title: 8E-8J-9H-9J_18mo_M_ATAC_2

city: LA JOLLA

first: Maria Luisa

last: Amaral

address: 9500 GILMAN DR

description:
Library name: XH_408
snATAC-seq

data_processing:
For male scATAC-seq samples, paired-end sequencing reads were aligned to the mm10 reference genome using Bowtie2 (Langmead 2012). From the filtered BAM files, we processed the data using SnapATAC2 (v 2.5.1)(Zhang 2024), following the official SnapATAC2 documentation. Barcode processing and fragment generation were performed, and doublets were removed using Scrublet. Nuclei with fewer than 1,000 fragments, more than 100,000 fragments, or a TSS enrichment score below 5 were discarded. For female 10X Multiome samples, we processed the CellRanger output directly using SnapATAC2, ensuring consistency between modalities. Fragment files were imported, and doublets were identified and removed using SnapATAC2's built-in method. TSS enrichment scores were computed using SnapATAC2’s function, and cells with fewer than 1,000 fragments, more than 15,000 fragments, or a TSS enrichment score below 5 were removed. Read counting and clustering were performed using a cell-by-bin matrix at 500-bp resolution, which was binarized for clustering. Bins overlapping the ENCODE blacklist (mm10) were removed to eliminate problematic regions. Read coverage normalization was performed using a log10(count +1) transformation followed by Z-score scaling, and bins with extreme Z-scores greater than 2 were filtered out. Feature selection was performed by retaining the top 700,000 most variable features. For dimensionality reduction, the Jaccard Index was computed, followed by diffusion maps for embedding. The top 20 eigenvectors were selected based on variance explained, and 20 nearest neighbors were computed per nucleus. The Leiden algorithm was applied for clustering, and clusters were annotated using known marker genes. Batch effects between male and female samples were corrected using Harmony prior to clustering. Low-quality clusters, including those with low TSS enrichment or suspected doublets, were removed from downstream analysis.
Assembly: mm10
Supplementary files format and content: Each .h5ad file is an AnnData object generated using SnapATAC2 and contains processed single-nucleus ATAC-seq data for a given sample. These files enable downstream analysis and visualization as described in the SnapATAC2 tutorials (https://kzhang.org/SnapATAC2/tutorials/).

source_name: Anterior hippocampus (AHC)

extract_protocol:
All experimental procedures using live animals were performed at the Salk Institute, and were approved by the Animal Care and Use Committee (IACUC). The Salk Institute has approved Assurance from NIH Office of Protection from Research Risks (D16-00328). C57BL/6J male and female mice were purchased from the Jackson Laboratory at 7, 38 and 63 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light cycles with food ad libitum until brain extraction (housing conditions: temperature of 21–23 °C, relative humidity of 61–63%). For synchronizing the estrous cycle in females ahead of brain extraction, females were exposed to male bedding for three days such that they would be in di-estrous at time of dissection. All animals were dissected between 1 and 5 pm to ensure similarity of circadian rhythm. Brains were extracted at 2, 9 or 18 months of age, sliced coronally at 600 µm and regions dissected in an ice-cold dissection buffer as previously described (Liu et al., Nature 2021) according to the Allen Brain Reference Atlas CCF (version 3)59 (CCFv3). Dissected tissue corresponding to the same region (across the anterior posterior axis) from each animal was collected across brain slabs and stored at -80 ºC. For nuclei isolation, region pools from 3–14 animals were processed for each of 2–3 biological replicas per region. Comprehensive brain dissection metadata are provided in Supplementary Table 1. No statistical methods were used to predetermine sample sizes. We empirically determined the number of animals needed to obtain sufficient nuclei from each brain region to run single nuclei sequencing experiments. We use two to three biological replicas for all single-cell epigenomic experiments to achieve minimum reproducibility for large-scale projects. Blinding and randomization was not performed during handling of the tissue samples. Additionally, all dissected regions were previously digitally registered into CCFv3 using ITK-SNAP60 (v.4.0.0) at 25 μm resolution.
Nuclei were pelleted with a swinging bucket centrifuge (500g, 5 min, 4°C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (1mM DTT (D9779, Sigma), 0.2% IGEPAL-CA630 (Sigma), 1X complete EDTA-free protease inhibitor (05056489001, Roche) and 5% BSA (A7906, Sigma) in PBS) and pelleted again (500g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were resuspended in 500 uL of tagmentation buffer (36.3 mM Tris-acetate, pH 7.8 (BP152, Thermo Fisher Scientific), 72.6mM Potassium-acetate (P5708, Sigma), 12.1 mM Magnesium-acetate (M2545, Sigma), 17.6% DMF (DX1730, EMD Millipore) in molecular biology-grade water) and counted using a hemocytometer. Concentration was adjusted to 2000 nuclei/uL, and 2000 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1 uL of barcoded Tn5 transposomes were added using a BenchSmart 96 (Mettler Toledo, RRID:SCR_018093; table S26), mixed five times, and incubated for 60 min at 37°C with 500 rpm shaking . To inhibit the Tn5 reaction, 10 uL of 40 mM EDTA was added to each well with a BenchSmart 96 and mixed 5 times, then incubated at 37°C for 15 min with 500 rpm shaking. Next, added 20 ul 2x sort buffer (2 % BSA, 2 mM EDTA in PBS), mix 5x and combine in a reagent reservoir. If processing two or more samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together, stained nuclei suspension with 3 uM Draq7 (1:100, 7406, Cell Signalling). Sort 20 nuclei per well into eight 96-well plates (total of 768 wells, 15,360 nuclei per sample) containing 10.5 ml EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation.
After addition of 1 uL 0.2%SDS (15553035, Thermo Fisher Scientific) to each well, samples were incubated at 55°C for 7 min with 500 rpm shaking. Next, 1 uL 12.5%Triton-X () was added to each well to quench the SDS. Next, 12.5 ml NEBNext High-Fidelity 2X~ PCR Master Mix (M0541, NEB) were added and samples were PCR-amplified (72°C 5 min, 98°C 30 s, (98°C 10 s, 63°C 30 s, 72°C 60 s) X 12 cycles, held at 12°C). After PCR, contents in all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit dsDNA HS Assay Kit (Invitrogen) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 (Illumina) and NovaSeq6000 (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

treatment_protocol: No treatment was applied to mice

value: Anterior hippocampus (AHC)

tag: age

tag: Sex

value: male


title: AML87_NK

status: Public on May 02 2025

type: SRA

city: Vienna

first: Kaan

last: Boztug

state: Vienna

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute

description: ATAC-seq

library_source: genomic

data_processing:
Sequencing adapter trimming and initial filtering with fastp ver 0.20.1
Alignment with bowtie 2 ver 2.4.4 to GRCh38 using the --very-sensitive parameter
PCR duplicate marking with samblaster ver 0.1.24
Sorting and filtering based on ENCODE blacklisted regions (PMID: 31249361) with samtools ver 1.12.
Indexing using samtools ver 1.12.
Peak calling using MACS2 v2.2.7.1 with flags --nomodel --keep-dup auto --extsize 147
workflow can be found at: https://zenodo.org/records/13763301
Assembly: GRCh38
Supplementary files format and content: Peak files in BED format generated with MACS2

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: Fresh-frozen bone marrow mononuclear cells were rapidly thawed and resuspended in IMDM. Cells were subsequently washed once with PBS. Blasts populations were identified via flow-cytometry using a routine diagnostics panel and subsequently 50.000 blasts were sorted for DNA-isolation and library prepration.

extract_protocol:
We performed DNA-islation and library prepration on 50.000 sorted blasts using the Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina, CA, USA) as described by Shashikant et al. (PMID:  30948010)
Library construction was performed as described in Shashikant et al. (PMID:  30948010)

tag: tissue

value: Bone marrow

tag: cell type

value: leukemic blast

tag: genotype

value: normal karyotype


title: 8E-8J-9H-9J_18mo_M_ATAC_1

state: CA

country: USA

institute: UCSD

description:
Library name: XH_406
snATAC-seq

organism: Mus musculus

value: WT

tag: batch


title: KP primary cell line with non-targeting control, shNTC, IgG CUT&RUN

city: New Haven

first: Siyuan

last: Wang

state: CT

address: 333 Cedar Street

department: Department of Genetics and Department of Cell Biology

institute: Yale University

description:
Library name: IgG_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus

data_processing:
CUT&RUN reads were analyzed for quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trimmomatic. Reads were then aligned to mm9 and K-12 E. coli genome U00096.3 by Bowtie2 version 2.3.4. Picard version 2.27.4 was used to down-sample the reads so that the read depths of E. coli sequences from different samples matched each other. SAMTools version 1.11 was then used to convert to BAM format, index, isolate uniquely mapped paired reads, and remove duplicates. MACS2 version 2.2.7.1 was used to call sample narrow peaks, using IgG as an input. Read counts across genomic intervals and peak visualization were performed using deepTools version 3.3110, and .bw files were visualized using the Integrative Genomics Viewer.
Assembly: mm9
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Run

source_name: KP LUAD primary cell line (31671)

growth_protocol: Cell lines were cultured in DMEM (Corning, 10-013-CV) containing 10% (vol/vol) FBS (Gibco, 26140-079) and 1% (vol/vol) Penicillin-Streptomycin (ThermoFisher, 15140-122) at 37 °C with 5% CO2. Cells were passaged whenever they reached confluency.

extract_protocol:
CUT&RUN was performed using the Epicypher CUTANATM ChIC/CUT&RUN Kit (14-1048) according to the manufacturer’s specifications with the following conditions and modifications: For binding to the Concanavalin beads, 500,000 cells per sample were prepared, counted twice by hemacytometer, and averaged. Nuclei were prepared according to the Epicypher Cut and Run Manual Appendix. Nuclei were incubated with activated beads. 0.1 E. coli spike in DNA ng was added to each sample. The following antibodies (0.5 ug of antibody per reaction) were used:IgG Control antibody: CUTANATM Kit Rabbit IgG CUT&RUN Negative Control Antibody; RNF2 antibody: CST RING1B (D22F2) XP® Rabbit mAb #5694; H3K4me3 antibody: Epicypher Rabbit Polyclonal H3K4me3 13-0041; H3K27me3 antibody: CST Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733; H2AK119ub antibody: CST Ubiquityl-Histone H2A (Lys119) (D27C4) Rabbit mAb #8240; BMI-1 antibody: Active Motif BMI-1 antibody (mAb) 39993; RNA Pol II p-ser5: Abcam Anti-RNA polymerase II phosphor-S5 EPR19015
Libraries were prepared using the Epicypher CUTANATM CUT&RUN Library Prep Kit (14-1001) according to the manufacturer’s specifications with the following modification: SPRI-select beads were used after library preparation to perform 200-700 bp size selection to enrich for DNA fragments from CUT&RUN and remove any adapter dimers or high molecular weight DNA. Library quality was analyzed using Agilent Tapestation D1000 High Sensitivity Tapes (#5067-5584). Sequencing was performed with 10 million reads ordered per sample, 150 bp paired-end reads, on an Illumina NovaSeq 6000.

treatment_protocol: KP cells were seeded in 6-well plates (Falcon, 353046) with a density of 50,000 cells/well. Cells were infected with lentivirus at different titers 24 hours after seeding. Stable transfected cells were selected with 6 μg/mL puromycin (Gibco, A11138-03) for 48-72 hours after lentiviral transfection. Cell pellets were collected after 48 hours of selection for quantitative RT-PCR validation and after 72 hours of selection for western blot validation.

tag: cell line

value: KP LUAD primary cell line (31671)

value: KrasLSL-G12D/WT; Trp53flox/flox

tag: treatment

value: shNTC


title: 8E-8J-9H-9J_9mo_M_ATAC_2

description:
Library name: MM_291
snATAC-seq


title: KP primary cell line with non-targeting control, shNTC, H2AK119ub CUT&RUN

description:
Library name: H2AK119ub_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, IgG CUT&RUN

description:
Library name: IgG_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: KP primary cell line with non-targeting control, shNTC, RNAPolII_pSer5 CUT&RUN

description:
Library name: RNAPolII_pSer5_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: AML57_UBTF

description: ATAC-seq

value: trisomy 8, UBTF


title: AML64_NK

description: ATAC-seq


title: AML04_NK

description: ATAC-seq


title: AML76_KMT2Ar

description: ATAC-seq


title: AML67_KMT2Ar

description: ATAC-seq


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, H2AK119ub CUT&RUN

description:
Library name: H2AK119ub_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: KP primary cell line with non-targeting control, shNTC, BMI1 CUT&RUN

description:
Library name: BMI1_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: AML89_RUNX1

description: ATAC-seq


title: AML52_KMTA2Ar

description: ATAC-seq


title: AML98_CBFB

description: ATAC-seq


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, BMI1 CUT&RUN

description:
Library name: BMI1_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: AML50_GLISr

description: ATAC-seq


title: KP primary cell line with non-targeting control, shNTC, H3K27me3 CUT&RUN

description:
Library name: H3K27me3_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: AML60_CBFB

description: ATAC-seq


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, H3K27me3 CUT&RUN

description:
Library name: H3K27me3_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: KP primary cell line with non-targeting control, shNTC, H3K4me3 CUT&RUN

description:
Library name: H3K4me3_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: AML54_KMT2Ar

description: ATAC-seq


title: AML07_KMT2Ar

description: ATAC-seq


title: AML88_mono7

description: ATAC-seq

value: monosomy 7


title: AML20_NK

description: ATAC-seq


title: KP primary cell line with non-targeting control, shNTC, RNF2 CUT&RUN

description:
Library name: RNF2_KP_shNTC
The KP cell line is stably transfected with shNTC hairpin with lentivirus


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, RNF2 CUT&RUN

description:
Library name: RNF2_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: RLP_9mo_F_RNA_rep1

description:
Library name: MM_1042_1_2
10X Multiome RNA

library_source: transcriptomic

data_processing:
Single-nucleus RNA-seq (snRNA-seq) data were generated using the 10X Genomics Multiome platform and processed with Cellranger-arc v2.0.2 to generate raw gene expression matrices. The data were aligned and quantified using the mouse reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0). Doublets were identified and removed using DoubletFinder from the Cell Ranger output for each sample65. Downstream analysis was performed using Seurat v5 in R. Individual samples were then merged into a single Seurat object. Quality control was applied to remove low-quality nuclei, filtering out cells with fewer than 500 or more than 6000 detected genes, and cells with >10% mitochondrial reads. Normalization was performed using the SCTransform (SCT) workflow, which models technical noise while preserving biological variation. Dimensionality reduction was carried out with PCA, and the top 30 components were used to compute a shared nearest neighbor (SNN) graph for clustering using the Leiden algorithm. UMAP was used for visualization. Following initial clustering, further manual filtering was applied to remove remaining doublets and low-quality subclusters. Specifically, subclusters containing >50% cells with low UMI counts or high doublet scores were excluded.
Assembly: mm10
Supplementary files format and content: These files are filtered_feature_bc_matrix.h5 files generated using the cellranger-arc count pipeline (v2.0.2, 10x Genomics). Each file corresponds to a single multiome sample and contains filtered gene expression and chromatin accessibility matrices. Filtering was performed automatically by Cell Ranger ARC based on quality metrics to retain high-confidence cells.

molecule: polyA RNA

source_name: DR+LC+PAG+PCG (PAG/PCG)

extract_protocol:
All experimental procedures using live animals were performed at the Salk Institute, and were approved by the Animal Care and Use Committee (IACUC). The Salk Institute has approved Assurance from NIH Office of Protection from Research Risks (D16-00328). C57BL/6J male and female mice were purchased from the Jackson Laboratory at 7, 38 and 63 weeks of age and maintained in the Salk animal barrier facility on 12-h dark light cycles with food ad libitum until brain extraction (housing conditions: temperature of 21-23C, relative humidity of 61-63%). For synchronizing the estrous cycle in females ahead of brain extraction, females were exposed to male bedding for three days such that they would be in di-estrous at time of dissection. All animals were dissected between 1 and 5 pm to ensure similarity of circadian rhythm. Brains were extracted at 2, 9 or 18 months of age, sliced coronally at 600 µm and regions dissected in an ice-cold dissection buffer as previously described (Liu et al., Nature 2021) according to the Allen Brain Reference Atlas CCF (version 3)59 (CCFv3). Dissected tissue corresponding to the same region (across the anterior posterior axis) from each animal was collected across brain slabs and stored at -80C. For nuclei isolation, region pools from 3-14 animals were processed for each of 2?3 biological replicas per region. Comprehensive brain dissection metadata are provided in Supplementary Table 1. No statistical methods were used to predetermine sample sizes. We empirically determined the number of animals needed to obtain sufficient nuclei from each brain region to run single nuclei sequencing experiments. We use two to three biological replicas for all single-cell epigenomic experiments to achieve minimum reproducibility for large-scale projects. Blinding and randomization was not performed during handling of the tissue samples. Additionally, all dissected regions were previously digitally registered into CCFv3 using ITK-SNAP60 (v.4.0.0) at 25um resolution.
Nuclei were pelleted with a swinging bucket centrifuge (1000g, 10 min, 4°C; 5920R, Eppendorf). Nuclei pellets were resuspended in sort buffer (1% BSA, 2uM 7-AAD, 1x cOmplete EDTA?free protease inhibitor and 1U/uL RNasin in PBS) and stained 10 mins on ice. Nuclei were sorted, and 120,000 nuclei were collected in 90 uL of collection buffer (5% BSA and 5U/uL RNasin). Nuclei were centrifuged (500 × g for 5 min at 4°C), and resuspended in nuclei permeabilization buffer (1mM DTT (D9779, Sigma), 0.2% IGEPAL-CA630 (Sigma), 1X cOmplete EDTA-free protease inhibitor (05056489001, Roche) and 5% BSA (A7906, Sigma) in PBS) incubated on ice for 1 min. Added 900 uL wash buffer and and pelleted again (500g, 5 min, 4°C; 5920R, Eppendorf). The nuclei were resuspended in 10uL of 1X Nuclei Buffer and counted using a hemocytometer. A total of 18,000 nuclei were loaded per tagmentation reaction loaded onto a Chromium Controller (10x Genomics) for downstream 10X Multiome ATAC and gene expression workflows. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Invitrogen) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that proper fragment sizes. Libraries were sequenced using the NextSeq500 and a NovaSeq6000 (Illumina).

value: DR+LC+PAG+PCG (PAG/PCG)

value: female


title: AML59_CBFB

description: ATAC-seq


title: RLP_9mo_F_RNA_rep2

description:
Library name: MM_1023_1_2
10X Multiome RNA


title: RLP_2mo_F_RNA_rep2

description:
Library name: MM_1091_1_2
10X Multiome RNA


title: AML82_NK

description: ATAC-seq


title: AML95_MECOM1

description: ATAC-seq

value: inv(3)(q21q26) RPN1/MECOM


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, H3K4me3 CUT&RUN

description:
Library name: H3K4me3_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: AML62_DEKNUP214

description: ATAC-seq


title: RLP_18mo_F_RNA_rep2

description:
Library name: MM_1067_1_2
10X Multiome RNA


title: RLP_2mo_F_RNA_rep1

description:
Library name: MM_983_1_2
10X Multiome RNA


title: AML63_NUP98

description: ATAC-seq


title: AML58_NK

description: ATAC-seq


title: NAC_9mo_F_RNA_rep2

description:
Library name: MM_1088_1_2
10X Multiome RNA

source_name: Nucleus Accumbens (ACB)

value: Nucleus Accumbens (ACB)


title: AML66_CBFB

description: ATAC-seq


title: AML77_trisomy8

description: ATAC-seq

value: trisomy 8


title: AML44_NUP98r

description: ATAC-seq


title: NAC_2mo_F_RNA_rep1

description:
Library name: MM_944_1_2
10X Multiome RNA


title: AML13_KMT2Ar

description: ATAC-seq


title: NAC_18mo_F_RNA_rep2

description:
Library name: MM_1089_1_2
10X Multiome RNA


title: AML39_DEKNUP214

description: ATAC-seq


title: NAC_9mo_F_RNA_rep1

description:
Library name: QY_1586_1_2
10X Multiome RNA


title: KP primary cell line with Rnf2 knockdown, shRnf2-3, RNAPolII_pSer5 CUT&RUN

description:
Library name: RNAPolII_pSer5_KP_shRnf2
The KP cell line is stably transfected with shRnf2-3 hairpin with lentivirus


title: NAC_18mo_F_RNA_rep1

description:
Library name: MM_1065_1_2
10X Multiome RNA


title: AML84_complex

description: ATAC-seq

value: complex


title: HCP_9mo_F_RNA_rep3

description:
Library name: EE_177_1_2
10X Multiome RNA

source_name: Posterior hippocampus (PHC)

value: Posterior hippocampus (PHC)


title: S_PR6_SFM

city: Toronto

first: Stewart

last: Russell

state: ON

address: 790 Bay St

country: Canada

institute: create fertility centre

data_processing:
Pre-and post-alignment QA/QC, genome mapping, and alignment of the raw sequencing data were performed using the Partek® Flow® Genomic Analysis Software. Raw sequencing data (unaligned reads in FASTQ format) underwent quality assurance and quality control (QA/QC), and bases were trimmed from the 3’ end based on a Phred quality score of 20 and minimum read length of 25 bases. Trimmed reads were then aligned to the human genome (GRCh38/hg38 Genome Reference Consortium Human Build 38 Organism: Homo sapiens) using the Spliced Transcripts Alignment to a Reference (STAR) (408) version 2.5.3a index with the default mapping parameters. The resulting aligned reads underwent post-alignment QA/QC to assess the number of reads per sample and quality of alignment. Aligned reads were then quantified to the annotation model hg38 Ensembl Transcripts (release 108) to acquire gene counts using the following input parameters: strict paired-end compatibility, require junction reads to match introns, no strand specificity, minimal read overlap with the feature value set at 100% of read length, and the filter features value set at 10. Some samples (N=40) with low reads (≤15 million reads) or poor alignment (≤30% alignment) following post-alignment QA/QC for the initial NovaSeq run underwent library preparation once more and were re-sequenced on the Illumina NextSeq 550 System for 75 cycles paired-end. Similarly, the raw sequencing data for these 40 samples were then imported into the Partek® Flow® workflow and incorporated with the NovaSeq data to re-acquire final gene counts as previously described.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw count table

molecule: total RNA

source_name: endometrial stromal cells

extract_protocol:
Total RNA (N=138) was isolated from uncultured (P0) and in vitro 48-hour-treated cells (Supplementary Table SIII) following established protocols from the Total RNA Purification Micro Kit (Norgen Biotek) and RNA integrity was assessed using the Agilent RNA 6000 Pico Kit and the Agilent 5200 Bioanalyzer System (Agilent Technologies Inc). Approximately 1.5-2 ng of total RNA per sample was used to generate libraries for RNA sequencing, employing the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio Inc.). The library preparation protocol recommended by the kit was followed, with a modification to reduce reagent volumes to 1/5 of the recommended amounts
Approximately 1 µL from each library was pooled and the pooled library underwent purification using the DNA Clean & Concentrator-5™ kit (Zymo Research) and the average library size was determined using the Agilent 5200 Bioanalyzer System and the Agilent DNF-474 HS NGS Fragment Kit (Agilent Technologies Inc). For quality control and normalization of all RNA libraries, the purified pooled library underwent preliminary sequencing using the Illumina NextSeq 550 System (Illumina, Inc.) for 75 cycles. The pooled library was first diluted to 4 nM in nuclease-free water and was denatured and diluted following the standard normalization method for the NextSeq 500/550 High Output v2 (75 Cycles) sequencing reagent kit (Illumina, Inc.). The final loading concentration was 1.6 pM of the denatured pooled libraries with 1% PhiX control spike-in (sequencing control).

value: endometrial stromal cells

value: proliferative phase, patient experiencing recurrent implantation failure

value: passage 1, serum-free media treatment

value: SFM


title: HCP_9mo_F_RNA_rep1

description:
Library name: QY_1584_1_2
10X Multiome RNA

value: WT


title: S_PR6_HPL

value: passage 1, human platelet lysate treatment

value: HPL


title: HCP_2mo_F_RNA_rep2

description:
Library name: MM_990_1_2
10X Multiome RNA


title: S_PR6_P0

value: passage 0


title: HCP_2mo_F_RNA_rep1

description:
Library name: MM_1040_1_2
10X Multiome RNA


title: AML47_CBFB

description: ATAC-seq

value: Bone marrow

value: leukemic blast


title: E_PR6_HPL

source_name: endometrial epithelial cells

value: endometrial epithelial cells


title: E_PR6_SFM


title: NAC_2mo_F_RNA_rep2

description:
Library name: MM_991_1_2
10X Multiome RNA

value: female


title: HCP_18mo_F_RNA_rep2

description:
Library name: MM_1090_1_2
10X Multiome RNA


title: E_PR6_P0


title: HCP_18mo_F_RNA_rep1

description:
Library name: MM_1029_1_2
10X Multiome RNA


title: HCA_9mo_F_RNA_rep2

description:
Library name: MM_1021_1_2
10X Multiome RNA

value: Anterior hippocampus (AHC)


title: HCA_9mo_F_RNA_rep1

description:
Library name: QY_1602_1_2
10X Multiome RNA


title: S_PR5_HPL


title: S_PR5_SFM


title: S_PR5_P0


title: HCA_2mo_F_RNA_rep2

description:
Library name: QY_1590_1_2
10X Multiome RNA


title: E_PR5_HPL


title: HCA_2mo_F_RNA_rep1

description:
Library name: MM_1086_1_2
10X Multiome RNA


title: AML26_CBFB

description: ATAC-seq


title: AML74_UBTF

description: ATAC-seq

value: normal karyotype, UBTF


title: HCP_9mo_F_RNA_rep2

description:
Library name: MM_1044_1_2
10X Multiome RNA


title: HCA_18mo_F_RNA_rep2

description:
Library name: MM_1066_1_2
10X Multiome RNA


title: HCA_18mo_F_RNA_rep1

description:
Library name: MM_1035_1_2
10X Multiome RNA


title: E_PR5_SFM


title: E_PR5_P0


title: S_PR4_HPL


title: FC_2mo_F_RNA_rep2

description:
Library name: QY_1594_1_2
10X Multiome RNA

source_name: Frontal Cortex (FC)

value: Frontal Cortex (FC)


title: FC_9mo_F_RNA_rep1

description:
Library name: QY_1606_1_2_3
10X Multiome RNA


title: S_PR4_P0


title: S_PR4_SFM


title: FC_2mo_F_RNA_rep1

description:
Library name: MM_986_1_2
10X Multiome RNA


title: E_PR4_HPL


title: FC_18mo_F_RNA_rep2

description:
Library name: MM_1068_1_2
10X Multiome RNA


title: FC_18mo_F_RNA_rep1

description:
Library name: QY_1695_1_2
10X Multiome RNA


title: S_PR3_HPL


title: E_PR4_P0


title: ENT_9mo_F_RNA_rep3

description:
Library name: EE_178_1_2
10X Multiome RNA

source_name: Entorhinal cortex (ENT)

value: Entorhinal cortex (ENT)


title: ENT_9mo_F_RNA_rep2

description:
Library name: QY_1617_1_2
10X Multiome RNA


title: ENT_9mo_F_RNA_rep1

description:
Library name: MM_1092_1_2
10X Multiome RNA


title: E_PR3_P0


title: ENT_2mo_F_RNA_rep1

description:
Library name: MM_1039_1_2
10X Multiome RNA


title: E_PR4_SFM


title: ENT_2mo_F_RNA_rep2

description:
Library name: MM_1004_1_2_3
10X Multiome RNA


title: ENT_18mo_F_RNA_rep3

description:
Library name: EE_174_1_2
10X Multiome RNA


title: ENT_18mo_F_RNA_rep2

description:
Library name: QY_1699_1_2
10X Multiome RNA


title: FC_9mo_F_RNA_rep2

description:
Library name: KA_37_1_2
10X Multiome RNA


title: E_PR2_HPL


title: S_PR2_HPL


title: CP_9mo_F_RNA_rep3

description:
Library name: EE_176_1_2
10X Multiome RNA

source_name: Caudate Putamen (CP)

value: Caudate Putamen (CP)


title: E_PR2_SFM


title: ENT_18mo_F_RNA_rep1

description:
Library name: MM_1031_1_2
10X Multiome RNA


title: S_PR1_SFM

value: endometrial stromal cells


title: E_PR2_P0

value: proliferative phase, patient experiencing recurrent implantation failure


title: CP_9mo_F_RNA_rep1

description:
Library name: QY_1596_1_2
10X Multiome RNA


title: CP_9mo_F_RNA_rep2

description:
Library name: QY_1607_1_2
10X Multiome RNA


title: E_PR3_HPL


title: CP_2mo_F_RNA_rep2

description:
Library name: MM_987_1_2
10X Multiome RNA


title: E_PR1_P0


title: S_PR3_SFM

value: passage 1, serum-free media treatment


title: E_PR3_SFM

value: SFM


title: CP_18mo_F_RNA_rep2

description:
Library name: QY_1697_1_2
10X Multiome RNA

value: WT


title: E_PR1_SFM


title: CP_2mo_F_RNA_rep1

description:
Library name: MM_941_1_2
10X Multiome RNA


title: S_PR1_HPL

value: passage 1, human platelet lysate treatment


title: S_C5_P0

value: proliferative phase, control patient with recent pregnancy


title: AMY_9mo_F_RNA_rep2

description:
Library name: QY_1615_1_2
10X Multiome RNA

source_name: Amygdala (AMY)

value: Amygdala (AMY)


title: AMY_9mo_F_RNA_rep1

description:
Library name: QY_1600_1_2
10X Multiome RNA


title: E_C5_HPL

value: HPL


title: CP_18mo_F_RNA_rep1

description:
Library name: MM_1094_1_2
10X Multiome RNA


title: E_C4_P0

value: passage 0


title: D61_24G_GEX

city: London

first: James

middle: Gervase

last: Nicholson

state: London

address: 4 Newark St,

department: Blizzard Institute

country: United Kingdom

institute: QMUL

description: Library name: D61_24G_GEX

library_source: transcriptomic single cell

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices for downstream pre-processing and analysis using the Seurat v5.0.1 R package
Assembly: GRCh38 human reference genome
Supplementary files format and content: cellranger output series matrix files

source_name: irradiated cerebral organoid

growth_protocol: Cerebral organoids were generated and cultured as per manufacturer’s instructions using the STEMdiff Cerebral Organoid Kit (StemCell Technologies, #08570) with minor adaptations. Briefly, for embryoid bodies (EB) generation, feeder-free EPSC were disso- ciated into single cells and 60,000 cells were plated into each well of a 96-well round-bottom ultra-low attachment plate (Corning) in seeding media (EB formation media+50 mM ROCK Inhibitor) and media was replenished every 2 days. When EB diameter R300 mm (day7–8), EBs were transferred to a 24-well ultra-low attachment plate (Corning) in a neural induction medium for 3–4 days. EBs were then embedded in Matrigel hESC-Qualified Matrix (Corning, #354277) droplets and transferred into a six-well ultra-low attachment plate (Corning) in a neural expansion medium for 3 days. After 3 days, the expansion medium was removed from the wells and re- placed with a maturation medium. The plate was transferred on an orbital shaker at 37C at 100 rpm.

extract_protocol:
COs for single-cell RNA sequencing were processed with the Brain Tumour Dissociation Kit (P) (Miltenyi Biotec,130-095-942) following the manufacturer’s protocol and using the gentle MACS dissociator.  24 hrs post-irradiation, 3-5 pooled COs were harvested and washed with D-PBS without calcium and magnesium. The organoids were then transferred into a C-Tube containing the pre-heated enzyme mix 1 followed by the gentleMACS Program m_brain_01, 37⁰C incubations under slow continuous rotation, gentleMACS Program m_brain_02, addition of enzyme mix 2 and gentle MACS Program m_brain_03. Single-cell suspension was passed through a 70µm strainer and centrifuged at 300g x for 10 minutes. CO cells were then resuspended in 0.04% BSA in DPBS, and viability and cell number were assessed with the Countess® II FL Automated Cell Counter using trypan blue. 100,000 cells were aliquoted into a new tube in 100µl to achieve a cell density of 1000 cells/µl as required by the 10X Genomics Single-cell RNA sequencing protocol, followed by a final count to ensure the correct number of cells.
Library preparation was performed at the Single Cell Genomics Facility (UCL, Cancer Institute) using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, 1000268) along with the Chromium Next GEM Chip G Single Cell Kit (10X Genomics, 1000120) according to the manufacturer’s instructions. Pooled samples libraries were sequenced with lane sequencing on Novaseq 6000 S4 (Novogene).

treatment_protocol: COs were irradiated at day 48 with 24 Gy or underwent sham irradiation (0 Gy). Irradiation was performed using X-Ray Biological Irradiator within the Queen Mary Biological Science Unit and radiation dose of 24 Gy was administered at 8.5Gy/min. After 24 hrs 3-5 pooled COs per condition were collected for processing.

value: Cerebral Organoid

value: Irradiated (24G)


title: E_C5_P0

value: endometrial epithelial cells


title: D61_0G_GEX

description: Library name: D61_0G_GEX

source_name: control cerebral organoid

value: control (0G)


title: AMY_2mo_F_RNA_rep2

description:
Library name: MM_1005_1_2
10X Multiome RNA

value: female


title: D19_24G_GEX

description: Library name: D19_24G_GEX


title: E_PR1_HPL


title: S_C3_HPL


title: D19_0G_GEX

description: Library name: D19_0G_GEX


title: AMY_2mo_F_RNA_rep1

description:
Library name: MM_979_1_2_3
10X Multiome RNA


title: AMY_18mo_F_RNA_rep3

description:
Library name: EE_173_1_2
10X Multiome RNA


title: AMY_2mo_F_RNA_rep3

description:
Library name: EE_175_1_2
10X Multiome RNA


title: Lung, SH.TBL15E

city: Badalona

first: Cristina

last: Vilaplana

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n, IGTP - Edifici Mar - UTE

country: Spain

institute: IGTP

data_processing:
Preprocessing of raw data included quality control through  MultiQC (v.1.9)
Illumina adapters were trimmed off with Trimmomatic (v.0.39)
Fastq files were aligned to GRCh38.89 human genome sequence through STAR (v.2.7.5b)
Genome_build: GRCh38.89
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Genes with mean raw counts that were below or equal to five were discarded as they were too lowly expressed to be reliably quantified and could interfere with the differential expression analysis

source_name: Lung Tissue

extract_protocol:
Granuloma TB lesions were removed and ~0.5 cm3 biopsy fragments of tissue samples  were kept on RNAlater solution (Qiagen) at 4ºC overnight for RNA-seq. Fresh tissue samples intended for RNA-seq were removed the following morning, for finally being stored at -80ºC. The mirVana miRNA Isolation Kit (Thermo Fisher Scientific) allowed the total-RNA isolation and recovery, followed by a genomic DNA digestion through DNA-free DNA Removal Kit (Thermo Fisher Scientific) considering manufacturer’s instructions, respectively. Total-isolated-RNA was diluted to reach a 25 ng/µl aliquot.
Libraries were constructed by the TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat) (Illumina) following the TruSeq Stranded Total RNA Sample Prep guide (Part #15031048 Rev. E), including a prior removal of ribosomal RNA through the RNA Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
RNA-seq was performed on an Illumina platform HiSeq 4000 (Illumina), at 50 million reads per sample, 100bp stranded paired-end reads

tag: individual

value: patient 15

tag: disease state

value: TB

value: Granuloma

tag: tissue location

value: External wall

value: Female

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Tuberculoma

tag: lesion size

tag: fresh necrosis

value: Yes

tag: granuloma biopsy culture

value: Negative


title: Lung, SH.TBL15I

tag: individual

tag: disease state

tag: tissue

tag: tissue location

value: Internal wall

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient


title: S_C3_SFM

value: endometrial stromal cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: E_C3_P0

value: endometrial epithelial cells

value: passage 0


title: Lung, SH.TBL14I

tag: individual

value: patient 14

tag: disease state

value: TB

value: Male

value: DS

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Cavitation

tag: lesion size

tag: fresh necrosis

tag: granuloma biopsy culture


title: S_C2_P0

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: Lung, SH.TBL15H

tag: individual

value: patient 15

tag: disease state

value: Healthy parenchyma

tag: tissue location

tag: age

tag: Sex

value: Female

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr


title: AMY_18mo_F_RNA_rep2

description:
Library name: QY_1701_1_2
10X Multiome RNA

tag: tissue

value: Amygdala (AMY)

tag: genotype

value: WT

value: female

tag: batch


title: Lung, SH.TBL14H

tag: individual

tag: disease state

tag: tissue location

tag: age

tag: Sex

value: Yes

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: Lung, SH.TBL11H

tag: individual

value: patient 11

tag: tissue

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

value: Positive


title: Lung, SH.TBL11E

tag: disease state

value: TB

value: Granuloma

tag: tissue location

value: External wall

tag: age

tag: Sex

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size

tag: fresh necrosis


title: S_C3_P0

tag: tissue

value: endometrial stromal cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 0

tag: treatment


title: E_C2_HPL

value: endometrial epithelial cells

value: passage 1, human platelet lysate treatment

value: HPL


title: Lung, SH.TBL13I

tag: individual

value: patient 13

tag: disease state

tag: tissue location

value: Internal wall

tag: age

value: Male

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

value: Cavitation

tag: granuloma biopsy culture


title: Lung, SH.TBL14C

tag: individual

value: patient 14

tag: disease state

tag: tissue

value: Center

tag: Sex

value: DS

value: Yes

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size

tag: fresh necrosis

value: Negative


title: Lung, SH.TBL15C

value: patient 15

value: TB

value: Granuloma

tag: tissue location

tag: age

value: Female

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

value: Tuberculoma


title: Lung, SH.TBL11I

tag: individual

value: patient 11

tag: disease state

tag: tissue

tag: Sex

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size

tag: granuloma biopsy culture

value: Positive


title: Lung, SH.TBL11C

tag: tissue location

tag: age

value: Male

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: fresh necrosis


title: S_C2_SFM

tag: tissue

value: endometrial stromal cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: Lung, SH.TBL14E

tag: individual

value: patient 14

tag: disease state

tag: tissue location

value: External wall

tag: age

tag: Sex

tag: drug sensitivity

value: No

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Cavitation

tag: lesion size

tag: granuloma biopsy culture


title: Lung, SH.TBL10H

tag: individual

value: patient 10

tag: disease state

tag: tissue

value: Healthy parenchyma

value: DS

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

value: Yes

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

value: yes

tag: fresh necrosis

value: Negative


title: Lung, SH.TBL10E

value: TB

value: Granuloma

tag: tissue location

tag: age

tag: Sex

value: Female

tag: drug sensitivity

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Tuberculoma

tag: lesion size


title: AMY_18mo_F_RNA_rep1

description:
Library name: MM_1064_1_2
10X Multiome RNA

tag: tissue

value: Amygdala (AMY)

tag: genotype

value: WT

value: female

tag: batch


title: E_C3_HPL

value: endometrial epithelial cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: E_C2_P0

value: passage 0


title: Lung, SH.TBL13H

tag: individual

value: patient 13

tag: disease state

value: Healthy parenchyma

tag: tissue location

tag: age

tag: Sex

value: Male

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

value: Cavitation

tag: fresh necrosis

tag: granuloma biopsy culture


title: Lung, SH.TBL10I

tag: individual

value: patient 10

tag: disease state

value: TB

tag: tissue

value: Granuloma

tag: tissue location

value: Internal wall

tag: age

value: DS

value: Yes

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size

value: Negative


title: Lung, SH.TBL13E

value: External wall

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: fresh necrosis


title: Lung, SH.TBL09H

tag: individual

value: patient 09

tag: disease state

tag: tissue

tag: tissue location

tag: age

value: Female

value: XDR

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: granuloma biopsy culture


title: S_C1_P0

value: endometrial stromal cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 0

tag: treatment


title: Lung, SH.TBL08H

tag: individual

value: patient 08

tag: disease state

value: Healthy parenchyma

tag: Sex

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: lesion size

tag: fresh necrosis


title: E_C1_HPL

tag: tissue

value: endometrial epithelial cells

tag: cell line

tag: cell type

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: E_C1_SFM

value: passage 1, serum-free media treatment

value: SFM


title: Lung, SH.TBL08E

tag: individual

tag: disease state

value: TB

value: Granuloma

tag: tissue location

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

value: Yes

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Cavitation

tag: granuloma biopsy culture

value: Negative


title: Lung, SH.TBL07H

tag: individual

value: patient 07

tag: disease state

tag: tissue

value: Female

value: DS

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: lesion size

tag: fresh necrosis


title: Lung, SH.TBL09E

value: patient 09

tag: tissue location

value: External wall

tag: age

tag: Sex

tag: drug sensitivity

value: XDR

tag: bmi

tag: smoking

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation


title: Lung, SH.TBL08I

tag: individual

value: patient 08

tag: disease state

tag: tissue

value: Internal wall

value: MDR

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: lesion size

tag: granuloma biopsy culture


title: Lung, SH.TBL09I

tag: tissue location

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: fresh necrosis


title: Lung, SH.TBL06H

tag: individual

value: patient 06

tag: disease state

tag: tissue

value: Healthy parenchyma

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: cavitation

tag: lesion size


title: E_C2_SFM

value: endometrial epithelial cells

tag: cell line

value: proliferative phase, control patient with recent pregnancy

tag: cell type

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: Lung, SH.TBL06E

tag: individual

tag: disease state

value: TB

value: Granuloma

tag: tissue location

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

value: Cavitation

tag: fresh necrosis

value: Yes

tag: granuloma biopsy culture

value: Negative


title: S_SRT5_HPL

tag: tissue

value: endometrial stromal cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

tag: cell type

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: E_SRT5_HPL


title: E_C1_P0

value: passage 0


title: Lung, SH.TBL06C

tag: individual

value: patient 06

tag: disease state

tag: tissue location

value: Center

tag: age

tag: Sex

value: Female

tag: drug sensitivity

value: DS

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: cavitation

tag: lesion size


title: Lung, SH.TBL05H

tag: individual

value: patient 05

tag: disease state

tag: tissue

value: Healthy parenchyma

value: MDR

tag: bmi

tag: smoking

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: fresh necrosis

tag: granuloma biopsy culture


title: S_SRT6_HPL

tag: cell line

tag: cell type

tag: treatment


title: Lung, SH.TBL05E

tag: individual

tag: disease state

value: TB

value: Granuloma

tag: tissue location

value: External wall

tag: age

tag: Sex

tag: drug sensitivity

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

value: yes

tag: cavitation

tag: lesion size


title: Lung, SH.TBL05I

tag: individual

tag: disease state

tag: tissue

value: Internal wall

tag: bmi

tag: smoking

value: Yes

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

value: Cavitation

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: E_SRT5_SFM

value: endometrial epithelial cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

tag: cell type

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: lib94761

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample. Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the GRCm38.91  mouse reference genome, using STAR v.2.4.2a40 and gene counts were generated using htseq-count41. Quality control (QC) and metrics analysis was performed using the Picard family of tools (v1.134, http://broadinstitute.github.io/picard/).
Assembly: GRCm38.91
Supplementary files format and content: *htseq_counts.txt

source_name: Splenocyte

growth_protocol: Dyrk1aflox (#027801) were obtained from Jackson Laboratories. Transgenic distal Lck-Cre (dLckCre) mice were previously reported. Mice were housed in the Benaroya Research Institute Vivarium in a speciﬁc-pathogen-free (SPF) animal room with unrestricted access to food and water. All murine experiments were performed on male and female mice between 7 and 24 weeks of age, with the approval of the IACUC of Benaroya Research Institute (Seattle, WA).

extract_protocol:
Cells were harvested at 0 and 5 hours and RNA isolated using Qiagen RNeasy kits (Qiagen). RNA was used to construct libraries using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), with reverse transcription followed by polymerase chain reaction amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).

treatment_protocol: Splenocytes were obtained from 8- to 12-week-old mice by crushing spleens through a 100-mm ﬁlter. Naïve CD4+CD62L+ T cells were isolated from splenocytes using CD4 negative enrichment kits (Stemcell Technologies, Vancouver, Canada) and CD62L microbeads (Miltenyi Biotec, San Diego, CA) per manufacturer’s instructions. Purity (>90%) was verified by ﬂow cytometry. Cells were cultured on polystyrene 96-well plates (Corning, Corning, NY) precoated with anti-CD3 and anti-CD28 antibody (5 mg/ml each, antibodies from BioXcell). Cells (10^5/well) were cultured in the presence of 5 mg/ml each anti-IL-12, anti-IFN-g, and anti-IL-4 antibody, 0.25 ng/ml TGF-b,  20 ng/ml each IL-6 and IL-1b (all cytokines from Peprotech).  Cells were fed with equal volumes of medium split 1:2 at day 3, and analyzed at day 4. Harmine or LCTB-21 were added as indicated at start of culture.

tag: Sex

value: male

tag: donor id

value: Splenocyte

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: Wildtype

tag: stimulation

value: Il-6, Il-1B, anti-Il-4, anti-Il-12, anti-IFNg, TGFb

tag: time point


title: Lung, SH.TBL07E

tag: individual

value: patient 07

tag: disease state

value: TB

tag: tissue

value: Granuloma

tag: tissue location

tag: age

value: Female

tag: drug sensitivity

value: DS

tag: bmi

tag: smoking

value: No

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: cavitation

tag: lesion size


title: E_SRT5_P0

tag: tissue

tag: cell line

tag: cell type

value: passage 0

tag: treatment


title: Lung, SH.TBL05C

tag: individual

value: patient 05

tag: disease state

tag: tissue location

value: Center

tag: age

tag: Sex

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

value: Yes

value: yes

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

value: Cavitation

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: Lung, SH.TBL07I

tag: individual

tag: disease state

tag: tissue

value: Internal wall

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: cavitation

tag: lesion size


title: lib94760

tag: Sex

value: male

tag: donor id

value: Splenocyte

tag: cell type

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: D1A dlckCre+

tag: stimulation

tag: time point


title: Lung, SH.TBL04H

tag: individual

value: patient 04

tag: disease state

value: TB

tag: tissue

value: Healthy parenchyma

tag: tissue location

tag: age

value: Male

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

value: Tuberculoma

tag: fresh necrosis

tag: granuloma biopsy culture


title: E_SRT4_HPL

tag: tissue

value: endometrial epithelial cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

tag: cell type

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: E_SRT4_SFM

value: passage 1, serum-free media treatment

value: SFM


title: Lung, SH.TBL04I

tag: individual

tag: disease state

value: Granuloma

tag: tissue location

value: Internal wall

tag: age

tag: Sex

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

value: Yes

tag: alcohol

tag: diabetes

value: No

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: cavitation

tag: lesion size

value: Negative


title: E_SRT4_P0

tag: tissue

tag: cell line

tag: cell type

value: passage 0

tag: treatment


title: Lung, SH.TBL04C

tag: individual

value: patient 04

tag: disease state

value: TB

tag: tissue location

value: Center

tag: age

tag: Sex

tag: drug sensitivity

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: fresh necrosis

tag: granuloma biopsy culture


title: lib94757

value: female

tag: donor id

tag: tissue

value: Splenocyte

tag: cell type

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: Wildtype

tag: stimulation

value: Il-6, Il-1B, anti-Il-4, anti-Il-12, anti-IFNg, TGFb

tag: time point


title: lib94758

tag: Sex

value: D1A dlckCre+


title: S_SRT3_HPL

value: endometrial stromal cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: lib94756


title: Lung, SH.TBL03I

tag: individual

value: patient 03

tag: disease state

value: Granuloma

tag: tissue location

value: Internal wall

tag: age

value: Male

tag: drug sensitivity

value: XDR

tag: bmi

tag: smoking

value: No

tag: alcohol

value: Yes

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: cavitation

value: Cavitation

tag: lesion size


title: S_SRT3_P0

tag: tissue

tag: cell line

tag: cell type

value: passage 0

tag: treatment


title: lib94754

tag: Sex

value: male

tag: donor id

value: Splenocyte

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: Wildtype

tag: stimulation

tag: time point


title: Lung, SH.TBL03E

tag: individual

tag: disease state

value: TB

tag: tissue location

value: External wall

tag: age

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: S_SRT3_SFM

tag: tissue

value: endometrial stromal cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

tag: cell type

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: RLP_18mo_F_RNA_rep1

description:
Library name: MM_1093_1_2
10X Multiome RNA

value: DR+LC+PAG+PCG (PAG/PCG)

tag: genotype

value: WT

tag: age

tag: Sex

value: female

tag: batch


title: lib94755

tag: donor id

tag: sort

tag: age (weeks)

tag: studygroup

value: D1A dlckCre+

tag: stimulation

value: Il-6, Il-1B, anti-Il-4, anti-Il-12, anti-IFNg, TGFb

tag: time point


title: E_SRT3_HPL

value: endometrial epithelial cells

value: passage 1, human platelet lysate treatment

value: HPL


title: S_SRT2_HPL


title: S_SRT2_SFM


title: Lung, SH.TBL02E

tag: individual

value: patient 02

tag: disease state

value: Granuloma

tag: tissue location

value: Male

tag: drug sensitivity

value: DS

tag: bmi

tag: smoking

value: Yes

tag: alcohol

tag: diabetes

tag: hcv

value: No

tag: hbv

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

value: yes

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Cavitation

tag: lesion size


title: Lung, SH.TBL02H

tag: individual

tag: disease state

value: TB

tag: tissue

value: Healthy parenchyma

tag: tissue location

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: lib94753

value: male

tag: donor id

value: Splenocyte

tag: cell type

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: Wildtype

tag: stimulation

tag: time point


title: lib94752

tag: Sex

tag: tissue

value: D1A dlckCre+


title: lib94751

value: female


title: S_SRT2_P0

value: endometrial stromal cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

value: passage 0

tag: treatment


title: Lung, SH.TBL02I

tag: individual

value: patient 02

tag: disease state

value: Granuloma

tag: tissue location

value: Internal wall

tag: age

value: Male

tag: drug sensitivity

value: DS

tag: bmi

tag: smoking

value: Yes

tag: alcohol

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: lesion size


title: Lung, SH.TBL04E

tag: individual

value: patient 04

tag: disease state

value: TB

tag: tissue

tag: tissue location

value: External wall

tag: age

tag: Sex

tag: drug sensitivity

value: MDR

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

value: No

tag: hcv

tag: hbv

value: yes

value: Tuberculoma

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: lib94750

value: female

tag: donor id

value: Splenocyte

tag: cell type

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: D1A dlckCre+

tag: stimulation

tag: time point


title: lib94759

tag: Sex

tag: tissue

value: Wildtype

value: Il-6, Il-1B, anti-Il-4, anti-Il-12, anti-IFNg, TGFb


title: E_SRT2_SFM

value: endometrial epithelial cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: Lung, SH.TBL01E

tag: individual

value: patient 01

tag: disease state

value: TB

value: Granuloma

tag: tissue location

value: External wall

tag: age

value: Male

tag: drug sensitivity

value: DS

tag: bmi

tag: smoking

value: Yes

tag: alcohol

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

value: Cavitation

tag: lesion size


title: Lung, SH.TBL01H

tag: individual

tag: disease state

tag: tissue

value: Healthy parenchyma

tag: tissue location

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

value: No

tag: hcv

tag: hbv

value: yes

tag: fresh necrosis

tag: granuloma biopsy culture

value: Negative


title: Lung, SH.TBL03C

value: patient 03

value: Center

value: XDR

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation


title: Lung, SH.TBL01I

tag: individual

tag: disease state

tag: tissue

tag: tissue location

value: Internal wall

tag: age

tag: Sex

tag: drug sensitivity

tag: bmi

tag: smoking

tag: alcohol

tag: diabetes

tag: hcv

tag: hbv

tag: lesion size

tag: fresh necrosis


title: E_SRT2_HPL

value: endometrial epithelial cells

tag: cell line

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium

tag: cell type

value: passage 1, human platelet lysate treatment

tag: treatment

value: HPL


title: S_SRT1_P0

value: endometrial stromal cells

value: passage 0


title: E_SRT2_P0


title: Lung, SH.TBL01C

tag: individual

value: patient 01

tag: disease state

value: TB

value: Granuloma

value: Male

value: DS

tag: tb symptoms

tag: relapse patient

tag: months time to scc

tag: time to scc

tag: multiple lesion xray

tag: lesion localization cxr

tag: presence cavities cxr

tag: infiltrates cxr

tag: signs bronchogenic dissmeniation cxr

tag: calcified granulomas cxr

tag: bronchiectasis cxr

tag: pleural affectation cxr

tag: months dx to surgery

tag: days surgery to discharge

tag: cavitation

tag: granuloma biopsy culture


title: lib94746

tag: Sex

value: male

tag: donor id

tag: tissue

value: Splenocyte

tag: cell type

value: CD4+ T cell

tag: sort

value: Naïve CD4+ T Cells

tag: age (weeks)

tag: studygroup

value: Wildtype

tag: stimulation

tag: time point


title: lib94747

value: D1A dlckCre+


title: E_SRT1_SFM

value: endometrial epithelial cells

tag: cell line

value: passage 1, serum-free media treatment

tag: treatment

value: SFM


title: Choroid plexus 24M 3

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.104) using STAR (v. 2.7.9a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Differentially expressed genes are produced with standard procedure of LRT with DEseq2 (v. 3.16) using GeneCount output from STAR (--quantMode)
Assembly: Rnor_6.0 (rn6) v.104
Supplementary files format and content: GeneCount files are tab-delimited text files for gene abundance for each samples for STAR raw count (QuantMode)
Supplementary files format and content: RSEM files are tab-delimited text files for gene abundance for each samples in TPM and FPKM
Supplementary files format and content: Differentially expressed gene table for all genes using LRT method with Ensembl ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj.

organism: Rattus norvegicus

source_name: Choroid plexus

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

value: Choroid plexus

tag: age

value: 84 weeks

tag: tissue type

value: Whole tissue

tag: genotype

value: Wistar


title: S_PR3_P0

value: endometrial stromal cells

value: proliferative phase, patient experiencing recurrent implantation failure

value: passage 0


title: Choroid plexus 24M 2

value: Male


title: Choroid plexus 24M 1


title: lib94749

value: female


title: S_PR2_SFM


title: S_SR6_P0

value: secretory phase, patient experiencing recurrent implantation failure


title: E_SR6_HPL

value: passage 1, human platelet lysate treatment

value: HPL


title: S_C5_HPL

value: proliferative phase, control patient with recent pregnancy


title: E_SRT1_P0

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium


title: Choroid plexus 18M 3

value: 60 weeks


title: S_PR2_P0


title: S_PR1_P0


title: Choroid plexus 18M 1


title: Choroid plexus 18M 2


title: E_SRT1_HPL

value: endometrial epithelial cells


title: E_C5_SFM

value: passage 1, serum-free media treatment

value: SFM


title: lib94748

value: Splenocyte

value: CD4+ T cell

value: Naïve CD4+ T Cells

value: D1A dlckCre+


title: Choroid plexus 12M 2

value: Choroid plexus

value: 48 weeks

value: Whole tissue

value: Wistar


title: E_SR6_SFM

value: secretory phase, patient experiencing recurrent implantation failure


title: S_SR5_HPL

value: endometrial stromal cells

value: passage 1, human platelet lysate treatment


title: S_C5_SFM

value: proliferative phase, control patient with recent pregnancy


title: E_SR6_P0

value: passage 0


title: S_C4_SFM


title: S_C4_HPL

value: HPL


title: E_SR5_HPL

value: endometrial epithelial cells


title: Choroid plexus 12M 1

value: Male


title: E_SR5_SFM

value: passage 1, serum-free media treatment

value: SFM


title: S_C4_P0


title: Choroid plexus 6M 3

value: 24 weeks


title: E_SR5_P0


title: E_SR4_P0


title: Choroid plexus 6M 2


title: E_C4_HPL


title: Choroid plexus 6M 1


title: Choroid plexus 12M 3


title: E_C4_SFM


title: Choroid plexus 3M 3

value: 12 weeks


title: S_SR3_HPL


title: S_SR3_P0


title: E_SR3_HPL


title: E_C3_SFM


title: S_SRT6_SFM

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium


title: Choroid plexus 1M 2

value: Choroid plexus

value: 4 weeks


title: E_SR3_P0


title: Choroid plexus 3M 2

value: Whole tissue


title: S_C2_HPL


title: S_SR2_SFM


title: S_SRT6_P0


title: S_SRT5_P0


title: E_SR2_HPL


title: NRP2neg CD4+ T cells 16h activation replicate 4

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
After QC and adapter trimming, alignment was performed using the 2-pass STAR aligner with the human reference genome.
Counts were normailzed for total read-depth using the DESeq2 method in the R Statistical Computing Environment.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include median of ratio values for each sample

source_name: CD4+ T cell

growth_protocol: Human CD4+ T cells were purified from freshly isolated PBMC and cultured in RPMI 1640 supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.75 g/l sodium bicarbonate, 100 U/ml penicillin/streptomycin, 0.1 mM non-essential amino acids and 50 µM 2-mercaptoethanol.

extract_protocol:
Total RNA was isolated using TRIZOL.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit following manufacturer's protocols.

treatment_protocol: Some CD4+ T cells were in vitro activated with 3 mcg/ml phytohemagglutinin for 16 hours. NRP2pos and NRP2neg cells were subsequently FACS-sorted and lyzed immediately in Trizol.

value: CD4+ T cell

tag: condition

value: stimulated


title: Choroid plexus 3M 1

value: Wistar


title: S_SRT4_HPL

value: endometrial stromal cells

value: passage 1, human platelet lysate treatment


title: S_C1_HPL

value: proliferative phase, control patient with recent pregnancy


title: NRP2neg CD4+ T cells 0h activation replicate 4

value: control


title: Choroid plexus 1M 3


title: S_C1_SFM


title: E_SR2_P0

value: endometrial epithelial cells

value: secretory phase, patient experiencing recurrent implantation failure

value: passage 0


title: S_SRT4_P0


title: E_SR3_SFM

value: passage 1, serum-free media treatment

value: SFM


title: Choroid plexus 1M 1

value: Male


title: E_SR2_SFM


title: S_SR1_SFM


title: S_SRT5_SFM

value: secretory phase, patient experiencing recurrent implantation failure and thin endometrium


title: NRP2neg CD4+ T cells 16h activation replicate 3


title: E_SRT3_SFM


title: S_SR3_SFM


title: E_SR1_HPL

value: HPL


title: NRP2pos CD4+ T cells 0h activation replicate 4


title: S_SR2_P0


title: 7H-8H-9G_9mo_M_ATAC_2

description: Library name: XH_449

library_source: genomic single cell

value: Amygdala (AMY)

value: WT

value: male

tag: batch


title: NRP2pos CD4+ T cells 16h activation replicate 4

value: CD4+ T cell

value: stimulated


title: S_SRT1_HPL

value: endometrial stromal cells


title: S_SRT4_SFM


title: NRP2pos CD4+ T cells 16h activation replicate 3


title: E_SR1_SFM


title: S_SRT1_SFM


title: E_SRT3_P0


title: NRP2pos CD4+ T cells 0h activation replicate 3


title: S_SR1_P0


title: NRP2pos CD4+ T cells 16h activation replicate 2


title: E_SR1_P0


title: S_SR6_HPL

value: passage 1, human platelet lysate treatment


title: 5E-6E_9mo_M_ATAC_1

description: Library name: XH_438

value: Caudate Putamen (CP)


title: NRP2neg CD4+ T cells 16h activation replicate 2


title: 5E-6E_9mo_M_ATAC_2

description: Library name: XH_448


title: NRP2neg CD4+ T cells 0h activation replicate 2

value: control


title: NRP2pos CD4+ T cells 0h activation replicate 2


title: NRP2neg CD4+ T cells 0h activation replicate 3


title: 3F-4E_9mo_M_ATAC_2

description: Library name: XH_450

value: Nucleus Accumbens (ACB)


title: PBMC, NR, TNFi, Pre, KAS29_KAS30_KAS31

city: Daejeon

first: Song

last: Woogil

address: KAIST, Daejeon 34141, Korea

department: Graduate School of Medical science and engineering

country: South Korea

institute: KAIST

description: 10x Genomics

data_processing:
All data were processed by cellranger v3.0.2 and manipulated and visualized by R v4.1.1 and Seurat v4.0.2.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

source_name: Blood (PBMC)

extract_protocol:
Single cell RNA was extracted from the PBMCs of the patients with ankylosing spondylitis
cDNA libraries were constructed using a single-cell RNA-seq kit, following standard protocols.

value: Blood (PBMC)

tag: disease state

value: Ankylosing Spondylitis (AS)


title: 3F-4E_9mo_M_ATAC_1

description: Library name: XH_440

tag: Sex


title: 7H-8H-9G_9mo_M_ATAC_1

description: Library name: XH_441


title: NRP2pos CD4+ T cells 16h activation replicate 1


title: S_SR4_HPL

value: secretory phase, patient experiencing recurrent implantation failure


title: S_SR5_SFM

value: passage 1, serum-free media treatment

value: SFM


title: S_SR5_P0

value: passage 0


title: NRP2pos CD4+ T cells 0h activation replicate 1


title: Cnt1

first: Silvia

last: Marino

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary University of London

data_processing:
Raw data was quality checked by FastQC v0.12.1 and trimmed using TrimGalore v0.6.10
Quantification of the counts was carried out using Salmon v1.10.2
Differential expression analysis was performed in DESeq2 using the Wald test, genes with no counts at all and counts per million (CPM) being 0 in more than half of the irradiated or control samples were filtered out.
Gene set enrichment analysis was performed using g:Profiler and the ranked DESeq2 Wald statistic of all genes
Assembly: genome GRCh38 (hg38) using Salmon v1.10.2
Supplementary files format and content: comma separated values of counts of the filtered genes for irradiated samples
Supplementary files format and content: comma separated values of counts of the filtered genes for control samples

source_name: Formalin fixed Paraffin embedded (FFPE) brain

growth_protocol: COs were developed from patient-derived expanded potential stem cell lines and were maintained in Stemcell™ mTeSR Plus medium.  For the development of COs, the STEMdiff™ Cerebral Organoid Kit was utilised and 1X Pen/Strep was added during the maintenance phase.

extract_protocol:
RNA from the FFPE tissue was extracted using Norgen FFPE RNA/DNA Purification plus kit.
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina NovaSeq6000PE150 technology.

treatment_protocol: Irradiation was performed using X-Ray Biological Irradiator from Queen Mary Biological Science Unit and radiation dose of 24Gy was administered at 8.5Gy/min. CO-related data were collected 4 weeks after the irradiation.

value: Control


title: PBMC, NR, TNFi, Post, KAS26_KAS27_KAS28

description: 10x Genomics


title: PBMC, NR, TNFi, Pre, KAS26_KAS27_KAS28

description: 10x Genomics


title: S_SR4_SFM


title: 2A-3A_9mo_M_ATAC_1

description: Library name: XH_401

source_name: Frontal cortex (FC)

value: Frontal cortex (FC)


title: PBMC, NR, TNFi, Post, KAS29_KAS30_KAS31

description: 10x Genomics


title: S_SR6_SFM


title: NRP2neg CD4+ T cells 0h activation replicate 1


title: 13D-14C_9mo_M_ATAC_2

description: Library name: XH_451

source_name: DR+LC+PAG+PCG (PAG/PCG)

value: DR+LC+PAG+PCG (PAG/PCG)

value: WT


title: 13D-14C_9mo_M_ATAC_1

description: Library name: XH_444

value: male


title: RT1

value: Formalin fixed Paraffin embedded (FFPE) brain

value: Irradiated


title: E_SR4_HPL

value: endometrial epithelial cells

value: passage 1, human platelet lysate treatment

value: HPL


title: RT2


title: 12D-13B_9mo_M_ATAC_2

description: Library name: XH_418

value: Entorhinal cortex (ENT)


title: S_SR4_P0

value: endometrial stromal cells


title: RT3


title: BSR166-Ad-950

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
For trimming we used FlexBar, which returned a greater number of reads, with a low number of singletons (< 2%) compared to the other adapters. Subsequently, the trimming and quality analysis of the reads by FASTQC and MULTIQC (EWELS et al., 2016) the files were aligned using the HISAT2 tool (Hierarchical Indexing for Transcript Alignment), which aligns the data in a hierarchical manner following a scheme of indexing based on the Burrows-Wheeler transformation and the Ferrafina-Manzini index (KIM, DAEHWAN; LANGMEAD; SALZBERG, 2015). The Stringtie platform was used to reconstruct the transcripts, calculate the number and size. The String Merge tool was used for concatenation, and Features Counts for counting readings in the alignment (LIAO; SMYTH; SHI, 2014). DESeq2 (v1.26.0) (LOVE et al., 2014) was used to estimate the change in feature expression between conditions.
Genome_build: Reads are in .fastq format and contain the raw base calls from sequencing. Alignment files are in .bam format and contain mapped reads.
Supplementary_files_format_and_content: Normalized abundance measurements are in .txt format as the output from DESeq2.

source_name: Frozen adrenocortical tumor tissue

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) following manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age at diagnosis (months)

tag: gender

value: female

tag: outcome

value: alive

tag: recurrence

value: absent


title: BSR167-Ad-487-08


title: 11E-11F-12E_9mo_M_ATAC_2

description: Library name: XH_414

source_name: Posterior hippocampus (PHC)

tag: tissue

value: Posterior hippocampus (PHC)


title: NRP2neg CD4+ T cells 16h activation replicate 1

tag: cell type

value: CD4+ T cell

value: stimulated


title: 2A-3A_9mo_M_ATAC_2

description: Library name: XH_452

value: Frontal cortex (FC)


title: E_SR4_SFM

source_name: endometrial epithelial cells

value: secretory phase, patient experiencing recurrent implantation failure

value: passage 1, serum-free media treatment

value: SFM


title: 12D-13B_9mo_M_ATAC_1

description: Library name: XH_416

value: WT

value: male


title: S_SR2_HPL

source_name: endometrial stromal cells


title: RT6

value: Formalin fixed Paraffin embedded (FFPE) brain

value: Irradiated


title: BSR165-Ad-150

value: present


title: PBMC, R, TNFi, Post, CITE, KAS07_KAS08

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

library_source: other

data_processing:
The sequenced reads were aligned using cellranger count (v7.1.0) to cellranger reference GRCh38 (GRCh38-2020-A).
Aligned files were aggregated with cellranger aggr (v7.1.0; --nosecondary)
Mulitplexed samples were seperated based on individual variants using souporcell, and annotate sample with
Assembly: hg38
Supplementary files format and content: Gene expression matrix

molecule: protein

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation.
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.1. The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on DNBSEQ-G400.

value: PBMC

tag: responsiveness

value: Responder

value: TNFi


title: BSR163-Ad-1993

value: female

value: alive


title: S_SR1_HPL

value: endometrial stromal cells

value: passage 1, human platelet lysate treatment

value: HPL


title: RT5


title: 11E-11F-12E_9mo_M_ATAC_1

description: Library name: XH_412

value: Posterior hippocampus (PHC)


title: BSR161-Ad-1340

value: deceased


title: RT7


title: 2A-3A_2mo_M_ATAC_2

description: Library name: XH_485

value: Frontal cortex (FC)


title: PBMC, R, TNFi, Pre/Post, CITE, KAS06_KAS07

value: TNFi or TNFi_base


title: RT4


title: RT8


title: BSR160-Ad-799


title: 2A-3A_2mo_M_ATAC_1

description: Library name: XH_483

value: WT


title: BSR164-Ad-2049

value: absent


title: BSR154-Ad-171


title: RT9

value: Formalin fixed Paraffin embedded (FFPE) brain


title: PBMC, NR, TNFi, Pre, CITE, KAS24_KAS25

value: Non responder


title: 12D-13B_2mo_M_ATAC_2

description: Library name: XH_486

source_name: Entorhinal cortex (ENT)

value: Entorhinal cortex (ENT)

value: male


title: 12D-13B_2mo_M_ATAC_1

description: Library name: XH_484


title: Cnt3

value: Control


title: BSR153-Ad-160-07


title: PBMC, NR, TNFi, Post, CITE, KAS24_KAS25

value: PBMC

value: TNFi


title: Cnt4


title: PBMC, NR, IL17i, Pre, CITE, KAS15_KAS16_KAS17


title: BSR147-Ad-164

value: female

value: present


title: 7H-8H-9G_18mo_M_ATAC_1

description: Library name: XH_437

source_name: Amygdala (AMY)

value: Amygdala (AMY)


title: 7H-8H-9G_18mo_M_ATAC_2

description: Library name: XH_439


title: Cnt6


title: PBMC, R, TNFi, Pre, CITE, KAS12_KAS13_KAS14

value: Responder


title: BSR140-Ad-2711

value: alive


title: 5E-6E_18mo_M_ATAC_1

description: Library name: XH_421

source_name: Caudate Putamen (CP)

value: Caudate Putamen (CP)


title: BSR139-Ad-2451


title: 5E-6E_18mo_M_ATAC_2

description: Library name: XH_423


title: Cnt7


title: PBMC, R, TNFi, Post, CITE, KAS12_KAS13_KAS14


title: PBMC, R, TNFi, Pre, CITE, KAS06_KAS08


title: BSR138-Ad-2329


title: 3F-4E_18mo_M_ATAC_2

description: Library name: XH_422

source_name: Nucleus Accumbens (ACB)

value: Nucleus Accumbens (ACB)


title: PBMC, NR, IL17i, Pre, CITE, KAS04


title: Cnt8


title: 3F-4E_18mo_M_ATAC_1

description: Library name: XH_420


title: BSR142-Ad-59-08


title: Cnt9


title: 2A-3A_18mo_M_ATAC_2

description: Library name: XH_454

value: Frontal cortex (FC)


title: Cnt5


title: PBMC, NR, IL17i, Post, CITE, KAS15_KAS16_KAS17


title: 2A-3A_18mo_M_ATAC_1

description: Library name: XH_453

value: WT


title: siRNA_bcat_BL37

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 7
siRNA_bcat_BL37

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic
Reads were aligned to mouse reference genome mm10 by STAR aligner
Gene counts were quantified by STRA
Assembly: mm10
Supplementary files format and content: TAB

source_name: liver

extract_protocol:
Using fresh frozen liver tissue, RNA was isolated using the RNeasy Mini kit (Qiagen) according to standard manufacturer protocols for tissue RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: strain

value: FVB/NJ


title: PBMC, NR, TNFi, Post, CITE, KAS04

value: Non responder


title: 13D-14C_18mo_M_ATAC_2

description: Library name: XH_443

value: DR+LC+PAG+PCG (PAG/PCG)


title: siRNA_bcat_BL38

description:
Library name: Sample 8
siRNA_bcat_BL38


title: siRNA_bcat_BL39

description:
Library name: Sample 9
siRNA_bcat_BL39


title: PBMC, NR, IL17i, Post, CITE, KAS04


title: PBMC, NR, TNFi, Pre, CITE, KAS04


title: siRNA_control_BL30

description:
Library name: Sample 5
siRNA_control_BL30


title: PBMC, NR, IL17i, Pre, CITE, KAS18_KAS19_KAS20


title: siRNA_control_BL31

description:
Library name: Sample 6
siRNA_control_BL31


title: PBMC, NR, IL17i, Post, CITE, KAS18_KAS19_KAS20


title: RT10

value: Formalin fixed Paraffin embedded (FFPE) brain

value: Irradiated


title: 13D-14C_18mo_M_ATAC_1

description: Library name: XH_442

value: male


title: RT11


title: Cnt11

value: Control


title: Cnt10


title: Cnt12


title: PBS_vehicle_BL28

description:
Library name: Sample 3
PBS_vehicle_BL28


title: siRNA_control_BL29

description:
Library name: Sample 4
siRNA_control_BL29


title: 12D-13B_18mo_M_ATAC_1

description: Library name: XH_417

value: Entorhinal cortex (ENT)


title: 12D-13B_18mo_M_ATAC_2

description: Library name: XH_419


title: 11E-11F-12E_18mo_M_ATAC_2

description: Library name: XH_415

value: Posterior hippocampus (PHC)


title: PBMC, NR, IL17i, Pre, CITE, KAS21_KAS22_KAS23

value: PBMC


title: PBS_vehicle_BL27

description:
Library name: Sample 2
PBS_vehicle_BL27


title: RT13


title: PBMC, NR, IL17i, Post, CITE, KAS21_KAS22_KAS23


title: PBS_vehicle_BL26

description:
Library name: Sample 1
PBS_vehicle_BL26


title: PBMC, NR, IL17i, Pre, CITE, KAS05


title: RT14


title: 11E-11F-12E_18mo_M_ATAC_1

description: Library name: XH_413


title: PBMC, NR, TNFi, Pre, CITE, KAS05


title: non-hematopoetic cells, 5TGM1 myeloma, 1 individual

city: New York

first: Gareth

last: Morgan

address: 550 1st Avenue

institute: NYU Langone Health

description:
Library name: Library6
10x Genomics

data_processing:
Gene expression count matrices were generated using cellranger v5 and processed in R using Seurat v4, including QC, library integration, data normalization, and clustering.
Assembly: Mouse mm39
Supplementary files format and content: filtered cellranger outputs (barcodes, features, matrix)

source_name: bone marrow

extract_protocol:
BM stroma cells were enriched by FACS sorting of live cells (Dapi-/Calcein+), which were negative for erythroid markers (CD71/Ter119) and immune lineage markers (CD45/CD3/B220/CD19/Gr1/CD11b).
Libraries were pooled as per 10x Chromium v3 protocol.

value: bone marrow

value: stromal

value: 5TGM1 injected

value: 7-8 weeks


title: PBMC, NR, TNFi, Post, CITE, KAS05

value: TNFi


title: POU2F1.BLC414

description:
Library name: Sample 5
POU2F1.BLC414

value: S45Y-beta-catenin + hMET + POU2F1 HCC model via SB-HDTVi


title: non-hematopoetic cells, PBS healthy, 1 individual

description:
Library name: Library5
10x Genomics


title: POU2F1.BLC413

description:
Library name: Sample 4
POU2F1.BLC413

value: liver


title: RT12


title: TUMOR.CTRL.BLC411

description:
Library name: Sample 3
TUMOR.CTRL.BLC411

value: FVB/NJ

value: S45Y-beta-catenin + hMET HCC model via SB-HDTVi


title: non-hematopoetic cells, 5TGM1 myeloma, 3 individuals, technical replicate of library 3

description:
Library name: Library4
10x Genomics


title: non-hematopoetic cells, 5TGM1 myeloma, 3 individuals

description:
Library name: Library3
10x Genomics


title: Arabidopsis, TSA,HTA12, 12DAG, Rep1

city: Xianyang

first: Mingming

last: Zhao

address: Taicheng Road,Yangling District

country: China

institute: Northwest A&F University China

description: Library name: 12DAG_TSA_HTA12_Rep1,ChIP

data_processing:
(1)Filter:ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of >20 for the final base.Reads shorter than 35 bp after trimming were discarded.(2)Alignment:The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using Bowtie2 and sorted and indexed using the samtools suite (version 1.17).(3)Remove: PCR duplicates were removed using Picard (version 3.0.0). (4)Callpeak:Peaks were identified using the “callpeak” function of MACS2 (version 2.2.6,). (5)Coverage tracks were calculated: normalizing using RPGC (effective genome size 119482912) –bin size 10, normalization method using RPGC reads per genome coverage), creating bigwig files.(6)Plot:The metagene results were drawn using deepTools(version 3.5.2).
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated using the Deeptools  (version 3.5.2).The BigWig files for making plot were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Generally, plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C. Plants used for ChIP-Seq and TSA treatments were grown in MS media supplemented with 1% sucrose under long-day photoperiod and ~21°C. In all cases, seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
1)Crosslink protein-DNA interactions with formaldehyde; 2) Fragment chromatin via sonication or enzymatic digestion; 3) Immunoprecipitate target protein-DNA complexes using specific antibodies; 4) Reverse crosslinking and purify DNA, followed by library construction for sequencing .
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling

tag: chip-antibody


title: Arabidopsis, TSA,HTA12, 12DAG, Rep2

description: Library name: 12DAG_TSA_HTA12_Rep2,ChIP


title: Arabidopsis, TSA,HTA67, 12DAG, Rep2

description: Library name: 12DAG_TSA_HTA67_Rep2,ChIP

value: CD771，杭州景杰


title: Arabidopsis, TSA,HTA67, 12DAG, Rep1

description: Library name: 12DAG_TSA_HTA67_Rep1,ChIP


title: TUMOR.CTRL.BLC410

description:
Library name: Sample 2
TUMOR.CTRL.BLC410

tag: treatment


title: non-hematopoetic cells, PBS healthy, 3 individuals

description:
Library name: Library1
10x Genomics

tag: age


title: Arabidopsis, TSA,H2A.Z, 12DAG, Rep2

description: Library name: 12DAG_TSA_H2A.Z_Rep2,ChIP


title: TUMOR.CTRL.BLC409

description:
Library name: Sample 1
TUMOR.CTRL.BLC409


title: BL_586 LNP-CTNNB1 R Phenotype

description:
Library name: Sample 5
BL_586 LNP-CTNNB1 R Phenotype

data_processing:
10X Space Ranger was used to generate the gene by spot count matrix
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: TSV file
Supplementary files format and content: features.tsv.gz: TSV file
Supplementary files format and content: matrix.mtx.gz: MTX file
Supplementary files format and content: H&E staining: TIF file
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue sections of 10um thickness were cut from mouse liver tumor FFPE blocks and were deparaffinized, H&E stained, then decrosslinked using standard 10X genomics protocols. Regions of interest (ROIs) were selected by outlining ~6.5mm2 areas.
Standard Visium CytAssist protocols were used for FFPE tissue for generation of sequence ready libraries. Quality control parameters were a DV200% >= 30%.

value: BL_586 LNP-CTNNB1 R Phenotype


title: BL_585 LNP-CTNNB1 R Phenotype

description:
Library name: Sample 4
BL_585 LNP-CTNNB1 R Phenotype

value: BL_585 LNP-CTNNB1 R Phenotype


title: Arabidopsis, TSA,H3K9K14Ac, 12DAG, Rep2

description: Library name: 12DAG_TSA_H3K9K14Ac_Rep2,ChIP


title: CTNNBT_MET_IRF2_4


title: POU2F1.BLC415

description:
Library name: Sample 6
POU2F1.BLC415


title: CTNNBT_MET_IRF2_1


title: Arabidopsis, TSA,H3K27Ac, 12DAG, Rep2

description: Library name: 12DAG_TSA_H3K27Ac_Rep2,ChIP

value: 39135，Active Motif


title: CTNNBT_MET_IRF2_3


title: Arabidopsis, TSA,H3K27Ac, 12DAG, Rep1

description: Library name: 12DAG_TSA_H3K27Ac_Rep1,ChIP


title: CTNNBT_MET_IRF2_2


title: CTNNBT_MET_CTRL_2


title: Arabidopsis, TSA,H3K9K14Ac, 12DAG, Rep1

description: Library name: 12DAG_TSA_H3K9K14Ac_Rep1,ChIP


title: BL_584 LNP-CTNNB1 NR phenotype

description:
Library name: Sample 2
BL_584 LNP-CTNNB1 NR phenotype

value: BL_584 LNP-CTNNB1 NR phenotype


title: non-hematopoetic cells, PBS healthy, 3 individuals, technical replicate of library 1

description:
Library name: Library2
10x Genomics


title: Arabidopsis, TSA,H2A.Z, 12DAG, Rep1

description: Library name: 12DAG_TSA_H2A.Z_Rep1,ChIP


title: BL_587 LNP-CTNNB1 NR phenotype

description:
Library name: Sample 3
BL_587 LNP-CTNNB1 NR phenotype

value: BL_587 LNP-CTNNB1 NR phenotype


title: CTNNBT_MET_CTRL_1


title: Arabidopsis, Mock,HTA12, 12DAG, Rep2

description: Library name: 12DAG_Mock_HTA12_Rep2,ChIP


title: Arabidopsis, Mock,HTA12, 12DAG, Rep1

description: Library name: 12DAG_Mock_HTA12_Rep1,ChIP


title: Arabidopsis, TSA,H3, 12DAG, Rep1

description: Library name: 12DAG_TSA_H3_Rep1,ChIP


title: Nrf2_Bcat_TREAT_BL_572


title: ChAT-GFP positive liver B cells, 4 hours post-PHX, rep 7

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

description:
Library name: 9_S50
Column name in raw_RSEM_counts.txt: X9_S50

data_processing:
Adaptor content was trimmed using Trim Galore (v 0.6.6) on paired reads with default parameters.
Trimmed reads were then aligned to the mm10_STAR_2.7.9a mouse reference using STAR (v 2.7.9a).
Gene counts and transcripts per million (TPM) normalization were determined using RSEM (v 1.3.0).
Assembly: mm10
Supplementary files format and content: raw_RSEM_counts.txt: tab-delimited text file containing raw counts (*_counts), TPM normalized (*_tpm), and FPKM normalized (*_fpkm) values for all samples.
Supplementary files format and content: Sample_.genes.results: tab-delimited file containing RSEM gene alignment outputs for each sample.

source_name: Liver

extract_protocol:
ChAT-GFP reporter mice were subjected to 70% PHX or Sham surgery and liver non-parenchymal cells were enriched as described above. B cells were stained and sorted on a BD FACSAria Fusion flow cytometry cell sorter at the Princess Margaret Flow Facility. RNA was extracted using the RNAeasy micro kit (QIAGEN) based on the manufacturer’s instructions.
Sample library preparation was performed using a Mammalian Low Input V2 Pico kit (Takara) based on the manufacturer’s instructions.

value: Liver

value: Male

value: B lymphocyte

tag: mouse id

value: PHX

tag: fraction

value: GFP-Pos