title: PBMC_Patient_7_Post

city: Bethesda

first: Mohamed-Reda

last: Benmebarek

state: MD

address: 10 Center Drive

department: Thoracic and GI Malignancies Branch

institute: NIH

description:
scRNA-Seq 5' v2
refdata-gex-GRCh38-2020-A

data_processing:
Raw scRNA-Seq data derived from 10x Genomics Single Cell Chromium 5' mRNA libraries was processed using Cell Ranger v6.1.2 run with default parameter settings and the GRCh38-2020-A transcriptome reference to generate the counts in the filtered_feature_bc_matrix.h5 files.
Assembly: hg38 (Cell Ranger version 6.1.2, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg38_6.1.2)
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in the h5 data format (one h5 file per sample).

source_name: PBMC

growth_protocol: PBMC and liver cancer tumor biopsy isolation

extract_protocol:
Prior to single cell RNA sequencing, patient PBMCs were processed and frozen by the NIH biobanking resource as described in Heinrich et al. 2022. PBMC samples were thawed at 37°C for rapid recovery and washed with FACS buffer (BD, Cat. No. 554656). Cell count and viability were assessed on a CellometerAuto200 (Nexcelom Bioscience). Prior to single cell sequencing, live cells were purified by magnetically depleting dead cells using a Dead Cell Removal Kit  (Miltenyi Biotec, Cat.No. 130-090-101) and sorted using an AutoMACS Pro (Miltenyi Bitoec) following the manufacturer’s instructions. Next, sorted cells were instantly transferred for single-cell cell capture and library preparation. For bulk RNA sequencing, RNA was extracted from fresh-frozen needle biopsy tumor samples at baseline and post-treatment, whereas RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of Bioanalyzer 2100 system (Agilent Technologies, California, USA).  Heinrich, B., et al. The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma. Gut 71, 1161-1175 (2022).
10x Genomics Single Cell Chromium 5' mRNA libraries were prepared as instructed by the 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). The scRNA-Seq samples were counted and diluted in PBS + 0.04% BSA, whereas the sample concentration and viability were assessed using the LunaFL fluorescent cell counter. The cellular samples were loaded in the lanes on the Chromium Connect according to the 10X Genomics 5’ v2 Single Cell User Guide with a single capture lane per sample targeting recovery of up to 6,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency. All steps of the library preparation were performed on the Connect and quality control were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide. Bulk RNA-Seq libraries were prepared using the NEB next Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instruction.

treatment_protocol: Tremilimumab + Durvalumab + Bevacuzumab

value: PBMC

value: Immunotherapy


title: PT75_Tumor

status: Public on Mar 14 2025

type: SRA

city: Baltimore

first: Roy

last: Elias

state: Maryland

address: 201 N Broadway

country: USA

institute: Johns Hopkins University

description:
Library name: NS129
column name in "tpm.txt" is library name

library_source: transcriptomic

data_processing:
FASTQ files were generated from the sequencer's output using Illumina bcl2fastq2 v.2.17.1.14 (RRID:SCR_015058) with default filters to select sequence reads for subsequent analyses. Trimgalore v0.6.7 (RRID:SCR_011847) was used to trim off the adaptor sequences and low-quality bases from the reads. The reads were aligned to the human reference genome (hg38) in a splice-aware fashion using RSEM v1.3.0 (RRID:SCR_000262) with STAR (RRID:SCR_004463) as the aligner. RSEM was also used for generating gene level expression estimates.
Assembly: hg38
Supplementary files format and content: txt files include tpm values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Tumor and normal adjacent tissue regions from nephrectomy specimens were identified on hematoxylin and eosin-stained slides by a genitourinary board-certified pathologist. These areas were macrodissected, and DNA/RNA were extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections using a DNA/RNA FFPE tissue kit (AllPrep DNA/RNA, Qiagen, Hilden, Germany).
Sequencing libraries were constructed using the Illumina TruSeq RNA exome kit (Illumina, Inc.)

tag: tissue

value: Tumor

tag: path grade

tag: Stage

tag: race

value: W

tag: Sex

value: Female

tag: sas

tag: amr

tag: eas

tag: eur

tag: afr

tag: ancestry bin

value: EUR

tag: age


title: 4112817

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

description: FL, cryo-preserved

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: Cy3, Cy5

molecule: genomic DNA

source_name: lymph node

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: FL, cryo-preserved


title: PBMC_Patient_7_Pre

library_source: transcriptomic single cell

tag: treatment

value: Untreated


title: PBMC_Patient_6_Post


title: GF_3X_PBS [ATAC_1_TGGATCTG]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

library_source: genomic

data_processing:
Paired-end ATAC-Seq reads were first assessed using FASTQC. Reads were trimmed using cutadapt to remove adapters and low quality reads below 30. Pair-end reads were then aligned against the GRCm39/mm10 mouse genome assembly with Bowtie (v2.3.0)84 in local mode, sensitive settings, and a maximum fragment size of 2000. Duplicated reads were marked using Picard (v.2.5.0). Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly paired, duplicated, aligned to mitochondrial genome, and/or aligned to ENCODE blacklist regions. Alignments with an insertion size of >100bp were removed to enrich for nucleosome-free reads. ATAC-Seq peaks were called for each replicate using MACS2, using --format BAMPE and --keep-dup all. IDR (v2.0.2) was used to determine consistency of peak detection between individual replicates and peaks with a threshold below 0.10 were merged between replicates for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: gzipped tagAlign file from Picard Suite that include the reads information.

organism: Mus musculus

growth_protocol: Adult male and female mice, and postnatal pups were used on a C57Bl/6J background (#000664, The Jackson Laboratory); NOD/ShiLtJ (#001976, The Jackson Laboratory) mice were obtained from the Jackson Laboratory. B6.Cg-Tg(Gfap-cre)73.12Mvs/J mice65 (The Jackson Laboratory, #012886) mice were crossed with B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J mice66 (The Jackson Laboratory, #007909) to generate Gfap(Cre/+);TdTomato(f/+) (TdTomatoGfap) mice. Postnatal pups were used from the NF-kB reporter strain FVB.Cg-Tg(HIV-EGFP,luc)8Tsb/J67 (The Jackson Laboratory, #027529) at P0-P3. Mice were kept in a pathogen-free facility at the Hale Building for Transformative Medicine at Brigham and Women’s Hospital in accordance with the IACUC guidelines. 10–12-week-old mice were used for stereotactic injection and EAE induction. Pups were sacrificed between P0-P3 for harvesting and culturing astrocytes. All procedures were reviewed and approved under the IACUC guidelines at Brigham and Women’s Hospital.

extract_protocol: After isolation of nuclei, transposition was performed using the kit (Illumina, #FC-121-1030). DNA was then amplified using NEBNext High Fidelity 2X PCR Master Mix (New England Biolabs, #M0541S) for 5 cycles. DNA quantity was then measured using a Viia 7 Real-Time PCR System (Thermo Fisher Scientific) and the number of cycles required to achieve 1/3 of maximal SYBR Green fluorescence was determined and libraries were amplified accordingly. TruSeq adaptors (universal: Ad1_noMX and barcoded: Ad2.1-Ad2.24) were used according to the Buenrostro protocol. Libraries were purified using MiniElute PCR Purification Kit (Qiagen, #28006) followed by double sided Agencourt AMPure XP bead purification (Beckman Coulter, #A63881) to remove primer dimers and large DNA fragments. Libraries were analyzed on a 2100 Bioanalyzer (Agilent Technologies) and High Sensitivity DNA Kit (Agilent Technologies, #5067-4626). Libraries were sequenced by Genewiz on an Illumina HiSeq 4000 by 2x75 bp paired end sequencing.

treatment_protocol: C57Bl/6J mice at age 10-12 weeks were anesthetized using 1-3% isoflurane mixed with oxygen. Heads were shaved and cleaned using 70% ethanol and Betadine (Thermo Fisher, #19-027132) followed by a medial incision of the skin to expose the skull. Mice were injected with 100 ng/mL IL-1β (R&D Systems, #401-ML-005, 100 µg/mL stock in PBS) and 50 ng/mL TNF-α (R&D Systems, #410-MT-010, 100 µg/mL stock in PBS) diluted in PBS or PBS. At day7, mice were re-injected (2X) or injected (1X) with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. For EAE experiments, mice were injected with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. The lateral ventricles were targeted bilaterally using the coordinates: +/- 1.0 (lateral), -0.44 (posterior), -2.2 (ventral) relative to Bregma. Mice were injected by two 5µL injections using a 25 µL Hamilton syringe (Sigma-Aldrich, #20787) on a stereotaxic alignment system (Kopf, #1900) and the incision was sutured.

tag: cell type

value: sorted astrocytes

tag: strain

value: female

value: 10 weeks

value: Germ Free Mice that are injected with PBS 3 times


title: PBMC_Patient_6_Pre


title: GF_3X_PBS [ATAC_1_GTCGTGAT]


title: PT73_Tumor

description:
Library name: NS125
column name in "tpm.txt" is library name


title: PT73_Normal

description:
Library name: NS126
column name in "tpm.txt" is library name

source_name: Normal

value: Normal


title: 4158726

description: FL, cryo-preserved


title: 4177810

description: FL, cryo-preserved


title: PBMC_Patient_5_Post


title: 4163297

description: FL, cryo-preserved


title: GF_3X_PBS [ATAC_1_GTAGAGGA]


title: 4158483

description: FL, cryo-preserved


title: PBMC_Patient_5_Pre


title: PT70_Normal

description:
Library name: NS120
column name in "tpm.txt" is library name


title: GF_3X_PBS [ATAC_1_AAGAGGCA]


title: PBMC_Patient_4_Post


title: GF_3X_Cytokine [ATAC_1_GTGTGGTG]

value: Germ Free Mice that are injected with TNFalpha stimulation 3 times


title: PT70_Tumor

description:
Library name: NS119
column name in "tpm.txt" is library name


title: 4112447

description: FL, cryo-preserved


title: PBMC_Patient_4_Pre


title: 4138652

description: FL, cryo-preserved


title: GF_3X_Cytokine [ATAC_1_AGGTTGGG]


title: PBMC_Patient_3_Post


title: GF_3X_PBS [ATAC_1_ACCACTGT]


title: 4131738

description: FL, cryo-preserved


title: PT67_Normal

description:
Library name: NS116
column name in "tpm.txt" is library name

value: Male


title: GF_3X_Cytokine [ATAC_1_GAGGGGTT]


title: 4164330

description: FL, cryo-preserved


title: PT67_Tumor

description:
Library name: NS115
column name in "tpm.txt" is library name


title: PBMC_Patient_3_Pre


title: GF_3X_Cytokine [ATAC_1_TGCTGGGT]


title: PT66_Tumor

description:
Library name: NS113
column name in "tpm.txt" is library name


title: PBMC_Patient_2_Post


title: GF_3X_Cytokine [ATAC_1_CCGTTTGT]


title: PT72_Tumor

description:
Library name: NS123
column name in "tpm.txt" is library name


title: PBMC_Patient_2_Pre


title: Heart tissue, doxorubicin treated biorep3

city: Cluj-Napoca

first: Emilia

last: Anca

state: Cluj

address: Clinicilor St. no. 7

country: Romania

institute: Faculty of Biology and Geology, Babes-Bolyai University

description: Library name: Doxorubicin 3

data_processing:
RNA-Seq was performed by Macrogen (Macrogen Amsterdam, The Netherlands). Libraries were prepared according to the standard protocol for the Watchmaker mRNA library (Watchmaker Genomics, Inc.) and sequenced on the Illumina NovaSeq6000 platform (Illumina, Inc.). The raw Fastq files were initially subjected to quality assessment via FastQC (Andrews, 2010), followed by trimming and filtering using Trimmomatic (Bolger et al., 2014) to eliminate low-quality bases and adapter sequences. The trimming parameters were as follows: ILLUMINACLIP:2:30:10, LEADING:10, TRAILING:10, SLIDINGWINDOW:4:15, HEADCROP:12, CROP:85 and MINLEN:36. The processed reads were then aligned using the STAR aligner (Dobin et al., 2013). To generate the genome index, the reference genome Rattus norvegicus mRatBN7.2 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015227675.2) FASTA file and the corresponding RefGene GTF annotation from UCSC were utilized (Perez et al., 2025). Gene-level quantification was subsequently performed with HTSeq (Putri et al., 2022), counting reads that mapped to exons (-t exon), associating counts with gene identifiers (-i gene_id), and resolving read overlaps using the union model (-m union).
Assembly: Rattus norvegicus mRatBN7.2
Supplementary files format and content: .tsv file of counts

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen) and the RNeasy Mini Kit (QIAGEN) using manufacturer’s instructions.
Libraries were prepared according to the standard protocol for the Watchmaker mRNA library (Watchmaker Genomics, Inc.) and sequenced on the Illumina NovaSeq6000 platform (Illumina, Inc.).

treatment_protocol: DOX group was treated with 3.75 mg/kg doxorubicin hydrochloride weekly, for 4 weeks via intravenous injection. Control group received saline injections using the same protocol.

value: heart


title: 4159170

description: FL, cryo-preserved


title: PT64_Normal

description:
Library name: NS110
column name in "tpm.txt" is library name

value: AFR


title: 4147081

description: FL, cryo-preserved


title: Heart tissue, doxorubicin treated biorep2

description: Library name: Doxorubicin 2


title: PBMC_Patient_1_Pre

value: PBMC


title: PBMC_Patient_1_Post

value: Immunotherapy


title: PT64_Tumor

description:
Library name: NS109
column name in "tpm.txt" is library name

value: Tumor


title: PT69_Tumor

description:
Library name: NS118
column name in "tpm.txt" is library name

value: W


title: PT63_Normal

description:
Library name: NS108
column name in "tpm.txt" is library name


title: 4149246

description: FL, cryo-preserved


title: PT63_Tumor

description:
Library name: NS107
column name in "tpm.txt" is library name


title: 4144366

description: FL, cryo-preserved


title: HF-5-blood

city: Wuhan

first: Si

last: Zhang

state: Hubei

address: Jiefang Avenue

country: China

institute: Huazhong University of Science and Technology

description:
normalized_blood_immune_cell_matrix.csv
barcode-9

data_processing:
Raw sequencing files were filtered for sequence quality, cells with <500 genes expressed or with high mitochondrial gene content were identified and removed from the datasets, and doublets with relatively high library size were also removed from the analysis.
Reads were then mapped to hg38 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).
Raw readcount tables were provided to the unsupervised clustering pipeline Seurat, and for each cell, the counts were normalized by the total counts and then multiplied by a scale factor of 100,000 before transforming to the log2 scale.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene expression for every single cell

source_name: peripheral blood from HF patient

extract_protocol:
Heart pieces were digested in RPMI-1640 medium containing 0.04 mg/ml Liberase TH (Roche, Switzerland) and 1 mg/ml DNase (Sigma, USA) in a 37-degree water bath with rotation for 7 minutes. The supernatant was obtained and then transferred to 5 ml of RPMI-1640 medium supplemented with 10% foetal bovine serum (Gibco, USA). After another 5-7 rounds of digestion with few residual tissue fragments, the cell suspensions were pooled and filtered two times through 70 μm and 40 μm strainers, sequentially (BD Falcon, USA). The cell suspensions were washed two times with PBS. Heart-infiltrating mononuclear cells and peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll Paque PREMIUM (GE, USA). Dead cells in cell suspensions were removed using a Dead Cell Removal Kit (Miltenyi Biotec, Germany) according to the manufacturer’s instructions.Processed cell suspension were encapsulated into droplets at a concentration of 700 cells/μL,which resulted in expected mRNA barcoding of ~6,000 single cells with a multiplet rate of 5.4%. After the RT step, the droplets were broken, and barcoded cDNA was purified with DynaBeads, followed by 14 cycles of PCR amplification. The resulting amplified cDNA was sufficient to construct 5’ gene expression libraries and T cell receptor-enriched libraries. The cDNA of single-cell transcriptomes was fragmented, double-sized selected with SPRI beads, and sequenced on an Illumina NextSeq platform. The cDNA of single-cell transcriptomes was fragmented, double-sized selected with SPRI beads, and sequenced on an Illumina NextSeq platform.
RNA libraries were prepared for sequencing using Illumina protocols

tag: disease

value: heart failure

tag: etiology

value: DCM

value: peripheral blood


title: PT62_Normal

description:
Library name: NS106
column name in "tpm.txt" is library name

tag: tissue

value: EUR


title: 4105105

description: FL, cryo-preserved

value: FL, cryo-preserved


title: Heart tissue, vehicle-treated biorep2

description: Library name: Control 2


title: Heart tissue, vehicle-treated biorep3

description: Library name: Control 3


title: HF-4-blood

description:
normalized_blood_immune_cell_matrix.csv
barcode-7

value: ICM


title: 4166503

description: FL, cryo-preserved


title: HF-3-blood

description:
normalized_blood_immune_cell_matrix.csv
barcode-5


title: 4188800

description: FL, cryo-preserved


title: Heart tissue, vehicle-treated biorep1

description: Library name: Control 1


title: 4199848

description: FL, cryo-preserved


title: PT62_Tumor

description:
Library name: NS105
column name in "tpm.txt" is library name

tag: path grade


title: HF-2-blood

description:
normalized_blood_immune_cell_matrix.csv
barcode-3


title: sdg2_Pol II Ser2p_rep2

city: beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

institute: Chinese Academy of Sciences

description: sdg2_Pol II Ser2p_merged.bw

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp.
Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Nuclei were extracted, and chromatin was sheared to generate 200-400bp fragments and immunoprecipitated with anti-RNA Pol II Ser5p (Abcam, ab5131) or anti-RNA Pol II Ser2p (Abcam, ab5095) antibody.
The immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

treatment_protocol: ChIP-seq was performed using 3-week-old seedlings, which were fixed with 1% formaldehyde.

value: Seedlings

tag: genotype

value: Pol II Ser2P (Abcam, ab5095)


title: 4170577

description: DLBCL, cryo-preserved

value: DLBCL, cryo-preserved


title: PT61_Normal

description:
Library name: NS104
column name in "tpm.txt" is library name

value: Normal

tag: Stage

tag: race

value: B

value: Female


title: HF-1-blood

description:
normalized_blood_immune_cell_matrix.csv
barcode-2


title: 4138527

description: DLBCL, cryo-preserved


title: Ctr-3-heart

description: heart tissue from normal heart

data_processing:
Raw sequencing files were filtered for sequence quality, cells with <500 genes expressed or with high mitochondrial gene content were identified and removed from the datasets, and doublets with relatively high library size were also removed from the analysis.
Reads were then mapped to hg38 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).
Raw readcount tables were provided to the unsupervised clustering pipeline Seurat, and for each cell, the counts were normalized by the total counts and then multiplied by a scale factor of 100,000 before transforming to the log2 scale.
Assembly: hg38
Supplementary files format and content: normalized_heart_immune_cell_matrix.csv: Matrix table with normalized gene expression for every single cell.
Supplementary files format and content: normalized_immune_cell_matrix.csv: Matrix table of all CD45+ immune cells.

source_name: normal heart

value: normal

value: heart


title: Heart tissue, doxorubicin treated biorep1

description: Library name: Doxorubicin 1


title: sdg2_Pol II Ser2p_rep1

description: sdg2_Pol II Ser2p_merged.bw


title: PT59_Normal

description:
Library name: NS100
column name in "tpm.txt" is library name

tag: Sex

tag: sas

value: AFR


title: h3.3ko;HTR5 K4A_Pol II Ser2p_rep1

description: h3.3ko;HTR5 K4A_Pol II Ser2p_merged.bw

value: h3.3ko;HTR5 K4A


title: Ctr-2-heart

description: heart tissue from normal heart


title: 4134434

description: DLBCL, cryo-preserved


title: 4176325

description: DLBCL, cryo-preserved


title: Ctr-1-heart

description: heart tissue from normal heart


title: PT59_Tumor

description:
Library name: NS99
column name in "tpm.txt" is library name

value: Tumor

tag: amr

tag: eas


title: 4175941

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_Pol II Ser2p_rep1

description: h3.3ko;HTR5_Pol II Ser2p_merged.bw


title: HF-5-heart

description: heart tissue from failing heart

source_name: failing heart

value: heart failure


title: 4141476

description: DLBCL, cryo-preserved


title: PT57_Normal

description:
Library name: NS96
column name in "tpm.txt" is library name

value: Male

tag: eur

tag: afr


title: HF-4-heart

description: heart tissue from failing heart


title: Col_Pol II Ser2p_rep2

description: Col_Pol II Ser2p_merged.bw

value: WT (Col)


title: HF-3-heart

description: heart tissue from failing heart


title: h3.3ko;HTR5_Pol II Ser2p_rep2

description: h3.3ko;HTR5_Pol II Ser2p_merged.bw


title: PT61_Tumor

description:
Library name: NS103
column name in "tpm.txt" is library name

tag: ancestry bin

tag: age


title: 4159421

description: DLBCL, cryo-preserved


title: PT57_Tumor

description:
Library name: NS95
column name in "tpm.txt" is library name


title: HF-2-heart

description: heart tissue from failing heart


title: h3.3ko;HTR5 K4A_Pol II Ser2p_rep2

description: h3.3ko;HTR5 K4A_Pol II Ser2p_merged.bw

tag: treatment


title: PT58_Tumor

description:
Library name: NS97
column name in "tpm.txt" is library name


title: sdg2_Pol II Ser5p_rep2

description: sdg2_Pol II Ser5p_merged.bw

value: Pol II Ser5P (Abcam, ab5131)


title: 4177842

description: DLBCL, cryo-preserved


title: Col_Pol II Ser2p_rep1

description: Col_Pol II Ser2p_merged.bw


title: PT56_Tumor

description:
Library name: NS93
column name in "tpm.txt" is library name


title: 4157186

description: DLBCL, cryo-preserved


title: WT_CoCl2_200uM_3

city: Durham

first: Chris

last: Corton

email: corton.chris@epa.gov, cortonchris@gmail.com, jie@liuonline.com, prpfeiffer@gmail.com, treasure.bailley@gmail.com

address: 109 TW Alexander Dr

institute: EPA

description: Library name: TC00003356_D07

data_processing:
Each FASTQ file was aligned to the probe sequences in the assay using HISAT2 v2.1.0 with spliced alignment disabled.
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: GRCh38
Supplementary files format and content: Human Whole Transcriptome v2.1
Supplementary files format and content: All samples are provided as a separate table of counts in CSV format, with rows corresponding to TempO-seq probe IDs, and columns corresponding to sample IDs

growth_protocol: MCF-7 cells (Synthego Inc., Redwood City, CA) were cultured in DMEM media (ThermoFisher, Durham, NC) supplemented with 10% FBS, 1 mM glutamine, 1 mM sodium pyruvate (Sigma, St. Louis, MO), and 1× antibiotic-antimycotic (ThermoFisher, Waltham, MA). Cells were plated at 8 × 10^4 cells per well in 24-well plates or 2 × 10^4 in 96-well plates. All treatments were carried out in at least three independent experiments using different batches of cells.

extract_protocol:
After 6 hours of exposure, media was removed, and cells were lysed in 0.3 mL Trizol, followed by RNA extraction.
Samples were analyzed by BioSpyder using a custom-attenuated version of the Human Whole Transcriptome v2.1 assay. Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a NovaSeqX Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: After 22 h of culture, when cells reached ~80% confluency, the medium was replaced with dosing solutions containing aliquots of the chemicals.

tag: cell line

value: WT

tag: chemical

tag: concentration

tag: treatment time

tag: replicate


title: PT58_Normal

description:
Library name: NS98
column name in "tpm.txt" is library name

tag: tissue

tag: path grade


title: sdg2_Pol II Ser5p_rep1

description: sdg2_Pol II Ser5p_merged.bw

tag: genotype


title: HF-1-heart

description: heart tissue from failing heart

tag: disease

tag: etiology

value: DCM


title: PT55_Normal

description:
Library name: NS92
column name in "tpm.txt" is library name

tag: Stage

tag: race

tag: Sex

tag: sas

tag: amr


title: WT_CoCl2_200uM_2

description: Library name: TC00003356_D06


title: 4140544

description: DLBCL, cryo-preserved


title: WT_CoCl2_200uM_1

description: Library name: TC00003356_D05


title: 4163639

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_Pol II Ser5p_rep2

description: h3.3ko;HTR5_Pol II Ser5p_merged.bw

value: Seedlings


title: 4111326

description: DLBCL, cryo-preserved


title: 4130051

description: DLBCL, cryo-preserved


title: PT54_Normal

description:
Library name: NS90
column name in "tpm.txt" is library name

tag: eas

tag: eur

tag: afr

tag: ancestry bin

tag: age


title: PT54_Tumor

description:
Library name: NS89
column name in "tpm.txt" is library name


title: HIF1A-null_CoCl2_200uM_2

description: Library name: TC00003356_D03

tag: cell line

tag: chemical

tag: concentration

tag: treatment time


title: PT52_Tumor

description:
Library name: NS85
column name in "tpm.txt" is library name

tag: tissue

tag: path grade


title: Col_Pol II Ser5p_rep2

description: Col_Pol II Ser5p_merged.bw

tag: genotype

tag: treatment


title: HIF1A-null_CoCl2_200uM_3

description: Library name: TC00003356_D04

tag: replicate


title: PT51_Normal

description:
Library name: NS84
column name in "tpm.txt" is library name

tag: Stage

tag: race

tag: Sex


title: h3.3ko;HTR5_Pol II Ser5p_rep1

description: h3.3ko;HTR5_Pol II Ser5p_merged.bw


title: PT56_Normal

description:
Library name: NS94
column name in "tpm.txt" is library name

tag: sas

tag: amr

tag: eas


title: HIF1A-null_CoCl2_200uM_1

description: Library name: TC00003356_D02


title: Col_Pol II Ser5p_rep1

description: Col_Pol II Ser5p_merged.bw


title: 4131257

description: DLBCL, cryo-preserved


title: 4107559

description: DLBCL, cryo-preserved


title: 4101316

description: DLBCL, cryo-preserved


title: PT49_Normal

description:
Library name: NS80
column name in "tpm.txt" is library name

tag: eur

tag: afr

tag: ancestry bin


title: WT_Wortmannin_1uM_3

description: Library name: TC00003356_C12

tag: cell line

tag: chemical

value: Wortmannin


title: HIF1A-null_Wortmannin_1uM_3

description: Library name: TC00003356_C09

tag: concentration

tag: treatment time


title: PT51_Tumor

description:
Library name: NS83
column name in "tpm.txt" is library name

tag: tissue

tag: path grade

tag: age


title: 4124188

description: DLBCL, cryo-preserved

value: DLBCL, cryo-preserved


title: h3.3ko;HTR5_H3K4me3_rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) or human (hg38) genome with Botiew2 version 2.4.2.
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
H3K4me3 peaks in WT were called using MACS2 version 2.1.2 with default parameters. Only peaks identified from both biological replicates were retained.
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp.
Spike-in normalization factors were used for the normalization of H3K4me3 ChIP-seq data. Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Assembly: TAIR10, hg38
Supplementary files format and content: bigwig

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-H3K4me3 (Abcam, ab8580).Mononucleosomes extracted from human HEK293 cells were added as a  “spike-in” reference before immunoprecipitation with anti-H3K4me3.
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

tag: genotype

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: 4179894

description: DLBCL, cryo-preserved


title: HIF1A-null_Wortmannin_1uM_2

description: Library name: TC00003356_C08

tag: replicate


title: PT55_Tumor

description:
Library name: NS91
column name in "tpm.txt" is library name

tag: Stage

tag: race

value: B

tag: Sex


title: WT_Wortmannin_1uM_2

description: Library name: TC00003356_C11


title: h3.3ko;HTR5 K4A_Pol II Ser5p_rep1

description: h3.3ko;HTR5 K4A_Pol II Ser5p_merged.bw

tag: treatment


title: h3.3ko;HTR5 K4A_H3K4me3_rep2

description: h3.3ko;HTR5 K4A_H3K4me3_merge.bw


title: sdg2_H3K4me3_rep1


title: PT50_Tumor

description:
Library name: NS81
column name in "tpm.txt" is library name

value: Female

tag: sas

tag: amr

tag: eas

tag: eur


title: 4167925

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_H3K4me3_rep1


title: PT48_Normal

description:
Library name: NS78
column name in "tpm.txt" is library name

value: Normal

tag: afr

tag: ancestry bin


title: 4197155

description: DLBCL, cryo-preserved


title: PT50_Normal

description:
Library name: NS82
column name in "tpm.txt" is library name


title: 4114033

description: DLBCL, cryo-preserved


title: WT_Ciclopirox_15uM_3

description: Library name: TC00003356_C06

tag: cell line

tag: chemical

value: Ciclopirox

tag: concentration

tag: treatment time


title: Col_H3K4me3_rep2

tag: tissue

tag: genotype


title: 4181460

description: DLBCL, cryo-preserved


title: HIF1A-null_Wortmannin_1uM_1

description: Library name: TC00003356_C07

tag: replicate


title: sdg2_H3K4me3_rep2

tag: chip antibody


title: PT47_Normal

description:
Library name: NS76
column name in "tpm.txt" is library name

tag: path grade

tag: Stage

tag: race

value: AFR

tag: age


title: PT48_Tumor

description:
Library name: NS77
column name in "tpm.txt" is library name

tag: Sex

tag: sas

tag: amr


title: WT_Ciclopirox_15uM_1

description: Library name: TC00003356_C04


title: h3.3ko;HTR5 K4A_H3K4me3_rep1 R1.fq.gz

description: h3.3ko;HTR5 K4A_H3K4me3_merge.bw

value: h3.3ko;HTR5 K4A


title: PT46_Normal

description:
Library name: NS74
column name in "tpm.txt" is library name

tag: eas

tag: eur

tag: afr


title: WT_Ciclopirox_15uM_2

description: Library name: TC00003356_C05

tag: cell line

tag: chemical


title: PT49_Tumor

description:
Library name: NS79
column name in "tpm.txt" is library name

value: Tumor

tag: ancestry bin


title: h3.3ko;HTR5 K4A_Input_rep2

description: h3.3ko;HTR5 K4A_H3K4me3_merge.bw

tag: tissue


title: 4167381

description: DLBCL, cryo-preserved


title: 4139696

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5 K4A_Input_rep1

description: h3.3ko;HTR5 K4A_H3K4me3_merge.bw

tag: genotype


title: Col_H3K4me3_rep1


title: 4198519

description: DLBCL, cryo-preserved


title: sdg2_Input_rep2


title: 4115001

description: DLBCL, cryo-preserved


title: PT47_Tumor

description:
Library name: NS75
column name in "tpm.txt" is library name


title: WT_DMSO_3

description: Library name: TC00003356_B10

value: DMSO

tag: concentration

tag: treatment time

tag: replicate


title: WT_Wortmannin_1uM_1

description: Library name: TC00003356_C10


title: PT44_Normal

description:
Library name: NS70
column name in "tpm.txt" is library name

tag: path grade

tag: Stage

value: Male


title: WT_DMSO_2

description: Library name: TC00003356_B09


title: sdg2_Input_rep1

tag: chip antibody


title: 4108101

description: DLBCL, cryo-preserved


title: 4146301

description: DLBCL, cryo-preserved


title: HIF1A-null_Ciclopirox_15uM_3

description: Library name: TC00003356_C03


title: PT46_Tumor

description:
Library name: NS73
column name in "tpm.txt" is library name

tag: race

tag: Sex

tag: age


title: HIF1A-null_Ciclopirox_15uM_2

description: Library name: TC00003356_C02


title: HIF1A-null_Ciclopirox_15uM_1

description: Library name: TC00003356_B12


title: PT45_Normal

description:
Library name: NS72
column name in "tpm.txt" is library name

tag: sas

tag: amr

tag: eas


title: Col_Input_rep1

value: WT (Col)


title: WT_DMSO_1

description: Library name: TC00003356_B11

tag: cell line


title: HTR5 K4A-GFP #2_IP

description: HTR5 K4A-GFP #2_IP vs Input.bw

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-GFP (Thermo Fisher Scientific, A11122).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

value: HTR5 K4A-GFP

value: GFP (Thermo Fisher Scientific, A11122)


title: h3.3ko;HTR5_Input_rep2


title: PT45_Tumor

description:
Library name: NS71
column name in "tpm.txt" is library name

tag: eur

tag: afr


title: 4147968

description: DLBCL, cryo-preserved

tag: tissue


title: 4158933

description: DLBCL, cryo-preserved


title: HIF1A-null_DMSO_2

description: Library name: TC00003356_B06

tag: genotype

tag: chemical


title: h3.3ko;HTR5_Input_rep1


title: PT44_Tumor

description:
Library name: NS69
column name in "tpm.txt" is library name

tag: ancestry bin


title: Col_Input_rep2


title: PT42_Tumor

description:
Library name: NS65
column name in "tpm.txt" is library name


title: HTR5-GFP #2_IP

description: HTR5-GFP #2_IP vs Input.bw


title: 4140531

description: DLBCL, cryo-preserved


title: 4109808

description: DLBCL, cryo-preserved


title: HIF1A-null_DMSO_1

description: Library name: TC00003356_B08

tag: concentration

tag: treatment time

tag: replicate


title: Young males treated with elamipretide replicate 4

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Raw methylation array data were normalized using SeSAMe (Zhou et al., 2018 Nucleic Acids Res. 46(20))
Normalized (SeSAMe, noob background subtraction): rds files

label: cy3, cy5

source_name: Hearts from 7-month-old male C57BL/6J mice

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from mouse hearts using the AllPrep DNA/RNA/Protein Mini Kit according to the manufacturer's protocol (Qiagen)

value: Hearts

tag: strain


title: 4176584

description: DLBCL, cryo-preserved


title: HTR5-GFP #1_IP

description: HTR5-GFP #1_IP vs Input.bw

value: Seedlings

tag: chip antibody


title: PT43_Normal

description:
Library name: NS68
column name in "tpm.txt" is library name

tag: path grade

tag: Stage

tag: race

tag: Sex


title: HTR5 K4A-GFP #2_Input

description: HTR5 K4A-GFP #2_IP vs Input.bw


title: PT41_Tumor

description:
Library name: NS63
column name in "tpm.txt" is library name

tag: sas

tag: amr

tag: eas

tag: age


title: HIF1A-null_DMSO_3

description: Library name: TC00003356_B07

tag: cell line


title: PT43_Tumor

description:
Library name: NS67
column name in "tpm.txt" is library name

tag: tissue

tag: eur

tag: afr


title: PT37_Normal

description:
Library name: NS57
column name in "tpm.txt" is library name

value: Locally Advanced

value: W

tag: ancestry bin

value: EUR


title: 4145528

description: DLBCL, cryo-preserved

value: DLBCL, cryo-preserved


title: 4104105

description: DLBCL, cryo-preserved


title: HTR5 K4A-GFP #1_IP

description: HTR5 K4A-GFP #1_IP vs Input.bw

tag: genotype


title: PT42_Normal

description:
Library name: NS66
column name in "tpm.txt" is library name

value: B


title: Young males treated with saline replicate 5


title: 4102009

description: DLBCL, cryo-preserved


title: PT41_Normal

description:
Library name: NS64
column name in "tpm.txt" is library name

value: Normal


title: Young males treated with saline replicate 4


title: HTR5-GFP #2_Input

description: HTR5-GFP #2_IP vs Input.bw


title: 4119279

description: DLBCL, cryo-preserved


title: Young males treated with elamipretide replicate 2


title: PT36_Normal

description:
Library name: NS55
column name in "tpm.txt" is library name


title: Old males treated with saline replicate 5

source_name: Hearts from 26-month-old male C57BL/6J mice


title: sdg2_BS-seq_rep1

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Reads were mapped to the Arabidopsis genome (TAIR10) with BS-Seeker2 version 2.1.8 using default parameters
Duplicated reads were filtered with Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged. CG, CHG, and CHH methylation levels were calculated with CGmaptools (version 0.1.2)
Methylation data were visualized with ggplot2 in R (version 1.1.1106).
Assembly: TAIR10
Supplementary files format and content: CGmap

extract_protocol:
Genomic DNA was extracted from 3-week-old seedlings with Quick-DNA Plant/Seed Miniprep Kit (ZYMO, D6020).
200ng fragmented genomic DNA (200bp-500bp) was used for library preparation with VAHTS universal Pro DNA library prep kit for Illumina (Vazyme, ND608). NEBNext Multiplex Oligos for Illumina (NEB, E7535) were used for adapter ligation. After purification with VAHTS DNA Clean Beads (Vazyme N411), bisulfite conversion was performed with EZ DNA Methylation-Gold Kit (ZYMO, D5005), followed by DNA purification and PCR amplification.


title: Young males treated with elamipretide replicate 3


title: PT37_Tumor

description:
Library name: NS56
column name in "tpm.txt" is library name


title: HTR5 K4A-GFP #1_Input

description: HTR5 K4A-GFP #1_IP vs Input.bw


title: HTR5-GFP #1_Input

description: HTR5-GFP #1_IP vs Input.bw


title: 4176133

description: DLBCL, cryo-preserved


title: sdg2_BS-seq_rep2


title: 4169012

description: DLBCL, cryo-preserved


title: 4137230

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_BS-seq_rep1


title: Young females treated with saline replicate 4

source_name: Hearts from 7-month-old female C57BL/6J mice


title: Young males treated with saline replicate 1


title: h3.3ko;HTR5 K4A_Pol II Ser5p_rep2

description: h3.3ko;HTR5 K4A_Pol II Ser5p_merged.bw

tag: treatment

value: Pol II Ser5P (Abcam, ab5131)


title: Old females treated with saline replicate 5

source_name: Hearts from 26-month-old female C57BL/6J mice

tag: strain


title: PT35_Normal

description:
Library name: NS53
column name in "tpm.txt" is library name


title: Young males treated with saline replicate 3


title: PT35_Tumor

description:
Library name: NS52
column name in "tpm.txt" is library name


title: h3.3ko;HTR5_BS-seq_rep2


title: Young males treated with saline replicate 2


title: PT33_Tumor

description:
Library name: NS49
column name in "tpm.txt" is library name

value: Female


title: PT32_Normal

description:
Library name: NS48
column name in "tpm.txt" is library name


title: Old females treated with elamipretide replicate 4


title: h3.3ko;HTR5 K4A_BS-seq_rep2

description: h3.3ko;HTR5 K4A_merged.CGmap.gz

value: h3.3ko;HTR5 K4A


title: 4107137

description: DLBCL, cryo-preserved


title: PT36_Tumor

description:
Library name: NS54
column name in "tpm.txt" is library name

value: Tumor


title: h3.3ko;HTR5 K4A_BS-seq_rep1

description: h3.3ko;HTR5 K4A_merged.CGmap.gz


title: 4187640

description: DLBCL, cryo-preserved


title: 4176046

description: DLBCL, cryo-preserved


title: Old males treated with elamipretide replicate 5


title: PT32_Tumor

description:
Library name: NS47
column name in "tpm.txt" is library name


title: 4105746

description: DLBCL, cryo-preserved


title: 4117030

description: DLBCL, cryo-preserved


title: Col_BS-seq_rep2


title: PT31_Tumor

description:
Library name: NS46
column name in "tpm.txt" is library name


title: Old females treated with saline replicate 4


title: 4184094

description: DLBCL, cryo-preserved


title: Col_BS-seq_rep1


title: PT30_Normal

description:
Library name: NS45
column name in "tpm.txt" is library name


title: sdg2_ATAC-seq_rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Reads mapped to chloroplast and mitochondria genome were removed and duplicated reads were filtered with Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized with RPKM. Average ATAC-seq profiles were generated using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol:
Three-week old seedlings were chopped in lysis buffer (15 mM Tris-HCl pH 7.5,20 mM NaCl, 80 mM KCl, 0.5 mM Spermine, 0.2% Triton X-100, 5 mM β-ME,protease inhibitor cocktail). After being filtered with a 30μm filter (CellTrics),nuclei were stained with DAPI and subjected to fluorescence-activated cell sorting (FACS). 50,000 nuclei per sample were collected and mixed with Tn5 transposase (Mei5bio, MF650-01), after 20 minutes of incubation at 37°C, tagmented DNA was recovered with ChIP DNA Clean & Concentrator kit (ZYMO, D5205).
After PCR amplification, sequencing libraries were purified with VAHTS DNA Clean Beads (Vazyme N411)


title: 4128852

description: DLBCL, cryo-preserved


title: Old females treated with elamipretide replicate 3


title: PT30_Tumor

description:
Library name: NS44
column name in "tpm.txt" is library name


title: PT29_Tumor

description:
Library name: NS42
column name in "tpm.txt" is library name


title: 4121621

description: DLBCL, cryo-preserved


title: Old females treated with elamipretide replicate 2


title: h3.3ko;HTR5_ATAC-seq_rep2


title: 4193638

description: DLBCL, cryo-preserved


title: Old males treated with elamipretide replicate 4


title: PT28_Tumor

description:
Library name: NS41
column name in "tpm.txt" is library name


title: Young females treated with saline replicate 3


title: sdg2_ATAC-seq_rep1


title: PT27_Normal

description:
Library name: NS40
column name in "tpm.txt" is library name


title: 4130194

description: DLBCL, cryo-preserved


title: Young males treated with elamipretide replicate 1


title: h3.3ko;HTR5_ATAC-seq_rep1


title: h3.3ko;HTR5 K4A_ATAC-seq_rep2

description: h3.3ko;HTR5 K4A_ATAC-seq_merge.bw


title: Old males treated with elamipretide replicate 3


title: 4183136

description: DLBCL, cryo-preserved


title: 4130865

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5 K4A_ATAC-seq_rep1

description: h3.3ko;HTR5 K4A_ATAC-seq_merge.bw


title: PT27_Tumor

description:
Library name: NS39
column name in "tpm.txt" is library name


title: Col_ATAC-seq_rep2

value: Col


title: Old females treated with saline replicate 3


title: 4128849

description: DLBCL, cryo-preserved


title: PT24_Tumor

description:
Library name: NS35
column name in "tpm.txt" is library name


title: Old males treated with elamipretide replicate 2


title: 4199714

description: DLBCL, cryo-preserved


title: PT21_Tumor

description:
Library name: NS31
column name in "tpm.txt" is library name


title: Col_ATAC-seq_rep1


title: Old males treated with saline replicate 4


title: sdg2_RNA-seq_rep3

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version0.20.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10.
Transcripts per million (TPM) values were generated using R.
Differential gene expression analysis was performed using DESeq2 version 1.26.0.
Assembly: TAIR10
Supplementary files format and content: TPM_for_all_samples.txt

extract_protocol:
Total RNA was extracted from 3-week-old seedlings with Minibest plant RNA extraction kit (Takara, 9769)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction


title: 4173863

description: DLBCL, cryo-preserved


title: PT19_Normal

description:
Library name: NS29
column name in "tpm.txt" is library name

value: Male

value: AFR


title: PT19_Tumor

description:
Library name: NS28
column name in "tpm.txt" is library name


title: sdg2_RNA-seq_rep2


title: Old males treated with saline replicate 3


title: PT16_Normal

description:
Library name: NS25
column name in "tpm.txt" is library name


title: 4171586

description: DLBCL, cryo-preserved


title: 4188879

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_RNA-seq_rep3


title: PT16_Tumor

description:
Library name: NS24
column name in "tpm.txt" is library name


title: PT24_Normal

description:
Library name: NS36
column name in "tpm.txt" is library name


title: 4171810

description: DLBCL, cryo-preserved


title: Young females treated with elamipretide replicate 4


title: 4116268

description: DLBCL, cryo-preserved


title: h3.3ko;HTR5_RNA-seq_rep2


title: Young females treated with saline replicate 2


title: PT15_Tumor

description:
Library name: NS22
column name in "tpm.txt" is library name


title: h3.3ko;HTR5_RNA-seq_rep1


title: Old males treated with elamipretide replicate 1


title: h3.3ko;HTR5 K4A_RNA-seq_rep3


title: 4168738

description: DLBCL, cryo-preserved


title: PT14_Tumor

description:
Library name: NS21
column name in "tpm.txt" is library name


title: Old females treated with saline replicate 1


title: 4171946

description: DLBCL, cryo-preserved


title: PT13_Tumor

description:
Library name: NS19
column name in "tpm.txt" is library name


title: h3.3ko;HTR5 K4A_RNA-seq_rep2


title: 4135099

description: DLBCL, cryo-preserved


title: Old females treated with saline replicate 2


title: sdg2_RNA-seq_rep1


title: Old males treated with saline replicate 2


title: h3.3ko;HTR5 K4A_RNA-seq_rep1


title: 4166706

description: DLBCL, cryo-preserved


title: PT8_Normal

description:
Library name: NS11
column name in "tpm.txt" is library name


title: 4138464

description: DLBCL, cryo-preserved


title: Col_RNA-seq_rep3

value: WT (Col)


title: Old males treated with saline replicate 1


title: 4122063

description: DLBCL, cryo-preserved


title: Young females treated with elamipretide replicate 3


title: PT15_Normal

description:
Library name: NS23
column name in "tpm.txt" is library name


title: Young females treated with saline replicate 1


title: Col_RNA-seq_rep2


title: 4189035

description: DLBCL, cryo-preserved


title: PT6_Tumor

description:
Library name: NS8
column name in "tpm.txt" is library name


title: Old females treated with elamipretide replicate 1


title: Col_RNA-seq_rep1


title: 4166940

description: DLBCL, cryo-preserved


title: PT5_Tumor

description:
Library name: NS7
column name in "tpm.txt" is library name


title: PT2_Normal

description:
Library name: NS4
column name in "tpm.txt" is library name


title: Young females treated with elamipretide replicate 2


title: 4120157

description: DLBCL, cryo-preserved


title: Young females treated with elamipretide replicate 1


title: 4107990

description: DLBCL, cryo-preserved


title: PT2_Tumor

description:
Library name: NS3
column name in "tpm.txt" is library name


title: 4135278

description: DLBCL, cryo-preserved


title: MGH721 (npp-16ΔIDR OE) adult day 1 animals, Replicate 4

first: Fasih

middle: Mubtasim

last: Ahsan

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Fastq read quality control, adapter trimming, quality score filtering, and quasi-alignment were all performed using custom UNIX/Bash shell scripts on the Mass General Brigham ERISTwo Scientific Computing CentOS 7 Linux Cluster. Reads were analyzed for quality control using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC v1.191. Reads were then filtered for Illumina adapter contamination, truncated short reads or low quality base calls using BBDuk (BBTools). The subsequently trimmed and cleaned reads were then quasi-aligned to the Caenorhabditis elegans reference transcriptome annotation (WBcel235, Ensembl Release 105) using Salmon v1.9.03, correcting for GC content and sequencing bias using the command parameters ‘--gcBias’ and ‘--seqBias’.
All statistical analyses and visualizations were generated using the R v4.3.2 (www.r-project.org) Bioconductor v3.18 statistical environment on a local machine through Jupyter Notebook v6.4.10 (https://jupyter.org). Quasi-aligned transcript quantification files for each sample were collapsed into gene-level count matrices using R package tximport v1.30.0, and paired differential expression was calculated using R package DESeq2 v1.42.1 with a design formula of ‘∼ Genotype’. Genes were considered differentially expressed with a Benjamini-Hochberg False Discovery Rate (FDR) corrected P value < 0.05 and an absolute log2 transformed fold change of 1.
Volcano plots were generated using R package ggplot2 v3.5.0, heatmaps were generated using R package pheatmap v1.0.12, and Venn diagrams were generated using R package ggvenn v0.1.10. Gene set overrepresentation analyses for genes identified as differentially expressed (with thresholds set as indicated above) between npp-16 OE and npp-16∆IDR OE were performed using R package clusterProfiler v4.10.1 for Gene Ontology (GO) terms, and R package ReactomePA v1.46.0 for Reactome-based pathway terms. Visualizations were post-edited for font, sizing, and appearance using Adobe Illustrator and the Adobe Creative Cloud Suite.
All custom bash scripts, Jupyter Notebook files, and processed fastq and transcript count files used in these analyses will be provided upon reasonable request by the corresponding author.
Assembly: ce11/WBcel235 (Ensembl Release 105)
Supplementary files format and content: Raw gene-level collapsed read counts for all 12 samples in matrix format (rows are samples, columns are WormBase Gene ID). Values represent raw read counts collapsed for each transcript from the WBcel235 (Ensembl Release 105) assembly to gene-level estimates using Salmon. 12 samples total (4 N2, 4 MGH558, 4 MGH721).
Supplementary files format and content: Salmon output generated quant.sf files are included for each sample. These files include (1) the transcript Wormbase Sequence ID, (2) the transcript length, (3) the effective length averaged for each gene-level, (4) the normalized transcript per million (TPM) abundance, and (5) the raw number of reads binned per transcript.

organism: Caenorhabditis elegans

source_name: Whole organism lysate

growth_protocol: C. elegans wild-type (N2 - Bristol), npp-16 OE (MGH558), and npp-16 IDR deletion OE (MGH721) nematodes were grown and maintained at 20°C on Nematode Growth Media (NGM) seeded with Escherichia coli OP50-1 as previously described (Soukas et al., 2009). Animals were synchronized by hypochlorite bleach treatment of a population of gravid adults. Animals were collected in M9 medium, centrifuged at 4400 rpm for 1 minute and resuspended in 6 mL 1.3% bleach, 250 mM NaOH for 1 minute of vigorous shaking. Bleach solution exposure and shaking step was repeated after one wash in M9. After second bleach step, pellet was resuspended in minimal M9 by gentle pipetting, and washed in M9 four times. Eggs were resuspended in 12 mL M9, and solution was left to rotate overnight for 23 hours at 20°C.

extract_protocol:
Worms were collected in TRIzol Reagent (Invitrogen), flash frozen in liquid nitrogen, and stored at -80°C prior to RNA isolation. Samples were lysed using metal beads and the Tissuelyser I system (Qiagen). RNA was isolated from lysate using Direct-zol RNA Miniprep kit (Zymo) and stored at -80°C prior to library preparation. Total RNA samples were evaluated for quality control using a NanoDrop One C Microvolume UV-Vis Spectrophotometer (ThermoFisher Scientific), with an A260/A280 > 1.9 and an A260/A230 > 2.2. Approximately 1 ug of RNA per sample was submitted to Genewiz (Azenta) for QC, library preparation, and total mRNA sequencing.
All total RNA quality control, mRNA-sequencing library preparation, and Illumina sequencing was performed by Genewiz (Azenta). Samples were first verified for RNA integrity scores greater than 8.5 using an Agilent Tapestation 4200, and a DV200 score greater than 70.0. Illumina library preparation was performed using polyA selection for mRNA species. Approximately 20 million paired-end, 150 base pair reads were obtained per sample, with ≥ 80% of bases passing a Phred quality score ≥ Q30.

treatment_protocol: Nematodes were synchronized as described in the growth protocol and plated onto 10 cm OP50-1 NGM agar plates from L1 of development to adult day 1 stage. Four independent biological replicate experiments were performed, using independently synchronized animals, OP50-1 seeded cultures, and prepared NGM agar plates for each experiment.

value: Whole organism lysate

value: Integrated transgenic overexpression of NPP-16/CeNUP50 bearing a deletion of the intrinsically disordered region (IDR) FG domain, missing amino acids 245-354.


title: PT1_Normal

description:
Library name: NS2
column name in "tpm.txt" is library name


title: PT1_Tumor

description:
Library name: NS1
column name in "tpm.txt" is library name


title: mouse mammary epithelial cells, HC11, 4C, Wnt4, rep2

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description: Library name: HC11_4C_Wnt4_rep2

data_processing:
For processing raw 4C-seq data, the publicly available 4C mapping pipeline for mapping (mm9) and filtering 4C data was used (https://github.com/deWitLab/4C_mapping) using default settings. The R package PeakC was used to analyze processed triplicates of 4C-seq data and identify significantly interacting regions within a window size of 400kb (https://github.com/deWitLab/peakC).
Assembly: mm9
Supplementary files format and content: Data structure processed 4C text file is as follows: coordinates fragment_read count  Note that the genome is 'cut' up in fragments by an restriction enzyme and the reads are aligned to this digested genome. Thus the coordinate refers to a relevant fragment.
Library strategy: 4C-Seq

source_name: mammary gland

growth_protocol: Mammary epithelial BC44 cells (a kind gift of Marie-Anne Deugnier, Institute Curie, Paris, France) were cultured in RPMI1640 + L-Glut (Fisher, 11973466), supplemented with 10% FBS (Gibco, cat# 10270-106) and 5g/ml insulin (Sigma-Aldrich, cat. #I9278). HC11 mammary epithelial cells were also cultured in RPMI1640 + L-Glut with 10% FBS and 5g/ml insulin, with the addition of 10ng/ml EGF (Peprotech, cat. #AF-100-15-B). Cells were dissociated with 0.05% trypsin and split 1:10 every 3 days.

extract_protocol:
1x10e6 BC44 or HC11 cells were crosslinked with 2% (v/v) formaldehyde in PBS/10% FBS for 10min at RT in 15cm cell culture dishes while shaking. Cells were isolated by using a cell scraper, lysed for 10min in lysis buffer and homogenized with a dounce-homogenizer. Nuclei were digested with 200U DpnII (NEB) in DpnII buffer (NEB) complemented with 0.3% SDS and 2% Triton X-100 for 4hr, an additional 200U DpnII O/N and another 200U DpnII for 4 hr the following day at 37C while shaking. The first ligation was performed with 100U T4 DNA ligase O/N at 16C in a total volume of 15ml. Following decrosslinking and phenol/chloroform extraction, the DNA was digested with NlaIII in Cutsmart buffer (NEB) O/N at 37C while shaking. After digestion a second ligation was carried out with T4 DNA ligase (Thermo Scientific) in a total volume of 15ml O/N at 16C. DNA was isolated via phenol/chloroform extraction and purified with the ChIP DNA Clean & Concentrator Kit (Zymo Research).
50-100ng DNA template per reaction and 1ug in total was used to amplify PCR-specific libraries for the Wnt4 promoter viewpoint with the Expand Long Template PCR system (Sigma) using specific primers. Successful reactions were pooled and purified with the High-pure PCR Product Purification Kit (Sigma). Equal amounts of libraries were combined, and all library preparation and sequencing steps were performed by MAD: Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam. Note that paired-end sequencing was performed for cost-effectiveness, only single reads needed for analysis so only the R1 .fastq files were used for data processing.

value: mammary gland

tag: cell type

value: mammary epithelial cells


title: PT8_Tumor

description:
Library name: NS10
column name in "tpm.txt" is library name

tag: path grade

value: Locally Advanced


title: MGH721 (npp-16ΔIDR OE) adult day 1 animals, Replicate 3


title: mouse mammary epithelial cells, BC44, 4C, Wnt4, rep3

description: Library name: BC44_4C_Wnt4_rep3


title: mouse mammary epithelial cells, HC11, 4C, Wnt4, rep1

description: Library name: HC11_4C_Wnt4_rep1


title: 4113140

description: DLBCL, cryo-preserved


title: 4120193

description: DLBCL, cryo-preserved


title: A2780 cells, SCR-6920 48 hours, replicate 3

city: Shanghai

first: Weijie

last: Chen

address: Furonghua Road 118

institute: Simcere Zaiming Pharmaceutical Co.

data_processing:
For RNA analysis, raw reads were mapped to the human reference genome (GRCm38) by Hisat2
Read count extraction and normalization were performed using htseq-count
Assembly: GRCm38
Supplementary files format and content: tab-delimited Excel files includes raw counts for each sample
Supplementary files format and content: tab-delimited Excel files includes FPKM values for each sample

source_name: cell line

growth_protocol: A2780 cells were maintained in 1640 with 10% FBS with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (#74134, Qiagen) according to the manufacturer’s protocol
RNA-seq libraries were prepared using the Illumina TrueSeq Stranded mRNA LT Sample Preparation Kit (Illumina)

treatment_protocol: A2780 cells were treated with SCR-6920 (1 μM) for 48 hours.

value: cell line

value: ovarian cancer cell

value: WT


title: 4133263

description: DLBCL, cryo-preserved

value: DLBCL, cryo-preserved


title: MGH721 (npp-16ΔIDR OE) adult day 1 animals, Replicate 2


title: mouse mammary epithelial cells, BC44, 4C, Wnt4, rep2

description: Library name: BC44_4C_Wnt4_rep2


title: MGH721 (npp-16ΔIDR OE) adult day 1 animals, Replicate 1


title: mouse mammary epithelial cells, BC44, 4C, Wnt4, rep1

description: Library name: BC44_4C_Wnt4_rep1


title: 4161781

description: DLBCL, cryo-preserved


title: A2780 cells, SCR-6920 48 hours, replicate 1


title: MGH558 (npp-16 OE) adult day 1 animals, Replicate 3

value: Integrated transgenic overexpression of a full length copy of NPP-16/CeNUP50


title: A2780 cells, SCR-6920 48 hours, replicate 2


title: MGH558 (npp-16 OE) adult day 1 animals, Replicate 4


title: mouse mammary epithelial cells, HC11, 4C, Wnt4, rep3

description: Library name: HC11_4C_Wnt4_rep3


title: mammary gland, puberty, basal

description: Library name: puberty basal cells ATACseq

data_processing:
Sequencing data were processed using the ATAC-Seq pipeline of the Kundaje lab (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters and mouse genome version mm9.
Assembly: mm9
Supplementary files format and content: bigwig files containing mapped reads are provided for pubertal mammary epithelial luminal, stromal and basal cells

source_name: FVB, puberty, mammary gland, female

growth_protocol: were maintained on an FVB/N background under standard housing conditions in either open or filtertop cages, with 12hr light/dark cycle and ad libitum access to food and water.

extract_protocol:
ATAC-seq samples were prepared according to the protocol from Buenrostro et al. Briefly, freshly sorted cells were washed once in 50ul ice-cold PBS and gently resuspended in 50ul cold lysis buffer (10mM Tris-HCl, pH 7.4; 10mM NaCl; 3mM MgCl2 and 0.1% NP-40) to isolate nuclei.
The transposase reaction (Illumina Nextera DNA Library Preparation Kit, FC-121-1030) was performed for 30min at 30°C and DNA was purified using MinElute PCR purification columns (Qiagen, #28004). DNA fragments were amplified using NEBNext Ultra II Q5 Master Mix (#M05445) and custom primers (see accompanying publication). The following PCR conditions were used: 72°C for 5min; 98°C for 30sec, 8 cycles of 98°C for 10sec, 63°C for 30sec and 72°C for 1min. Libraries were purified with the MinElute PCR purification kit. An additional, single left-sided purification with AMPure XP beads (Beckman Coulter #A63880) was performed to remove primer dimers. Libraries were quantified with qRT-PCR before paired-end sequencing on an Illumina NextSeq 550 system (2 x 75bp, performed by MAD: Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam).

treatment_protocol: The 3rd and 4th mammary gland fat pads from 6 puberty (p35) FVB/N mice were dissected, chopped to small pieces and incubated for 2hr at 37°C in an orbital shaker in a digestion mix composed of DMEM/F12, 5% FBS, 1% Penicillin / Streptomycin, 25mM HEPES and 300U/ml Collagenase IV. Red blood cells were lysed with ACK Lysing Buffer and single cell suspensions were generated by consecutive digestion steps with Trypsin-EDTA and DNAseI. Cells were stained in HBSS containing 10% FBS with the following antibodies (eBioscience): anti-Mouse CD45-Biotin (clone 30-F11), anti-Mouse CD31-Biotin (clone 390), anti-Mouse TER-119-Biotin (clone Ter-119), anti-Mouse CD326-PE (clone G8.8), anti-Mouse CD49f-FITC (clone GoH3) and Streptavidin-APC. DAPI was used for live/dead cell discrimination. 55,000 luminal, basal and stromal cells were sorted into ice-cold 10mM HEPES containing 10% FBS using a BD FACSAria III equipped with a 100m nozzle at 20psi. FITC: excitation with 488nm laser, emission detected using a 530/30nm bandpass filter; PE: excitation with 561nm laser, emission detected using a 582/15nm bandpass filter; DAPI: excitation with 407nm laser, emission detected using a 450/50nm bandpass filter; APC: excitation with a 633nm laser, emission detected using a 660/20nm bandpass filter. Cells were sorted with a plate voltage of 2500V using the 4-Way Purity precision mode.

value: FVB, puberty, mammary gland, female

value: FACS sorted basal cells

value: wildtype


title: A2780 cells, control, replicate 3


title: mammary gland, puberty, luminal

description: Library name: puberty luminal cells ATACseq

value: FACS sorted luminal cells


title: Dam_only_AML12_shMatr3_rep2

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

data_processing:
DamID-seq reads were mapped to mouse reference genome (mm10) using Bowtie (v1.2.3).
Duplicate reads were excluded and kept only one read for each genomic site.
To visualize the DamID signals, the log2 ratio of Dam-Lamin B1 over unfused Dam was calculated for each 50kb bin using bedtools (v2.29.2).

source_name: AML12 cells

growth_protocol: The mouse hepatocyte cell line alpha mouse liver 12 (AML12; CRL-2254, ATCC, Manassas, VA) were cultured in DMEM/F12 (11320033, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (16140071, Gibco, Grand Island, NY), ITS Liquid Media Supplement (100×, 41400045, Gibco), and 40 ng/ml dexamethasone (D4902, Sigma, Darmstadt, Germany) at 37℃ and 5% CO2.

extract_protocol:
The DNA samples were extracted with phenol chloroform
The libraries were constructed with VAHTS Universal DNA Library Prep Kit for MGI.
DamID-Seq

treatment_protocol: Dam-fusion protein-expressing vectors were first introduced to 200w cells by lentivirus-based system for stably expression of Dam-Lamin B1 and Dam-only proteins, separately. After 3 days of lentivirus transduction, cells were harvest for gDNA isolation. Then the gDNA was digested with DpnI overnight at methylated GATCs, and dsAdR adaptors were ligated to the end of gDNA fragments. Followed by DpnII digestion, the fragments containing unmethylated GATCs were destroyed and the gDNA fragments containing methylated GATCs were specifically amplified by PCR.

value: hepatocyte

value: stably expression of Dam-Lamin B1 proteins; MATR3 Knock-down


title: A2780 cells, control, replicate 2


title: Dam_only_AML12_shMatr3_rep1


title: MGH558 (npp-16 OE) adult day 1 animals, Replicate 1


title: A2780 cells, control, replicate 1


title: MG isolated from MNU-injured retina, AAV2-aProx1 Ab injected

city: Daejeon

first: Jin Woo

last: Kim

state: Daejeon

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
Library name: library5
raw file accessions are available in file on series

data_processing:
Pooled and size-selected sequencing libraries were sequenced on an Illumina NextSeq 550 instrument using a High Output kit (Illumina) with 38-bp paired-end reads setting. Sequencing reads from single-cell RNA-Seq libraries were aligned to the mouse reference genome (version mm10 from the UCSC) using RSEM (version 1.3.1) with STAR (version 2.7.9a) aligner with default parameters for paired-end reads 74. The matrix of raw counts was transformed into Seurat object for the downstream analysis.
Assembly: genome build number: GRCm38
Supplementary files format and content: The processed data are provided as gene_TPM.csv files. Each file is a comma-separated values (CSV) format, where rows correspond to gene names, and columns correspond to cell IDs. The values represent gene expression levels quantified as Transcripts Per Million (TPM).

molecule: polyA RNA

source_name: retina

extract_protocol:
Freshly prepared samples were resuspended in the resuspension buffer (PBS containing 0.04% BSA and 0.5U/ml RNase inhibitor). Dissociated cells were then filtered through a 50-ml cell filter. Single-cells were sorted using a BD FACSAria Fusion (BD Biosciences) into 96 well PCR plates.
Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the Smart-seq2 protocol with few modifications. Revers transcription (20U/µl Maxima H minus transcriptase, 1M Betaine, 5mM MgCl2, 1μM template switching oligo, additional 0.8U/μl RNase Inhibitor), template switching reaction and PCR pre-amplification (KAPA HiFi HotStart (Roche), 18 cycles) were performed according to the protocol. The PCR products in each well was cleaned up using 0.6× SPRI beads (2% Sera-Mag Speed Beads (Cytiva), 1M NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.01% NP40, 0.05% Sodium Azide, 22% w/v PEG 8000). The quality of cDNA libraries was assessed by quantitative PCR with a primer pair of GAPDH. 50–100 pg of each cDNA library were used to generate the Illumina sequencing library using EZ-Tera XT DNA library preparation kits (Enzynomics). After the final PCR amplification, samples were pooled and cleaned by MinElute PCR purification kit (Qiagen).

value: retina

value: AAV2-aProx1 Ab + MNU


title: N2 wildtype adult day 1 animals, Replicate 3

value: Whole organism lysate

value: N2 (Bristol)


title: IgG control for group2_rep3

city: Houston

first: Shu-Hsia

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist

description: group 2

data_processing:
Sequencing was performed on the Illumina Hiseq X Ten at 150bp paired-end reads with 20M read depth
Both library preparation and sequencing were performed by Novogene (Sacramento, California)
All samples had Q30 > 90%.
Alignment via HISAT2
Assembly via cufflinks
Assembly: hg38
Supplementary files format and content: csv, count table

source_name: Cell line

growth_protocol: U937 cells mainted in RPMI 1640 media

extract_protocol:
Cell pelets were resuspended in Trizol and RNA isolated using chloroform extraction
NEBNext Ultra DNA Library Prep Kit for Illumina

treatment_protocol: AML cells were pretreated with 50 ng/ml IFNg followed by treatment with 5 mg/ml LILRB3 antibodies for 72 hours

value: IgG

tag: stimulation

value: 50 ng/mL IFNy


title: N2 wildtype adult day 1 animals, Replicate 4


title: Dam_LaminB_AML12_shMatr3_rep2

value: stably expression of  Dam-only proteins; MATR3 Knock-down


title: Dam_LaminB_AML12_shMatr3_rep1


title: IgG control for group2_rep2

description: group 2


title: MG isolated from MNU-injured retina, AAV2-Ctrl Ab injected, rep1

description:
Library name: library3
raw file accessions are available in file on series

value: AAV2-Ctrl Ab + MNU


title: N2 wildtype adult day 1 animals, Replicate 2


title: Dam_only_AML12_Ctrl_rep2

value: stably expression of  Dam-only proteins


title: IgG control for group2_rep1

description: group 2


title: MG isolated from healthy retina, AAV2-Ctrl Ab injected

description:
Library name: library1
raw file accessions are available in file on series

value: AAV2-Ctrl Ab


title: MG isolated from healthy retina, AAV2-aProx1 Ab injected

description:
Library name: library2
raw file accessions are available in file on series

value: AAV2-aProx1 Ab


title: origa-255-39

city: Seville

first: Rafael

middle: G

last: Albaladejo

state: Seville

address: c/Profesor García González 2

department: Biología Vegetal y Ecología

country: Spain

institute: Universidad de Sevilla

description:
Library name: origa-255-39
column name in raw_counts_All_samples.txt: origa255-39

data_processing:
Quality check with FastQC
Cleaning and removal of contaminant reads with Rcorrector + Fastp + SortMeRNA + Kraken
Normalization with Trinity
Assembly: de novo assembly with Trinity + Oases. Remove redundancy with EvidentialGene
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Helianthemum origanifolium

source_name: adult leaves

growth_protocol: Seeds were subjected to mechanical scarification with fine-grained sandpaper and germinated on sterile Petri plates with moist filter paper. Five days later, the seedlings were transferred to soil-filled pots containing a 3:1:1 ratio of soil:sand:perlite, and cultivated in a greenhouse at 22/25ºC (night/day), 40-60% relative humidity, and natural daylight. At 446 days after sowing, leaves from 3-5 apical node were selected for RNA isolation and stored at -80ºC until processing.

extract_protocol:
RNeasy Plant Mini Kit (QIAGEN, Crawley, UK)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, the first-strand cDNA was synthesised using random hexamer primers followed by the second-strand cDNA synthesis. The library was prepared following the steps of end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The Novogene NGS RNA Library Prep Set was employed for library preparation.

value: adult leaves


title: N2 wildtype adult day 1 animals, Replicate 1


title: mammary gland, puberty, stromal

description: Library name: puberty stromal cells ATACseq

value: FVB, puberty, mammary gland, female

value: FACS sorted stromal cells


title: LILRB3 agonist_rep3

description: group 2

value: LILRB3 agonist


title: molle256-29

description:
Library name: molle256-29
column name in raw_counts_All_samples.txt: molle256-29

organism: Helianthemum marifolium subsp. molle


title: 4193646

description: DLBCL, cryo-preserved

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

source_name: lymph node

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: DLBCL, cryo-preserved


title: Dam_LaminB_AML12_Ctrl_rep2

value: hepatocyte

value: stably expression of Dam-Lamin B1 proteins


title: LILRB3 agonist_rep2

description: group 2


title: MGH558 (npp-16 OE) adult day 1 animals, Replicate 2

value: Integrated transgenic overexpression of a full length copy of NPP-16/CeNUP50


title: MG isolated from MNU-injured retina, AAV2-Ctrl Ab injected, rep2

description:
Library name: library4
raw file accessions are available in file on series

value: retina


title: origa-255-38

description:
Library name: origa-255-38
column name in raw_counts_All_samples.txt: origa255-38


title: molle256-27

description:
Library name: molle256-27
column name in raw_counts_All_samples.txt: molle256-27


title: Dam_LaminB_AML12_Ctrl_rep1


title: molle254-25

description:
Library name: molle254-25
column name in raw_counts_All_samples.txt: molle254-25


title: LILRB3 agonist_rep1

description: group 2


title: IgG control for group1_rep3

description: group 1


title: 06 RB06

type: RNA

hyb_protocol: Standard protocol from Nanotring nCounter protocol

data_processing: nSolver program from nanostring was used for data processing

source_name: TI-Tregs from SB1 tumors

label_protocol: Cells were YFP+. No other labeling was used.

growth_protocol: SB1 tumors were grown in RPMI medium supplemented with 10%FCS, 1%L-glutamine and 1% penicillin/streptomycin before implantation into flank of C57bl/6 mice

extract_protocol: Tumors were harvested and processed into single cell suspension. Treated with DNAse/Collagenase mixture before FACS sorting by YFP signal. RNA extraction ensued.

treatment_protocol: No treatment

value: Kdr(+/+)xFoxp3(yfp-cre) mice


title: Dam_only_AML12_Ctrl_rep1


title: IgG control for group1_rep1

description: group 1

value: IgG


title: origa-247-31

description:
Library name: origa-247-31
column name in raw_counts_All_samples.txt: origa247-31


title: 05 RB05

scan_protocol: Standard protocol from Nanotring nCounter protocol


title: andal261-08

description:
Library name: andal261-08
column name in raw_counts_All_samples.txt: andal261-08

organism: Helianthemum marifolium subsp. andalusicum


title: molle254-22

description:
Library name: molle254-22
column name in raw_counts_All_samples.txt: molle254-22


title: origa-247-33

description:
Library name: origa-247-33
column name in raw_counts_All_samples.txt: origa247-33


title: IgG control for group1_rep2

description: group 1

value: 50 ng/mL IFNy


title: andal261-06

description:
Library name: andal261-06
column name in raw_counts_All_samples.txt: andal261-06


title: LILRB3 antagonist_rep3

description: group 1

value: LILRB3 antagonist


title: marif085-15

description:
Library name: marif085-15
column name in raw_counts_All_samples.txt: marif085-15

organism: Helianthemum marifolium subsp. marifolium


title: LILRB3 antagonist_rep2

description: group 1


title: marif085-12

description:
Library name: marif085-12
column name in raw_counts_All_samples.txt: marif085-12


title: marif089-17

description:
Library name: marif089-17
column name in raw_counts_All_samples.txt: marif089-17


title: andal260-03

description:
Library name: andal260-03
column name in raw_counts_All_samples.txt: andal260-03


title: LILRB3 antagonist_rep1

description: group 1


title: 03 RB03

value: Kdr(fl/fl)xFoxp3(yfp-cre) mice


title: 04 RB04


title: 12 h Neurons following Insulin exposure

status: Public on Mar 13 2025

first: Norman

last: Haughey

address: 2912 Saint Paul St

institute: Johns Hopkins School of Medicine

data_processing:
Paired-end 100nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Rattus norvegicus sequence Rnor_6.0 with CLCGenomicsServer 8.0.1 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 8.0.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v6.5
Assembly: RAT_GENOME_(NCBI)-Rnor_6.0
Supplementary files format and content: Skhu-RAT-FPKM-LogQuant-Signals .txt file, quantile normalized log2 FPKM values, 0 ignored as Null

source_name: hippocampal neurons

growth_protocol:
growth protocol astrocytes: Astrocytes were seeded at 5 x10^4 cells per well on 6-well plates coated with PDL in DMEM/F12 (Gibco BRL) supplemented with 10% FBS, D-glucose (final concentration 25 mM) (Sigma), and 1% antibiotic/antimitotic solution (104 Unit of penicillin G/ml, 10 mg streptomycin/ml and 25 mg amphotericin B/ml) (Sigma).
growth protocol neurons: Hippocampal neurons seeded at 8x10^5 /well in 6-well plates coated with PEI and in serum free Neurobasal medium containing 1% B27.

extract_protocol:
Total RNA was extracted  from primary cultured Rattus hippocampal astrocytes, and neurons using a RNeasy Mini Kit following the manufacturer's protocol (Qiagen, Venlo, Limburg)
Illumina TruSeq Stranded Total RNA with RIBO-ZERO depletion & fragmentation

treatment_protocol:
treatment protocol astrocytes: Astrocytes were treated with saline or 200 nM insulin (Sigma) at time points 6 and 12 h. Four hours before treatment, media was changed to DMEM/F12 (Gibco BRL) supplemented with 2% FBS, D-glucose (final concentration 5 mM) (Sigma), and 1% antibiotic/antimitotic solution (104 Unit of penicillin G/ml, 10 mg streptomycin/ml and 25 mg amphotericin B/ml) (Sigma).
treatment protocol neurons: Hippocampal neurons were treated with saline or 200 nM insulin (Sigma) at 0, 6 or 12 h. Four hours before treatment, media was changed to serum free Neurobasal medium containing 1% B27 (insulin-free).

value: hippocampal neurons

value: primary cutured cells

value: neuron

tag: timepoint

value: Insulin treatment


title: Control Neurons (saline treatment)

value: 0 min

value: Untreated


title: 6 h Neurons following Insulin exposure

value: 6 h


title: 12 h Astrocytes following Insulin exposure

source_name: hippocampal astrocytes

value: hippocampal astrocytes

value: astrocyte


title: Control Astrocytes (saline treatment)


title: 6 h Astrocytes following Insulin exposure


title: marif089-18

description:
Library name: marif089-18
column name in raw_counts_All_samples.txt: marif089-18

value: adult leaves


title: 02 RB02

first: Mohamed-Reda

address: 10 Center Drive

institute: NIH


title: siG1_1

city: Seattle

first: Alison

last: Paquette

state: WA

address: 1900 Ninth Avenue

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

data_processing:
Fastq sequencing files were aligned to GrCh38 using kallisto with bias correction.
Estimated transcript abundances were condensed to Ensembl Gene IDs as length scaled transcripts per million using the tximport package.
Assembly: GRCh38
Supplementary files format and content: .csv file that contains lengthscaledTPM counts

source_name: placenta

growth_protocol: BeWo cells were purchased from ATCC (CCL-98) and stored in LN2 prior to initiation of cell culture. Cells were grown in Ham’s F12K complete media (Thermo Fisher, #21127022; 10% Fetal Bovine Serum [FBS]/1X Penicillin/Streptomycin) in 10 cm tissue culture treated plates (Fisher Scientific, #08772E) and cultured at 370C at 5% CO2.

extract_protocol:
RNA was isolated using the Zymo Direct-zol Mini-prep kit (Zymo-Catalog # RD2051
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were treated with: 1) DMSO (0.1%) or 50uM Forskolin for 48h, 2) GCM1 siRNA or non-targeting siRNA for 24h. The order and timing of treatments are indicated for each sample.

value: placenta

value: BeWo

value: choriocarcinoma

value: GCM1 siRNA for 24h


title: siG1_3


title: NT_1

value: Non-targeting  siRNA for 24h


title: NT_3_F1

value: 50uM Forskolin for 48h then non-targeting siRNA for 24h


title: NT_3_Si1

value: Non-targeting siRNA for 24h then 50uM Forskolin for 48h


title: G1_2_Si1

value: GCM1 siRNA for 24h then 50uM Forskolin for 48h


title: NT_2_Si1


title: siG1_2


title: NT_2_F1


title: NT_1_Si1


title: G1_1_Si1


title: G1_3_F1

value: 50uM Forskolin for 48h then GCM1 siRNA for 24h


title: F_3_48

value: 50uM Forskolin for 48h


title: F_2_48


title: G1_2_F1


title: G1_1_F1


title: andal260-01

description:
Library name: andal260-01
column name in raw_counts_All_samples.txt: andal260-01


title: F_1_48


title: D_1_48

value: DMSO 0.1% for 48h


title: M58_72_100

data_processing:
Fastq sequencing files were aligned to GrCh38 using kallisto with bias correction.
Estimated transcript abundances were condensed to Ensembl Gene IDs as length scaled transcripts per million using the tximport package.
Assembly: GRCh38
Supplementary files format and content: .csv file of lengthscaledTPM counts

source_name: Placenta

growth_protocol: Cells were cultured in IMDM with 10% FBS and 1% penicillin/streptomycin and incubated at 37 °C with 5% CO2 and ambient O2

treatment_protocol: Cells were treated with 0nM, 10nM, or 100nM CRH for 24 or 72hrs. Cells collected from 8 placentas (4 male and 4 female) were each treated with the 6 treatment combinations (24hr- 0nM, 10nM, 100nM CRH and 72hr- 0nM, 10nM, 100nM CRH).

value: Placenta

value: Primary Trophoblasts

value: Syncytiotrophoblasts

tag: time point

value: 100nM CRH

tag: Sex

value: male


title: D_3_48


title: M58_72_10

value: 10nM CRH


title: 01 RB01

last: Benmebarek

value: Kdr(fl/fl)xFoxp3(yfp-cre) mice


title: M58_24_100


title: NT_1_F1

value: placenta

value: BeWo


title: NT_3

value: choriocarcinoma


title: NT_2

value: Non-targeting  siRNA for 24h


title: G1_3_Si1


title: M58_72_0

value: 0nM CRH


title: M58_24_0


title: M58_24_10


title: M56_24_10


title: M56_72_10


title: M56_72_100


title: M02_72_100


title: D_2_48


title: M56_24_100


title: M56_72_0


title: M02_24_0


title: M01_24_10


title: M01_72_0


title: F49_72_100

value: female


title: M56_24_0


title: M02_72_0


title: F49_72_0


title: M01_72_100


title: M02_24_100


title: M01_24_100


title: M01_24_0


title: M01_72_10


title: F49_24_0


title: F47_72_10


title: F49_24_10


title: F47_72_0


title: F49_72_10


title: F47_72_100


title: F47_24_100


title: F47_24_10


title: F25_72_0


title: F47_24_0


title: M02_72_10


title: F25_24_10


title: F25_24_100


title: M02_24_10


title: F25_24_0


title: F12_72_100


title: F49_24_100


title: F12_72_0


title: F12_72_10


title: F12_24_10


title: F12_24_0


title: IER3 knockdown in SK-N-BE(2) RNA-seq Replicate 4

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
FASTQ files were mapped against a reference human genome hg38 with the splice-aware aligner STAR (v2.7.10a) to generate BAM files
Obtained aligned files (BAM format) were subjected to quantification using featureCounts from Subread package (v2.0.3). The reads were quantified for Gencode transcript annotation release v46 (corresponds to genome hg38).
Generated matrix file from read quantification was then used for differential expression (DE) analysis. DE analysis was performed using Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix containing tab-delimited data includes raw read count values for individual genes in each Sample.

growth_protocol: SH-SY5Y, SKNBE2 and HeLa cells were routinely cultured in DMEM media supplemented with 10% FBS.

extract_protocol:
The cells from both contrl and IER3sh stable cell lines were collected  and Total RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System. For RNA sequencing.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat # RS-122-2201). mRNA sequencing on 100PE of DNBseq platform.

treatment_protocol: Stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

value: cell line

value: ShRNA


title: IER3 knockdown in SK-N-BE(2) RNA-seq Replicate 3


title: IER3 knockdown in SK-N-BE(2) RNA-seq Replicate 2


title: SK-N-BE(2) control RNA-seq Replicate 1

value: Untreated


title: IER3 knockdown in SH-SY5Y RNA-seq Replicate 3


title: IER3 knockdown in SH-SY5Y RNA-seq Replicate 4


title: SK-N-BE(2) control RNA-seq Replicate 2


title: IER3 knockdown in SH-SY5Y RNA-seq Replicate 1


title: IER3 knockdown in SH-SY5Y RNA-seq Replicate 2


title: SH-SY5Y control RNA-seq Replicate 2


title: F25_72_100


title: F25_72_10


title: IER3 pulldown in SK-N-BE(2) ChIP-seq Replicate 2

data_processing:
FASTQ files were mapped against a reference human genome hg38 with bowtie2 (v2.4.4) using --end-to-end --very-sensitive --no-mixed --no-discordant parameteres to generate BAM files.
Obtained aligned files (BAM format) were subjected to duplicate removal using Picard (v2.21.6). The hg38 blacklist regions are reremoved from BAM files using BEDTools (v2.30.0)
Peaks (narrowPeak) are called by comparing IER3sh pulldown samples and Input samples in individual cell lines using MACS3 callpeak -q 0.01 parameters.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Supplementary files format and content: MACS Peaks

extract_protocol:
DNA from the INPUT and IER3 pulldown ChIP samples were extarcted using phenol-choloform extraction followed by Ethanol precipitaion and the final pellet was dissolved in nuclease free water.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: All the three cell lines used are wild type and untreated cell lines.

tag: chip antibody

value: IER3 polyclonal antibody (Invitrogen, #PA5-20391)

value: ChIP Antibody


title: SH-SY5Y control RNA-seq Replicate 1


title: IER3 pulldown in SH-SY5Y ChIP-seq Replicate 2


title: SH-SY5Y Input ChIP-seq Replicate 2


title: SK-N-BE(2) Input ChIP-seq Replicate 2


title: IER3 pulldown in SH-SY5Y ChIP-seq Replicate 1


title: SK-N-BE(2) Input ChIP-seq Replicate 1


title: IER3 pulldown in HeLa ChIP-seq Replicate 1

value: HeLa


title: HeLa Input ChIP-seq Replicate 1


title: IER3 pulldown in HeLa ChIP-seq Replicate 2


title: F12_24_100

value: Placenta

value: Primary Trophoblasts

value: Syncytiotrophoblasts


title: SH-SY5Y Input ChIP-seq Replicate 1


title: K35 S. epi

city: Krakow

first: Piotr

last: Brzoza

address: Gronostajowa 7

department: Department of Immunology

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

data_processing:
For raw reads: Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2). Quality trimming of the reads has not been performed.
Further data processing was performed using the Galaxy platform .
Reads of low quality (Phred Score <20 or length <20bp) were filtered out with Trim Galore!, alignment was achieved using HISAT2  against hg38 human genome assembly , and raw counts were compiled via featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Organoid primary keratinocyte culture

growth_protocol: Human epidermis was treated with TrypLE-Select (Thermofisher) to isolate epidermal cells. Cells were cultured in serum free KGM-Gold medium (Lonza Group Ltd.) to generate passage 1 cells.  The keratinocytes were then plated at density of 1×10^5 cells per well on permeable inserts (12-mm-diameter, 0.4mm pore size; Millipore, Millicell culture inserts) in CnT Prime Epidermal Keratinocyte Medium (CellnTec). Cells were cultured at 37°C in presence of 5% CO2 until confluence. Polarized skin structures that resemble in vivo stratified epidermis were generated by air-liquid interface cultures grown in 3D Prime Medium (CellnTec) for 10 days.

extract_protocol:
RNA was isolated using the Total RNA Zol-Out kit (A&A Biotechnology) according to the manufacturer’s instruction.
TrueSeq Stranded mRNA (illumina) kita was used for library preparation. 200ng of RNA was used per sample.

treatment_protocol: Bacteria were grown in tryptic soy broth (TSB, Sigma) for 24 hrs  to a stationary phase of growth, followed by two washes in PBS. Bacterial treatment was performed by adding 20µl of 2.5x10^6 CFU/ml (5x10^4 CFU per sample), or 20µl PBS as a vehicle control, to the model apical aspect. Keratinocytes were then incubated for 24 hr while exposed to microbial challange.

value: Organoid primary keratinocyte culture

value: S. epidermidis


title: IER3 pulldown in SK-N-BE(2) ChIP-seqReplicate 1


title: M54 PBS

value: PBS/control


title: M54 S. aur

value: S. aureus


title: K35 S. aur


title: HeLa Input ChIP-seq Replicate 2


title: Mouse colon, CAC+Erl70 4

city: Galveston

first: Haiping

last: Hao

address: 301 University Blvd

institute: UTMB NGS Core

data_processing:
Sequencing reads were trimmed for low quality bases and Illumina adapters using cutadapt v1.15.
STAR 2.7.10a
DESeq2 v1.38.3
Gene ontology and KEGG pathway enrichment of gene lists was completed with Enrichr.
Assembly: GRCm39
Supplementary files format and content: Excel files containing gene lists, id, mean base, log2 fold change, and p-values.

source_name: Colon

growth_protocol: Six-week-old male C57BL/6J mice were housed in the UTMB Animal Facility with a 12-hour light/dark cycle, temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and their colon tissues snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen colon tissue using the PureLink RNA Mini Kit (Thermo Fisher).
RNA libraries were prepared using the NEBNext Ultra II RNA Kit per manufacturer's protocol.

treatment_protocol: There were three groups of 4 mice receiving the following treatments: (1) vehicle control mice received AIN-93G basal diet, (2) CAC mice were additionally subjected to AOM 7.4 mg/kg i.p. followed by 2.5% DSS in drinking water for 2 cycles of 7 days each with intermittent 2-week intervals of normal drinking water, and (3) CAC+Erl70 mice received the same AOM/DSS regimen but were fed AIN-93G diet containing 70 ppm erlotinib.

value: Colon

value: Colonocytes

value: WT

value: Male

value: AOM/DSS + AIN-93G Diet pre-mixed with Erlotinb 70 ppm


title: K35 PBS


title: HEK293 miRNA from virus infected nuclear fraction biol rep 3

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

library_source: other

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
sequences were aligned to human miRNAs using bowtie2 and quantified using bedtools coverage
normalized counts in excel file
Assembly: hg38
Supplementary files format and content: raw counts file

molecule: other

growth_protocol: HEK293 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol:
After PR8 infection for 16 hrs, cells were fractionated into cytplasmic and nuclear fractions. First AGO proteins were enriched by immunoprecipitation with T6B peptide. The RNA was isolated and small RNA libraries were genereated.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: PR8 IAV virus treatment at MOI 10

tag: ip molecule

value: T6B peptide

value: PR8 IAV infection

tag: fraction

value: nuclear fraction


title: M36 S. aur


title: M36 S. epi


title: M36 PBS


title: Mouse colon, CAC+Erl70 3


title: P5-1 Product scRNA-seq

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

data_processing:
FASTQ files were analyzed with the 10× Genomics Cell Ranger (v7.1.0) software pipeline, including demultiplexing and read alignment to the CAR-augmented human reference genome GRCh38.p13 to detect endogenous and CAR RNAs.
The GD2-CAR sequence was indexed with the human reference genome (GRCh38.p13) to generate a chimeric reference before data pre-processing and read alignment. Alignment to the chimeric reference followed the 10x Genomics standard, using Cell Ranger (v7.1.0) and tertiary analysis with Seurat tools. Cells with raw UMI > 0 matching the GD2-CAR sequence were identified as CAR+ cells. Before cell clustering, quality controls were conducted in Seurat (v4.0). Genes detected in fewer than 10 cells and cells with >10% mitochondrial raw unique molecular identifiers (UMIs) were removed to exclude low-quality or dying cells. UMI counts were log-normalized. Cells with <1,500 or >7,500 genes were excluded. Doublets were identified using DoubletFinder. The top 2,000 genes with the greatest variability were retained and scaled (linear transformation) for clustering and integration. Cells in pre-infusion product samples were integrated using harmony. When clustering CAR NKT product samples, principal component analysis (PCA) and unsupervised Louvain clustering analysis with a resolution of 0.5 were performed on the scaled data. A total of 10 clusters were identified from 24 pre-infusion product samples. Cells in each cluster were projected onto a two-dimensional UMAP. Seurat function CellCycleScoring was used to evaluate differences in cell cycle phase gene expression.
B cells, red blood cells, and monocytes were filtered out by removing cells where HBB, CD79A, MS4A1, CD19, CD22, CD14, and MS4A7 reads were > 0.
Assembly: hg38
Supplementary files format and content: Products_integrated.metadata.csv, contains cells metadata from the integrated Product samples

source_name: CAR-NKT

growth_protocol: PBMCs were isolated from peripheral blood leukapheresis products using Ficoll gradient purification, and NKTs were isolated using a special lot of anti-iNKT microbeads (Miltenyi Biotec, tested according to FDA guidelines by BioReliance) and the CliniMACS instrument (Miltenyi Biotec). Enriched NKTs were then stimulated with α-galactosylceramide (Glycosyn, cGMP grade)-pulsed PBMCs and cultured with IL2 and IL21 (NCI, 200 U ml−1 and CellGenix, 10 ng ml−1, respectively). Cells were transduced with retroviral particles encoding the GD2-CAR.15 construct in RetroNectin-coated plates (Takara Bio) for 72 h and then washed, replated, and cultured for 9-15 days. CAR-NKT products that did not expand sufficiently by day 10 were restimulated with α-galactosylceramide-pulsed PBMCs or aAPCs and further expanded until sufficient numbers were met for the assigned DL.

extract_protocol:
Cells were dissociated and RNAseq libraries were prepared according to manufacturer’s protocols using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics).
scRNA-seq libraries were prepared according to Chromium Next GEM Single Cell 5` Reagent Kit v2 (10x Genomics). Libraries were sequenced on NovaSeq6000.

value: CAR-NKT

tag: sample type

value: Product


title: HEK293 miRNA from virus infected nuclear fraction biol rep 1

tag: cell line


title: Mouse colon, CAC+Erl70 1

tag: tissue


title: HEK293 miRNA from virus infected cytoplasmic fraction biol rep 4

value: cytoplasmic fraction


title: HEK293 miRNA from virus infected cytoplasmic fraction biol rep 3


title: HEK293 miRNA from virus infected cytoplasmic fraction biol rep 2


title: Mouse colon, CAC 3

value: AOM/DSS + AIN-93G Diet


title: Mouse colon, CAC 4


title: HEK293 miRNA from control nuclear fraction biol rep 4

value: Control cells


title: Mouse colon, CAC 2


title: HEK293 miRNA from control nuclear fraction biol rep 3


title: Mouse colon, CAC 1


title: HEK293 miRNA from control nuclear fraction biol rep 2


title: Mouse colon, Control 3

value: AIN-93G Diet