title: Fn14 Knockout LX-2 replicate 1

city: Perth

first: Nathan

middle: Michael

last: Main

address: 305, Bentley WA 6102

institute: Curtin Medical Research Institute

description: Library name: 1-2KO-LX-2-1

data_processing:
Quality assessment of the sequencing data was performed using FastQC v0.10.1.
Pass-filter paired-end FASTQ files were processed with Cutadapt v1.9.1 to remove adapter sequences, PCR primer-derived sequences, bases with quality scores <20, and reads shorter than 75 bp after trimming.
Short-read alignment was performed using HISAT2 v2.0.1 against the human reference genome GRCh38.p13/hg38.
Gene-level read counts were generated using HTSeq v0.6.1 with gene annotation files supplied by Azenta/GENEWIZ. FPKM expression values were calculated from HTSeq read counts.
Differential expression analysis was performed using the DESeq2 Bioconductor package. Genes with adjusted P values <0.05 were considered differentially expressed.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: tab-delimited text file includes FPKM expression values for all samples

growth_protocol: LX-2 cells were grown in reduced-serum medium consisting of EBM-2 (Lonza, CC-3162) supplemented with EGM-2 MV BulletKit (Gibco, CC-4176) components containing 2% bovine serum albumin (Gibco, CC-4176).

extract_protocol:
Total RNA was extracted using the Isolate II RNA Mini Kit (Bioline, BIO-52072)
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: Cells were cultured for 24 hours prior to treatment with 100 ng/mL TWEAK or vehicle control (PBS) for 2 hours.

tag: cell line

value: Hepatic Stellate Cells

value: Fn14 KO

value: PBS


title: Fn14 Knockout LX-2 replicate 3

status: Public on Jun 17 2026

type: SRA

state: WA

country: Australia

description: Library name: 1-2KO-LX-2-3

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: genotype

tag: treatment


title: Healthy human donor (2), CAR T cells, MAFF, RNA

city: Stanford

first: Oliver

last: Takacsi-Nagy

state: CA

address: 234 Pasteur Dr. (BMI 4600)

department: Pathology

country: USA

institute: Stanford University School of Medicine

description:
Library name: Acute_2I-MAFF_RNA
Column name in both processed data files: 'Acute_2I'

data_processing:
Basecalls were performed using bcl-convert Version 4.4.6 from Illumina
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

source_name: Primary Human T Cell

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with CD19-expressing Nalm6 targets (leukemia cell line, 1:8 Effector:Target ratio, 72-hour co-culture).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and RNA was isolated using Qiagen RNeasy Micro or Mini Kits, including DNase treatment.
25-100ng of RNA based on Qubit quantification (Thermo Fisher) was inputted into the Illumina Stranded mRNA Prep workflow and resultant libraries were quantified by Qubit and size-verified on an Agilent TapeStation. Sequencing was performed on a NovaSeq X (Illumina) with the following read structure: 151 bp Read 1, 12 bp i7 Index, 24 bp i5 Index, 151 bp Read 2.

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which healthy human donor they were isolated from and which transcription factor they were edited to express.

value: Primary Human T Cell

tag: individual

value: Healthy Donor 2

tag: tf expressed

value: MAFF


title: Colostrum C002

city: Singapore

first: Jia Ming

last: Low

address: NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228

country: Singapore

institute: National University Hospital

description:
Library name: C002_BM_T1
Colostrum

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files were processed using Cell Ranger (10x Genomics)
Gene expression matrices were imported into Seurat (v4.4.0)
Cells with fewer than 250 detected genes, fewer than 500 UMIs, or greater than 10% mitochondrial transcripts were excluded.
Data were normalized, scaled, and integrated across samples using standard Seurat workflows.
Dimensionality reduction was performed using principal component analysis and Uniform Manifold Approximation and Projection (UMAP).
Cell clusters were identified and annotated on canonical marker gene expression.
Annotated datasets were exported as count matrices, metadata tables, and a Seurat object for public deposition.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains gene expression count matrices;
Supplementary files format and content: barcodes.tsv.gz contains cell barcodes; features.tsv.gz contains gene features;
Supplementary files format and content: cell_metadata.csv.gz contains cell-level annotations;
Supplementary files format and content: sample_metadata.csv.gz contains sample-level metadata;
Supplementary files format and content: MILK_final_annotated_seurat_object_CORRECTED.rds contains the annotated Seurat object used for downstream analyses.

molecule: total RNA

source_name: Breast milk

growth_protocol: Lactating mothers were recruited under an institutional review board approved study. Human breast milk and peripheral blood samples were collected longitudinally across lactation.

extract_protocol:
Cells were isolated from fresh breast milk and peripheral blood mononuclear cells. Single-cell suspensions were processed according to standard laboratory protocols prior to sequencing.
Single-cell libraries were generated using the 10x Genomics Chromium platform according to the manufacturer's instructions.

treatment_protocol: No experimental treatment was administered. Samples were collected observationally.

tag: tissue

value: Breast milk

tag: Sex

value: female

tag: Stage

value: Colostrum

value: wild type


title: Healthy human donor (2), CAR T cells, FOSL1, RNA

description:
Library name: Acute_2H-FOSL1_RNA
Column name in both processed data files: 'Acute_2H'


title: Puck_240129_32

city: New Haven

first: Hattie

last: Chung

state: CT

address: 300 George St

institute: Yale University

description: Library name: 2024-03-02_Puck_240129_32

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Ovary

growth_protocol: Female C57BL/6 mice were maintained under SPF conditions on a 12-hour light-dark cycle with standard chow and water provided ad libitum.

extract_protocol:
10µm frozen sections were cut on the cryostat
Spatial transcriptome libraries were prepared using the Slide-seq V2 protocol

treatment_protocol: Mice were staged near-daily for their estrous cycle and harvested at the estrus or metestrus stage via intracardial perfusion with PBS. Ovaries were fresh frozen embedded in OCT.

value: Ovary

value: Metestrus

tag: batch

tag: group

value: Middle


title: Fn14 Knockout LX-2 replicate 4

description: Library name: 1-2KO-LX-2-4


title: Puck_240129_26

description: Library name: 2024-03-02_Puck_240129_26


title: Puck_240129_29

description: Library name: 2024-03-02_Puck_240129_29

value: Old


title: Healthy human donor (2), CAR T cells, GFP, RNA

description:
Library name: Acute_2E-GFP_RNA
Column name in both processed data files: 'Acute_2E'

value: GFP


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 13-0

city: la jolla

first: Yanmiao

last: Du

address: 4254 Urey Hall, 9500 Gilman Drive

department: Department of Chemistry and Biochemistry/Cellular and Molecular Medicine

institute: UCSD

description:
Library name: ChIP_PFC_MOR-LPS_M_13-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

library_source: genomic

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore (v0.6.7, --paired --fastqc).
Reads were aligned to Mus musculus mm10 using Bowtie2 (v2.4.5). PCR duplicates were removed with SAMtools (v1.15.1) markdup. Reads overlapping ENCODE mm10 blacklist (v2) were excluded with BEDTools subtract (v2.30.0). Coverage profiles were generated with bedtools genomecov and converted to BigWig with bedGraphToBigWig.
Peak calling: MACS2 (v2.2.7.1; -q 0.05 -g mm) against matched pooled Input controls.
Differential H3K27ac analysis: consensus peak set constructed in DiffBind (v3.10.1) with condition-aware merging. Read counts quantified with DiffBind (dba.count, summarizeOverlaps); peaks retained if >= 15 reads in >= 80% of samples within any condition. Differential peaks identified via DESeq2 (dba.analyze); FDR < 0.05. Peaks annotated with ChIPpeakAnno (v3.32.1) and EnsDb.Mmusculus.v79.
Transcription factor regulatory influence assessed with Taiji (v1.2.0) integrating H3K27ac enhancers and RNA-seq expression. TF activity quantified as personalized PageRank scores (z-score normalized, capped at +/-2).
Assembly: mm10
Supplementary files format and content: narrowPeak files (MACS2 peak calls); bigWig coverage tracks (bedtools genomecov + bedGraphToBigWig)

molecule: genomic DNA

source_name: prefrontal cortex

growth_protocol: Male and female C57BL/6NTac mice (Taconic, Hudson, NY) were bred at the University of Pennsylvania and group-housed (3-5/cage) under a 12-h light/dark cycle (lights on at 0700) with ad libitum access to food and water. All procedures were approved by the University of Pennsylvania Animal Care and Use Committee.

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). ~10,000 NeuN+ nuclei per replicate were lysed and digested with MNase (88216, Thermo Fisher) in the presence of CaCl2; reaction quenched with EDTA. Chromatin IP was performed using 0.125 ug anti-H3K27ac antibody (39135, Active Motif) coupled to 5 uL protein A Dynabeads (10001D, Thermo Fisher), following the MOWChIP-seq protocol.
ChIP-seq libraries were constructed from purified ChIP DNA (~10,000 NeuN+ nuclei) and input DNA (~2,000 nuclei). PFC libraries used xGen 2S DNA Library Prep Kit (10009877, IDT); hippocampus, hypothalamus, and striatum libraries used ThruPLEX DNA-Seq kit (R400674, Takara Bio). Fragment size verified on TapeStation (Agilent) with High Sensitivity DNA Analysis Kit; primer-dimers removed with SPRIselect beads. Libraries quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 nt, ~15 million reads per library).

treatment_protocol: Perinatal morphine exposure: 8-12-week-old female mice were implanted with osmotic minipumps (Alzet model 1004) delivering morphine sulfate (10 mg/kg/day, NIDA Drug Supply) or saline, then co-housed with drug-naive males. Pups were transferred to drug-naive surrogates within 4-8 hours of birth. Postnatal morphine (10 mg/kg SC, 10 mL/kg) or saline was administered twice daily (09:00 and 17:00) from PND1 through the morning of PND14, after which mice underwent spontaneous opioid withdrawal. In adulthood, mice were assigned to four groups: SAL-SAL (saline/saline), SAL-LPS (saline/LPS challenge), MOR-SAL (morphine/saline), or MOR-LPS (morphine/LPS challenge). Brain tissues were collected 2 hours after adult LPS or saline injection.

value: prefrontal cortex

value: MOR-LPS


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 18-1

description:
Library name: ChIP_PFC_MOR-LPS_F_18-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 14-0

description:
Library name: ChIP_PFC_MOR-LPS_M_14-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (2), CAR T cells, BATF, RNA

description:
Library name: Acute_2D-BATF_RNA
Column name in both processed data files: 'Acute_2D'

value: BATF


title: Healthy human donor (2), CAR T cells, FOS, RNA

description:
Library name: Acute_2C-FOS_RNA
Column name in both processed data files: 'Acute_2C'

value: FOS


title: Fn14 Knockout LX-2 replicate 2

description: Library name: 1-2KO-LX-2-2

value: Hepatic Stellate Cells

value: Fn14 KO

value: PBS


title: Puck_240129_27

description: Library name: 2024-03-02_Puck_240129_27


title: Fn14α Knockout LX-2 replicate 4

description: Library name: 1KO-LX-2-4

value: Fn14alpha KO


title: Fn14α Knockout LX-2 replicate 3

description: Library name: 1KO-LX-2-3


title: Puck_240129_24

description: Library name: 2024-03-02_Puck_240129_24


title: Healthy human donor (2), CAR T cells, JUN, RNA

description:
Library name: Acute_2B-JUN_RNA
Column name in both processed data files: 'Acute_2B'

value: Primary Human T Cell

value: Healthy Donor 2

value: JUN


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 16-4

description:
Library name: ChIP_PFC_MOR-LPS_F_16-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: Fn14α Knockout LX-2 replicate 2

description: Library name: 1KO-LX-2-2


title: Puck_240129_23

description: Library name: 2024-02-27_Puck_240129_23

value: Ovary


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 15-3

description:
Library name: ChIP_PFC_MOR-LPS_F_15-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_240129_22

description: Library name: 2024-02-27_Puck_240129_22

value: Metestrus


title: Healthy human donor (2), CAR T cells, JUN-FOS-BATF, RNA

description:
Library name: Acute_2A-JUN-FOS-BATF_RNA
Column name in both processed data files: 'Acute_2A'

value: JUN-FOS-BATF


title: Healthy human donor (1), CAR T cells, BATF2, RNA

description:
Library name: Acute_1K-BATF2_RNA
Column name in both processed data files: 'Acute_1K'

value: Healthy Donor 1


title: Aged mouse brain Xenium cohort

type: RNA

city: Irvine

first: Saurabh

last: Chatterjee

state: California

address: 847 Health Sciences Road

department: Department of Environmental and Occupational Health

institute: University of California, Irvine

description: Aged cohort from Xenium run ChatS_10032025; sample_map.csv includes control_1-control_4 and heatstress_1-heatstress_4 across areas 1-4. Heat-stress mice received periodic heat exposure at approximately 40 deg C for 3 hours/day for 14-15 days; slide ID 0069982; panel Xenium Mouse Brain Gene Expression (mBrain_v1.1); instrument XETG00221; analysis software xenium-4.0.1.0.

hyb_protocol: The Xenium Mouse Brain Gene Expression panel (mBrain_v1.1; 247 predesigned targets; chemistry v1) was used by the UCI Genomics Research and Technology Hub for in situ probe hybridization. Panel probes were hybridized to target RNAs, washed, ligated/circularized, and amplified by rolling-circle amplification according to the 10x Genomics Xenium workflow before imaging and decoding.

scan_protocol: Imaging, decoding, quality score generation, and segmentation were performed using the Xenium Analyzer system. Instrument software version 4.0.1.4; analysis software xenium-4.0.1.0; instrument serial XETG00221; pixel size 0.2125 um; z-step size 3.0 um.

data_processing: Decoded transcripts and cell segmentation outputs were generated by Xenium Onboard Analysis version xenium-4.0.1.0. Processed outputs for each cohort include cell_feature_matrix.h5, MEX matrix files, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and coordinates.csv.

source_name: brain

extract_protocol: tissue preparation protocol: FFPE mouse brain tissue sections were processed by the UCI Genomics Research and Technology Hub using the 10x Genomics Xenium FFPE tissue preparation workflow. Sections were mounted on Xenium slides, baked/deparaffinized, rehydrated, subjected to target retrieval and enzymatic permeabilization, post-fixed, and equilibrated for in situ hybridization.

treatment_protocol: Heat-stress mice received periodic heat exposure at approximately 40 deg C for 3 hours/day for 14-15 days. Control and heat-stress sample annotations are recorded in sample_map.csv.

value: brain

tag: tissue preservation method

value: FFPE

value: control and periodic heat exposure (~40 deg C, 3 hours/day for 14-15 days)


title: Wildtype LX-2 treated with TWEAK replicate 4

description: Library name: WT-LX-2-TWK-4

value: WT

value: TWEAK (100ng/mL, 2 hours)


title: Puck_240129_21

description: Library name: 2024-02-27_Puck_240129_21

value: Old


title: Puck_240108_35

description: Library name: 2024-02-27_Puck_240108_35

value: Young


title: Wildtype LX-2 treated with TWEAK replicate 3

description: Library name: WT-LX-2-TWK-3

value: Hepatic Stellate Cells


title: Healthy human donor (1), CAR T cells, MAFF, RNA

description:
Library name: Acute_1I-MAFF_RNA
Column name in both processed data files: 'Acute_1I'

value: MAFF


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 12-2

description:
Library name: ChIP_PFC_MOR-LPS_F_12-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: MOR-LPS


title: Healthy human donor (1), CAR T cells, FOSL1, RNA

description:
Library name: Acute_1H-FOSL1_RNA
Column name in both processed data files: 'Acute_1H'

value: Primary Human T Cell


title: H3K27ac ChIP-seq striatum, SAL-SAL, male, replicate 5-3

description:
Library name: ChIP_Striatum_SAL-SAL_M_5-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

source_name: striatum

value: striatum

value: wild type

value: SAL-SAL


title: Wildtype LX-2 treated with TWEAK replicate 2

description: Library name: WT-LX-2-TWK-2


title: Wildtype LX-2 treated with TWEAK replicate 1

description: Library name: WT-LX-2-TWK-1


title: Wildtype LX-2 replicate 4

description: Library name: WT-LX-2-4

value: PBS


title: Puck_240108_27

description: Library name: 2024-02-27_Puck_240108_27

value: Ovary

value: Metestrus


title: Healthy human donor (1), CAR T cells, FOSL1-BATF-MAFA, RNA

description:
Library name: Acute_1F-FOSL1-BATF-MAFA_RNA
Column name in both processed data files: 'Acute_1F'

value: Healthy Donor 1


title: Healthy human donor (1), CAR T cells, MAFF-ATF3-BATF2, RNA

description:
Library name: Acute_1G-MAFF-ATF3-BATF2_RNA
Column name in both processed data files: 'Acute_1G'


title: Wildtype LX-2 replicate 3

description: Library name: WT-LX-2-3


title: Puck_240108_26

description: Library name: 2024-02-27_Puck_240108_26

value: Estrus


title: H3K27ac ChIP-seq striatum, SAL-SAL, male, replicate 1-3

description:
Library name: ChIP_Striatum_SAL-SAL_M_1-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_240108_25

description: Library name: 2024-02-27_Puck_240108_25


title: Wildtype LX-2 replicate 2

description: Library name: WT-LX-2-2

value: WT


title: Input control striatum, SAL-SAL, male

description:
Library name: Input_Striatum_SAL-SAL_M
Input control (pooled)


title: Healthy human donor (1), CAR T cells, GFP, RNA

description:
Library name: Acute_1E-GFP_RNA
Column name in both processed data files: 'Acute_1E'

value: GFP


title: Healthy human donor (1), CAR T cells, BATF, RNA

description:
Library name: Acute_1D-BATF_RNA
Column name in both processed data files: 'Acute_1D'

value: BATF


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 9-4

description:
Library name: ChIP_Striatum_SAL-SAL_F_9-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_240108_20

description: Library name: 2024-02-27_Puck_240108_20

value: Young


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 9-2

description:
Library name: ChIP_Striatum_SAL-SAL_F_9-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_240108_07

description: Library name: 2024-02-13_Puck_240108_07

value: Old


title: MSC culture supernatant was collected, centrifuged, and stored at -80°C.rep2

city: boston

first: Bin

last: Song

address: 55 Fruit Street

institute: Massachusetts General Hospital

description: Library name: MSC-CM-2

data_processing:
Using cutadapt, remove reads with a proportion of N bases greater than 0.1, remove adapter sequences; after trimming adapters, retain reads with a length of 18 ~ 35 bp.
Assembly: Homo sapiens
Supplementary files format and content: Raw Counts

molecule: cytoplasmic RNA

source_name: culture supernatant

extract_protocol:
Total RNA was isolated and purified following the manufacturer’s procedure. The RNA amount and purity of each sample was evaluated using NanoDrop ND-1000(NanoDrop, Wilmington, DE, USA). The RNA fragment integrity was evaluated through Bioanalyzer 4200 (Agilent,CA,USA). The obtained total RNA were denaturated at 70℃ for 2 min with DNA 3’ Adapters , and then mixed with T4 RNA Ligase 2, truncated K227Q (NEB, M0351L, USA) at room temperature. The 3’ adapter ligation reaction was performed at 16℃ more than 8 hours. The rest of 3’ Adapters were removed by RTP at 37℃ for 30 min. The 5’ adapters and the products from last step were ligation with T4 RNA Ligase 1 (NEB,M0204L,USA) at 37℃ for 60 min following with n reaction carried by SuperScript II Reverse Transcriptase (Thermo,18064014,USA) at 50℃ for 60 min, and at 80 ℃ for 10 min. The cDNA products were amplified using Phusion® High-Fidelity DNA Polymerase (NEB,M0530L,USA). Specifically, the denaturation temperature was 98℃ for 30 sec with an annealing temperature of 60℃ for 30 sec, and the extension was carried out for 15 sec at 72℃ for 10-16 cycles. The final 5 minute extension was then done at 72℃.
The PCR products were purified and enriched through PAGE electrophoresis. The sequencing strategy was Single-end 50 bp for Illumina Hiseq 2500 following the vendor’s recommended protocol.

value: culture supernatant

value: Human umbilical cord-derived mesenchymal stem cells


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 9-0

description:
Library name: ChIP_Striatum_SAL-SAL_F_9-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: MSC culture supernatant was collected, centrifuged, and stored at -80°C.rep1

description: Library name: MSC-CM-1


title: 293T culture supernatant was collected, centrifuged, and stored at -80°C.rep3

description: Library name: H293-CM-3

value: Human Embryonic Kidney Cell


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 4-1

description:
Library name: ChIP_Striatum_SAL-SAL_F_4-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 293T culture supernatant was collected, centrifuged, and stored at -80°C.rep2

description: Library name: H293-CM-2


title: Healthy human donor (3), CAR T cells, JUN+FOS+BATF, RNA

description:
Library name: Chronic_HA_3I-JUN+FOS+BATF_RNA
Column name in both processed data files: Donor3_JUN+FOS+BATF

data_processing:
Basecalls were performed using bcl-convert Version 4.3.6 from Illumina and samples demultiplexed using Fulcrum Genomics fqtk v0.3.1.
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with GD2-expressing Nalm6 targets for two days and then challenged a second time for three days (engineered leukemia cell line, 1:4 Effector:Target ratio).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and preserved in Zymo DNA/RNA shield. RNA extraction was performed by Plasmidsaurus.
Performed by Plasmidsaurus. The general workflow consisted of: reverse transcription, second strand synthesis, tagmentation, indexing and amplification.

value: Primary Human T Cell

value: Healthy Donor 3

value: JUN+FOS+BATF


title: Input control striatum, SAL-SAL, female

description:
Library name: Input_Striatum_SAL-SAL_F
Input control (pooled)

value: striatum

value: wild type

value: SAL-SAL


title: 293T culture supernatant was collected, centrifuged, and stored at -80°C.rep1

description: Library name: H293-CM-1


title: Puck_240108_14

description: Library name: 2024-02-12_Puck_240108_14

value: Ovary


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 10-1

description:
Library name: ChIP_Striatum_SAL-SAL_F_10-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (3), CAR T cells, JUN, RNA

description:
Library name: Chronic_HA_3F-JUN_RNA
Column name in both processed data files: Donor3_JUN

value: JUN


title: Healthy human donor (3), CAR T cells, BATF, RNA

description:
Library name: Chronic_HA_3E-BATF_RNA
Column name in both processed data files: Donor3_BATF


title: H3K27ac ChIP-seq striatum, SAL-LPS, male, replicate 5-2

description:
Library name: ChIP_Striatum_SAL-LPS_M_5-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: 10x lib 8, donor E20, healthy

city: Rehovot

first: Liran

last: Shlush

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description: Library name: 10x_lib_8_donor_E20_blood_sample_1

data_processing:
Count matrices were generated using 10x Genomics' Cell Ranger v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
As each 10x scRNA library contained pooled cells of multiple individuals, both Vireo (https://github.com/single-cell-genetics/vireo) and Souporcell (https://github.com/wheaton5/souporcell) were used (on each 10x library separately) to cluster cells based on SNPs found in the sequenced RNA. Cells that were identified as doublets by Vireo or Souporcell were discarded.
As part of additional doublet detection, A metacell model was constructed using Metacell with a target metacell size of 50 cells, including cells previously identified as doublets. Metacells containing at least threefold more doublet-marked cells than expected from the overall doublet rate were classified as doublet-enriched. All cells that belonged to a doublet metacell were then marked as doublets. We also identified doublet metacells based on the expression of marker genes of two cell states
We filtered out cells with at least 15% mitochondrial and MALAT1 expression, then removed mitochondrial and ribosomal genes and further filtered cells with ≤500 UMIs.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad file (https://anndata.readthedocs.io/en/stable/) containing count matrix and cell metadata.

source_name: peripheral blood

growth_protocol: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) were isolated from peripheral blood of healthy adult donors by magnetic enrichment. Cells were pre-stimulated overnight in StemSpan SFEM II medium supplemented with SCF, FLT3L, TPO, IL-3, SR1, and UM729 before being transduced with a CellTaggin lentiviral library. Following lentiviral barcoding, GFP⁺ transduced cells were single-cell sorted into 384-well plates and cultured in StemSpan SFEM II supplemented with defined cytokine combinations. Cells were maintained at 37°C and 5% CO₂ and sampled longitudinally at 2–3 time points during differentiation.

extract_protocol:
At each sampling time point, half of the cells from each culture well cells were harvested and pooled for single-cell RNA sequencing. Cell suspensions were washed and processed immediately for Chromium Single Cell 3′ library preparation according to the manufacturer's instructions. For final time points, a fraction of cells was additionally collected for genomic DNA extraction and CellTag barcode recovery.
Single-cell RNA-seq libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). 10,000 - 20,000 cells were loaded for GEM generation. Following reverse transcription, cDNA amplification, and library construction according to the manufacturer's protocol, libraries were sequenced on an Illumina NovaSeq 6000 platform. Transcriptomic libraries captured both cellular mRNA and expressed CellTag barcode sequences.

treatment_protocol: CD34⁺ cells were transduced with the CellTag-V1 lentiviral barcode library on retronectin-coated plates in the presence of LentiBoost and protamine sulfate. After transduction, single GFP⁺ cells were sorted and cultured under distinct cytokine stimulation conditions designed to promote different myeloid differentiation trajectories. Cytokine compositions varied between experimental conditions as described in Supplementary Table S3.

value: peripheral blood

value: male

value: immune cells

tag: age

tag: disease state

value: healthy


title: Puck_240108_10

description: Library name: 2024-02-12_Puck_240108_10

value: Estrus

value: Young


title: H3K27ac ChIP-seq striatum, SAL-LPS, male, replicate 5-0

description:
Library name: ChIP_Striatum_SAL-LPS_M_5-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Fn14α Knockout LX-2 replicate 1

description: Library name: 1KO-LX-2-1

value: Hepatic Stellate Cells

value: Fn14alpha KO

value: PBS


title: Healthy human donor (3), CAR T cells, FOS, RNA

description:
Library name: Chronic_HA_3D-FOS_RNA
Column name in both processed data files: Donor3_FOS

value: Primary Human T Cell

value: Healthy Donor 3

value: FOS


title: 10x lib 8, donor E1, healthy

description: Library name: 10x_lib_8_donor_E1_blood_sample_1

value: female


title: Input control prefrontal cortex, MOR-LPS, female

description:
Library name: Input_PFC_MOR-LPS_F
Input control (pooled)

value: prefrontal cortex

value: wild type

value: MOR-LPS


title: Healthy human donor (1), CAR T cells, ATF3, RNA

description:
Library name: Acute_1J-ATF3_RNA
Column name in both processed data files: 'Acute_1J'

value: Healthy Donor 1


title: Puck_240108_03

description: Library name: 2024-02-12_Puck_240108_03

value: Ovary

value: Old


title: H3K27ac ChIP-seq striatum, SAL-LPS, male, replicate 1-4

description:
Library name: ChIP_Striatum_SAL-LPS_M_1-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum

value: SAL-LPS


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, RNA

description:
Library name: Chronic_HA_3C-JUN-FOS-BATF_RNA
Column name in both processed data files: Donor3_JUN-FOS-BATF

value: JUN-FOS-BATF


title: H3K27ac ChIP-seq striatum, SAL-SAL, male, replicate 3-2

description:
Library name: ChIP_Striatum_SAL-SAL_M_3-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-SAL


title: 10x lib 7, donor E17, healthy

description: Library name: 10x_lib_7_donor_E17_blood_sample_1

value: peripheral blood

value: male

value: immune cells

value: healthy


title: Input control striatum, SAL-LPS, male

description:
Library name: Input_Striatum_SAL-LPS_M
Input control (pooled)


title: Puck_230807_03

description: Library name: 2024-02-12_Puck_230807_03

value: Estrus


title: 10x lib 7, donor E16, healthy

description: Library name: 10x_lib_7_donor_E16_blood_sample_1


title: Puck_230913_06

description: Library name: 2023-12-17_Puck_230913_06


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 9-3

description:
Library name: ChIP_Striatum_SAL-LPS_F_9-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: MSC culture supernatant was collected, centrifuged, and stored at -80°C.rep3

description: Library name: MSC-CM-3

value: culture supernatant

value: Human umbilical cord-derived mesenchymal stem cells


title: Puck_240108_24

description: Library name: 2024-02-27_Puck_240108_24

value: Young


title: Healthy human donor (3), CAR T cells, GFP, RNA

description:
Library name: Chronic_HA_3A-GFP_RNA
Column name in both processed data files: Donor3_GFP

value: Primary Human T Cell

value: Healthy Donor 3

value: GFP


title: 10x lib 7, donor E15, healthy

description: Library name: 10x_lib_7_donor_E15_blood_sample_1


title: PM104_001

description: Library name: 2023-12-17_PM104_001

value: Ovary


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 9-1

description:
Library name: ChIP_Striatum_SAL-LPS_F_9-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: Healthy human donor (1), CAR T cells, JUN, RNA

description:
Library name: Acute_1B-JUN_RNA
Column name in both processed data files: 'Acute_1B'

value: Healthy Donor 1

value: JUN


title: Healthy human donor (2), CAR T cells, JUN+FOS+BATF, RNA

description:
Library name: Chronic_HA_2I-JUN+FOS+BATF_RNA
Column name in both processed data files: Donor2_JUN+FOS+BATF

value: Healthy Donor 2

value: JUN+FOS+BATF


title: 10x lib 6, donor E3, healthy

description: Library name: 10x_lib_6_donor_E3_blood_sample_1

value: peripheral blood


title: A0064_045

description: Library name: 2023-12-17_A0064_045

value: Metestrus

value: Middle


title: Puck_240108_17

description: Library name: 2024-02-12_Puck_240108_17

value: Old


title: H3K27ac ChIP-seq striatum, SAL-SAL, female, replicate 10-3

description:
Library name: ChIP_Striatum_SAL-SAL_F_10-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum

value: SAL-SAL


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 4-4

description:
Library name: ChIP_Striatum_SAL-LPS_F_4-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: Healthy human donor (2), CAR T cells, JUN+BATF, RNA

description:
Library name: Chronic_HA_2H-JUN+BATF_RNA
Column name in both processed data files: Donor2_JUN+BATF

value: JUN+BATF


title: A0029_047

description: Library name: 2023-12-17_A0029_047

value: Estrus

value: Young


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 4-0

description:
Library name: ChIP_Striatum_SAL-LPS_F_4-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (2), CAR T cells, JUN+FOS, RNA

description:
Library name: Chronic_HA_2G-JUN+FOS_RNA
Column name in both processed data files: Donor2_JUN+FOS

value: Primary Human T Cell

value: JUN+FOS


title: 10x lib 6, donor E14, healthy

description: Library name: 10x_lib_6_donor_E14_blood_sample_1

value: male

value: immune cells

value: healthy


title: A0029_042

description: Library name: 2023-12-17_A0029_042

value: Ovary


title: Healthy human donor (2), CAR T cells, JUN, RNA

description:
Library name: Chronic_HA_2F-JUN_RNA
Column name in both processed data files: Donor2_JUN

value: Healthy Donor 2

value: JUN


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 3-1

description:
Library name: ChIP_Striatum_SAL-LPS_F_3-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: 10x lib 5, donor E9, healthy

description: Library name: 10x_lib_5_donor_E9_blood_sample_1

value: peripheral blood


title: A0029_028

description: Library name: 2023-12-17_A0029_028

value: Metestrus

value: Old


title: Healthy human donor (2), CAR T cells, BATF, RNA

description:
Library name: Chronic_HA_2E-BATF_RNA
Column name in both processed data files: Donor2_BATF

value: BATF


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 2-2

description:
Library name: ChIP_Striatum_SAL-LPS_F_2-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum

value: SAL-LPS


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 2-0

description:
Library name: ChIP_Striatum_SAL-LPS_F_2-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 10x lib 5, donor E7, healthy

description: Library name: 10x_lib_5_donor_E7_blood_sample_1


title: A0029_020

description: Library name: 2023-12-17_A0029_020

value: Estrus

value: Middle


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 10-4

description:
Library name: ChIP_Striatum_SAL-LPS_F_10-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 10-2

description:
Library name: ChIP_Striatum_SAL-LPS_F_10-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_230913_07

description: Library name: 2023-11-28_Puck_230913_07

value: Young


title: 10x lib 4, donor E4, healthy

description: Library name: 10x_lib_4_donor_E4_blood_sample_1

value: female


title: PM104_004

description: Library name: 2023-11-28_PM104_004


title: 10x lib 4, donor E13, healthy

description: Library name: 10x_lib_4_donor_E13_blood_sample_1

value: male


title: A0064_042

description: Library name: 2023-11-28_A0064_042


title: H3K27ac ChIP-seq striatum, SAL-LPS, female, replicate 10-0

description:
Library name: ChIP_Striatum_SAL-LPS_F_10-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (1), CAR T cells, JUN+FOS+BATF, RNA

description:
Library name: Chronic_HA_1I-JUN+FOS+BATF_RNA
Column name in both processed data files: Donor1_JUN+FOS+BATF

value: Primary Human T Cell

value: Healthy Donor 1

value: JUN+FOS+BATF


title: 10x lib 4, donor E12, healthy

description: Library name: 10x_lib_4_donor_E12_blood_sample_1

value: immune cells

value: healthy


title: A0064_039

description: Library name: 2023-11-28_A0064_039

value: Ovary


title: H3K27ac ChIP-seq striatum, MOR-SAL, male, replicate 8-0

description:
Library name: ChIP_Striatum_MOR-SAL_M_8-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: 10x lib 6, donor E2, healthy

description: Library name: 10x_lib_6_donor_E2_blood_sample_1

value: peripheral blood


title: Healthy human donor (1), CAR T cells, JUN+BATF, RNA

description:
Library name: Chronic_HA_1H-JUN+BATF_RNA
Column name in both processed data files: Donor1_JUN+BATF

value: JUN+BATF


title: 10x lib 4, donor E1, healthy

description: Library name: 10x_lib_4_donor_E1_blood_sample_1


title: A0064_038

description: Library name: 2023-11-28_A0064_038

value: Metestrus


title: H3K27ac ChIP-seq striatum, MOR-SAL, male, replicate 17-4

description:
Library name: ChIP_Striatum_MOR-SAL_M_17-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum


title: Puck_240129_36

description: Library name: 2024-03-02_Puck_240129_36

value: Estrus


title: Healthy human donor (1), CAR T cells, JUN+FOS, RNA

description:
Library name: Chronic_HA_1G-JUN+FOS_RNA
Column name in both processed data files: Donor1_JUN+FOS

value: JUN+FOS


title: 10x lib 3, donor E2, healthy

description: Library name: 10x_lib_3_donor_E2_blood_sample_1


title: Input control striatum, MOR-SAL, male

description:
Library name: Input_Striatum_MOR-SAL_M
Input control (pooled)


title: A0064_037

description: Library name: 2023-11-28_A0064_037

value: Middle


title: 10x lib 5, donor E8, healthy

description: Library name: 10x_lib_5_donor_E8_blood_sample_1


title: Healthy human donor (1), CAR T cells, JUN, RNA

description:
Library name: Chronic_HA_1F-JUN_RNA
Column name in both processed data files: Donor1_JUN

value: JUN


title: A0029_026

description: Library name: 2023-12-17_A0029_026


title: Healthy human donor (2), CAR T cells, FOS, RNA

description:
Library name: Chronic_HA_2D-FOS_RNA
Column name in both processed data files: Donor2_FOS

value: Healthy Donor 2

value: FOS


title: 10x lib 3, donor E11, healthy

description: Library name: 10x_lib_3_donor_E11_blood_sample_1

value: female


title: 10x lib 5, donor E1, healthy

description: Library name: 10x_lib_5_donor_E1_blood_sample_1


title: Healthy human donor (2), CAR T cells, JUN-FOS-BATF, RNA

description:
Library name: Chronic_HA_2C-JUN-FOS-BATF_RNA
Column name in both processed data files: Donor2_JUN-FOS-BATF

value: Primary Human T Cell

value: JUN-FOS-BATF


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 7-1

description:
Library name: ChIP_PFC_MOR-LPS_F_7-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: MOR-LPS


title: A0029_043

description: Library name: 2023-11-28_A0029_043

value: Ovary

value: Young


title: H3K27ac ChIP-seq striatum, MOR-SAL, male, replicate 17-0

description:
Library name: ChIP_Striatum_MOR-SAL_M_17-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: 10x lib 3, donor E10, healthy

description: Library name: 10x_lib_3_donor_E10_blood_sample_1

value: peripheral blood

value: male

value: immune cells

value: healthy


title: Healthy human donor (2), CAR T cells, FOS+BATF, RNA

description:
Library name: Chronic_HA_2B-FOS+BATF_RNA
Column name in both processed data files: Donor2_FOS+BATF

value: FOS+BATF


title: Healthy human donor (1), CAR T cells, BATF, RNA

description:
Library name: Chronic_HA_1E-BATF_RNA
Column name in both processed data files: Donor1_BATF

value: Healthy Donor 1

value: BATF


title: A0029_036

description: Library name: 2023-11-28_A0029_036

value: Estrus


title: H3K27ac ChIP-seq striatum, MOR-SAL, female, replicate 7-2

description:
Library name: ChIP_Striatum_MOR-SAL_F_7-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum


title: Healthy human donor (1), CAR T cells, FOS, RNA

description:
Library name: Chronic_HA_1D-FOS_RNA
Column name in both processed data files: Donor1_FOS

value: Primary Human T Cell

value: FOS


title: 10x lib 2, donor E1, healthy

description: Library name: 10x_lib_2_donor_E1_blood_sample_1

value: female


title: A0029_035

description: Library name: 2023-11-28_A0029_035

value: Old


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, female, replicate 15-1

description:
Library name: ChIP_PFC_MOR-LPS_F_15-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: MOR-LPS


title: Input control striatum, SAL-LPS, female

description:
Library name: Input_Striatum_SAL-LPS_F
Input control (pooled)

value: wild type

value: SAL-LPS


title: Healthy human donor (1), CAR T cells, JUN-FOS-BATF, RNA

description:
Library name: Chronic_HA_1C-JUN-FOS-BATF_RNA
Column name in both processed data files: Donor1_JUN-FOS-BATF

value: JUN-FOS-BATF


title: H3K27ac ChIP-seq striatum, MOR-SAL, female, replicate 16-1

description:
Library name: ChIP_Striatum_MOR-SAL_F_16-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-SAL


title: Healthy human donor (2), CAR T cells, GFP, RNA

description:
Library name: Chronic_HA_2A-GFP_RNA
Column name in both processed data files: Donor2_GFP

value: Healthy Donor 2

value: GFP


title: 10x lib 1, donor E5, healthy

description: Library name: 10x_lib_1_donor_E5_blood_sample_1

value: peripheral blood

value: immune cells

value: healthy


title: H3K27ac ChIP-seq striatum, MOR-SAL, female, replicate 15-4

description:
Library name: ChIP_Striatum_MOR-SAL_F_15-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_230810_11

description: Library name: 2023-09-27_Puck_230810_11

value: Ovary

value: Metestrus


title: Puck_240108_33

description: Library name: 2024-02-27_Puck_240108_33

value: Young


title: Healthy human donor (1), CAR T cells, FOS+BATF, RNA

description:
Library name: Chronic_HA_1B-FOS+BATF_RNA
Column name in both processed data files: Donor1_FOS+BATF

value: Primary Human T Cell

value: Healthy Donor 1

value: FOS+BATF


title: 10x lib 1, donor E1, healthy

description: Library name: 10x_lib_1_donor_E1_blood_sample_1

value: female


title: Puck_240108_32

description: Library name: 2024-02-27_Puck_240108_32


title: Puck_230810_09

description: Library name: 2023-09-27_Puck_230810_09

value: Estrus

value: Middle


title: Input control striatum, MOR-SAL, female

description:
Library name: Input_Striatum_MOR-SAL_F
Input control (pooled)

value: striatum

value: wild type


title: Healthy human donor (1), CAR T cells, GFP, RNA

description:
Library name: Chronic_HA_1A-GFP_RNA
Column name in both processed data files: Donor1_GFP


title: CN1

city: Hefei

first: Zhang

last: luyuan

state: Anhui

address: Anhui Medical University, Meishan Road, Hefei, Anhui, China

country: China

institute: The First Affiliated Hospital of Anhui Medical University

description:
Library name: CN1
FACS-sorted peripheral blood NK cells from a patient with CHB, sequenced on Illumina NovaSeq 6000 with PE150 reads

data_processing:
Raw reads were preprocessed by removing adaptor sequences, trimming low-quality bases at the 3′ end, removing reads shorter than 25 bp, and filtering rRNA reads.
Clean reads were aligned to the human reference genome using HISAT2 (v2.0.4).
Alignment files were processed using samtools (v1.9) and sambamba (v0.6.4).
Gene expression levels were quantified using StringTie (v1.3.3b), normalized by the TMM method, and reported as FPKM values.
Differential expression analysis was performed using edgeR, and genes with Q-value ≤ 0.05 and |log2 fold change| ≥ 1 were considered differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene count for all Samples

growth_protocol: Peripheral blood samples were collected from patients with chronic hepatitis B (CHB) or CHB-MASLD at the First Affiliated Hospital of Anhui Medical University. Peripheral blood mononuclear cells (PBMCs) were isolated by density-gradient centrifugation, and NK cells were sorted as CD3−CD56+ cells by flow cytometry.

extract_protocol:
Total RNA was extracted from FACS-sorted peripheral blood NK cells using MJzol Animal RNA Isolation Kit according to the manufacturer’s instructions, followed by purification with RNAClean XP Kit and RNase-Free DNase Set. RNA integrity was assessed using Agilent 2100 Bioanalyzer or Agilent 4200 TapeStation, and RNA quantity and purity were measured using Qubit 2.0 and NanoDrop ND-2000.
mRNA was enriched from purified total RNA using VAHTS mRNA Capture Beads (Human/Mouse/Rat). RNA-seq libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina. Library concentration was measured using Qubit 2.0, and fragment size distribution was assessed using Agilent 4200 TapeStation. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: No in vitro treatment was applied before RNA extraction. Freshly isolated NK cells were directly processed for RNA extraction.

value: NK cell


title: H3K27ac ChIP-seq striatum, SAL-SAL, male, replicate 3-0

description:
Library name: ChIP_Striatum_SAL-SAL_M_3-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-SAL


title: H3K27ac ChIP-seq striatum, MOR-SAL, female, replicate 15-0

description:
Library name: ChIP_Striatum_MOR-SAL_F_15-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-SAL


title: Puck_230810_08

description: Library name: 2023-09-27_Puck_230810_08

value: Old


title: Homo sapiens HFF cell, infected with TGGT1_245740 knockout T. gondii RH strain, biological replicate 3

city: China

first: Jing

last: Li

address: No. 182, Tianmu Mountain Road, Xihu District, Hangzhou City, Zhejiang Province, Hangzhou Medical College

institute: Laboratory of Pathogenic Biology, School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, China.

description: Library name: HFF_KO245740inf_Rep3

data_processing:
Illumina Casava 1.8 software used for basecalling
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: skin

growth_protocol: Human HFF-1 foreskin fibroblast cells cultured in DMEM + 10% FBS + 1% penicillin-streptomycin at 37°C, 5% CO₂. Confluent monolayers were used for infection assays.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer's protocols.

treatment_protocol: Three groups: 1) Uninfected HFF negative control; 2) HFF infected with WT RH tachyzoites (MOI=1:1) ; 3) HFF infected with TGGT1_245740 KO tachyzoites (MOI=1:1). Cells harvested at 24h post-infection.

value: skin

value: human foreskin fibroblast

value: wild-type human cell

value: Infected with TGGT1_245742 KO T. gondii RH strain


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 8-3

description:
Library name: ChIP_Striatum_MOR-LPS_M_8-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: Ramos VRC01_ADT

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Library name: s002_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.

library_source: other

data_processing:
Cellranger v6.1.2 multi was used to obtain antigen barcode counts using the antigen barcode library and VDJ library. The VDJ reference that was used with multi was created using the fetch-imgt utility of cell ranger 6.0.2 for Macaca mulatta on 17th March 2023. The constant region sequences from Ramesh et al. were added to the IMGT sequences. Since the multi option is only available with newer versions of cellranger which have specific requirements for VDJ reference, we used another VDJ reference comprised of heavy chain V gene sequences from Cirelli et al., KimDB v1.1, and IMPre in addition to IMGT sequences to start with a comprehensive database for assembly with cellranger v3.1.0. The assembled sequences were once again annotated with the Cirelli et al. database using IgBLAST v1.21.0. The sequences were filtered to keep only those that were productive and with a predicted CDR3 region. After filtering Ig sequences, cells with only a single heavy and a single light chain were used downstream.
Assembly: mmul10
Supplementary files format and content: Processed data files include per-sample outputs from Cell Ranger v6.1.2 multi. Count matrices are provided in Market Exchange Format (MEX): barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and antigen barcode features), and matrix.mtx.gz (sparse UMI count matrix). V(D)J outputs are provided as: airr_rearrangement.tsv (BCR rearrangements in AIRR Community standard format), filtered_contig_annotations.csv (per-contig V(D)J gene annotations), filtered_contig.fasta (filtered contig sequences), and clonotypes.csv (clonotype assignments). All files are prefixed with a sample identifier (s001–s008) corresponding to the sample listed in each GEO record.
Library strategy: CITE-seq

molecule: other

source_name: Ramos VRC01

extract_protocol:
PBMCs were isolated from WB post BG505 vaccination.
Single cell suspensions of FACS enriched memory B cells were prepared and loaded onto the 10X Genomics Chromium Controller using the Chromium NextGEM Single Cell 5’ Library & Gel Bead kit to capture individual cells and barcoded gel beads within droplets. For RM experiments, counting steps were skipped due to low number of antigen specific B cells isolated via FACS. VDJ and feature barcode libraries were prepared according to manufacturer instructions. They were then sequenced on an Illumina NovaSeq 6000 with a paired-end 26x91 configuration targeting a depth of 5,000 reads for both surface barcode libraries and VDJ libraires. Cell Ranger software was used to perform demultiplexing of cellular transcript data, as well as mapping and annotation of UMIs and transcripts for downstream data analysis.

value: Ramos VRC01


title: Puck_230810_06

description: Library name: 2023-09-27_Puck_230810_06

value: Ovary


title: Homo sapiens HFF cell, infected with TGGT1_245740 knockout T. gondii RH strain, biological replicate 2

description: Library name: HFF_KO245740inf_Rep2

value: Infected with TGGT1_245741 KO T. gondii RH strain


title: Wildtype LX-2 replicate 1

description: Library name: WT-LX-2-1

value: Hepatic Stellate Cells

value: WT

value: PBS


description:
Library name: Acute_1C-FOS_RNA
Column name in both processed data files: 'Acute_1C'

value: Primary Human T Cell

value: Healthy Donor 1

value: FOS


title: Ramos VRC01_BCR

description:
Library name: s002_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.

data_processing:
Cellranger v6.1.2 multi was used to obtain antigen barcode counts using the antigen barcode library and VDJ library. The VDJ reference that was used with multi was created using the fetch-imgt utility of cell ranger 6.0.2 for Macaca mulatta on 17th March 2023. The constant region sequences from Ramesh et al. were added to the IMGT sequences. Since the multi option is only available with newer versions of cellranger which have specific requirements for VDJ reference, we used another VDJ reference comprised of heavy chain V gene sequences from Cirelli et al., KimDB v1.1, and IMPre in addition to IMGT sequences to start with a comprehensive database for assembly with cellranger v3.1.0. The assembled sequences were once again annotated with the Cirelli et al. database using IgBLAST v1.21.0. The sequences were filtered to keep only those that were productive and with a predicted CDR3 region. After filtering Ig sequences, cells with only a single heavy and a single light chain were used downstream.
Assembly: mmul10
Supplementary files format and content: Processed data files include per-sample outputs from Cell Ranger v6.1.2 multi. Count matrices are provided in Market Exchange Format (MEX): barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and antigen barcode features), and matrix.mtx.gz (sparse UMI count matrix). V(D)J outputs are provided as: airr_rearrangement.tsv (BCR rearrangements in AIRR Community standard format), filtered_contig_annotations.csv (per-contig V(D)J gene annotations), filtered_contig.fasta (filtered contig sequences), and clonotypes.csv (clonotype assignments). All files are prefixed with a sample identifier (s001–s008) corresponding to the sample listed in each GEO record.
Library strategy: BCR-Seq


title: Homo sapiens HFF cell, infected with TGGT1_245740 knockout T. gondii RH strain, biological replicate 1

description: Library name: HFF_KO245740inf_Rep1

value: Infected with TGGT1_245740 KO T. gondii RH strain


title: Puck_230810_02

description: Library name: 2023-09-27_Puck_230810_02

value: Estrus

value: Middle


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 8-1

description:
Library name: ChIP_Striatum_MOR-LPS_M_8-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum

value: wild type


title: Puck_230714_39

description: Library name: 2023-09-05_Puck_230714_39


title: Ramos RA1_ADT

description:
Library name: s001_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.

source_name: Ramos RA1

value: Ramos RA1


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 6-4

description:
Library name: ChIP_Striatum_MOR-LPS_M_6-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Homo sapiens HFF cell, infected with Toxoplasma gondii RH wild-type tachyzoite, biological replicate 3

description: Library name: HFF_WTinf_Rep3

value: skin

value: human foreskin fibroblast

value: wild-type human cell

value: Infected with WT T. gondii RH strain


title: Puck_230714_29

description: Library name: 2023-09-05_Puck_230714_29

value: Ovary

value: Metestrus

value: Young


title: Homo sapiens HFF cell, infected with Toxoplasma gondii RH wild-type tachyzoite, biological replicate 2

description: Library name: HFF_WTinf_Rep2


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 6-0

description:
Library name: ChIP_Striatum_MOR-LPS_M_6-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: Puck_230714_28

description: Library name: 2023-09-05_Puck_230714_28


title: NK cells from CHB-MASLD patient 3

description:
Library name: nk6
FACS-sorted peripheral blood NK cells from a patient with CHB-MASLD, sequenced on Illumina NovaSeq 6000 with PE150 reads

data_processing:
Raw reads were preprocessed by removing adaptor sequences, trimming low-quality bases at the 3′ end, removing reads shorter than 25 bp, and filtering rRNA reads.
Clean reads were aligned to the human reference genome using HISAT2 (v2.0.4).
Alignment files were processed using samtools (v1.9) and sambamba (v0.6.4).
Gene expression levels were quantified using StringTie (v1.3.3b), normalized by the TMM method, and reported as FPKM values.
Differential expression analysis was performed using edgeR, and genes with Q-value ≤ 0.05 and |log2 fold change| ≥ 1 were considered differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Processed data files include gene expression quantification matrices generated from RNA-seq data. Expression values were normalized and reported as FPKM.
Supplementary files format and content: Supplementary processed files may include differential expression analysis results, including log2 fold change, statistical significance, and adjusted Q-values for genes identified in the comparison between CHB and CHB-MASLD NK cells.

value: peripheral blood

value: NK cell

value: CHB-MASLD


title: Puck_230714_23

description: Library name: 2023-09-05_Puck_230714_23


title: NK cells from CHB-MASLD patient 2

description:
Library name: nk5
FACS-sorted peripheral blood NK cells from a patient with CHB-MASLD, sequenced on Illumina NovaSeq 6000 with PE150 reads


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 14-4

description:
Library name: ChIP_Striatum_MOR-LPS_M_14-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Homo sapiens HFF cell, uninfected control, biological replicate 3

description: Library name: HFF_Control_Rep3

value: uninfected, no parasite infection


title: NK cells from CHB-MASLD patient 1

description:
Library name: nk3
FACS-sorted peripheral blood NK cells from a patient with CHB-MASLD, sequenced on Illumina NovaSeq 6000 with PE150 reads


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 14-2

description:
Library name: ChIP_Striatum_MOR-LPS_M_14-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Homo sapiens HFF cell, uninfected control, biological replicate 2

description: Library name: HFF_Control_Rep2


title: NK cells from CHB patient 3

description:
Library name: CN2-NK
FACS-sorted peripheral blood NK cells from a patient with CHB, sequenced on Illumina NovaSeq 6000 with PE150 reads

value: CHB


title: Puck_230517_38

description: Library name: 2023-06-20_Puck_230517_38

value: Estrus

value: Buck


title: Puck_230517_39

description: Library name: 2023-06-22_Puck_230517_39


title: NK cells from CHB patient 2

description:
Library name: CN1-NK
FACS-sorted peripheral blood NK cells from a patient with CHB, sequenced on Illumina NovaSeq 6000 with PE150 reads


title: Homo sapiens HFF cell, uninfected control, biological replicate 1

description: Library name: HFF_Control_Rep1


title: Puck_230517_37

description: Library name: 2023-06-20_Puck_230517_37


title: Input control striatum, MOR-LPS, male

description:
Library name: Input_Striatum_MOR-LPS_M
Input control (pooled)

value: striatum

value: wild type


title: OCI-AML-3 DKO HiC

city: Chicago

first: Feng

last: Yue

address: 420 E. Superior St.

institute: Northwestern University

description: Library name: OCI-AML-3-DKO-HiC

data_processing:
HiC raw pair-end FASTQ files were trimmed using trimGalore (v.0.6.10) to remove adaptor sequences and quality control was subsequently performed using FastQC (v.0.12.1).
Trimmed Hi-C data was processed using our in-house runHiC pipeline (v.0.8.7), detailed at (https://xiaotaowang.github.io/HiC_pipeline/quickstart.html). In short, hg38 genome alignment was performed using BWA-MEM (v.0.7.17). Aligned read pairs underwent filtering, deduplication and assembly. Identical restriction fragment mappings were removed. Read pairs were binned at multiple resolutions (5kb to 50Mb) with simultaneous ICE normalization. The process yielded ICE-normalized matrices in .mcool format for subsequent analysis. Hi-C contact maps were converted from aligned read pairs using Juicer Tools (v1.22.01) and were used for visualization with KR normalization.
Assembly: hg38
Supplementary files format and content: mcool

growth_protocol: U937 cells and MOLM-13 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS). THP-1 cells were maintained in RPMI-1640 supplemented with 10% FBS and 50nM BME. OCI-AML-3 cells were cultured in MEM α supplemented with 20% FBS. All cell cultures were supplemented with 1X Antibiotic-Antimycotic and were grown in 37°C with 5% CO2.

extract_protocol:
In-situ Hi-C was performed using the Arima-HiC+ Kit (Arima, A51008-ARI) following manufacturer protocol. In brief, one million cells were crosslinked with 2% formaldehyde as described above. Cell lysis, nuclear permeabilization, chromatin digestion and biotin ligation were all performed according to manufacturer protocol. DNA shearing was performed using Vibra-Cell (Sonics & Maerials, VCX750) in 32% Amplitude for in total 1 minute to produce ~400-600bp of fragments.
Biotin enrichment was then performed using streptavidin-coated enrichment beads supplied in the Arima Hi-C kit according to the manufacturer’s protocol. On-bead library preparation was performed using KAPA HyperPrep (Roche, 7962363001) following the adjusted protocol supplied by Arima.

value: AML


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 13-0

description:
Library name: ChIP_Striatum_MOR-LPS_M_13-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: NK cells from CHB patient 1

description:
Library name: 0707nk
FACS-sorted peripheral blood NK cells from a patient with CHB, sequenced on Illumina NovaSeq 6000 with PE150 reads


title: Puck_230517_36

description: Library name: 2023-06-20_Puck_230517_36

value: Old


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 7-1

description:
Library name: ChIP_Striatum_MOR-LPS_F_7-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor5, T651M Group, 48 Hour Timepoint

city: Bethesda

first: Skyler

middle: Alexander

last: Kuhn

state: Maryland

address: 9000 Rockville Pike, BG 29B RM 1NN20

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Donor5_TM_T48_S30
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_TM_T48_S30

data_processing:
Sequencing adapters and low-quality bases were trimmed using Cutadapt v1.18.
Trimmed reads were aligned to the GENCODE (9) GRCh38.p13 primary human reference genome with STAR v2.7.6a in two-pass basic mode.
PCR duplicates were marked using Picard’s MarkDuplicate utility.
Gene expression levels were quantified with RSEM v1.3.3 using v41 of GENCODE's comprehensive annotation.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

source_name: blood

growth_protocol: Human monocyte-derived dendritic cells (MDDCs) were generated from cryopreserved human monocytes obtained from 5 donors. After thawing, monocytes were washed with PBS and cultured at 1 x 10^6 cells/mL in DC medium consisting of RPMI + Glutamax, 5% FBS, 15 mM HEPES, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 ug/mL streptomycin, supplemented with IL-4 (20 ng/mL) and GM-CSF (20 ng/mL). Cells were cultured for 5 days with replacement of half of the medium and addition of fresh cytokines every other day. Nonadherent dendritic cells were harvested by centrifugation and resuspended in DC medium. Resulting cells were >95% CD11c+/CD209+ by flow cytometry. For RNA-seq experiments, MDDCs were plated at 1 x 10^6 cells/well in 12-well plates.

extract_protocol:
Cells were harvested by centrifugation and lysed in 1 mL TRIzol reagent per sample, then stored at -80 C until extraction. For RNA isolation, samples were mixed with 200 uL 1-bromo-3-chloropropane and centrifuged at 4 C for 15 minutes at 16,000 x g. The aqueous phase was collected and passed through a QIAshredder column at 21,000 x g for 2 minutes. RNA was purified using the Qiagen AllPrep DNA/RNA system with an additional on-column DNase I treatment. RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA 6000 Pico kit and quantified using the Quant-iT RiboGreen RNA assay.
Sequencing libraries were prepared from 200 ng total RNA using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer’s protocol. Libraries were quality checked by Agilent Bioanalyzer, quantified by KAPA SYBR FAST qPCR, pooled, and sequenced as paired-end reads on Illumina platforms, with final sequencing performed on a NovaSeq 6000 (2 x 100 bp).

treatment_protocol: Human MDDCs were mock-infected or infected with Powassan virus (POWV) at an MOI of 0.1 in a small volume for 1 hour at 37 C and 5% CO2 with occasional gentle rocking. In experiments involving inhibitor treatment, MDDCs were pretreated with ruxolitinib (10 ug/mL) for 1 hour prior to infection and maintained in the culture for the duration of the experiment.

value: blood

value: monocyte-derived dendritic cells

tag: time

value: Hour 48


title: OCI-AML-3 WT HiC

description: Library name: OCI-AML-3-WT-HiC


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 16-4

description:
Library name: ChIP_Striatum_MOR-LPS_F_16-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: MOLM13 SKO HiC

description: Library name: MOLM13-SKO-HiC


title: Donor4, T651M Group, 48 Hour Timepoint

description:
Library name: Donor4_TM_T48_S29
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_TM_T48_S29


title: Puck_230517_23

description: Library name: 2023-06-20_Puck_230517_23

value: Ovary


title: MOLM13 WT HiC

description: Library name: MOLM13-WT-HiC


title: Donor3, T651M Group, 48 Hour Timepoint

description:
Library name: Donor3_TM_T48_S28
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_TM_T48_S28


title: Puck_230406_08

description: Library name: 2023-06-20_Puck_230406_08

value: Young


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 16-0

description:
Library name: ChIP_Striatum_MOR-LPS_F_16-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: Donor2, T651M Group, 48 Hour Timepoint

description:
Library name: Donor2_TM_T48_S27
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_TM_T48_S27


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 15-3

description:
Library name: ChIP_Striatum_MOR-LPS_F_15-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: OCI-AML-3 sgSUV39H1/2 DKO Cells, Replicate 1

description: Library name: OCI-AML-3-DKO-Rep1

data_processing:
RNA-Seq raw pair-end FASTQ files underwent quality control using fastp (version 0.23.4) with default settings to remove low-quality reads and trim adapters.
Cleaned RNA-Seq data were aligned to the reference genome hg38 using STAR (version 2.7.11b) with default parameters. Gene expression quantification was determined with featureCounts from the subread package (version 2.0.6), considering only the properly mapped pair-end read counts
Assembly: hg38
Supplementary files format and content: tab-delimited file including raw reads

extract_protocol:
One million cells were stabilized in RNAprotect (Qiagen, 76526) and were stored in -80C prior to extraction. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, 75134) and the RNA integrity was evaluated using RNA ScreenTape Analysis (Agilent, 5067-5576).
Library preparation was then performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina, in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs #E7490) following manufacturer’s protocol.


title: Puck_230406_06

description: Library name: 2023-06-20_Puck_230406_06


title: Puck_230406_01

description: Library name: 2023-06-20_Puck_230406_01


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 15-1

description:
Library name: ChIP_Striatum_MOR-LPS_F_15-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor5, WT Group, 48 Hour Timepoint

description:
Library name: Donor5_WT_T48_S25
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_WT_T48_S25

value: WT


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 12-2

description:
Library name: ChIP_Striatum_MOR-LPS_F_12-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_230223_01

description: Library name: 2023-06-20_Puck_230223_01


title: OCI-AML-3 sgControl Cells, Replicate 1

description: Library name: OCI-AML-3-sgControl-Rep1


title: Donor4, WT Group, 48 Hour Timepoint

description:
Library name: Donor4_WT_T48_S24
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_WT_T48_S24


title: Input control striatum, MOR-LPS, female

description:
Library name: Input_Striatum_MOR-LPS_F
Input control (pooled)


title: MOLM13 sgSUV39H1 SKO Cells, Replicate 2

description: Library name: MOLM13-SKO-Rep2


title: 514-L-mKO-sol

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: 514-L-mKO-sol
2x150 Paired-End

data_processing:
Sequencing was performed on the Illumina NovaSeq platform using a 2x150 Paired-End configuration
Raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the reference genome (mm10) using the STAR aligner v.2.5.2b.
Assembly: mm10
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: TPM_values.csv

source_name: Muscle

growth_protocol: Mice were housed at 23˚C or 30˚C in ventilated cages under a 12 h – 12 h light/dark cycle. Mice were fed a standard diet (Lab Diet 5008) with free access to food and water unless specified.

extract_protocol:
Total RNA were extracted using Rneasy kit (QIAGEN)
ERCC RNA Spike-In Mix (ThermoFisher) was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR Kit (Qiagen). RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina according to manufacturer’s instructions.

value: Muscle


title: Input control hypothalamus, SAL-SAL, male

description:
Library name: Input_Hypothalamus_SAL-SAL_M
Input control (pooled)

source_name: hypothalamus

value: hypothalamus

value: SAL-SAL


title: 512-RR-ctrl-sol

description:
Library name: 512-RR-ctrl-sol
2x150 Paired-End


title: MOLM13 sgControl Cells, Replicate 2

description: Library name: MOLM13-sgControl-Rep2


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, male, replicate 5-3

description:
Library name: ChIP_Hypothalamus_SAL-SAL_M_5-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor1, WT Group, 48 Hour Timepoint

description:
Library name: Donor1_WT_T48_S21
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_WT_T48_S21


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, male, replicate 3-2

description:
Library name: ChIP_Hypothalamus_SAL-SAL_M_3-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: MOLM13 sgControl Cells, Replicate 1

description: Library name: MOLM13-sgControl-Rep1


title: Donor5, MOCK Group, 48 Hour Timepoint

description:
Library name: Donor5_mock_T48_S20
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_mock_T48_S20

value: MOCK


title: 508-R-ctrl-sol

description:
Library name: 508-R-ctrl-sol
2x150 Paired-End

value: mKO


title: U937 sgSUV39H1/2 DKO Cells, TPA treated, Replicate 3

description: Library name: U937-DKO-TPA-Rep3


title: Donor4, MOCK Group, 48 Hour Timepoint

description:
Library name: Donor4_mock_T48_S19
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_mock_T48_S19


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 9-4

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_9-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 9-2

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_9-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 508-N-mKO-sol

description:
Library name: 508-N-mKO-sol
2x150 Paired-End


title: U937 sgSUV39H1/2 DKO Cells, TPA treated, Replicate 2

description: Library name: U937-DKO-TPA-Rep2


title: 508-L-ctrl-sol

description:
Library name: 508-L-ctrl-sol
2x150 Paired-End


title: U937 sgSUV39H1/2 DKO Cells, TPA treated, Replicate 1

description: Library name: U937-DKO-TPA-Rep1


title: Donor2, MOCK Group, 48 Hour Timepoint

description:
Library name: Donor2_mock_T48_S17
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_mock_T48_S17


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 9-0

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_9-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 498-R-ctrl-sol

description:
Library name: 498-R-ctrl-sol
2x150 Paired-End


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 4-1

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_4-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, TPA treated, Replicate 3

description: Library name: U937-SKO-TPA-Rep3


title: Donor1, MOCK Group, 48 Hour Timepoint

description:
Library name: Donor1_mock_T48_S16
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_mock_T48_S16


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 10-3

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_10-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, TPA treated, Replicate 2

description: Library name: U937-SKO-TPA-Rep2


title: Donor5, T651M Group, 24 Hour Timepoint

description:
Library name: Donor5_TM_T24_S15
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_TM_T24_S15

value: Hour 24


title: 498-N-mKO-sol

description:
Library name: 498-N-mKO-sol
2x150 Paired-End


title: Input control hypothalamus, SAL-SAL, female

description:
Library name: Input_Hypothalamus_SAL-SAL_F
Input control (pooled)


title: 494-R-mKO-sol

description:
Library name: 494-R-mKO-sol
2x150 Paired-End


title: U937 sgSUV39H1 SKO Cells, TPA treated, Replicate 1

description: Library name: U937-SKO-TPA-Rep1


title: Donor4, T651M Group, 24 Hour Timepoint

description:
Library name: Donor4_TM_T24_S14
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_TM_T24_S14


title: 494-N-mKO-sol

description:
Library name: 494-N-mKO-sol
2x150 Paired-End


title: U937 sgControl Cells, TPA treated, Replicate 3

description: Library name: U937-sgControl-TPA-Rep3


title: H3K27ac ChIP-seq hypothalamus, SAL-SAL, female, replicate 10-1

description:
Library name: ChIP_Hypothalamus_SAL-SAL_F_10-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor3, T651M Group, 24 Hour Timepoint

description:
Library name: Donor3_TM_T24_S13
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_TM_T24_S13


title: 494-L-ctrl-sol

description:
Library name: 494-L-ctrl-sol
2x150 Paired-End


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, male, replicate 3-3

description:
Library name: ChIP_Hypothalamus_SAL-LPS_M_3-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: U937 sgControl Cells, TPA treated, Replicate 2

description: Library name: U937-sgControl-TPA-Rep2


title: KO_S_3

city: Guangzhou

first: Jinwen

last: Kang

state: Guangdong

address: 483 Wushan Road, Tianhe District

institute: South China Agricultural University

description: Library name: D3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Uterus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug oftotal RNA was used forthe construction ofsequencing libraries.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

value: Uterus

value: Primary cell

value: Stromal Cells

value: PIEZO1 Knockout


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, male, replicate 11-0

description:
Library name: ChIP_Hypothalamus_SAL-LPS_M_11-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: KO_S_2

description: Library name: D2


title: U937 sgControl Cells, TPA treated, Replicate 1

description: Library name: U937-sgControl-TPA-Rep1

value: AML


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, male, replicate 1-4

description:
Library name: ChIP_Hypothalamus_SAL-LPS_M_1-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor5, WT Group, 24 Hour Timepoint

description:
Library name: Donor5_WT_T24_S10
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_WT_T24_S10

value: blood

value: monocyte-derived dendritic cells


title: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-3

city: Shanghai, P.R. China

first: weiying

last: meng

address: 1239 Siping Road, Shanghai, P.R. China

institute: Tongji University

description: Library name: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-3

data_processing:
To investigate the alternative splicing induced by depletion of PUS proteins or SMD2, we performed splicing analysis using rMATS (v4.3.0) on RNA-seq data aligned with HISAT2-generated BAM files. rMATS identifies and quantifies five distinct types of alternative splicing events: skipped exon (SE), alternative 3’ splice sites (A3SS), alternative 5’ splice sites (A5SS), retained intron (RI), and mutually exclusive exon (MXE). Percent spliced-in (PSI) values were calculated from junction-only reads, and differential inclusion levels (ΔPSI) between KO and control samples were used to quantify changes in splicing events. Events with a false discovery rate (FDR) ≤ 0.05 were considered statistically significant. Representative splicing events were visualized using rmats2sashimiplot (https://github.com/Xinglab/rmats2sashimiplot).
Assembly: hg38

source_name: cell line

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, C11995500CP) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S; BasalMedia, S110JV)，HuCCT1 cells were maintained in RPMI-1640 medium (ThermoFisher, C11875500BT) supplemented with 10% FBS and 1% P/S. All cell lines were incubated at 37°C in a humidified atmosphere with 5% CO2. Cells were passaged every 2-3 days when they reached approximately 90% confluency.

extract_protocol:
Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.
Total RNA was extracted from HEK293T and HuCCT1 cells using TRIzol™ reagent according to the manufacturer’s instructions. RNA-seq library preparation was conducted using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s protocol. This process included ribosomal RNA depletion to enrich the library for mRNA and pre-mRNAs. After rRNA depletion, the RNA was fragmented and denatured to generate appropriate RNA fragments for cDNA synthesis. First-strand cDNA was synthesized, and an A-tail was subsequently added to the 3’ end of the cDNA to facilitate adapter ligation. Illumina sequencing adapters were then ligated to the cDNA fragments, and the adapter-ligated library was amplified via PCR to enrich for the desired fragments. The final RNA-seq library was quantified and normalized to ensure uniform sequencing depth across samples. High-throughput sequencing was performed on the Illumina HiSeq 6500 platform.See the article for detailed instructions.

value: cell line


title: KO_S_1

description: Library name: D1


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, male, replicate 1-2

description:
Library name: ChIP_Hypothalamus_SAL-LPS_M_1-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-2

description: Library name: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-2

treatment_protocol: Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.


title: KO_NON_S_3

description: Library name: C3


title: Donor4, WT Group, 24 Hour Timepoint

description:
Library name: Donor4_WT_T24_S9
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_WT_T24_S9

value: WT


title: Input control hypothalamus, SAL-LPS, male

description:
Library name: Input_Hypothalamus_SAL-LPS_M
Input control (pooled)


title: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-1

description: Library name: RNA-seq-HEK293T-SNRPD2KO-WTSMD2-1


title: Donor3, WT Group, 24 Hour Timepoint

description:
Library name: Donor3_WT_T24_S8
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_WT_T24_S8


title: KO_NON_S_2

description: Library name: C2


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, male, replicate 1-0

description:
Library name: ChIP_Hypothalamus_SAL-LPS_M_1-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-3

description: Library name: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-3


title: Donor2, WT Group, 24 Hour Timepoint

description:
Library name: Donor2_WT_T24_S7
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_WT_T24_S7


title: KO_NON_S_1

description: Library name: C1


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 9-1

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_9-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-2

description: Library name: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-2


title: Donor1, WT Group, 24 Hour Timepoint

description:
Library name: Donor1_WT_T24_S6
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_WT_T24_S6


title: Ctrl_S_3

description: Library name: B3


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 3-1

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_3-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor2, T651M Group, 24 Hour Timepoint

description:
Library name: Donor2_TM_T24_S12
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_TM_T24_S12


title: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-1

description: Library name: RNA-seq-HEK293T-SNRPD2KO-MutSMD2-1


title: Donor5, MOCK Group, 24 Hour Timepoint

description:
Library name: Donor5_mock_T24_S5
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor5_mock_T24_S5


title: Donor1, T651M Group, 24 Hour Timepoint

description:
Library name: Donor1_TM_T24_S11
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_TM_T24_S11


title: Ramos RA1_BCR

description:
Library name: s001_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.

value: Ramos RA1


title: Ctrl_S_2

description: Library name: B2


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 2-0

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_2-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hypothalamus


title: RNA-seq-HEK293T-SNRPD2KO3

description: Library name: RNA-seq-HEK293T-SNRPD2KO3


title: Donor4, MOCK Group, 24 Hour Timepoint

description:
Library name: Donor4_mock_T24_S4
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor4_mock_T24_S4


title: Ctrl_S_1

description: Library name: B1


title: Homo sapiens HFF cell, infected with Toxoplasma gondii RH wild-type tachyzoite, biological replicate 1

description: Library name: HFF_WTinf_Rep1

value: skin

value: human foreskin fibroblast

value: wild-type human cell

value: Infected with WT T. gondii RH strain


title: H3K27ac ChIP-seq striatum, MOR-LPS, male, replicate 17-1

description:
Library name: ChIP_Striatum_MOR-LPS_M_17-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: striatum

value: MOR-LPS


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 10-4

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_10-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: RNA-seq-HEK293T-SNRPD2KO2

description: Library name: RNA-seq-HEK293T-SNRPD2KO2


title: Donor3, MOCK Group, 24 Hour Timepoint

description:
Library name: Donor3_mock_T24_S3
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_mock_T24_S3

value: MOCK

value: Hour 24


title: Ctrl_NON_S_3

description: Library name: A3

value: Uterus

value: Primary cell

value: Stromal Cells


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 10-2

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_10-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: RNA-seq-HEK293T-SNRPD2KO1

description: Library name: RNA-seq-HEK293T-SNRPD2KO1

value: cell line


title: Input control hypothalamus, SAL-LPS, female

description:
Library name: Input_Hypothalamus_SAL-LPS_F
Input control (pooled)


title: Ctrl_NON_S_2

description: Library name: A2

value: WT


title: RNA-seq-HEK293T-Ctrl3

description: Library name: RNA-seq-HEK293T-Ctrl3


title: Donor2, MOCK Group, 24 Hour Timepoint

description:
Library name: Donor2_mock_T24_S2
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_mock_T24_S2

value: blood

value: monocyte-derived dendritic cells


title: Donor1, MOCK Group, 24 Hour Timepoint

description:
Library name: Donor1_mock_T24_S1
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_mock_T24_S1


title: Puck_230517_33

description: Library name: 2023-06-20_Puck_230517_33

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

value: Ovary

value: Estrus

value: Buck

value: Old


title: H3K27ac ChIP-seq striatum, MOR-LPS, female, replicate 16-2

description:
Library name: ChIP_Striatum_MOR-LPS_F_16-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore (v0.6.7, --paired --fastqc).
Reads were aligned to Mus musculus mm10 using Bowtie2 (v2.4.5). PCR duplicates were removed with SAMtools (v1.15.1) markdup. Reads overlapping ENCODE mm10 blacklist (v2) were excluded with BEDTools subtract (v2.30.0). Coverage profiles were generated with bedtools genomecov and converted to BigWig with bedGraphToBigWig.
Peak calling: MACS2 (v2.2.7.1; -q 0.05 -g mm) against matched pooled Input controls.
Differential H3K27ac analysis: consensus peak set constructed in DiffBind (v3.10.1) with condition-aware merging. Read counts quantified with DiffBind (dba.count, summarizeOverlaps); peaks retained if >= 15 reads in >= 80% of samples within any condition. Differential peaks identified via DESeq2 (dba.analyze); FDR < 0.05. Peaks annotated with ChIPpeakAnno (v3.32.1) and EnsDb.Mmusculus.v79.
Transcription factor regulatory influence assessed with Taiji (v1.2.0) integrating H3K27ac enhancers and RNA-seq expression. TF activity quantified as personalized PageRank scores (z-score normalized, capped at +/-2).
Assembly: mm10
Supplementary files format and content: narrowPeak files (MACS2 peak calls); bigWig coverage tracks (bedtools genomecov + bedGraphToBigWig)

value: striatum


title: Ctrl_NON_S_1

description: Library name: A1


title: H3K27ac ChIP-seq hypothalamus, SAL-LPS, female, replicate 10-0

description:
Library name: ChIP_Hypothalamus_SAL-LPS_F_10-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hypothalamus


title: RNA-seq-HEK293T-Ctrl2

description: Library name: RNA-seq-HEK293T-Ctrl2


title: A-08

city: Xi'an

first: Jidong

state: Shaanxi

address: NO.157, Xiwu Road

institute: Xi'an Jiaotong University

description:
Library name: Sample 6
10x Genomics

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Low quality bases were trimmed by using trimmomatic (version: 0.38) (The options and parameters used to filter raw reads were: ILLUMINACLIP:MeRIP-PE.fa:2:30:10:1:true SLIDINGWINDOW:30:15 AVGQUAL:15 LEADING:15 TRAILING:15 HEADCROP:8 MINLEN:30
Clean reads were mapped to GRCm39(GenCode vM29) using hisat2 with default parameters.
The R package exomePeak was used to call peaks and detect differential peaks  from filtered alignment files. The annotation file used to annotate the peaks was downloaded from GenCode (vM29). Only peaks with p < 0.05 and foldchange >=1.5 were identified as being significantly differential peaks
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: femoral head cartilage

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018)
The MeRIP libraries using eluted RNA were constructed using SMARTer Stranded Total RNA-Seq Kit version 2 (Takara/Clontech) according to the manufacturer’s protocol.

value: femoral head cartilage

value: primary cells

value: Cartilage progenitor cells(CPCs), Chondrocytes, Immune cells(ImmuneCells)

value: femoral head necrosis


title: OCI-AML-3 sgSUV39H1/2 DKO Cells, Replicate 2

description: Library name: OCI-AML-3-DKO-Rep2

value: AML


title: KO_S_3

description: Library name: D3

value: Uterus

value: Primary cell

value: Stromal Cells

value: PIEZO1 Knockout


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 8-2

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_8-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: A-07

description:
Library name: Sample 5
10x Genomics

value: femoral neck fracture


title: KO_S_2

description: Library name: D2


title: RNA-seq-HEK293T-Ctrl1

description: Library name: RNA-seq-HEK293T-Ctrl1

value: cell line


title: A-06

description:
Library name: Sample 4
10x Genomics


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 8-0

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_8-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: KO_S_1

description: Library name: D1


title: U937 sgSUV39H1/2 DKO Cells, ATAC Replicate 1

description: Library name: U937-DKO-ATAC-Rep1

data_processing:
ATAC-Seq raw pair-end FASTQ files were trimmed using trimGalore (v.0.6.10) to remove adaptor sequences and quality control was subsequently performed using FastQC (v.0.12.1).
Trimmed ATAC-Seq reads were processed using the ENCODE ATAC-Seq pipeline. Trimmed reads were aligned to the hg38 reference genome, followed by removal of duplicates and unmapped. Peak calling was performed, and IDR filtering was performed across the duplicates to identify highly reproducible peaks.
Assembly: hg38
Supplementary files format and content: IDR peaks

growth_protocol: U937 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS). THP-1 cells were maintained in RPMI-1640 supplemented with 10% FBS and 50nM BME. All cell cultures were supplemented with 1X Antibiotic-Antimycotic and were grown in 37°C with 5% CO2.

extract_protocol:
ATAC-Seq was performed as described previously with slight adjustments. Quarter of a million cells were used and lysed on ice for total of 20 minutes under 0.1% Tween-20, 0.1% NP-40 and 0.01% Digitonin. The intact nuclei were then collected for tagmentation using 5uL of Tagment DNA TDE1 Enzyme (Illumina).
Total DNA were extracted and library preparation was then performed using Nextera XT DNA Library Preparation Kit (Illumina). All ATAC-Seq experiments were performed in duplicates.


title: KO_NON_S_3

description: Library name: C3


title: A-03

description:
Library name: Sample 3
10x Genomics


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 6-3

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_6-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: A-02

description:
Library name: Sample 2
10x Genomics


title: KO_NON_S_2

description: Library name: C2


title: U937 sgSUV39H1 SKO Cells, ATAC Replicate 2

description: Library name: U937-SKO-ATAC-Rep2


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 17-2

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_17-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: A-01

description:
Library name: Sample 1
10x Genomics


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 17-0

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_17-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: KO_NON_S_1

description: Library name: C1


title: U937 sgControl Cells, ATAC Replicate 2

description: Library name: U937-sgControl-ATAC-Rep2


title: MDA-F4-3

city: IOWA CITY

first: Shanshan

last: Liu

state: IA

address: 431 Newton Road

institute: The University of Iowa

description:
Library name: Sample6
MDA.F4.3

data_processing:
1. Evaluate sequence quality, trim reads and map reads to genome 2. Generate hit counts for genes/exons 3. Compare gene/exon hit counts and analyze gene ontology
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug pf total RNA was used for the construction of sequencing libraries.
1. Ribosomal RNA depletion; 2. RNA Fragmentation and random priming; 3. First and second strand cDNA synthesis; 4. End repair, 5’Phosphorylation, and dA-Tailing; 5. Adaptor ligation, PCR enrichment, and sequencing

value: FABP4 binding

value: breast cancer cells

value: WT

value: cell sorting


title: Ctrl_S_3

description: Library name: B3


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 13-3

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_13-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). ~10,000 NeuN+ nuclei per replicate were lysed and digested with MNase (88216, Thermo Fisher) in the presence of CaCl2; reaction quenched with EDTA. Chromatin IP was performed using 0.125 ug anti-H3K27ac antibody (39135, Active Motif) coupled to 5 uL protein A Dynabeads (10001D, Thermo Fisher), following the MOWChIP-seq protocol.
ChIP-seq libraries were constructed from purified ChIP DNA (~10,000 NeuN+ nuclei) and input DNA (~2,000 nuclei). PFC libraries used xGen 2S DNA Library Prep Kit (10009877, IDT); hippocampus, hypothalamus, and striatum libraries used ThruPLEX DNA-Seq kit (R400674, Takara Bio). Fragment size verified on TapeStation (Agilent) with High Sensitivity DNA Analysis Kit; primer-dimers removed with SPRIselect beads. Libraries quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 nt, ~15 million reads per library).

value: hypothalamus


title: MDA-F4-2

description:
Library name: Sample5
MDA.F4.2


title: U937 sgControl Cells, ATAC Replicate 1

description: Library name: U937-sgControl-ATAC-Rep1


title: Ctrl_S_2

description: Library name: B2


title: Input control hypothalamus, MOR-SAL, male

description:
Library name: Input_Hypothalamus_MOR-SAL_M
Input control (pooled)


title: THP-1 sgSUV39H1/2 DKO Cells, Replicate 3

description: Library name: THP-1-DKO-Rep3


title: MDA-F4-1

description:
Library name: Sample4
MDA.F4.1


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 13-1

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_13-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Ctrl_S_1

description: Library name: B1