title: cLNs_ BCG+Mtb+aCD4_13_Edge lesion_rep1

description:
Library name: DSP-1001510800105-F-C09_S299_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C11

status: Public on Feb 11 2026

type: RNA

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

scan_protocol: Following treatment and lysis, gene expression was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: THP1 treated with Abacavir|Emtricitabine 0.5|0.1 uM for 24.0 h

label_protocol: biotin labeling. Processing was done by th Broad Institute as previously described (10.1016/j.cell.2017.10.049)

growth_protocol:
HepG2 cells (5000 cells/well; ATCC, HB-8065) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC, cat. no.  30-2003), supplemented with 10% FBS and 1% P/S  at 37°C, 5% CO2.
HK-2 cells (5000 cells/well; ATCC, cat. no. CRL-2190) were cultured in Keratinocyte Serum Free Medium (K-SFM), Kit (Gibco, cat. no. 17005-042)  at 37°C, 5% CO2.
THP-1 cells (10,000 cells/well; ATCC, cat. no. TIB-202) were cultured in RPMI-40 medium (Gibco, cat. no. 11875-093) supplemented with 10% fetal bovine serum (FBS, Gibco, cat. no. 10438026) and 1% penicillin/streptomycin (P/S, Corning, cat. no. 30-002) at 37°C, 5% CO2. Macrophage differentiation was induced in vitro with phorbol-12-myristate-13-acetate (PMA, 50 ng/mL; Sigma) for 72 hours at 37°C in 5% CO2

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

treatment_protocol: After 24 hours of culture for HepG2 and HK-2 cells, and 72 hours for THP-1 macrophages, the cells were placed in their respected culture media supplemented with 2% FBS for 16 hours. Subsequently, they were treated for 6 or 24 hours with either vehicle (DMSO) or with ART medications at a concentration of 0.1, or 0.5 µM.

tag: cell line

tag: treatment

value: Abacavir|Emtricitabine 0.5|0.1 uM

tag: duration

tag: plate

tag: well


title: Kidney ECs from Control mouse 1 on HFD

type: SRA

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Zimbabwe

institute: keio university

description: Library name: WT_kidneyEC_1

library_source: transcriptomic

data_processing:
DEGs, heatmaps, and PCAs were analyzed using the DESeq2 package version 1.28.13. The enrichment of GO biological processes and the correlation network of enriched GO terms were analyzed with the clusterProfiler package, version 3.16.14, with p values of 0.01 and 0.05 and q-values of 0.05 (BH methods).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include a gene-level count matrix generated from RNA-seq data. The matrix contains raw and normalized read counts for each gene across all samples. Differential expression analysis was performed using DESeq2, and result tables include gene symbols, log2 fold changes, p-values, and adjusted p-values (BH method).

organism: Mus musculus

source_name: kidney

growth_protocol: Mice were maintained under a 12-h light/dark cycle with ad libitum access to food and water. At 8 weeks of age, mice were switched from a standard chow diet to a high-fat diet (HFD; 60% kcal fat) and were maintained on this diet for 4 weeks before tissue collection for RNA-sequencing.

extract_protocol:
Endothelial cells (ECs) were isolated from collagenase-digested whole kidneys via magnetic-activated cell sorting (MACS) using a CD31 antibody. Total RNA was subsequently extracted from the purified ECs using ISOGEN reagent for library preparation.
The libraries were sequenced for 100 cycles (paired ends) using a NovaSeq

tag: tissue

value: kidney

tag: cell type

value: endothelial cell

tag: genotype

value: wild-type littermate

value: High-fat diet

tag: batch


title: PETER001_THP1_24H_X1_B46:C14

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

source_name: THP1 treated with Elvitegravir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: cLNs_ BCG+Mtb+aCD4_15_Edge lesion_rep2

city: Cairns

first: Andreas

last: Kupz

state: Queensland

address: McGregor Road, Smithfield

department: Australian Institute of Tropical Health and Medicine

country: Australia

institute: James Cook University

description:
Library name: DSP-1001510800105-F-C11_S301_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue

data_processing:
Slides were stained with barcoded probes and fluorescent markers
ROIs were selected on the GeoMx instrument and UV light releases barcodes from chosen areas
The released barcodes were quantified
FASTQfiles.gz
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatia bar codes
Supplementary files format and content: Feature.tsv.gz: List of gene ID
Library strategy: Spatial Transcriptomics

source_name: Cervical Lymph Nodes (cLNs)

growth_protocol: C57BL/6 mice were 1) untreated mice (Normal); 2) unvaccinated and Mtb-infected (Mtb); 3)  unvaccinated, immunosuppressed with anti-CD4 mAb and Mtb-infected (Mtb+aCD4); 4) vaccinated with BCG,  immunosuppressed with anti-CD4 mAb and Mtb-infected (BCG+aCD4+Mtb); 5) vaccinated with PE25,  immunosuppressed with anti-CD4 mAb and Mtb-infected (PE25+aCD4+Mtb). Mice were unvaccinated or vaccinated, 60 days post-vaccination some mice were Mtb-infected and/or immunosupressed with weekly intra-peritoneal injections of aCD4 mAb for 120 days.

extract_protocol:
Samples were Fixed in 4% paraformaldehyde for 24 hours, transfer to 70% ethanol and embbeding in parafin. Then slides were cut and sent to Nanostring (Seattle) where they were stained and data was generated
Sample transcriptome sequence libraries were done following the manufacturer products by Nanstring Seattle.

treatment_protocol: After treatment period mice cLNs were collected

value: Cervical Lymph Nodes (cLNs)

value: C57BL/6 mice


title: cLNs_ BCG+Mtb+aCD4_12_Lesion_rep2

description:
Library name: DSP-1001510800105-F-C08_S298_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ BCG+Mtb+aCD4_10_Lesion_rep1

description:
Library name: DSP-1001510800105-F-C06_S296_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C09

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine

source_name: THP1 treated with Dolutegravir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Dolutegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_24H_X1_B46:C06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir

source_name: THP1 treated with Abacavir|Dolutegravir 0.5|0.1 uM for 24.0 h

value: Abacavir|Dolutegravir 0.5|0.1 uM


title: cLNs_ BCG+Mtb+aCD4_11_Normal in disease__rep1

description:
Library name: DSP-1001510800105-F-C07_S297_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ Naïve_8_Normal_rep1

description:
Library name: DSP-1001510800105-F-C04_S294_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue

value: No Treament


title: PETER001_THP1_24H_X1_B46:C07


title: cLNs_ Naïve_9_Normal_rep2

description:
Library name: DSP-1001510800105-F-C05_S295_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C04


title: PETER001_THP1_24H_X1_B46:C05


title: PETER001_THP1_24H_X1_B46:C08


title: cLNs_ Mtb+aCD4_6_Edge lesion_rep3

description:
Library name: DSP-1001510800105-F-C03_S293_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ BCG+Mtb+aCD4_16_Edge lesion_rep3

description:
Library name: DSP-1001510800105-F-C12_S302_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C01

description: L1000 inferred profile; pert_id: DMSO

source_name: THP1 treated with DMSO 0.5 uM for 24.0 h

value: DMSO 0.5 uM


title: cLNs_ Mtb+aCD4_3_Lesion_rep2

description:
Library name: DSP-1001510800105-F-B12_S290_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C02

description: L1000 inferred profile; pert_id: DMSO


title: cLNs_ Mtb+aCD4_5_Lesion_rep3

description:
Library name: DSP-1001510800105-F-C02_S292_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:C03

description: L1000 inferred profile; pert_id: DMSO


title: cLNs_ Mtb+aCD4_4_Edge lesion_rep2

description:
Library name: DSP-1001510800105-F-C01_S291_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B21

description: L1000 inferred profile; pert_id: Water

source_name: THP1 treated with Water 0.01 uM for 24.0 h

value: Water 0.01 uM


title: cLNs_ Mtb+aCD4_2_Lesion_rep1

description:
Library name: DSP-1001510800105-F-B11_S289_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ Mtb+aCD4_1_Edge lesion_rep1

description:
Library name: DSP-1001510800105-F-B10_S288_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B20

description: L1000 inferred profile; pert_id: Water


title: cLNs_ PE25+Mtb+aCD4_20_Edge lesion_rep3

description:
Library name: DSP-1001510800105-F-B09_S287_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B17

description: L1000 inferred profile; pert_id: Dolutegravir

source_name: THP1 treated with Dolutegravir 0.1 uM for 24.0 h

value: Dolutegravir 0.1 uM


title: cLNs_ PE25+Mtb+aCD4 _19_Lesion_rep3

description:
Library name: DSP-1001510800105-F-B08_S286_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ PE25+Mtb+aCD4_17_Lesion_rep2

description:
Library name: DSP-1001510800105-F-B06_S284_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B19

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_24H_X1_B46:B15

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir

source_name: THP1 treated with Cobicistat|Elvitegravir 0.1|0.1 uM for 24.0 h

value: Cobicistat|Elvitegravir 0.1|0.1 uM


title: cLNs_ PE25+Mtb+aCD4_18_Edge lesion_rep2

description:
Library name: DSP-1001510800105-F-B07_S285_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B18


title: PETER001_THP1_24H_X1_B46:B13


title: cLNs_ PE25+Mtb+aCD4_14_Edge lesion_rep1

description:
Library name: DSP-1001510800105-F-B03_S281_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ PE25+Mtb+aCD4_16_Lesion_rep1

description:
Library name: DSP-1001510800105-F-B05_S283_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B12

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine

source_name: THP1 treated with Cobicistat|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Cobicistat|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_24H_X1_B46:B16


title: cLNs_ PE25+Mtb+aCD4_15_Normal in disease__rep1

description:
Library name: DSP-1001510800105-F-B04_S282_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B11


title: cLNs_ Mtb_13_Edge lesion_rep3

description:
Library name: DSP-1001510800105-F-B02_S280_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue

value: Mtb


title: PETER001_THP1_24H_X1_B46:B10


title: cLNs_ Mtb_12_Edge lesion_rep2

description:
Library name: DSP-1001510800105-F-B01_S279_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ Mtb_10_Edge lesion_rep1

description:
Library name: DSP-1001510800105-F-A11_S277_001.fatq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B14


title: PETER001_THP1_24H_X1_B46:B08

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM for 24.0 h


title: cLNs_ Mtb_9_Lesion_rep2

description:
Library name: DSP-1001510800105-F-A10_S276_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: cLNs_ Mtb_11 _Lesion_rep3

description:
Library name: DSP-1001510800105-F-A12_S278_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B07

value: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM


title: PETER001_THP1_24H_X1_B46:B05

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM for 24.0 h


title: cLNs_ Mtb_7_Normal in disease__rep1

description:
Library name: DSP-1001510800105-F-A08_S274_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: PETER001_THP1_24H_X1_B46:B04

value: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:B06


title: cLNs_ Mtb_8_Lesion_rep1

description:
Library name: DSP-1001510800105-F-A09_S275_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: MKO3

city: Hangzhou City

first: Xiang

last: An

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Library name: MKO3

data_processing:
recommendations and index codes were added to attribute sequences to each sample.
Assembly: genome-version GRCm39
Supplementary files format and content: htseq-count V0.11.2 was used to count the reads numbers mapped to each gene.

source_name: Bone marrow-derived macrophage(BMDM)

growth_protocol: BMDMs were harvested and differentiated from bone marrow cells of mice in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (P/S), and 2% M‐CSF conditioned medium or 20ng/ml M-CSF for 7 days.

extract_protocol:
The total RNA of cells was isolated by using TRIzol reagent according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s

treatment_protocol: WT and MKO BMDMs were serum and M-CSF starved for 4 h followed by 50 ng/ml M-CSF stimulation for 12 h

value: Bone marrow-derived macrophage(BMDM)

value: M-CSF


title: MKO1

description: Library name: MKO1


title: MKO2

description: Library name: MKO2


title: PETER001_THP1_24H_X1_B46:A21

description: L1000 inferred profile; pert_id: Ritonavir

source_name: THP1 treated with Ritonavir 0.5 uM for 24.0 h

value: Ritonavir 0.5 uM


title: PETER001_THP1_24H_X1_B46:A18

description: L1000 inferred profile; pert_id: Abacavir

source_name: THP1 treated with Abacavir 0.5 uM for 24.0 h

value: Abacavir 0.5 uM


title: PETER001_THP1_24H_X1_B46:A19


title: PETER001_THP1_24H_X1_B46:A17


title: WT2

description: Library name: WT2


title: WT3

description: Library name: WT3


title: WT1

description: Library name: WT1


title: KGMKPMG3

city: BERKELEY

first: Matangi

last: Kumar

state: CA

address: Rm 596, Minor Hall

department: Vision Science

institute: UC Berkeley

description:
Library name: Control_3
column name in normalizedPrimaryMG.csv: Control_3

data_processing:
The raw base call files were demultiplexed via Illumina bcl2fastq2 (v2.20). Adapter trimming and quality filtering were performed with Trim Galore (v0.6.6). Quality metrics were assessed with FastQC (v0.11.9).
Assembly: mouse genome (mm39, UCSC) via STAR (v2.7.1a).
Supplementary files format and content: csv files include normalized counts for each sample

source_name: Retina

growth_protocol: For Samples 8-10: Primary mouse Müller glia were isolated from postnatal day 8–10 C57BL/6J pups [26–28]. Retinas were dissociated with papain (Worthington, Columbus, OH) into a single-cell suspension. The cells were plated on 6-well plates coated with 0.1% gelatin in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Waltham, MA) supplemented with 10% fetal bovine serum (FBS) (Avantor Seradigm; Radnor, PA) and 1% penicillin–streptomycin (Gibco, Waltham, MA). Cultures were maintained at 37°C in a humidified 5% CO₂ incubator. Once confluent, the cells were passaged onto fresh gelatin-coated plates.

extract_protocol:
neural retinas (n = 4 per pooled sample) were dissected free of retinal pigment epithelium. Retinal tissue was dissociated into single cells via a papain dissociation system (Worthington, Columbus, OH), passed through a 40 µm cell strainer, and washed with PBS containing 0.5% bovine serum albumin (BSA). Dead cells and debris were depleted with the Dead Cell Removal Kit (Miltenyi Biotech, Bergisch Gladbach, Germany). The remaining cell suspension was incubated on ice for 10 min  with 15 µL of anti-GLAST (ACSA-1)-APC antibody at a 1:50 dilution (Miltenyi Biotech) protected from light. After washing, the cells were centrifuged (300g , 5 min), resuspended in 90 µL of MACS buffer and 10 µL of anti-APC microbeads (Miltenyi Biotech), and then incubated at 4°C for 15 min. Following a wash, the cells were passed through an LS column (Miltenyi Biotech) in a QuadroMACS separator. Unlabeled (GLAST⁻) cells were collected as flow-through; the column was washed 3x with 3 mL of MACS buffer. GLAST⁺ Müller glia were eluted with 5 mL of MACS buffer via a plunger. Total RNA from enriched Müller glia was extracted via the Arcturus™ PicoPure RNA Isolation Kit (Thermo Fisher, Waltham, MA).
RNA quality was assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and samples with an RNA integrity number (RIN) of 7.0 were used for library construction. cDNA was synthesized and amplified via the SMARTer v4 Ultra-Low Input RNA Kit (Clontech, Mountain View, CA). cDNA was fragmented on a Diagenode Bioruptor Pico (Diagenode, Denville, NJ), and sequencing libraries were prepared with the KAPA HyperPrep DNA Kit (Roche, Basel, Switzerland). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 S4 flow cell (QB3 Genomics Core, UC Berkeley; RRID: SCR_022170) to generate 150 bp paired-end reads.

treatment_protocol: For samples 1-7: Sham-injected control mice received a corneal incision created with a sterile 31 G paracentesis needle without silicone oil. pharmaceutical-grade silicone oil (Alcon, Fort Worth, TX) was injected into the anterior chambers of both eyes using a 33 G Hamilton glass syringe (Reno, NV), avoiding contact with the lens and corneal endothelium. Chronic mild OHT was induced by injecting 1.2 µL of silicone oil.

value: Retina

value: primary Muller glia

value: Muller glia

value: WT


title: PETER001_THP1_24H_X1_B46:A20


title: PETER001_THP1_24H_X1_B46:A16


title: KGMKPMG2

description:
Library name: Control_2
column name in normalizedPrimaryMG.csv: Control_2


title: PETER001_THP1_24H_X1_B46:A15

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: KGMKOHT2MG

description:
Library name: OHT_2
column name in normalized_macs.csv: OHT_2

value: Silicone Oil-Injected


title: KGMKPMG1

description:
Library name: Control_1
column name in normalizedPrimaryMG.csv: Control_1


title: PETER001_THP1_24H_X1_B46:A14

value: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: KGMKOHT3MG

description:
Library name: OHT_3
column name in normalized_macs.csv: OHT_3


title: PETER001_THP1_24H_X1_B46:A13


title: KGMKWT3MG

description:
Library name: SHAM_3
column name in normalized_macs.csv: SHAM_3

value: Sham-injected


title: PETER001_THP1_24H_X1_B46:A12

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 24.0 h


title: KGMKOHT1MG

description:
Library name: OHT_1
column name in normalized_macs.csv: OHT_1


title: PETER001_THP1_24H_X1_B46:B09

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate


title: KGMKWT2MG

description:
Library name: SHAM_2
column name in normalized_macs.csv: SHAM_2


title: PETER001_THP1_24H_X1_B46:A11

value: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM


title: PETER001_THP1_24H_X1_B46:A10


title: KGMKWT1MG

description:
Library name: SHAM_1
column name in normalized_macs.csv: SHAM_1


title: PETER001_THP1_24H_X1_B46:A09

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:A08

value: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM


title: Tibialis anterior muscle, septic mouse#3, Day 1

city: Kobe

first: Yuko

last: Ono

state: Hyogo

address: Kusunoki-cho 7-5-2

department: Department of Disaster and Emergency Medicine

country: Japan

institute: Kobe University

description:
Library name: CS03
CS03

data_processing:
First, sequence quality was checked using FastQC v0.11.8 and MultiQC v1.12 with --export option. Next, Trimmomatic v0.39 was used to remove adapter sequences and PRINSEQ-lite v0.20.4 was used to remove the poly A/T tail, short sequence length reads, and trim low-quality bases at the extremity of the reads. Reads were aligned to the Mus musculus reference genome (mm39) using STAR v2.7.9a.
Gene expression levels were calculated using the featureCount function from the Subread v1.6.0 and normalized to cpm (counts per million).
Assembly: mm39
Supplementary files format and content: csv files include CPM values for each sample

source_name: Tibialis anterior muscle

extract_protocol:
Total RNA was extracted from tibialis anterior muscle harvested from sham or septic mice using Isogen (Cat# 311-02501, Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Cat No.7760) following manufacturer's protocol and index codes were added to attribute sequences to each sample. Finally, The resulting libraries were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The purified libraries were sequenced on a Novaseq 6000 (Illumina) with a 150-base pair-end read setting.

value: Tibialis anterior muscle

value: wild type

value: Septic mice received an intraperitoneal injection of cecal slurry at 1.0 mg/g body weight.


title: PETER001_THP1_24H_X1_B46:A06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir|Emtricitabine

source_name: THP1 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:A07


title: PETER001_THP1_24H_X1_B46:A05


title: PETER001_THP1_24H_X1_B46:A04


title: Tibialis anterior muscle, septic mouse#1, Day 1

description:
Library name: CS01
CS01


title: Tibialis anterior muscle, sham control mouse#3, Day 1

description:
Library name: C03
C03

value: Control mice received an intraperitoneal injection of vehicle (7.5% glycerol-PBS).


title: Tibialis anterior muscle, septic mouse#2, Day 1

description:
Library name: CS02
CS02


title: Tibialis anterior muscle, sham control mouse#1, Day 1

description:
Library name: C01
C01


title: Tibialis anterior muscle, sham control mouse#2, Day 1

description:
Library name: C02
C02


title: Fpr2-KO SuHx2

city: Wenzhou

first: jiafei

last: lu

state: Zhejiang

address: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Lucheng District, Wenzhou, Zhejiang 325027, China.

institute: wenzhou medical university

description:
Library name: Fpr2-KO SuHx2
T

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: RV

growth_protocol: WT and Fpr2-KO female mice were maintained under normoxic conditions for 21 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: WT and Fpr2-KO female mice were maintained under hypoxic conditions with Sugen injection (20 mg/kg) for 21 days.

value: RV

value: SuHx 3W


title: PETER001_HK2_6H_X1.A2_B46:H21

description: L1000 inferred profile; pert_id: DMSO

source_name: HK2 treated with DMSO 0.5 uM for 6.0 h

value: DMSO 0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:H20

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_HK2_6H_X1.A2_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: HK2 treated with Darunavir 0.1 uM for 6.0 h

value: Darunavir 0.1 uM


title: Fpr2-KO SuHx1

description:
Library name: Fpr2-KO SuHx1
S


title: PETER001_HK2_6H_X1.A2_B46:H17


title: PETER001_HK2_6H_X1.A2_B46:H19

description: L1000 inferred profile; pert_id: DMSO


title: Fpr2-KO Ctr2

description:
Library name: Fpr2-KO Ctr2
R

value: Ctr


title: WT SuHx2

description:
Library name: WT SuHx2
X


title: Fpr2-KO Ctr1

description:
Library name: Fpr2-KO Ctr1
Q


title: PETER001_HK2_6H_X1.A2_B46:H16


title: PETER001_HK2_6H_X1.A2_B46:H15

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

source_name: HK2 treated with Emtricitabine|Ritonavir 0.1|0.5 uM for 6.0 h

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: WT SuHx1

description:
Library name: WT SuHx1
W


title: PETER001_HK2_6H_X1.A2_B46:H12

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 6.0 h


title: WT Ctr2

description:
Library name: WT Ctr2
V


title: PETER001_HK2_6H_X1.A2_B46:H13


title: LOXL2, Knockout, Replicate12

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

data_processing:
Please see methods
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each samples

source_name: TMJ

extract_protocol:
Please see methods
Please see methods

value: TMJ


title: PETER001_HK2_6H_X1.A2_B46:H14


title: WT Ctr1

description:
Library name: WT Ctr1
U

value: WT


title: LOXL2, Knockout, Replicate11


title: PETER001_HK2_6H_X1.A2_B46:H11

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:H10


title: PETER001_HK2_6H_X1.A2_B46:H09

description: L1000 inferred profile; pert_id: Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:H08

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: LOXL2, Knockout, Replicate8


title: LOXL2, Knockout, Replicate9


title: LOXL2, Knockout, Replicate10


title: LOXL2, Knockout, Replicate7


title: PETER001_HK2_6H_X1.A2_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

source_name: HK2 treated with Darunavir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: LOXL2, Knockout, Replicate6


title: PETER001_HK2_6H_X1.A2_B46:H04


title: PETER001_HK2_6H_X1.A2_B46:H07


title: PETER001_HK2_6H_X1.A2_B46:H05


title: LOXL2, Knockout, Replicate4


title: LOXL2, Knockout, Replicate5


title: LOXL2, Knockout, Replicate3


title: PETER001_HK2_6H_X1.A2_B46:H03

description: L1000 inferred profile; pert_id: Water

source_name: HK2 treated with Water 0.01 uM for 6.0 h

value: Water 0.01 uM


title: LOXL2, Knockout, Replicate2


title: PETER001_HK2_6H_X1.A2_B46:H02

description: L1000 inferred profile; pert_id: Water


title: PETER001_HK2_6H_X1.A2_B46:G21

description: L1000 inferred profile; pert_id: DMSO


title: LOXL2, Knockout, Replicate1


title: LOXL2, Control, Replicate8

value: Control


title: PETER001_HK2_6H_X1.A2_B46:G20

description: L1000 inferred profile; pert_id: DMSO


title: LOXL2, Control, Replicate7


title: PETER001_HK2_6H_X1.A2_B46:G19

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_HK2_6H_X1.A2_B46:G18

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 6.0 h

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:G15

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:G16


title: LOXL2, Control, Replicate4


title: LOXL2, Control, Replicate3


title: PETER001_HK2_6H_X1.A2_B46:G13

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: LOXL2, Control, Replicate6


title: PETER001_HK2_6H_X1.A2_B46:G12

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:G14


title: LOXL2, Control, Replicate5


title: LOXL2, Control, Replicate1


title: PETER001_HK2_6H_X1.A2_B46:G11

value: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: LOXL2, Control, Replicate2


title: X2_AMPK-KO_MK8722_rep4

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ-file generation and demultiplexing using bcl-convert v. 4.0.3
Align to genome and determine transcript and gene counts with the nfcore-rnaseq pipeline v. 3.10.1 using the STAR->Salmon workflow.
Assembly: GRCm38
Supplementary files format and content: Salmon quantification file
Supplementary files format and content: tsv file with gene counts
Supplementary files format and content: file linking transcripts to genes

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Total RNA was isolated using QIAwave RNeasy kit (QIAGEN, 74536) with on-column DNAse treatment using Qiagen RNase-Free DNase set (QIAGEN, 79256) following manufacturer’s protocol.
Messenger RNA sequencing libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan Life Sciences, 0520) as recommended by the manufacturer. Libraries were quantified with Qubit fluorometer (ThermoFisher Scientific, Waltham, USA), quality checked using a TapeStation instrument (Agilent Technologies, Waldbronn, Germany) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina, San Diego, USA).

value: Mouse Embryonic Fibroblasts

value: AMPK KO

tag: passage

tag: rin


title: X2_Wild-type_MK8722_rep4

value: Wild type


title: PETER001_HK2_6H_X1.A2_B46:G17


title: PETER001_HK2_6H_X1.A2_B46:G09

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 6.0 h


title: X2_AMPK-KO_Torin-1_rep4


title: X2_Wild-type_Torin-1_rep4


title: X2_Wild-type_DMSO-control_rep4

value: DMSO (control)


title: PETER001_HK2_6H_X1.A2_B46:G08

value: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:G07


title: X2_AMPK-KO_Torin-1_rep3


title: X2_Wild-type_Torin-1_rep3


title: PETER001_HK2_6H_X1.A2_B46:G06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir

source_name: HK2 treated with Darunavir|Emtricitabine|Ritonavir 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:G05


title: PETER001_HK2_6H_X1.A2_B46:G04


title: PETER001_HK2_6H_X1.A2_B46:G03

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:G02

value: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: X2_AMPK-KO_DMSO-control_rep4


title: X2_Wild-type_DMSO-control_rep2


title: PETER001_HK2_6H_X1.A2_B46:F21

description: L1000 inferred profile; pert_id: Wortmannin

source_name: HK2 treated with Wortmannin 5 uM for 6.0 h

value: Wortmannin 5 uM


title: PETER001_HK2_6H_X1.A2_B46:F17

description: L1000 inferred profile; pert_id: Bictegravir

source_name: HK2 treated with Bictegravir 0.5 uM for 6.0 h

value: Bictegravir 0.5 uM


title: X2_Wild-type_DMSO-control_rep3


title: X2_Wild-type_MK8722_rep2


title: X2_AMPK-KO_Torin-1_rep2


title: X2_AMPK-KO_MK8722_rep3


title: X2_Wild-type_MK8722_rep3


title: PETER001_HK2_6H_X1.A2_B46:F20


title: PETER001_HK2_6H_X1.A2_B46:G01


title: PETER001_HK2_6H_X1.A2_B46:F16


title: X2_AMPK-KO_DMSO-control_rep3


title: X2_AMPK-KO_Torin-1_rep1


title: X2_AMPK-KO_DMSO-control_rep2


title: X2_Wild-type_DMSO-control_rep1


title: PETER001_HK2_6H_X1.A2_B46:F18


title: PETER001_HK2_6H_X1.A2_B46:F13

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: HK2 treated with Elvitegravir 0.1 uM for 6.0 h

value: Elvitegravir 0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:F14


title: PETER001_HK2_6H_X1.A2_B46:F15


title: X2_AMPK-KO_MK8722_rep2


title: X2_Wild-type_Torin-1_rep2


title: PETER001_HK2_6H_X1.A2_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: HK2 treated with Darunavir|Ritonavir 0.1|0.5 uM for 6.0 h

value: Darunavir|Ritonavir 0.1|0.5 uM


title: X2_AMPK-KO_DMSO-control_rep1


title: PETER001_HK2_6H_X1.A2_B46:F08


title: X2_AMPK-KO_MK8722_rep1


title: PETER001_HK2_6H_X1.A2_B46:F10

description: L1000 inferred profile; pert_id: Elvitegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:F06

description: L1000 inferred profile; pert_id: Dolutegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: X2_Wild-type_Torin-1_rep1


title: X1_Wild-type_DMSO-control_rep4

source_name: MEF

extract_protocol:
Total RNA was isolated using QIAwave RNeasy kit (QIAGEN, 74536) with on-column DNAse treatment using Qiagen RNase-Free DNase set (QIAGEN, 79256) following manufacturer’s protocol.
ssRNA-seq; Messenger RNA sequencing libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan Life Sciences, 0520) as recommended by the manufacturer. Libraries were quantified with Qubit fluorometer (ThermoFisher Scientific, Waltham, USA), quality checked using a TapeStation instrument (Agilent Technologies, Waldbronn, Germany) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina, San Diego, USA).

value: MEF


title: PETER001_HK2_6H_X1.A2_B46:F03

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: X1_Wild-type_DMSO-control_rep3


title: PETER001_HK2_6H_X1.A2_B46:F02

value: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:F04

value: Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: X1_Tfeb-Tfe3-KO_DMSO-control_rep4

value: Tfeb/Tfe3 KO


title: PETER001_HK2_6H_X1.A2_B46:F05


title: PETER001_HK2_6H_X1.A2_B46:F07


title: X1_Wild-type_MK8722_rep4


title: X2_Wild-type_MK8722_rep1


title: PETER001_HK2_6H_X1.A2_B46:F01


title: X1_Tfeb-Tfe3-KO_DMSO-control_rep3


title: PETER001_HK2_6H_X1.A2_B46:E21

description: L1000 inferred profile; pert_id: Rapamycin

source_name: HK2 treated with Rapamycin 5 uM for 6.0 h

value: Rapamycin 5 uM


title: X1_Tfeb-Tfe3-KO_MK8722_rep4


title: X1_Wild-type_Torin-1_rep4


title: PETER001_HK2_6H_X1.A2_B46:E20


title: X1_Tfeb-Tfe3-KO_DMSO-control_rep2


title: X1_Wild-type_Torin-1_rep3


title: PETER001_HK2_6H_X1.A2_B46:E18

description: L1000 inferred profile; pert_id: Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Tenofovir Disoproxil Fumarate 0.1 uM for 6.0 h

value: Tenofovir Disoproxil Fumarate 0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:E19


title: PETER001_HK2_6H_X1.A2_B46:E17


title: X1_Wild-type_DMSO-control_rep2


title: X1_Wild-type_MK8722_rep3


title: PETER001_HK2_6H_X1.A2_B46:E16


title: X1_Wild-type_MK8722_rep2


title: PETER001_HK2_6H_X1.A2_B46:E15

description: L1000 inferred profile; pert_id: Cobicistat

source_name: HK2 treated with Cobicistat 0.1 uM for 6.0 h

value: Cobicistat 0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:E13


title: X1_Tfeb-Tfe3-KO_Torin-1_rep4


title: X1_Tfeb-Tfe3-KO_MK8722_rep3


title: PETER001_HK2_6H_X1.A2_B46:E14


title: PETER001_HK2_6H_X1.A2_B46:E12

description: L1000 inferred profile; pert_id: Bictegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:E10

value: Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:E11


title: X1_Tfeb-Tfe3-KO_Torin-1_rep3


title: X1_Tfeb-Tfe3-KO_Torin-1_rep2


title: X1_Tfeb-Tfe3-KO_MK8722_rep2


title: X1_Tfeb-Tfe3-KO_DMSO-control_rep1


title: PETER001_HK2_6H_X1.A2_B46:E09

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine

source_name: HK2 treated with Bictegravir|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Bictegravir|Emtricitabine 0.5|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:E08


title: X1_Wild-type_Torin-1_rep2

value: Wild type


title: PETER001_HK2_6H_X1.A2_B46:E06

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: X1_Wild-type_DMSO-control_rep1

value: DMSO (control)


title: X1_Wild-type_MK8722_rep1


title: PETER001_HK2_6H_X1.A2_B46:E07


title: X1_Wild-type_Torin-1_rep1


title: X1_Tfeb-Tfe3-KO_Torin-1_rep1


title: High fat diet liver,snATACseq

city: Changchun

first: Peng

last: Chen

address: Xinmin Street 126

department: Department of genetics

institute: Jilin University

library_source: genomic

data_processing:
The scRNA-seq were processed by CellRanger (v7.0.1) with Mus musculus genome assembly GRCm38 (mm10) as the reference.
For snATACseq,raw sequencing reads were aligned to Mus musculus genome assembly GRCm38 (mm10), while peaks were quantified using Cellranger with default parameters. Genomic annotation was obtained from Ensembl v79For Seurat (v4.1.1) and Signac (1.3.0) were utilized in the analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: scRNA-seq data were processed as expression matrix and snATAC-seq were processed as matrix with fragment files.

molecule: genomic DNA

source_name: liver

extract_protocol:
For the purpose of single-cell RNA sequencing (scRNA-seq) four mice from each diet group were fasted overnight and then anesthetized using sodium pentobarbital (5% 0.05 mL/g mice weight) at 15 weeks of age. Their livers were perfused and harvested for the subsequent analysis. Post-perfusion, liver tissues from the mice were surgically excised and finely diced into ~1mm3 fragments on a chilled surface. These fragments then underwent enzymatic disintegration for 15 minutes at 37℃, employing a Liver Dissociation Kit (Miltenyi Biotec) in conjunction with gentle shaking. Following digestion, the samples were passed through a 100-µm cell strainer. The resulting liver cell suspension was collected and subjected to centrifugation at a speed of 30g for 2 minutes, followed by a red blood cell-lysis step and centrifuged at 300g for 5 minutes. The final cellular pellet was resuspended in a medium composed of 2% BSA in RPMI 1640 (Sigma-Aldrich).
The cell suspensions from 4 mice in a group were pooled together and loaded into a Chromium Controller (10X Genomics) to generate single-cell gel beads, following the manufacturer's instructions. We used Single Cell 3' Library and Gel Bead Kit V3.1 for this process. Single-cell RNA-seq libraries were subsequently constructed and sequenced using an Illumina Novaseq6000 sequencer with a paired-end 150 bp strategy, produced a minimum of 150 gigabases worth of sequencing data for each group. These steps were carried out by CapitalBio Technology in Beijing.snATAC-seq was carried out on liver tissue samples extracted from same mice in scRNA-seq. Nuclei suspensions from mice were prepared following the 10x Genomics protocol and pooled together. It was directly used for generating single-nuclei ATAC-seq libraries. These libraries were assembled utilizing Chromium Next GEM Chip H and the Chromium Controller, with the samples subsequently being barcoded. DNA fragments were amplified, and sequencing libraries were constructed as per Chromium NextGEM Single Cell ATAC Reagent Kits v1.1 instructions. The final pooled libraries were sequenced on the Illumina NovaSeq platform with paired-end 50 approach.

value: liver

value: high fat diet


title: PETER001_HK2_6H_X1.A2_B46:E02

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine

source_name: HK2 treated with Cobicistat|Elvitegravir|Emtricitabine 0.1|0.1|0.1 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:D19

description: L1000 inferred profile; pert_id: Vorinostat

source_name: HK2 treated with Vorinostat 5 uM for 6.0 h

value: Vorinostat 5 uM


title: PETER001_HK2_6H_X1.A2_B46:E05

value: Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:E04


title: High fat diet liver,scRNAseq

library_source: transcriptomic single cell


title: High iron diet liver,scRNAseq

value: high iron diet


title: X1_Tfeb-Tfe3-KO_MK8722_rep1


title: control liver,scRNAseq

value: chow diet


title: PETER001_HK2_6H_X1.A2_B46:E03


title: PETER001_HK2_6H_X1.A2_B46:E01


title: PETER001_HK2_6H_X1.A2_B46:D21


title: PETER001_HK2_6H_X1.A2_B46:D20


title: PETER001_HK2_6H_X1.A2_B46:D15

description: L1000 inferred profile; pert_id: Cobicistat|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: BMDM, WT, KAT8-inhibitor, R848-1

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: RNA-seq gene_expression.txt

source_name: bone marrow

growth_protocol: BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml).

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit (MagBeads) (Cat#T102096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

treatment_protocol: BMDMs pretreatment with DMSO and KAT8-inhibitor were stimulated with R848(100ng/ml) for 6h

value: bone marrow

value: BMDM

value: Mouse primary bone marrow-derived macrophages

value: WT

value: pretreatment with KAT8-inhibitor, R848(100ng/ml) for 6h


title: High iron diet liver,snATACseq


title: PETER001_HK2_6H_X1.A2_B46:D18

description: L1000 inferred profile; pert_id: Efavirenz

source_name: HK2 treated with Efavirenz 0.5 uM for 6.0 h

value: Efavirenz 0.5 uM


title: BMDM, WT, KAT8-inhibitor, R848-3


title: PETER001_HK2_6H_X1.A2_B46:D17


title: BMDM, WT, DMSO, R848-2

value: pretreatment with DMSO, R848(100ng/ml) for 6h


title: BMDM, WT, KAT8-inhibitor, R848-2


title: PETER001_HK2_6H_X1.A2_B46:D16


title: control liver,snATACseq


title: BMDM, KAT8-cKO, R848-2

treatment_protocol: WT and KAT8 deficient BMDMs were stimulated with R848(100ng/ml) for 6h or not.


title: PETER001_HK2_6H_X1.A2_B46:D11

description: L1000 inferred profile; pert_id: Efavirenz|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 6.0 h


title: BMDM, KAT8-cKO, UT-2

value: UT


title: PETER001_HK2_6H_X1.A2_B46:D14

value: Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: BMDM, KAT8-cKO, UT-1


title: PETER001_HK2_6H_X1.A2_B46:D13


title: PETER001_HK2_6H_X1.A2_B46:D08

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 6.0 h


title: BMDM, WT, DMSO, R848-1


title: PETER001_HK2_6H_X1.A2_B46:D12

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: BMDM, WT, R848-2


title: PETER001_HK2_6H_X1.A2_B46:D10


title: PETER001_HK2_6H_X1.A2_B46:D07

value: Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:D09


title: BMDM, WT, DMSO, R848-3


title: PETER001_HK2_6H_X1.A2_B46:D05

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine

source_name: HK2 treated with Efavirenz|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Efavirenz|Emtricitabine 0.5|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:D04


title: BMDM, WT, UT2


title: BMDM, KAT8-cKO, R848-1


title: PETER001_HK2_6H_X1.A2_B46:D06


title: WT,psoriasis,skin

source_name: Ear skin

treatment_protocol: A daily topical dose of 30 mg IMQ cream (5%) (Shichuan MedShine Pharmaceuticals Co.) per ear for three consecutive days. At day 4, ears were collected for RNA isolation.

value: Ear skin

value: IMQ-induced psoriasis


title: KAT8-cKO,psoriasis,skin


title: BMDM, WT, UT1


title: BMDM, WT, R848-1


title: PETER001_HK2_6H_X1.A2_B46:D02


title: PETER001_HK2_6H_X1.A2_B46:C21

description: L1000 inferred profile; pert_id: Genistein

source_name: HK2 treated with Genistein 5 uM for 6.0 h

value: Genistein 5 uM


title: PETER001_HK2_6H_X1.A2_B46:D01


title: Background_control_Bcells_WT_rep1_72h_post_activation

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: RNA from the RNA/DNA hybrids (S9.6 IP)

library_source: other

data_processing:
Reads were mapped to the reference mouse genome (GRCm38) using the STAR short read aligner (version STAR 2.4.0b)
Quality control, read processing and filtering, visualization of the results was performed using custom scripts and elements of the RSeQC, BEDtools and SAMtools packages.
For every biological replicate the coresponding RNaseH control signal was subtracted from the actual experiment.
Assembly: mm10 - GRCm38 primary assembly
Supplementary files format and content: .bw (bigWig) format -an indexed binary wiggle file
Library strategy: DRIPc-seq (Sanz LA et al. 2019)

molecule: other

source_name: in vitro activated primary splenic B-cells 3 days post activation

growth_protocol: Splenic naïve B-cells were prepared using the CD43 negative selection commercial kit (Miltenyi Biotec.; 130-090-862).

extract_protocol:
After 72h h, the culture medium was removed, and cells were washed once with cold PBS and twice with TE buffer (10 mM Tris [pH 8.0] and 1 mM EDTA). Cell lysis was performed directly on the plate by adding 0.5 ml of lysis buffer (TE supplemented with 0.625% SDS and 0.0625 mg/ml 7 Proteinase K), and the suspension was immediately transferred to a fresh 2 ml tube and incubated for 4.5 h at 37°C with gentle mixing every 15 min.
genomic DNA was purified by phenol:chloroform:isoamyl alcohol (25:24:1) extraction and ethanol precipitation. Precipitated DNA was washed with 70% ethanol, air-dried, and resuspended in 30 µl of TE buffer. Next, pure gDNA was sheared by sonication using Bioruptor Plus with a water-cooling system (Diagenode) as the following: 3 µg gDNA diluted to 200 µl in TE was placed in 1.5 ml DNA LoBind Tubes (Eppendorf) and subjected to 30 cycles of sonication (30 s ON, 90 s OFF) in “Low” mode. The length of fragments after sonication was evaluated by running DNA samples before and after shearing on a 1.5% agarose gel in 1X TAE (40 mM Tris [pH 8.0], 20 mM acetic acid, and 2 mM EDTA) at 70-80 V. To ensure specificity, nucleic acids are pre-treated with Ribonuclease H (RNase H) (NEB, cat. No. M0297S) to eliminate RNA:DNA hybrids from the mixture. In this process, 4 μg of digested gDNA is incubated with 4 μL of NEB RNase H for 4 hours at 37°C. Following this treatment, proceed with the S9.6 immunoprecipitation step, processing both the control, RNase H-treated samples alongside the experimental samples. Afterward, 4 µg of fragmented gDNA was mixed with 10 µg of S9.6 antibody, diluted to a final volume of 1 ml with binding buffer (20 mM HEPES [pH 7.4], 150 mM NaCl, and 0.05% Triton X-100), and incubated overnight with gentle rotation in a refrigeration cabinet. The next day, input fractions that contained S9.6 were added to 50 µl of M2 anti-FLAG Magnetic Beads (Sigma) or Protein G Dynabeads (Thermo), respectively, and incubated for 2 h. Additionally, a second set of negative controls were prepared by incubating 4 µg of sonicated gDNA with beads without the bait. Following incubation, the unbound fraction was removed, and beads were washed three times with 500 µl of binding buffer for 5 min with gentle rotation in a refrigeration cabinet. Elution was performed by adding 125 µl of elution buffer (50 mM Tris [pH 8], 1 mM EDTA, 0.5% SDS, and 0.64 mg/ml Proteinase K) for 45 min at 55°C. Two replicates of each sample were pooled and purified using a DNA clean and concentrator kit (Zymo Research) according to the manufacturer’s protocol. After elution with 30 µl of elution buffer (Zymo Research), half of the eluate was treated with 2 µl of DNAse I (1 U/µl) in 1X DNase I digestion buffer (Thermo Fisher Scientific) for 1 h at 37°C. For DNase I inactivation, 1 µl of 0.5 M EDTA was added for 10 min at 65°C. RNA was purified using the RNA clean and concentrator kit (Zymo Research). The purified RNA underwent NGS library preparation and subsequent sequencing, which was conducted commercially by Azenta Life Sciences using their strand-specific protoco

treatment_protocol: Cells, isolated from WT and Het mice, were activated for 72hours by incubation with LPS and IL4 (20 µg/ml LPS and 20 ng/ml IL-4 final concentration) prior to experiment. Next, cells were collected by trypsinization, washed in PBS and counted.


title: Background_control_Bcells_WT_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)

value: in vitro activated primary splenic B-cells 3 days post activation


title: PETER001_HK2_6H_X1.A2_B46:C20


title: Background_control_Bcells_Het_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)

value: DIS3 G766R/+ heterozygous


title: PETER001_HK2_6H_X1.A2_B46:C16

description: L1000 inferred profile; pert_id: Emtricitabine

source_name: HK2 treated with Emtricitabine 0.1 uM for 6.0 h

value: Emtricitabine 0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:C15

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

source_name: HK2 treated with Elvitegravir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: RNaseH_control_Bcells_WT_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: PETER001_HK2_6H_X1.A2_B46:C19


title: PETER001_HK2_6H_X1.A2_B46:C18


title: PETER001_HK2_6H_X1.A2_B46:C13


title: PETER001_HK2_6H_X1.A2_B46:C17


title: RNaseH_control_Bcells_Het_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: RNaseH_control_Bcells_Het_rep1_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: PETER001_HK2_6H_X1.A2_B46:C14


title: RNaseH_control_Bcells_WT_rep1_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: PETER001_HK2_6H_X1.A2_B46:C11

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

source_name: HK2 treated with Abacavir|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Abacavir|Emtricitabine 0.5|0.1 uM


title: DRIPc-seq_Bcells_Het_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)

value: activation in 20 ug/ml LPS and 20 ng/ml IL-4 for 72h


title: PETER001_HK2_6H_X1.A2_B46:C12


title: Background_control_Bcells_Het_rep1_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: DRIPc-seq_Bcells_WT_rep2_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: PETER001_HK2_6H_X1.A2_B46:D03


title: DRIPc-seq_Bcells_WT_rep1_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: DRIPc-seq_Bcells_Het_rep1_72h_post_activation

description: RNA from the RNA/DNA hybrids (S9.6 IP)


title: MicroC_Bcells_WT_rep2

data_processing:
Raw Hi-C reads were trimmed using TrimGalore (v0.6.7) (Krueger; Martin, 2011). The fastq files were processed using the Juicer Pipeline (v2.13.07) {Durand N, 2016}, using default options and aligned to the GRCm38/mm10 genome assembly.
The processing was performed without any input for restriction enzyme sites as MicroC uses the Micrococcal Nuclease (MNase) which does not cleave at specific cut-sites
Assembly: mm10 - GRCm38 primary assembly
Supplementary files format and content: .hic format - indexed binary format of contact matrix heatmaps
Library strategy: MicroC

extract_protocol:
cells, isolated from WT and Het mice, were activated for 72hours by incubation with LPS and IL4 (20 µg/ml LPS and 20 ng/ml IL-4 final concentration) prior to experiment. Next, cells were collected by trypsinization, washed in PBS and counted. For crosslinking, 300 mM DSG (ThermoScientific) solution in DMSO (100x) was prepared freshly and diluted to 1x in room temperature PBS. Cellular pellet was resuspended in DSG solution and incubated for 35 minutes on rotating wheel at room temperature. Next 16% methanol-free formaldehyde (Thermo Scientific) was added to a mixture to a final concentration of 1% and incubated for next 10 minutes on rotating wheel at room temperature. To quench the crosslinking reaction, Tris pH 7.5 was added to a final concentration of 0.375 M and incubated on rotating wheel for 5 minutes at room temperature. Next, cells were centrifuged at 4oC, washed once with ice-cold PBS and re-counted. Cells were divided into 5 mln cells portions, pelleted, snap frozen and stored at -80°C until needed.
MicroC was performed according to (Goel et al, 2023) with minor modifications. 10 million crosslinked activated B cells from WT and Het mice were resuspended in MB#1 buffer (10 mM Tris pH 7.5, 50 mM NaCl, 5 mM NgCl2, 1mM CaCl2, 0.1% Igepal, EDTA-free protease inhibitor cocktail (Roche)) and incubated on ice for 20 minutes to isolate nuclei. After one wash with MB#1 buffer, nuclei were resuspended in MB#1 buffer containing MNAse and incubated for 20 minutes in 37oC with 1000 rpm rotation in thermoblock to digest chromatin. Reaction was stopped by addition of 4mM EGTA and 10 minutes incubation at 65oC. Next, nuclear pellet was washed twice in MB#2 buffer (10 mM Tris pH 7.5, 50 mM NaCl, 10 mM MgCl2, BSA), resuspended in 100 ul Repair End Master Mix (1x NEB 2.1, 2mM ATP, 5mM DTT, 50 U PNK), incubated at 37oC for 15 mins with shaking 1000 rpm. Next, 50 U Klenow was added and incubated for next 15 mins at 37oC with shaking 1000 rpm. To biotinylate, Biotin Master Mix (66 nM Biotin-dATP, 66 nM Biotin-dCTP, 66 nM dTTP, 66 nM dGTP, T4 DNA ligase buffer, 33 ug BSA) was added and incubated 45 mins 25oC with shaking 1000 rpm. To quench the reaction EDTA was added to final concentration of 30 mM, incubated at 65oC for 20 minutes and the chromatin pellet was washed once with MB#3 buffer (50 mM Tris pH 7.5, 10 mM MgCl2, 50 ug BSA). Next, the chromatin pellet was resuspended in Ligation Master Mix (T4 buffer, 100 ug BSA, 10 000 U T4 DNA ligase), incubated for 2.5 hours at 25oC and centrifuged. The chromatin pellet was resuspended in Exonuclease Master Mix (NEBuffer 1, 1000 U Exonuclease III), incubated for 15 mins at 37oC and centrifuged. Next, the samples were incubated overnight at 65oC in Reverse crosslinking solution (1% SDS, 200 mM NaCl, 520 ug Proteinase K, 26 ug RNAseA), DNA was purified on 1.0x AmPure beads to enrich for dinucleosome fraction. Prior to library preparation 10-15ug biotinylated chromatin was pull-down using Dynabeads MyOne Streptavidin T1 for 30 mins incubation at room temperature, washed twice with 1xTWB (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA pH 8.0, 0.1% Tween-20) and once with 10 mM Tris pH 7.5. Library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to manufacturer protocol.

treatment_protocol: Ex vivo activation of B lymphocytes for class switch recombination, proliferation studies and RNA sequencing and was achieved by culturing them in RPMI 1640 containing 15% FBS supplemented with 100 nM 2-mercaptoethanol, 20 µg/ml LPS and 20 ng/ml IL-4 for 72h.

value: activation in 20 µg/ml LPS and 20 ng/ml IL-4 for 72h


title: PETER001_HK2_6H_X1.A2_B46:C09

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine

source_name: HK2 treated with Dolutegravir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Dolutegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:C10


title: PETER001_HK2_6H_X1.A2_B46:C08


title: MicroC_Bcells_Het_rep2


title: MicroC_Bcells_WT_rep1


title: PETER001_HK2_6H_X1.A2_B46:C06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir

source_name: HK2 treated with Abacavir|Dolutegravir 0.5|0.1 uM for 6.0 h

value: Abacavir|Dolutegravir 0.5|0.1 uM


title: PETER001_HK2_6H_X1.A2_B46:C07


title: MicroC_Bcells_Het_rep1


title: PETER001_HK2_6H_X1.A2_B46:C05


title: PETER001_HK2_6H_X1.A2_B46:C04


title: PETER001_HK2_6H_X1.A2_B46:C01

description: L1000 inferred profile; pert_id: DMSO

source_name: HK2 treated with DMSO 0.5 uM for 6.0 h

value: DMSO 0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:B21

description: L1000 inferred profile; pert_id: Water

source_name: HK2 treated with Water 0.01 uM for 6.0 h

value: Water 0.01 uM


title: F3_rep2

city: Boulder

first: Thomas

last: Cech

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

description: Library name: FBD33317_b797ddda_baf645db_barcode03

data_processing:
For post-sequencing analysis, data were basecalled on the command-line interface of the CU Boulder BioFrontiers Institute FIJI Compute Cluster. Basecalling was performed using Dorado v0.7.4 hac_5mC_5hmC model. Reads were aligned to the GRCh38 human genome assembly using Samtools v1.3.1. Methylation data were extracted using the Dorado v0.7.4 modkit pileup command. Downstream analyses were conducted in R version 2024.12.0+467.
Assembly: GRCh38
Supplementary files format and content: Processed files are .bed files output from Dorado v0.7.4 modkit pileup command. Global genome methylation was measured by taking the number of CpGs called as 5mC methylated over the total number of CpG sites called.

growth_protocol: All cells were maintained in DMEM media supplemented with 10% fetal bovine serum, 1X pencillin-streptomycin and 1X GlutaMAX-I at 37 °C with 5% CO2. Note that the parental U2OS cell line (generous gift from the Rippe lab, University of Heidelberg, Germany) contains a lacO-array incorporated into the genome that has enriched K27 methylation, but this is not pertinent to the current study.

extract_protocol:
Firstly, cells were trypsinized and genomic DNA was extracted as in Laird et al., 1991 Nucleic Acids Research. In brief, cells were lysed and digested overnight at 37 °C in a buffer containing 0.2% SDS and 100 µg/mL proteinase K. DNA was then precipitated in 100% isopropanol.
Libraries were prepared using Oxford Nanopore Technologies Native Barcoding Kit 24 V14 (SQK-NBD114.24) per manufacturer’s instructions. Libraries were barcoded, pooled, and loaded onto an Oxford Nanopore Technologies MinION Flow Cell (R10.4.1, FLO-MIN114). Libraries were sequenced for 48 h at a rate of 400-450 bases per second with live basecalling off. Approximately 500 Mb of data per genome were collected, representing ~0.1X genome coverage for an accurate and precise measure of global DNA methylation (per Faulk., 2023 Genome Research).

treatment_protocol: untreated controls

value: heterozygous DNMT1-Halo knock-in

value: untreated


title: WT_U2OS_rep2

description: Library name: FBD33317_b797ddda_baf645db_barcode02

value: WT

value: wild type


title: FL6

city: ChongQing

first: Zhen

last: Zou

address: Medical College Road, Yuzhong District

department: Institute of Life Sciences

institute: ChongQing Medical University

description:
autophagy-1-tpm.txt
Apoptosis expression_matrix_annot

data_processing:
The data were analyzed on the online platform of Majorbio Cloud Platform (www.majorbio.com)
Differential gene is used to mine the differential gene data of Meji Biotech cloud platform for expression difference statistics (padjust≤0.05,DESeq2,FC≥2)
The LPS group was used as the difference group, and the WT+LPS group was used as the control, and the rising gene set was established for apoptosis cluster analysis（Hierarchical clustering;complete;euclidean)
Autophagy-related genes were screened from the expression of all genes, gene sets were established, and then expression clustering analysis was performed in four sets of samples（Hierarchical clustering;complete;euclidean)
Assembly: GRCm39
Supplementary files format and content:
ZIP1_icKO_vs_WT text file includes raw counts and tpm for each Sample
ZIP1_icKO_LPS_vs_WT_LPS text file includes raw counts and tpm for each Sample
gene.count.matrix.annot text file includes raw counts for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA was measured by Nanodrop2000, RNA integrity was measured by agarose gel electrophoresis, and RIN value was measured by Agilent2100. A single library construction requires a total amount of RNA ≥ 1ug, a concentration of ≥ 35ng/μL, OD260/280≥1.8, OD260/230≥1.0.
Eukaryotic mRNA sequencing is based on the Illumina Novaseq 6000 sequencing platform, which sequences all mRNAs transcribed by specific tissues or cells of eukaryotes at a certain time, and the sequencing experiment uses the Illumina TruseqTM RNA sample prep kit method for library construction

value: Lung

value: alveolar epithelial cells

value: vehicle


title: ZL1

value: Slc39a1flox/flox; Sfptc-CreERT2

value: LPS 1Day


title: FL5


title: FZ19


title: ZL3


title: E8_rep2

description: Library name: FBD33317_b797ddda_baf645db_barcode01

value: homozygous DNMT1-Halo knock-in


title: ZL4


title: F3_rep1

description: Library name: 27041df051fcbfbdc0a1e7834770b19fcce07b2c_SQK-NBD114-24_barcode03


title: PETER001_HK2_6H_X1.A2_B46:C02

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_HK2_6H_X1.A2_B46:C03

description: L1000 inferred profile; pert_id: DMSO


title: WT_U2OS_rep1

description: Library name: 27041df051fcbfbdc0a1e7834770b19fcce07b2c_SQK-NBD114-24_barcode02


title: Z17


title: FL3


title: PETER001_HK2_6H_X1.A2_B46:B20

description: L1000 inferred profile; pert_id: Water


title: PETER001_HK2_6H_X1.A2_B46:B19

description: L1000 inferred profile; pert_id: Water


title: F3_5azaC_24h_rep2

description: Library name: SQK-NBD114-24_barcode18

treatment_protocol: U2OS cell lines were treated with 4 µM GSK or 5-azaC inhibitor (dissolved in DMSO) for the time indicated. DMSO vehicle controls were treated with the same concentration of DMSO as corresponding inhibitor treatment groups for 24 hours before harvest.

value: 5azaC 24h


title: E8_rep1

description: Library name: 27041df051fcbfbdc0a1e7834770b19fcce07b2c_SQK-NBD114-24_barcode01


title: Z10


title: WT 23


title: F3_DMSOvehiclefor5azaC_rep1

description: Library name: SQK-NBD114-24_barcode16

value: DMSO


title: F3_5azaC_4h_rep2

description: Library name: SQK-NBD114-24_barcode17

value: 5azaC 4h


title: PETER001_HK2_6H_X1.A2_B46:B18

description: L1000 inferred profile; pert_id: Dolutegravir

source_name: HK2 treated with Dolutegravir 0.1 uM for 6.0 h

value: Dolutegravir 0.1 uM


title: WT 22


title: PETER001_HK2_6H_X1.A2_B46:B17


title: F3_GSK_4h_rep1

description: Library name: SQK-NBD114-24_barcode14

value: GSK 4h


title: PETER001_HK2_6H_X1.A2_B46:B16


title: WT 21


title: F3_GSK_24h_rep1

description: Library name: SQK-NBD114-24_barcode15

value: GSK 24h


title: F3_DMSOvehicleforGSK_rep1

description: Library name: SQK-NBD114-24_barcode13


title: E8_DMSOvehiclefor5azaC_rep1

description: Library name: SQK-NBD114-24_barcode12


title: B-cells day5 post in vtiro activation DIS3 +/+ rep3

description:
d5_Bcells_ResultsOrdered.tsv
Actd5_wtBcells_ResultsOrdered.tsv

data_processing:
RNA sequencing reads were mapped using STAR split read aligner (2.7.10a) to a mm10 mouse reference genome (GRCm38 primary assembly).
Reads were counted onto a gencode gene annotation (vM6 basic annotation) using FeatureCount (subread package release 2.0.0)
Differential expression RNA-seq analyses were performed using DESeq2 R package.
Assembly: mm10 - GRCm38 primary assembly
Supplementary files format and content: tab delimited fiel containg DESeq resutls output with additional table of noralized counts per gene

source_name: in vitro activated B-cells 5 days post activation

extract_protocol:
Total RNA from collected tissues and primary cultures was isolated using a standard TRIzol protocol
rRNA depleted, strand specyfic, paired-end libraries

value: primary B-cells

value: B-cells


title: E8_5azaC_24h_rep2

description: Library name: SQK-NBD114-24_barcode11


title: PETER001_HK2_6H_X1.A2_B46:B14

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir

source_name: HK2 treated with Cobicistat|Elvitegravir 0.1|0.1 uM for 6.0 h

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

value: Cobicistat|Elvitegravir 0.1|0.1 uM


title: E8_DMSOvehiclefor5azaC_rep2

description: Library name: SQK-NBD114-24_barcode09


title: E8_5azaC_4h_rep2

description: Library name: SQK-NBD114-24_barcode10


title: E8_GSK_24h_rep2

description: Library name: SQK-NBD114-24_barcode08


title: PETER001_HK2_6H_X1.A2_B46:B15


title: B-cells day5 post in vtiro activation DIS3 +/+ rep2

value: in vitro activated B-cells 5 days post activation


title: PETER001_HK2_6H_X1.A2_B46:B13


title: E8_DMSOvehicleforGSK_rep2

description: Library name: SQK-NBD114-24_barcode06


title: B-cells day5 post in vtiro activation DIS3 +/+ rep1


title: E8_GSK_4h_rep2

description: Library name: SQK-NBD114-24_barcode07


title: PETER001_HK2_6H_X1.A2_B46:B12

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine

source_name: HK2 treated with Cobicistat|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Cobicistat|Emtricitabine 0.1|0.1 uM


title: E8_5azaC_4h_rep1

description: Library name: SQK-NBD114-24_barcode04


title: E8_5azaC_24h_rep1

description: Library name: SQK-NBD114-24_barcode05


title: B-cells day5 post in vtiro activation DIS3 G766R/+ rep3

description:
d5_Bcells_ResultsOrdered.tsv
Actd5_hetBcells_ResultsOrdered.tsv

value: DIS3 G766R/+ heterozygous


title: E8_GSK_24h_rep1

description: Library name: SQK-NBD114-24_barcode03


title: PETER001_HK2_6H_X1.A2_B46:B11


title: B-cells day5 post in vtiro activation DIS3 G766R/+ rep2


title: B-cells day5 post in vtiro activation DIS3 G766R/+ rep1


title: E8_GSK_4h_rep1

description: Library name: SQK-NBD114-24_barcode02


title: PETER001_HK2_6H_X1.A2_B46:B10


title: B-cells day 3 post in vtiro activation DIS3 +/+ rep3

description:
d3_Bcells_ResultsOrdered.tsv
Actd3_wtBcells_ResultsOrdered.tsv

source_name: in vitro activated B-cells 3 days post activation


title: PETER001_HK2_6H_X1.A2_B46:B09

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM for 6.0 h


title: Assembled + Stimulated Rep 1

city: Novara

first: Andrea

last: Cochis

address: Corso Trieste 15/A

department: Department of Health Science

country: Italy

institute: University of Eastern Piedmont

description: Library name: A+S_rep1

data_processing:
Fastq files were analyzed with RSEM v. 1.3.1
RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the human GRCh38 / hg38 genome (Ensembl v100 database)
RSEM was launched with the following parameters --phred33-quals -p 21 --output-genome-bam --strandedness reverse --calc-ci --ci-memory 12288 --sort-bam-by-coordinate --sort-bam-memory-per-thread 4G --time --estimate-rspd --append-names --paired-end –star
Assembly: GRCh38 / hg38 genome (Ensembl v100 database)
Supplementary files format and content: Genes_TPM.xlsx = File containing the normalized counts of gene quantification in TPM in all samples.

source_name: hBMSCs

growth_protocol: hBMSCs from a 58-year-old male donor were expanded in $\alpha$MEM with 10% FBS and 5 ng/mL bFGF. Spheroids were fabricated using AggreWell™ 400 (approx. 260 cells per spheroid) and cultured for 24 hours in chondropermissive medium before assembly.

extract_protocol:
RNA was isolated from constructs using a standardized protocol (Trizol). RIN values were >= 9
Ribosomal RNA depletion was performed using the Illumina™ Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus Kit.

treatment_protocol: Spheroids were encapsulated in a fibrin matrix (2.5 mg/mL). Groups were either randomly dispersed, assembled into circular patterns using acoustic standing waves, or assembled and then stimulated with sound for 2 days.

value: hBMSCs

value: sound-guided assembly + acoustic stimulation


title: Assembled Spheroids Replicate 1

description: Library name: A_rep1

value: sound-guided assembly


title: Assembled + Stimulated Rep 2

description: Library name: A+S_rep2


title: Assembled Spheroids Replicate 2

description: Library name: A_rep2


title: Dispersed Spheroids Replicate 2

description: Library name: D_rep2

value: random distribution


title: Dispersed Spheroids Replicate 1

description: Library name: D_rep1


title: PETER001_HK2_6H_X1.A2_B46:B08

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

value: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM


title: B-cells day 3 post in vtiro activation DIS3 +/+ rep2

value: in vitro activated B-cells 3 days post activation


title: B-cells day 3 post in vtiro activation DIS3 +/+ rep1


title: PETER001_HK2_6H_X1.A2_B46:B07


title: E8_DMSOvehicleforGSK_rep1

description: Library name: SQK-NBD114-24_barcode01

value: homozygous DNMT1-Halo knock-in

value: DMSO


title: PETER001_HK2_6H_X1.A2_B46:B06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM for 6.0 h


title: LMNAC KO, untreated, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: RNA.KO.unt.3

data_processing:
RNA-seq data were aligned against the hg19 version of the human genome using bowtie2 and RSEM v1.2.12 software
Assembly: hg19
Supplementary files format and content: RSEM counts for all genes in tab-delimited format

extract_protocol:
Total RNA for lamin A/C knockout experiments was isolated from 2×10^6 cells using a PureLink RNA Mini Kit (Invitrogen, 12183025) according to the manufacturer’s protocol
Sequencing library preparation was done using the QuantSeq 3’-mRNA-Seq Library Prep kit  (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: lmnac genotype

value: KO

value: untreated

tag: replicate


title: HMGB2_DSG-whole

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

description: Library name: HMGB2_DSG-whole

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
Paired-end reads were processed for adapter removal and mapped to the hg38 reference genome using Bowtie2.
RPKM normalized bigwigs were generated using deeptools.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Lung Tissue

extract_protocol:
For HMGB2 ChIPmentation, cells were initially fixed with 1.5 mM EGS at room temperature for 20 minutes, followed by 1% formaldehyde for 10 minutes
Antibody incubation, washes, Tagmentation and DNA extraction were performed as described in the methods section

value: Lung Tissue

value: Human Embryonic Fibroblast


title: LMNAC KO, untreated, replicate 1

description: Library name: RNA.KO.unt.1


title: B-cells day 3 post in vtiro activation DIS3 G766R/+ rep3

description:
d3_Bcells_ResultsOrdered.tsv
Actd3_hetBcells_ResultsOrdered.tsv

value: primary B-cells

value: B-cells


title: PETER001_HK2_6H_X1.A2_B46:B05

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

institute: Icahn School of Medicine at Mount Sinai

value: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM


title: LMNAC KO, untreated, replicate 2

description: Library name: RNA.KO.unt.2


title: B-cells day 3 post in vtiro activation DIS3 G766R/+ rep2


title: LMNAC WT, G9ai treated, replicate 3

description: Library name: RNA.WT.G9ai.3

value: WT


title: PETER001_HK2_6H_X1.A2_B46:B04


title: B-cells day 3 post in vtiro activation DIS3 G766R/+ rep1

value: DIS3 G766R/+ heterozygous


title: naive B-cells DIS3 +/+ rep3

description:
d0_Bcells_ResultsOrdered.tsv
Actd3_wtBcells_ResultsOrdered.tsv

source_name: naive B-cells

value: naive B-cells


title: LMNAC WT, untreated, replicate 2

description: Library name: RNA.WT.unt.2


title: LMNAC WT, untreated, replicate 3

description: Library name: RNA.WT.unt.3


title: PETER001_HK2_6H_X1.A2_B46:A21

description: L1000 inferred profile; pert_id: Ritonavir

source_name: HK2 treated with Ritonavir 0.5 uM for 6.0 h

value: Ritonavir 0.5 uM


title: LMNAC WT, G9ai treated, replicate 2

description: Library name: RNA.WT.G9ai.2


title: LMNAC WT, untreated, replicate 1

description: Library name: RNA.WT.unt.1


title: PETER001_HK2_6H_X1.A2_B46:A20


title: naive B-cells DIS3 +/+ rep2


title: SPMS 1

city: Wroclaw

first: Lukasz

last: Laczmanski

address: Weigla 12

institute: Hirszfeld Institute of Immunology and Experimental Therapy

description:
Library name: probe 5
S22

data_processing:
To identify functionally relevant target genes of the differentially expressed miRNAs (RRMS vs SPMS), we filtered experimentally validated interactions from miRecords, miRTarBase, and TarBase databases using the multiMiR package and org.Hs.eg.db database in R (v4.4.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes the raw counts

source_name: plasma-derived EV

extract_protocol:
Total RNA, including miRNA, was extracted from plasma-derived EVs using the Total Exosome RNA & Protein Isolation Kit (Invitrogen, USA) employing acid-phenol:chloroform for organic extraction according to the manufacturer’s protocol. Briefly, ethanol was added to the aqueous phase obtained from acid-phenol:chloroform extraction and passed through a glass-fiber filter cartridge, which immobilized the RNA. The filter was subsequently washed, and RNA, including the small RNA fraction, was eluted using a low ionic-strength buffer.
RNA sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Switzerland) following the manufacturer’s protocol. Li-braries were sequenced on the Illumina NextSeq 500/550 platform using Mid Output kits (v2.5). Image processing, base calling, and demultiplexing were performed with NextSeq Control Software (Illumina, San Diego, CA, USA).

value: plasma-derived EV

tag: subject group

value: SPMS


title: SPMS 2

description:
Library name: probe 6
S29


title: PETER001_HK2_6H_X1.A2_B46:A19


title: RRMS 1

description:
Library name: probe 4
R8

value: RRMS


title: naive B-cells DIS3 +/+ rep1


title: PETER001_HK2_6H_X1.A2_B46:A18

description: L1000 inferred profile; pert_id: Abacavir

source_name: HK2 treated with Abacavir 0.5 uM for 6.0 h

value: Abacavir 0.5 uM


title: Control 2

description:
Library name: probe 2
K24

value: healthy controls (HC)


title: naive B-cells DIS3 G766R/+ rep3

description:
d0_Bcells_ResultsOrdered.tsv
Actd3_hetBcells_ResultsOrdered.tsv


title: Control 3

description:
Library name: probe 3
K49


title: Control 1

description:
Library name: probe 1
K17


title: PETER001_HK2_6H_X1.A2_B46:A17


title: naive B-cells DIS3 G766R/+ rep2


title: naive B-cells DIS3 G766R/+ rep1


title: MOLM-13 rep2

city: Houston

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

institute: Baylor College of Medicine

data_processing:
Steps were performed using an eCLIP processing pipeline, with custon scripts available at https://github.com/VanNostrandLab/eclip , based off of the published analysis pipeline described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209.
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming. Command: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 18 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes 10nt from 3' end to account for possible UMIs on 3' end of read). Command:  cutadapt -j 8 -u -10 -o clip1.trim.fastq.gz - --report minimal
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn clip1.trim.fastq.gz
Unique genomic mapping (takes repeat-removed raeds and maps to the reference genome). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.genome.map/ --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn clip1.repeat.unmap.fastq
Sorting (sorts genome mapped output file). Command: samtools sort -@ 8 -m 2G -o clip1.genome.map.bam clip1.genome.map/Aligned.out.bam
Indexing: indexes sorted bam file. Command: samtools index clip1.genome.map.bam
PCR duplicate removal (uses UMI that was appended to read name to remove PCR duplicate reads that map to the same position and have the same UMI). Command: umi_tools dedup --random-seed 1 --stdin clip1.genome.map.bam --method unique --stdout clip1.bam > /dev/null
Index bam file. Command: samtools index input1.bam
Create bigwig from bam file. Command: b2bw --bam clip1.bam --cpus 1
Peak calling (runs CLIPper peak calling algorithm). Command: clipper --species hg19 --processors 8 --bam clip1.bam --outfile clip1.peak.bed
Peak processing (input normalization and identification of reproducible peaks). Command: process_peak --outdir /storage/vannostrand/software/eclip/tests/hg19/--read_type SE --species hg19 --report test.peak.summary.html --ip_bams clip1.bam clip2.bam --input_bams input1.bam input2.bam --peak_beds clip1.peak.bed clip2.peak.bed --ids clip1 clip2
Assembly: UCSC version hg19
Supplementary files format and content: bigwig format contains genome browser coverage (in reads per million); bed format contains peak locations of reproducible RBP binding signal

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), L-glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were UV cross-linked then flash-frozen in liquid nitrogen, followed by lysis, RNAse I treatment, and immunoprecipitation (IP) for DDX6.
eCLIP was performed as described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209. IP fragments were ligated to 3' RNA adapters and RNA was isolated and reverse-transcribed following SDS-PAGE and Western blot. cDNA products were ligated to 5' adapters and PCR-amplified.

value: AML

tag: rip antibody

value: Novus DDX6 cat. # NB200-192


title: MOLM-13 input


title: MOLM-13 rep1


title: PETER001_HK2_6H_X1.A2_B46:A15

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:A16


title: p7_Plasmocytoma

data_processing:
saples were mapped with STAR split read alligner
mapped reads were processed, QC and filtered by custom scripts empling elements of SAMtools, bedtools, Bwtool, RSeQC packages
Differential expression analysis was performed using the DESeq2 bioconductor package
genomic structural variants were called using SVDetect
mait-pair reads preprocessed using Nxtrim
Genome_build: human samples were mapped to the GRCh38 reference geneome murine samples were mapped to the GRCm38 reference geneome

source_name: murine Pristane induced peritoneal plasmocytoma

growth_protocol: Mice were injected 3 times intraperitoneally, in 2-month intervals, with 0.5 ml of pristane oil (2,6,10,12-tetramethylpentadecane) to induce the development of mouse plasmacytoma (MPC), an established murine model of multiple myeloma. The ascit was collected by paracentesis.

extract_protocol: RNA was isolated using TRIreagent DNA was extracted

value: Peritoneal plasma cells

tag: dis3 genotype/expressed variant

tag: strain

value: BALB/C


title: Liver, septic mouse, Day 1

description: Library name: Liver

data_processing:
FASTX-Toolkit v0.0.14 was used to remove primer sequences and sickle v1.33 was used to remove low-quality reads, and short sequence length reads. After filtering, paired-end reads were joined using FLASH v1.2.11. The Qiime2 program was used to remove chimeric and noise sequences, generate ASVs, and match them against the Greengenes v13_8 database to add taxonomic information.
Assembly: Greengenes v13_8
Supplementary files format and content: Excel files include taxonomy and read counts of ASVs for each sample.

organism: mouse metagenome

source_name: Liver

extract_protocol:
Total RNA was extracted from tibialis anterior muscle, blood, liver, and spleen obtained from septic mice and cecal slurry stock using Isogen (Cat# 311-02501, Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions, followed by reverse transcription to cDNA. Reverse transcription was performed using 1 μg of total RNA, random primers (Cat# 3801, Takara Bio, Kusatsu, Japan), RNase inhibitors (Cat# 10777019, Thermo Fisher Scientific), a deoxynucleotide mix (Cat# 639125, Takara Bio), and Moloney murine leukemia virus reverse transcriptase (Cat# 28025013, Thermo Fisher Scientific).
Sequencing libraries were prepared by 2-step tailed PCR method targeting the V3/V4 region of the bacterial 16s rRNA gene, following the 16S metagenomic sequencing library preparation protocol for the Illumina MiSeq system. The libraries were sequenced on a MiSeq (Illumina) with a 300-base pair-end read setting.

value: Liver

value: wild type

value: Septic mice received an intraperitoneal injection of cecal slurry at 1.0 mg/g body weight.


title: SPMS 3

description:
Library name: probe 7
S50


title: Spleen, septic mouse, Day 1

description: Library name: Spleen

source_name: Spleen

value: Spleen


title: p25_Plasmocytoma


title: PETER001_HK2_6H_X1.A2_B46:A14

tag: cell line

value: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: Tibialis anterior muscle, septic mouse, Day 1

description: Library name: TA

source_name: Tibialis anterior muscle

value: Tibialis anterior muscle

tag: treatment


title: Blood, septic mouse, Day 1

description: Library name: Blood

source_name: Blood

value: Blood


title: Cecal slurry stock, mice

description: Library name: CS

source_name: Cecal slurry stock

value: Cecal slurry stock

value: No treatment


title: p18_Plasmocytoma


title: SW620-Mouse4

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 4.0). First, Illumina BCL files were de-multiplexed and converted to FASTQs using mkfastq. Second, FASTQs were then used to quantify gene expression using Cell Ranger count and the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference. Lastly, cellranger aggr took outputs from multiple runs of cellranger count, and normalized these runs to the same sequencing depth and recomputed the gene-barcode matrices and analysis on the combined data.  Then we selected cells that had a mitochondrial read rate and expressed genes to filter out low-quality cells from our data set. Count data of each cell was first scaled and then log transformed using the R package Seurat (v4.0.4). Normalized and scaled data were used for all downstream analyses. Monocle 2 Pseudo time analysis was performed with five types of cells markers to the ordering genes function.
assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: xenografts tumor

extract_protocol:
Single cells were dissociated with tumor dissociation kit (Miltenyi Biotec). Then blood cells and mose cells were removed with magnetic beads separation. Finally, live human SW620 cells were counted and diluted in 1x phosphate-buffered saline (PBS) to 700-1200 cells per μL.
The cell suspension was loaded in Chromium Next GEM Chip G and sorted in the Chromium Controller from 10X Genomics. The Cell-Gel Beads in Emulsion (GEMs) were then incubated to generate the barcoded cDNA. cDNA was cleaned using Dynabeads and washed, followed by cDNA amplification and SPRIselection. The retrieved cDNA was enzymatically fragmented, end-repaired, poly-A tailed, and ligated. Size selection, adaptor ligation, and amplification were done. Sequencing was done using HiSeq X Ten System (Illumina) according to 10X Genomics specifications. All quality control steps were carried out using Qsep100 System (BIOptic) with High Resolution Cartridge, whereas the concentration was calculated using Qubit 4.0 Fluorometer with Kit High Sensitivity assays.

value: xenografts tumor

value: colorectal cancer

value: WT cell line


title: PETER001_HK2_6H_X1.A2_B46:A13

tag: duration


title: PETER001_HK2_6H_X1.A2_B46:A12

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 6.0 h

tag: plate


title: SW620-Mouse3


title: HaCaT, Ro60 and La sequential IP (control)

city: Frederick

first: Sandra

middle: L

last: Wolin

state: Maryland

address: 1050 Boyles Street, BLDG 560 Room 11-39

department: NCI

institute: NIH

description: Library name: Ro60_La_control

data_processing:
Demultiplexing and adapter trimming by Ultraplex v1.2.5.
Read alignment to UCSC hg38 using Novoalign v4.03.08 (parameters -t 15,3 -l 15 -x 4 -g 20 -s 1 -o SAM -R 0 -r All --umi2 bc --matchReward 3 --softclip 0,0).
Deduplication by UMI using UMI-tools v1.1.5.
Read counting for annotations using featureCounts of Subread v2.0.6 with -M --fraction.
Assembly: hg38
Supplementary files format and content: Tab-separated count tables.

source_name: HaCaT

extract_protocol:
Cells were washed once in Dulbecco’s Phosphate-Buffered Saline (Gibco) and harvested in NET-2 (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2.5 mM MgCl2, 0.5 % NP-40) containing 1 mM phenylmethylsulfonyl fluoride (PMSF) and protease inhibitor cocktail. Cells were sonicated in a Bioruptor (Diagenode) and the lysate cleared by centrifuging for 5 min at 10,000 x g at 4 °C. Lysates were incubated with MagStrep Streptactin XT beads (IBA) for 1.5 hrs at 4 °C with rotation. After washing three times with NET-2, beads were incubated with NET-2 containing 50 mM biotin (Sigma) for 30 minutes at 4°C to elute Twin-Strep-Ro60 RNPs. To isolate La-containing RNPs, half the eluate was incubated with Protein G Dynabeads (Thermo Fisher Scientific) pre-coupled to a patient anti-La serum (a gift of John Harley, University of Cincinnati) at 4 °C for 1.5 hours with rotation. The remaining eluate was incubated with Protein G Dynabeads (Thermo Fisher Scientific) coupled to normal human sera. After three washes with NET-2, RNAs were extracted with phenol:chloroform:isoamyl alcohol (25:24:1) followed by addition of glycoblue (Invitrogen) and ethanol precipitation.
The cDNA library was prepared as described by Buchbender et al. (10.1016/j.ymeth.2019.10.003) except that 20 ng of purified RNA was ligated to the 3’ adapter with T4 RNA ligase 2 (truncated KQ) (New England Biolabs).

value: HaCaT

value: human keratinocyte

value: RO60-/- + twin-strep-RO60

tag: antibody

value: normal human sera


title: SW620-Mouse2

tag: tissue


title: SW620-Mouse1

tag: cell type


title: MMTV-PyMT WT Tumors Rep2

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

hyb_protocol: FFPE tissue sections from three wild type PyMT primary tumors were mounted on fiducial bead-coated MERSCOPE slides and prepared following Vizgen’s MERSCOPE User Guide for FFPE tissue processing. To ensure optimal hybridization, tissue sections underwent a clearing process to remove lipids and proteins that could interfere with imaging. This involved incubation in a Clearing Premix containing Proteinase K at 47°C overnight, followed by a 3-hour photobleaching step to eliminate background fluorescence. The samples were then incubated in a fresh Clearing Premix solution, with additional Proteinase K treatment at 37°C for an extended period, ensuring optimal conditions for subsequent hybridization and imaging.

scan_protocol: Imaging was performed on the MERSCOPE platform according to the MERSCOPE Instrument User Guide. Each field of view was imaged in seven 1.5 μm-thick z planes at 60× magnification. Images were processed and decoded to identify RNA spots with xyz coordinates and gene assignments using Vizgen's Merlin software.

data_processing: To improve the MERSCOPE onboard cell segmentation, we re-segmented the data using Cellpose2 v2.2.3 implemented in Vizgen vpt v1.2.2 pipeline. The obtained cell_by_gene matrix and metadata were used to create the AnnData object and downstream analysis such as quality control, clustering, differential gene expression was performed using Scanpy v1.9.3

source_name: Breast tumor

value: FFPE Embedded Tumor


title: MMTV-PyMT WT Tumors Rep3


title: PETER001_HK2_6H_X1.A2_B46:A11

value: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM

tag: well


title: MMTV-PyMT WT Tumors Rep1


title: PETER001_HK2_6H_X1.A2_B46:A09

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 6.0 h


title: PETER001_HK2_6H_X1.A2_B46:A10