title: Healthy Control 10_L3_ADT

description:
Library name: HC10_CS_csp_S16_L003
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: adt

value: Endometrium

value: CD45+ Cells

value: XX

tag: treatment

value: Healthy Control


title: Healthy Control 12_L2_ADT

status: Public on Mar 10 2026

type: SRA

city: Birmingham

first: Rebecca

last: Asiimwe

state: Alabama

address: 1720 2nd Ave South

department: Surgery

country: USA

institute: The University of Alabama at Birmingham

description:
Library name: HC12-FB_S9_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

library_source: other

data_processing:
Reads from single-cell RNA-seq experiments of each Healthy Control and Uterus Transplant library were pre-processed and aligned against the GRCh38 human reference and quantified using Cell Ranger (v.6.1.1) from 10x Genomics
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files (tsv) and matrix files (mtx): *_barcodes.tsv.gz: cellular barcodes present in dataset; *_features.tsv.gz: IDs of quantified genes; *_matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs and columns correspond to the cellular barcodes
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
Endometrial biopsies were collected with a Pipelle® suction curette (Cooper Surgical; Ref. 8200) in the clinical setting and transported to the laboratory in DPBS with calcium and magnesium (DPBS+/+; Gibco™; Cat. 14-040-133) on ice. Multiple passes of the suction curette were performed to acquire sufficient tissue for multimodal analysis. Endometrial biopsies were then digested to isolate cells for downstream analysis including sorting, flow cytometry, or in vitro incubation. Endometrial biopsies used for immunofluorescence microscopy were embedded in O.C.T. mounting media (Tissue-Tek; Cat. No. 4583) in a mold (Tissue-Tek; Cat. No. 4566). Molds were then placed in liquid nitrogen-cooled isopentane (Fisher Scientific; Cat. No. O3551-714 4). Frozen molds were stored at -800C until sectioned onto glass slides for imaging. Endometrial biopsies used for single cell isolation were processed into single cell suspensions for use in downstream single cell isolation techniques, such as scRNA-seq, spectral flow cytometric analysis, and in vitro culture. The biopsies were minced in a petri dish containing 2-3 mL of 370C-warmed DPBS with Calcium and Magnesium (DPBS+/+) on ice with a razor blade or scalpel and transferred to a 50 mL conical for digestion, also on ice. The petri dish was rinsed 4-5 times with 1 mL of 370C-warmed DPBS+/+ which was also transferred to the 50 mL conical. A 1:100 ratio of 5mg/mL Liberase (Sigma Aldrich; 723 SKU 5401127001) and a 1:1000 ratio of 1 mg/mL DNAse I (Sigma-Aldrich; SKU 724 11284932001) was added to the conical and inverted 2-3 times to mix. The conical 725 containing the minced biopsy and digestion media was then placed in a 370C shaking incubator at 240 RPMs and was inspected every 5 minutes to determine if the digestion had completed. If the digestion needed to continue, the conical was inverted 2-3 times to mix and placed back in the 370C shaking incubator at 240 RPMs. Digestion typically took 10-15 minutes on average. The digested sample was placed on ice and filtered through a 70 μm strainer (Stemcell Technologies; Cat. 27260) into a new 50 mL conical. The strainer was rinsed 5 times with 1 mL ice-cold DPBS+/+ before adding more ice-cold DPBS+/+ to the 50mL mark. The digested biopsy was then centrifuged at 300xg for 5 min at 4ºC. After centrifugation, the supernatant was aspirated without disturbing the pellet, which was then transferred to a 15mL conical and resuspended in 2 mL ACK lysis buffer (Quality Biological; Cat. 118-156-101) to incubate on ice for 2 minutes. After ACK lysis, 13 mL ice-cold DPBS without calcium and magnesium (DPBS-/-; Gibco™; Cat. 14-287-739 080) was added to the cell suspension. The 15 mL conical was then inverted 2-3 times to mix and was then centrifuged at 300xg for 5 min at 4ºC. The supernatant was aspirated without disturbing the cell pellet which was then resuspended in 0.5-1mL fresh sort buffer (ice-cold DPBS-/- + 0.04% (w/v) BSA (Jackson ImmunoResearch; Cat. 001-000-162)) for counting. Cells were counted by creating a 1:10 or 1:100 dilution with 0.04% Trypan blue in PBS (Gibco™; Ref. 15250-061). For the 1:10 dilution, 10 μL of the well-mixed cell suspension was added to 90 μL of 0.04% Trypan blue in PBS. For a 1:100 dilution, 10 μL of the 1:10 dilution was added to 90 μL of 0.04% Trypan blue in PBS. Cell counts were performed using a disposable Neubauer improved hemocytometer (INCYTO; DHC-N01-748 5), following the manufacturer’s instructions.
Live CD45+ cells were used for single-cell RNA sequencing after being FACS-enriched. Cells that were used in CITE-seq experiments were blocked with TruStain Fc block (BioLegend; Cat. 422301) for 30 minutes. Cells were then incubated with TotalSeq B™ Universal cocktail (BioLegend; Cat. 399904) in Cell Staining Buffer (Biolegend; Cat. 420201) and washed following the manufacturer’s protocol before being used for scRNA library preparation. Cells isolated for scRNA/CITE-seq were suspended in ice-cold cell sorting buffer. scRNA GEMs and libraries were prepared according to the manufacturer's instructions. 5' libraries were prepared according to 10x Genomics CG000331 protocol, using Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics; PN-1000263). 3' libraries were prepared using 10x Genomics CG000399 protocol, or CG000206 if a CITE-seq antibody panel was used with the appropriate 3’ GEM kit (10x Genomics; PN 1000121). Both 3' and 5' libraries used Dual Index Kit TT Set A (10x Genomics; PN 3000431). GEMs were created on either a Chromium Controller or Chromium X (10x Genomics). Either C1000 (Bio-rad) or SimpliAmp (Applied Biosystems) thermocyclers were used for library prep. Quality and concentrations of cDNA and final libraries were calculated from 2100 BioAnalyzer (Agilent) electrograms. Sequencing was performed on a NovaSeq 6000 (Ilumina)

tag: library type

value: ADT

value: TotalSeq™-B Human Universal Cocktail v.1

tag: tissue

tag: cell type

tag: genotype


title: Healthy Control 10_L2_ADT

description:
Library name: HC10_CS_csp_S16_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: FVF_DO9

city: Schlieren

first: Umesh

last: Ghoshdastider

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

description:
Library name: FVF_DO9
dial-out nested PCR for sgRNA amplification for P60

data_processing:
Bioinformatic analysis of single-cell RNA sequencing data: Raw sequencing data, consisting of BCL files, were demultiplexed using Illumina bcl2fastq v2.20 with default settings. One mismatch in the sample barcode sequences was allowed. The resulting fastq files were processed using the BD Rhapsody Pipeline (version 1.9.1) hosted at the Seven Brigdge’s cloud platform (https://www.sevenbridges.com/). A custom mouse reference genome, based on Gencode vM25 (GRCm38.p6), was generated and combined with the 720 sgRNAs sequences. Based on STAR aligner, a custom STAR reference genome was created and the Refined Putative Cell Calling option was disabled during the pipeline execution. For downstream analysis, unique molecular identifier (UMI) count data was corrected using BD Genomics Recursive Substitution Error Correction (RSEC). Processing PCR sgRNA dial-out data PCR dial-out data was processed using an in-house custom Python script as previously described (15). Three 9-nucleotide cell barcodes were extracted from the 97 possible barcodes from Read 1. One mismatch was allowed per barcode (Hamming distance of 1). The script also retrieved the 8-nucleotide UMI sequences from Read 1, as specified in the BD manual. For valid barcodes, sgRNAs were identified in Readd 2 by performing an exact match search for the 20-nucleotide sgRNA sequence. UMI counts per cell were deduplicated and sgRNA UMI counts per cell were computed. If multiple sgRNAs were detected for one cell, the cell was assigned to a specific sgRNA only if its UMI count exceeded the 99th percentile. Processing of single-cell RNA sequencing data The Scrublet Python package was used to remove doublets from each dataset separately. Genes expressed in a minimum of 5 cells were retained and an expected double rate of 20% (as estimated by BD Rhapsody) was applied. After filtering, seven P4 single-cell RNA-seq datasets and eight P60 datasets were merged using Seurat. Only cells containing detected sgRNAs and classified as singlets were selected for further analysis. Cells were filtered based on the following criteria: UMI counts > 500, UMI counts lower than the 0.99 quantile (to remove outliers) and mitochondrial gene content < 20%. Filtered datasets were then processed using Seurat’s standard pipeline. Gene expression was normalized using the NormalizeData function, which scales counts to 10,000 per cell followed by a natural log transformation (log1p). The FindVariableGenes function identified 2,000 highly variable genes, and data scaling was performed using ScaleData. Principal Component Analysis (PCA) was conducted with RunPCA and the ElbowPlot function was used to determine the top principal components that contributed to explaining the variance of the data for each dataset at P4 and P60. The FindNeighbors function was applied to identify nearest neighbors based in the selected principal components. Clustering was performed using FindClusters with Louvain modularity optimization. To visualize the data in two dimensions, UMAP (Uniform Manifold Approximation and Projection) was used. No batch effects were observed in the P4 and P60 datasets, so batch effect correction was not performed.
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: Comma-separated value files and matrix files with count numbers, *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.

molecule: other

organism: Mus musculus

source_name: mouse epidermis

growth_protocol: All mice were housed at the Laboratory Animal Services Center (LASC) of the University of Zurich in individually-ventilated cages in a humidity- and light-controlled environment (22˚C, 45-50%, 12 h light/dark cycle), and had access to food and water ad libitum.

extract_protocol:
P4 back skin was processed as previously described (15). Fat was scraped off and the back skin was washed once in cold PBS and then placed in dispase (Corning #354235) dermis-side facing down, incubated for 35 min at 37 °C on an orbital shaker. Next, epidermis was separated from dermis with fine forceps and placed in 4 ml 0.25% Trypsin-EDTA (1×, Gibco; 25200056) for 15 min at 37 °C with orbital shaking. Epidermis was torn into smaller pieces and washed with cold PBS, pipetted vigorously up and down to achieve a single-cell suspension. Suspension was filtered through a 70-µm and subsequently a 40-µm strainer (Corning; #431750, #431751). Suspension was then centrifuged for 10 min at 400 g and resuspended in FACS buffer (PBS + 2% chelexed FBS (FBS(-)) + DAPI). P60 back skin was processed as previously described (15). Back skin was harvested with surgical scissors and placed dermis-facing up on a styrofoam rack with pins. Fat was scraped off with a scalpel. Fat-free skin was then washed, dermis-side facing down in 1× PBS. Skin was then placed in the same orientation in 0.5% Trypsin-EDTA (10×, Gibco; 15400054) and incubated at 37 °C on an orbital shaker for 25 min (females) or 50 min (males). Using a glass microscopy slide, skin was secured to the bottom of the dish and scraped again with a scalpel until it started to diverge. Excess cold PBS with 2% FBS(-) was added to neutralize trypsin. Cell suspension was strained on ice first through a 70-µm strainer, washed with an additional 15 ml of cold 1× PBS with 2% FBS (-) and then filtered through a 40-µm strainer. Cell suspension was spun down at 400 g for 10 min and resuspended in FACS buffer. P4: a total of 18 injected P4 mice were collected and assessed in 7 independent single-cell RNA sequencing runs. P60: a total of 7 injected mice were collected and assessed in 8 independent single-cell RNA sequencing runs.
Library construction protocol for scRNA-seq: EGFP-positive cells were sorted on a BD FACSAria III using a 70-µm nozzle and processed for single-cell capture with a BD Rhapsody Single-Cell Analysis System using BD Rhapsody Cartridge Kit (#633733). For P4, 7 separate cartridges with an average of 76,613 cells were loaded. For P60, 8 cartridges with an average of 68,171 cells were loaded. Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Library construction protocol for RNA-seq: RNA was isolated from lysates from nontargeting control and Gm10076 C7 keratinocytes as described in the Ribosome profiling section using TRIzol®  LS Reagent (Invitrogen, 10296028) and column purified with a Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared and sequenced at Novogene. Library construction protocol for Other:  As previously described, the sgRNA-containing region was amplified from the BD Rhapsody beads using a nested KAPA Polymerase reaction. In the first polymerase reaction (PCR1), the Rhapsody beads from each separate cartridges were resuspended and distributed into 4 separate 50 µL reactions  (100 µl KAPA HiFi HotStart ReadyMix (Roche 07958935001), 6 µl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 6 µl reverse primer (5′-TCTTGTGGAAAGGACGA-3′, 10 μM), 12 μl Bead RT/PCR Enhancer reagent from BD Biosciences and 72 μl nuclease-free water for a total volume of 200 μl). PCR1 conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 25 cycles of denaturation 95 °C for 30 s, annealing 53 °C for 30 s, extension 72 °C for 20 s and a final extension of 10 min at 72 °C. The 4 x 50 µl PCR1 product was pooled, and beads were removed using a magnet. Amplicons were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instructions. 3 μl of cleaned up PCR1 was used as template for PCR 2 (25 µL KAPA HiFi HotStart Ready Mix, 2 μl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 2 μl reverse primer (CAGACGTGTGCTCTTCCGATCTCTTGTGGAAAGGACGAAACA*C*C*G-3′, 10 μM), 18 μl nuclease-free water) for a total volume of 50 μl. PCR2 conditions were as follows: initial denaturation at 95 °C for 3 min, followed by 10 cycles of denaturation 95 °C for 30 s, annealing 60 °C for 3 min, extension 72 °C for 60 s, and a final extension of 5 min at 72 °C. Agencourt AMPure XP beads were used to clean up PCR2 product according to the manufacturer’s instructions  before the indexing PCR. Indexing PCR was performed according to BD Biosciences ‘mRNA Targeted Library Preparation’ protocol (doc ID: 210968 rev. 3.0). Library construction protocol for Ribo-seq: Ribosome profiling was conducted with some adjustments of the original method (64, 65). For RNA digestion, cell lysates were incubated with 1 U/µg of RNase 1 (Epicentre/Lucigen, 10U/µL) for 45 minutes at room temperature. Reaction was stopped by adding 4 µL of SUPERase Inhibitor (20 U/µL, SUPERase-InTM RNase Inhibitor Thermo Scientific AM2694). To eliminate free nucleotides and isolate ribosome-protected fragments, the RNase I-treated samples were processed using Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). RNA extraction was performed utilizing TRIzol® LS Reagent (Invitrogen 10296028) in combination with the Direct-zolTM RNA MiniPrep kit (Zymo Research, R2052). Total RNA concentration was measured using QubitTM RNA broad range kit (Invitrogen, Q10210). Ribosome footprints were excised and extracted from a 15% TBE-UREA gel (Invitrogen, EC68852BOX) using the 20nt, 22nt, 27nt, 30nt and 60nt oligonucleotides mix as markers (1 µL of 10 µM dilution in 19µL RNase-free H2O). Extraction was performed overnight with RNA extraction buffer (300mM NaOAc pH=5.5, 1mM EDTA, 0.25% v/v SDS). T4 PNK (NEB, M0201S) end-healing reaction was performed on the ribosome footprints for 1 hour at 37˚C. Linker ligation reaction followed using T4 RnI truncated K227Q (NEB, M0351L) in combination with 20 µM of preadenylated linker for 3 hours at 22˚C (50% w/v PEG-8000, 10X T4 RNA ligase, preadenylated linker, T4 RnI truncated K227Q). Ribosomal RNA was depleted using biotinylated rRNA depletion oligos (2 µM) by mixing 10 µL of sample with 10 µL of oligo mix and incubated for 2 minutes at 80˚C, followed by a gradual decrease in temperature to 25˚C. MyOne Streptavidin dynabeads (Life Technologies, 65001) were used to recover the samples. Reverse transcription was performed on the Ribosomal RNA-free samples using SuperScriptTM IV Reverse Transcriptase (Invitrogen, 18090050). Footprints were excised and extracted from a 15% TBE-UREA gel. Extraction was performed overnight with DNA extraction buffer (10mM Tris-HCl pH=8, 300mM NaCl, 1mM EDTA). cDNA was circularized using CircLigase II (100 U/µL, Biosearch, CL4115K) for 1 hour at 60˚C. cDNA was amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific, F530S) using an individual index per sample. 6-12 cycle amplicons were visualized using an 8% TBE non-denaturing polyacrylamide gel to determine optimal cycle number. PCR was carried out with 7-9 cycles and analyzed on an 8% TBE non-denaturing polyacrylamide gel (Invitrogen, EC61252BOX). DNA was excised from gel and extracted using DNA extraction buffer by incubating overnight with gentle shaking. DNA was recovered and precipitated in 10 mM Tris-HCl pH=8. DNA was quantified using Qubit TM 1X dsDNA High Sensitivity Assay (Invitrogen, Q33230) and quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Samples were pooled and prepared for sequencing.

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_4

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

description: Library name: Sample_30

library_source: genomic

data_processing:
Trimming Illumina adapters with cutadapt
Trimming low quality tails with sickle (https://github.com/najoshi/sickle) (with -q 20 option)
Alignment with bowtie2 against version dm6 of the Drosophila melanogaster genome
Filtration of PCR duplicates and non-unique mapping with picard (https://broadinstitute.github.io/picard/)
Blacklist filtration with bedtools
Reproducible peaks calling was conducted against corresponding preimmune controls with IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr).  A soft p value threshold for MACS2 in IDR of 0.01, the IDR reproducibility threshold was set to 0.05 for true replicates and 0.01 for pseudoreplicates. All samples showed good reproducibility (the rescue ratio or/and the self consistency ratio were <2).
ChiP-Seq coverage tracks were obtained using deepTools (Ramírez et al. 2014) bamCoverage functions  with a bin width of 50 bps and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by IDR and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted using a ChIP DNA Clean &Concentrator kit (Zymo Research, USA).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with MagSelect XP beads (Magen). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from third-instar larvae. 500 milligrams of larvae was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, and 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized in a Potter and Dounce homogenizer with a tight pestle, filtered through a 100 µm Nylon Cell Strainer (Miltenyi Biotec, USA), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, and protease inhibitors) and one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, and protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, and protease inhibitors). The suspension of nuclei was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test the extent of sonication and measure the DNA concentration. Debris was removed by centrifugation at 14,000 x g, 4°C, for 10 min, and chromatin was pre-cleared with Protein G Dynabeads (Invitrogen, USA). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein G (rat anti-CP190, 1:300; rat anti-Su(Hw), 1:200; rat non-specific IgG) or Protein A (rabbit anti-HA, 1:500; rabbit anti-Pita, 1:200; rabbit non-specific IgG) Dynabeads (Thermo Fisher Scientific, USA) mixed with 200 µL of PBST. Then antibody–Dynabead complexes were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL nuclear lysis buffer (2 µL aliquots of pre-cleared chromatin as input material) were incubated overnight at 4°C with antibody–Dynabead complexes.

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rat

tag: strain

tag: antibody


title: FVF_DO8

description:
Library name: FVF_DO8
dial-out nested PCR for sgRNA amplification for P60


title: TBM, blood,  MPH016, D0

city: London

first: James

middle: Royce

last: Barnacle

state: London

address: Francis Crick Institute, 1 Midland Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description: Library name: DAV1202A67

library_source: transcriptomic

data_processing:
Raw data were processed using nf-core/rnaseq (v3.10.1) of the nf-core collection of workflows. This workflow used FASTQ files as input, performed quality control (QC), trimming and (pseudo-)alignment to the GRCh38 release 95 human reference genome, and produced a gene expression matrix and QC report. The pipeline was executed with Nextflow (v22.10.3). The output matrix was read into R (v4.2.0) in which subsequent analysis was done.
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: .csv file with samples as colnames and genes as rownames

molecule: total RNA

source_name: Blood

extract_protocol:
Whole blood was collected directly into PAXgene RNA tubes (QIAGEN/BD Biosciences) from 40 patients enrolled into the LASER-TBM trial. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN, Venlo, Netherlands). Samples were stored at -80˚C before and after RNA extraction. Quantity and quality of RNA was assessed using a Qubit fluorimeter (ThermoFisher) and Agilent 2100 Bioanalyzer. Samples with RNA integrity number (RIN) <7 were excluded.
RNA libraries were constructed using Tecan’s Universal Human Blood RNA-Seq kit. Ribosomal and globin RNA were removed using Tecan’s AnyDeplete system. DNA library size distribution was assessed using the D1000 TapeStation kit processed on the 4200 TapeStation (Agilent Technologies). The data were analysed by Agilent’s 4200 TapeStation Analysis Software. Concentration was measured using the QuantiFluor dsDNA System (Promega Corporation). Libraries were sequenced on an Illumina HiSeq4000 with a single-end 100 cycle read configuration.

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: female

tag: antibiotics

value: soc

tag: aspirin

value: no

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: TBM, blood,  MPH033, D0

description: Library name: DAV1202A65

tag: tissue

value: definite

value: positive


title: Healthy Control 10_L4_GEX

description:
Library name: HC10_CS_3p_S25_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

molecule: polyA RNA

tag: library type

value: RNA

tag: adt

value: Endometrium

tag: cell type

value: CD45+ Cells

tag: genotype

value: XX

tag: treatment

value: Healthy Control


title: FVF_DO6

description:
Library name: FVF_DO6
dial-out nested PCR for sgRNA amplification for P60

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: TBM, blood,  MPH013, D0

description: Library name: DAV1202A63

value: Blood

tag: patient id

tag: study

tag: timepoint

value: intensified


title: Healthy Control 10_L1_ADT

description:
Library name: HC10_CS_csp_S16_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: ADT

value: TotalSeq™-B Human Universal Cocktail v.1


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_3

description: Library name: Sample_29

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rat

tag: strain

tag: antibody


title: Healthy Control 10_L3_GEX

description:
Library name: HC10_CS_3p_S25_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_1

description: Library name: Sample_27


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_2

description: Library name: Sample_28


title: FVF_DO5

description:
Library name: FVF_DO5
dial-out nested PCR for sgRNA amplification for P60


title: FVF_DO4

description:
Library name: FVF_DO4
dial-out nested PCR for sgRNA amplification for P4


title: FVF_DO3

description:
Library name: FVF_DO3
dial-out nested PCR for sgRNA amplification for P4


title: CTCF_larvae_CTCFdeltaCP_4

description: Library name: Sample_26

value: dCTCFdeltaCP

value: rabbit

value: dCTCF (HA)


title: TBM, blood,  NSH003, D14

description: Library name: DAV1202A62

value: laser

tag: age

tag: Sex

value: female

tag: antibiotics

tag: aspirin

value: yes

tag: diagnosis

value: possible

tag: gxpu

value: negative

tag: mtb culture


title: TBM, blood,  NSH020, D0

description: Library name: DAV1202A61

tag: tissue

value: male

value: no

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: CTCF_larvae_CTCFdeltaCP_3

description: Library name: Sample_25

tag: genotype


title: FVF_DO10

description:
Library name: FVF_DO10
dial-out nested PCR for sgRNA amplification for P4

value: mouse epidermis

tag: cell type

value: skin cells

value: Pik3ca x LSLCas9


title: Healthy Control 10_L2_GEX

description:
Library name: HC10_CS_3p_S25_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

tag: treatment

value: Healthy Control


title: FVF_DO2

description:
Library name: FVF_DO2
dial-out nested PCR for sgRNA amplification for P4


title: Uterus Transplant 4_Biopsy 2_L1

description:
Library name: UTx04Bx02_S32_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

library_source: transcriptomic single cell

data_processing:
Reads from single-cell RNA-seq experiments of each Healthy Control and Uterus Transplant library were pre-processed and aligned against the GRCh38 human reference and quantified using Cell Ranger (v.6.1.1) from 10x Genomics
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files (tsv) and matrix files (mtx): *_barcodes.tsv.gz: cellular barcodes present in dataset; *_features.tsv.gz: IDs of quantified genes; *_matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs and columns correspond to the cellular barcodes

value: Uterus Transplant


title: CTCF_larvae_CTCFdeltaCP_2

description: Library name: Sample_24

value: whole organism

value: dCTCFdeltaCP

tag: development stage

value: larvae

tag: antibody source

value: rabbit

tag: strain

tag: antibody

value: dCTCF (HA)


title: Uterus Transplant 2_Biopsy 2_L2_4

description:
Library name: UTx02Bx02_28_S6_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Healthy Control 10_L1_GEX

description:
Library name: HC10_CS_3p_S25_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: TBM, blood,  NSH019, D14

description: Library name: DAV1202A60

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: female

tag: antibiotics

value: intensified

tag: aspirin

value: yes

value: definite

value: positive

value: negative


title: Uterus Transplant 2_Biopsy 2_L1_4

description:
Library name: UTx02Bx02_28_S6_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: tissue

value: Endometrium

value: CD45+ Cells


title: FVF_DO1

description:
Library name: FVF_DO1
dial-out nested PCR for sgRNA amplification for P4

value: mouse epidermis

value: skin cells

tag: genotype

value: Pik3ca x LSLCas9


title: FVF_WTA18

description:
Library name: FVF_WTA18
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4, secondary validation screen

tag: cell type


title: TBM, blood,  MPH011, D7

description: Library name: DAV1202A57

tag: diagnosis

value: probable

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: TBM, blood,  NSH019, D7

description: Library name: DAV1202A59


title: CTCF_larvae_CTCFdeltaCP_1

description: Library name: Sample_23

value: whole organism

value: dCTCFdeltaCP

tag: development stage

value: larvae

tag: antibody source

tag: strain

tag: antibody


title: TBM, blood,  NSH002, D14

description: Library name: DAV1202A58

value: Blood

tag: patient id

tag: study

tag: timepoint

tag: age


title: CP190_larvae_CTCFdeltaCP_4

description: Library name: Sample_22

tag: tissue

value: rat


title: FVF_WTA16

description:
Library name: FVF_WTA16
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60

tag: genotype


title: TBM, blood,  NSH015, D7

description: Library name: DAV1202A56

value: laser

tag: Sex

value: male

tag: antibiotics

tag: aspirin

value: no

value: possible


title: Uterus Transplant 2_Biopsy 2_L2_3

description:
Library name: UTx02Bx02_27_S26_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type

value: XX

tag: treatment

value: Uterus Transplant


title: TBM, blood,  NSH015, D0

description: Library name: DAV1202A55

value: intensified

tag: diagnosis

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Uterus Transplant 2_Biopsy 2_L1_3

description:
Library name: UTx02Bx02_27_S26_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells


title: CP190_larvae_CTCFdeltaCP_3

description: Library name: Sample_21

tag: development stage

tag: antibody source

tag: strain

tag: antibody


title: FVF_WTA15

description:
Library name: FVF_WTA15
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: TBM, blood,  NSH014, D7

description: Library name: DAV1202A54

tag: patient id

tag: study

tag: timepoint

tag: age

value: yes

value: definite

value: positive

tag: blood neutrophils


title: Uterus Transplant 2_Biopsy 2_L2_2

description:
Library name: UTx02Bx02_26_S22_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: tissue

tag: genotype


title: CP190_larvae_CTCFdeltaCP_2

description: Library name: Sample_20

value: whole organism

value: dCTCFdeltaCP

value: larvae

value: rat


title: TBM, blood,  MPH013, D7

description: Library name: DAV1202A53

value: Blood

value: laser

tag: Sex

value: female

tag: antibiotics

tag: aspirin

value: no

value: probable


title: CP190_larvae_CTCFdeltaCP_1

description: Library name: Sample_19


title: FVF_WTA17

description:
Library name: FVF_WTA17
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60 secondary validation library

tag: cell type


title: FVF_WTA13

description:
Library name: FVF_WTA13
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60


title: Uterus Transplant 2_Biopsy 2_L1_2

description:
Library name: UTx02Bx02_26_S22_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: XX

tag: treatment

value: Uterus Transplant


title: SuHw_adult_wt_2

description: Library name: Sample_18

value: dCTCFwt

value: adult

value: SuHw


title: TBM, blood,  GSH006, D56

description: Library name: DAV1202A52

value: male

value: intensified

value: yes

tag: diagnosis

value: definite

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: FVF_WTA12

description:
Library name: FVF_WTA12
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: SuHw_larvae_wt_2

description: Library name: Sample_16

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rat

tag: strain

tag: antibody


title: Uterus Transplant 2_Biopsy 2_L1_1

description:
Library name: UTx02Bx02_25_S20_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: CD45+ Cells


title: Uterus Transplant 2_Biopsy 2_L2_1

description:
Library name: UTx02Bx02_25_S20_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium


title: FVF_WTA11

description:
Library name: FVF_WTA11
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4


title: TBM, blood,  NSH003, D56

description: Library name: DAV1202A51

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

value: female

value: possible

value: negative

tag: blood neutrophils


title: FVF_WTA10

description:
Library name: FVF_WTA10
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4

tag: tissue

tag: genotype


title: TBM, blood,  GSH004, D7

description: Library name: DAV1202A50

tag: Sex

value: male

tag: antibiotics

tag: aspirin

value: no


title: TBM, blood,  MPH036, D14

description: Library name: DAV1202A49

value: intensified

value: yes

tag: diagnosis

tag: gxpu

value: positive

tag: mtb culture


title: CTCF_larvae_wt_4

description: Library name: Sample_14

value: dCTCFwt

tag: development stage

value: rabbit

value: dCTCF (HA)


title: Uterus Transplant 1_Biopsy 5_L1

description:
Library name: UTx01Bx05_S16_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type

value: XX

tag: treatment

value: Uterus Transplant


title: Uterus Transplant 1_Biopsy 5_L2

description:
Library name: UTx01Bx05_S16_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: CD45+ Cells


title: FVF_WTA8

description:
Library name: FVF_WTA8
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: FVF_WTA14

description:
Library name: FVF_WTA14
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60


title: FVF_WTA9

description:
Library name: FVF_WTA9
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60


title: SuHw_larvae_wt_1

description: Library name: Sample_15

value: whole organism

value: larvae

tag: antibody source

value: rat

tag: strain

tag: antibody

value: SuHw


title: TBM, blood,  MPH022, D14

description: Library name: DAV1202A48

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

value: male

value: soc

value: no

value: definite

value: negative

tag: hiv vl

tag: blood wcc


title: Uterus Transplant 1_Biopsy 2_L4

description:
Library name: UTx01_Bx02_5p_S13_L004
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: tissue

value: Endometrium

tag: genotype

value: XX


title: FVF_WTA6

description:
Library name: FVF_WTA6
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60


title: CTCF_larvae_wt_2

description: Library name: Sample_12

value: dCTCFwt

value: rabbit

value: dCTCF (HA)


title: CTCF_larvae_wt_3

description: Library name: Sample_13


title: Uterus Transplant 1_Biopsy 2_L2

description:
Library name: UTx01_Bx02_5p_S13_L002
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: CD45+ Cells

value: Uterus Transplant


title: SuHw_adult_wt_1

description: Library name: Sample_17

value: whole organism

value: adult


title: TBM, blood,  NSH018, D0

description: Library name: DAV1202A47

tag: age

tag: Sex

tag: antibiotics

value: intensified

tag: aspirin

value: yes

value: possible

tag: blood neutrophils


title: Uterus Transplant 1_Biopsy 2_L1

description:
Library name: UTx01_Bx02_5p_S13_L001
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type


title: TBM, blood,  NSH016, D0

description: Library name: DAV1202A44

value: Blood

value: laser

value: female

tag: diagnosis

value: probable

tag: gxpu

tag: mtb culture


title: CTCF_larvae_wt_1

description: Library name: Sample_11

tag: development stage

value: larvae

tag: antibody source

tag: strain

tag: antibody


title: TBM, blood,  NSH010, D14

description: Library name: DAV1202A46

tag: patient id

tag: study

tag: timepoint

value: soc

value: no

value: definite

value: positive

value: negative

tag: hiv vl


title: CP190_larvae_wt_4

description: Library name: Sample_10

tag: tissue

tag: genotype

value: dCTCFwt

value: rabbit


title: FVF_WTA4

description:
Library name: FVF_WTA4
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: FVF_WTA5

description:
Library name: FVF_WTA5
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60


title: TBM, blood,  MPH023, D14

description: Library name: DAV1202A43

tag: age

tag: Sex

tag: antibiotics

value: intensified

tag: blood wcc


title: Healthy Control 19_L4_5

description:
Library name: HC19-4_S4_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

tag: cell type

value: CD45+ Cells

value: XX

tag: treatment

value: Healthy Control


title: Uterus Transplant 1_Biopsy 2_L3

description:
Library name: UTx01_Bx02_5p_S13_L003
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Uterus Transplant


title: FVF_WTA2

description:
Library name: FVF_WTA2
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4


title: TBM, blood,  NSH002, D0

description: Library name: DAV1202A42

value: Blood

value: laser

value: female

tag: aspirin

value: yes

tag: diagnosis

value: probable

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: FVF_WTA3

description:
Library name: FVF_WTA3
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4


title: Healthy Control 19_L2_5

description:
Library name: HC19-4_S4_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Healthy Control 19_L1_5

description:
Library name: HC19-4_S4_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: CP190_larvae_wt_3

description: Library name: Sample_9

value: whole organism

tag: development stage

value: larvae

tag: antibody source

tag: strain

tag: antibody


title: CP190_larvae_wt_2

description: Library name: Sample_8

tag: tissue

value: dCTCFwt

value: rabbit


title: FVF_WTA1

description:
Library name: FVF_WTA1
scRNA-seq WTA of P4 skin, CROP-seq-CRE P4

value: mouse epidermis

value: skin cells

tag: genotype


title: Pita_larvae_wt_2

description: Library name: Sample_6

value: Pita


title: TBM, blood,  LH011, D14

description: Library name: DAV1202A40

tag: patient id

tag: study

tag: timepoint

tag: age

value: soc

value: no

value: definite

value: positive

value: negative

tag: hiv vl


title: TBM, blood,  MPH013, D14

description: Library name: DAV1202A41

value: Blood

tag: Sex

tag: antibiotics

value: intensified

tag: blood wcc


title: Healthy Control 19_L4_4

description:
Library name: HC19-3_S3_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

tag: cell type

value: CD45+ Cells

value: XX

tag: treatment

value: Healthy Control


title: CP190_larvae_wt_1

description: Library name: Sample_7

value: whole organism

value: larvae


title: Brg1-AID_CnR_MyoD-ER_4OHT_72h_T7

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 24

data_processing:
Basecalls performed using Bcl2fastq.
CUT&RUN and ATAC-Seq reads were aligned to the mm10 genome assembly using bowtie2.
CUT&RUN peaks were called using SICER (v2) with following configuration: For transcription factors and co-factors, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For histone modifications, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all CUT&RUN data.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM
Library strategy: CUT&Run

source_name: Brg1AID/AID preadipocytes

growth_protocol: Preadipocytes were maintained in growth media (DMEM plus 10% Foundation FBS).

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (#14-1048, Epicypher), following the manufacturer’s instructions with the following modifications. 0.5 million cells were used for each CUT&RUN reaction. Cells were gently fixed with 0.1% formaldehyde for 1 min. Cells were resuspended in cold Nuclei Extract Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MgCl2 supplemented with protease inhibitor and 0.5 mM Spermidine), lysed on ice for 10 mins, and centrifuged at 600 g for 3 min 4°C. Nuclei were resuspended in 100 uL cold Nuclei Extract Buffer and incubated with activated 10 uL/reaction Concanavalin A beads for 10 min at RT. The following steps are performed according to the manufacturer’s instructions.
Libraries were prepared following the instruction of CUTANA™ CUT&RUN Library Prep Kit for Illumina sequencing. CUT&RUN enriched DNA were used to construct libraries, using NEBNext® Ultra™ II DNA Library Prep kit (#E7645L, NEB) with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: MyoD-ER-T7 preadipocytes were grown in growth media (DMEM plus 10% Foundation FBS) for 2 days. On the day of experiments, growth medium was replaced with differentiation medium (DMEM plus 2% horse serum), and cells were rested for 3h. Cells were then pretreated with 1 µM BRM014 or 3 µM A-485 for 1h; 1 µM 5Ph-IAA for 2h; or 250 nM dCBP-1 for 3h, before 400 nM 4-OHT was added for 1h to induced MyoD nuclear translocation.

tag: cell line

value: Brg1AID/AID preadipocytes

value: Preadipocyte

tag: chip antibody


title: TBM, blood,  NSH009, D0

description: Library name: DAV1202A37

value: laser

value: male

tag: aspirin

value: yes

tag: diagnosis

value: possible

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: TBM, blood,  MPH033, D14

description: Library name: DAV1202A38

tag: tissue

tag: patient id

value: female

value: soc

value: no

value: definite


title: Brg1-AID_CnR_MyoD-ER_4OHT_72h_K4me1

description: Library name: Sample 23

value: Anti-H3K4me1 (13-0040, Epicypher)


title: Brg1-AID_CnR_MyoD-ER_4OHT_72h_K27ac

description: Library name: Sample 22

value: Anti-H3K27ac (ab4729, Abcam)


title: Healthy Control 19_L3_5

description:
Library name: HC19-4_S4_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells

tag: genotype


title: CTCF_adult_wt_2

description: Library name: Sample_4

value: dCTCFwt

tag: development stage

value: adult

tag: antibody source

value: rabbit

tag: strain

tag: antibody

value: dCTCF (HA)


title: Healthy Control 19_L2_4

description:
Library name: HC19-3_S3_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: XX

value: Healthy Control


title: Brg1-AID_CnR_MyoD-ER_4OHT_72h_IgG

description: Library name: Sample 21

value: Brg1AID/AID preadipocytes

value: Preadipocyte

value: Anti-IgG (13-0042K, Epicypher)


title: Pita_larvae_wt_1

description: Library name: Sample_5

value: whole organism

value: larvae

value: Pita


title: TBM, blood,  LH007, D0

description: Library name: DAV1202A36

value: Blood

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: male

tag: antibiotics

value: intensified

value: no

value: definite

value: positive

value: negative

tag: hiv vl

tag: blood wcc


title: Healthy Control 19_L1_4

description:
Library name: HC19-3_S3_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

tag: cell type

value: CD45+ Cells

tag: treatment


title: CTCF_adult_wt_1

description: Library name: Sample_3

value: dCTCFwt

value: adult

value: rabbit

value: dCTCF (HA)


title: Brg1-AID_CnR_MyoD-ER_4OHT_24h_T7

description: Library name: Sample 20

tag: cell line

value: Brg1AID/AID preadipocytes

value: Preadipocyte

tag: chip antibody


title: Pita_adult_wt_2

description: Library name: Sample_2

tag: tissue

value: whole organism

value: Pita


title: TBM, blood,  GSH011, D56

description: Library name: DAV1202A35

value: Blood

tag: patient id

value: laser

tag: aspirin

tag: diagnosis

value: probable

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: Healthy Control 19_L4_3

description:
Library name: HC19-2_S2_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: genotype

value: XX

value: Healthy Control


title: TBM, blood,  GSH011, D14

description: Library name: DAV1202A34

tag: study

tag: timepoint

tag: age

value: male

value: intensified

value: no


title: Pita_adult_wt_1

description: Library name: Sample_1

tag: development stage

tag: antibody source

tag: strain

tag: antibody


title: Healthy Control 19_L3_3

description:
Library name: HC19-2_S2_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

tag: cell type

value: CD45+ Cells

tag: treatment


title: larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_2

description: Library name: Sample 10

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The processed reads were aligned to the version dm6 of the Drosophila melanogaster genome using the splice-aware STAR algorithm (Dobin et al. 2013).
The gene read counts were calculated using the STAR quantMode option (--quantMode GeneCounts).
Assembly: dm6
Supplementary files format and content: Processed data are gene counts obtained using STAR quantMode.

extract_protocol:
50 ng of total RNA was used for isolation of mRNA using oligo(dT) Magnetic beads (NEB, USA) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared with the NEBNext® Ultra RNA Library Prep kit  (NEB, USA) per the manufacturer's instructions. Purified mRNA was used as a started material for library preparation. After first and second strands synthesis cDNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters were ligated, after which the material was purified with Ampure XP beads (Beckman Coulter). PCR amplification was performed using indexed primers for 12 cycles using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads, quantified using fluorometry with DS-11 (DeNovix, USA) and its quality was assessed on a Bioanalyzer 2100 system (Agilent).  Diluted libraries were clustered on a pair-read flowcell and sequenced using a NovaSeq 6000 system (Illumina, USA).

treatment_protocol: Total RNA was isolated using the TRI reagent (Molecular Research Center, USA) according to the manufacturer’s instructions. 100 mg of 3rd instar larvae was used for extraction procedure.

tag: tissue

value: larvae


title: Healthy Control 19_L2_3

description:
Library name: HC19-2_S2_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Brg1-AID_CnR_MyoD-ER_4OHT_24h_K4me1

description: Library name: Sample 19

tag: cell line

tag: chip antibody

value: Anti-H3K4me1 (13-0040, Epicypher)


title: TBM, blood,  MPH018, D7

description: Library name: DAV1202A32

tag: patient id

tag: Sex

tag: antibiotics

value: soc

tag: aspirin

tag: diagnosis

value: negative

tag: hiv vl

tag: blood wcc


title: TBM, blood,  GSH009, D14

description: Library name: DAV1202A33

tag: study

tag: timepoint

tag: age

value: female

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: Healthy Control 19_L3_4

description:
Library name: HC19-3_S3_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type

tag: genotype

tag: treatment


title: Brg1-AID_CnR_MyoD-ER_4OHT_24h_K27ac

description: Library name: Sample 18

tag: cell line

value: Brg1AID/AID preadipocytes

value: Preadipocyte

tag: chip antibody

value: Anti-H3K27ac (ab4729, Abcam)


title: Brg1-AID_CnR_MyoD-ER_4OHT_24h_IgG

description: Library name: Sample 17

value: Anti-IgG (13-0042K, Epicypher)


title: TBM, blood,  NSH010, D7

description: Library name: DAV1202A31

tag: tissue

value: Blood

tag: patient id

value: laser

tag: Sex

value: definite

value: positive


title: larvae_CTCFdeltaCP_PitadeltaCP1_2

description: Library name: Sample 8

value: whole organism

tag: development stage

tag: strain


title: larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_1

description: Library name: Sample 9


title: TBM, blood,  MPH010, D0

description: Library name: DAV1202A30

value: male

tag: antibiotics

tag: aspirin

value: no

tag: diagnosis

value: possible

tag: hiv vl

tag: blood wcc


title: Healthy Control 19_L3_2

description:
Library name: HC19-1_S1_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells

value: XX

value: Healthy Control


title: Healthy Control 19_L4_2

description:
Library name: HC19-1_S1_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Brg1-AID_CnR_MyoD-ER_4OHT_9h_K27ac

description: Library name: Sample 14

value: 4OHT (9h)


title: TBM, blood,  MPH029, D0

description: Library name: DAV1202A29

tag: study

tag: timepoint

tag: age

value: female

value: intensified

value: yes

tag: gxpu

value: negative

tag: mtb culture


title: TBM, blood,  NSH004, D14

description: Library name: DAV1202A28

value: Blood

value: soc

tag: blood neutrophils


title: Healthy Control 19_L2_2

description:
Library name: HC19-1_S1_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type

tag: genotype

tag: treatment


title: larvae_CTCFdeltaCP_SuHwdelta114_2

description: Library name: Sample 6

tag: tissue

value: larvae


title: Brg1-AID_CnR_MyoD-ER_4OHT_9h_IgG

description: Library name: Sample 13

tag: cell line

value: Brg1AID/AID preadipocytes

value: Preadipocyte

tag: chip antibody

value: Anti-IgG (13-0042K, Epicypher)


title: Healthy Control 19_L1_3

description:
Library name: HC19-2_S2_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Brg1-AID_CnR_MyoD-ER_4OHT_4h_T7

description: Library name: Sample 12

value: 4OHT (4h)


title: larvae_CTCFdeltaCP_2

description: Library name: Sample 4

value: whole organism

value: dCTCFdeltaCP

tag: development stage

tag: strain


title: larvae_CTCFdeltaCP_SuHwdelta114_1

description: Library name: Sample 5


title: larvae_CTCFdeltaCP_1

description: Library name: Sample 3


title: TBM, blood,  GSH002, D7

description: Library name: DAV1202A27

tag: patient id

value: laser

tag: Sex

value: male

tag: antibiotics

tag: aspirin

value: no

tag: diagnosis

value: possible


title: larvae_CTCFdeltaCP_PitadeltaCP1_1

description: Library name: Sample 7


title: Healthy Control 18_L4_1

description:
Library name: HC18-2B2_S7_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells

value: XX

value: Healthy Control


title: Healthy Control 19_L1_2

description:
Library name: HC19-1_S1_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Brg1-AID_CnR_MyoD-ER_4OHT_4h_K4me1

description: Library name: Sample 11

value: Anti-H3K4me1 (13-0040, Epicypher)


title: Brg1-AID_CnR_MyoD-ER_4OHT_9h_T7

description: Library name: Sample 16

value: 4OHT (9h)


title: Healthy Control 18_L3_1

description:
Library name: HC18-2B2_S7_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: TBM, blood,  NSH011, D56

description: Library name: DAV1202A26

value: Blood

tag: study

tag: timepoint

tag: age

value: intensified

value: definite

value: positive

value: negative

tag: hiv vl

tag: blood wcc


title: Brg1-AID_CnR_MyoD-ER_4OHT_9h_K4me1

description: Library name: Sample 15

value: Brg1AID/AID preadipocytes

tag: cell type

value: Preadipocyte


title: TBM, blood,  MPH023, D7

description: Library name: DAV1202A25

value: laser

value: female

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: Healthy Control 18_L2_1

description:
Library name: HC18-2B2_S7_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: tissue

tag: genotype

tag: treatment


title: Brg1-AID_CnR_MyoD-ER_4OHT_4h_K27ac

description: Library name: Sample 10

tag: cell line

value: 4OHT (4h)

tag: chip antibody

value: Anti-H3K27ac (ab4729, Abcam)


title: TBM, blood,  MPH033, D7

description: Library name: DAV1202A23

tag: patient id

tag: Sex

tag: antibiotics

value: soc

value: no


title: Brg1-AID_CnR_MyoD-ER_4OHT_4h_IgG

description: Library name: Sample 9

value: Anti-IgG (13-0042K, Epicypher)


title: larvae_wt_2

description: Library name: Sample 2

value: whole organism

value: dCTCFwt

tag: development stage

value: larvae

tag: strain


title: larvae_wt_1

description: Library name: Sample 1


title: Brg1-AID_CnR_MyoD-ER_4OHT_1h_T7

description: Library name: Sample 8

value: 4OHT (1h)


title: Healthy Control 1_L4

description:
Library name: HC01_S39_L004
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells

value: XX

value: Healthy Control


title: Brg1-AID_CnR_MyoD-ER_4OHT_1h_K4me1

description: Library name: Sample 7

value: Brg1AID/AID preadipocytes

value: Anti-H3K4me1 (13-0040, Epicypher)


title: TBM, blood,  MPH002, D0

description: Library name: DAV1202A22

value: Blood

tag: study

value: laser

tag: timepoint

tag: age

value: intensified

tag: aspirin

tag: diagnosis

value: possible

value: negative


title: Healthy Control 1_L3

description:
Library name: HC01_S39_L003
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: cell type


title: CIC02-Tagtociclib 200nM R2

city: Cambridge

first: Nicolas

last: Fernandez

state: MA

address: 71 Ames St, 8th floor

institute: Broad Institute of MIT and Harvard

description: Library name: RNA-C11

data_processing:
Trimmed reads were mapped to the Homo Sapiens GRCh38 (hg38) reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Differential expression was performed using the PyDESeq2 library in Python.
We first filtered for the top 10,000 expressing genes across three replicates of treated versus non-treated cell lines. We then followed the PyDESeq2 workflow to fit size factors, fit dispersion, and calculate log fold changes. A list of up- and down-regulated genes with an adjusted P value of < 0.05 and absolute value log2 fold change of > 0.5 was generated. We used the interactive heatmap Python library, Clustergrammer2, to hierarchically cluster our samples and visualize the differentially expressed gene expression data. Enrichment analysis was performed using the web tool Enrichr to identify transcription factors that may be upstream of the differentially expressed genes.
Assembly: Homo Sapiens GRCh38 (hg38)
Supplementary files format and content: Count table

extract_protocol:
Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

value: sarcoma

value: Tagtociclib 200nM


title: CIC02-DMSO R3

description: Library name: RNA-C9

value: DMSO


title: Brg1-AID_CnR_MyoD-ER_4OHT_1h_K27ac

description: Library name: Sample 6

value: Preadipocyte

value: Anti-H3K27ac (ab4729, Abcam)


title: Brg1-AID_CnR_MyoD-ER_4OHT_1h_IgG

description: Library name: Sample 5

value: 4OHT (1h)

value: Anti-IgG (13-0042K, Epicypher)


title: CIC02-Tagtociclib 200nM R3

description: Library name: RNA-C12


title: CIC02-Tagtociclib 200nM R1

description: Library name: RNA-C10


title: Healthy Control 18_L1_1

description:
Library name: HC18-2B2_S7_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells


title: TBM, blood,  MPH027, D7

description: Library name: DAV1202A20

value: female

value: soc

value: no

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


city: New Haven

first: Bao

last: Wang

state: Connecticut

address: 333 Cedar Street

department: Deparment of Laboratory Medicine

institute: Yale University

description:
Library name: all-wells
the dataset is multiplexed with 8 samples: MOCKDAY1, MOCKDAY2, MOCKDAY5, RV1ADAY1, RV1ADAY2, RV1ADAY5, RV+BX795DAY1, RV+BX795DAY2, specified in cell_metadata.csv column "sample"

data_processing:
Transcripts were mapped to both human genome and HRV-1A (KC894166.1). Alignment, demultiplexing, barcoding, gene counting  and aggregation were done via Parse Biosciences developed split-pipe v0.9.6p (currently Trailmaker(TM))
Analysis of multiplexed cell feature matrix was implemented using Seurat v4 in R version 4.3.
Assembly: GRCh38 (human), KC894166.1 (HRV-1A)
Supplementary files format and content: Comma delimited file of cell barcode: cell_metadata.csv, comma delited file of gene list: all_genes.csv, matrix file of cell x feature matrix: DGE.mtx
Supplementary files format and content: Cluster annotated R analysis object SeuratObject.rds

source_name: air-liquid interface organoid culture

growth_protocol: Primary nasal human airway epithelial cells from healthy adult donors were obtained from PromoCell. Cells were first expanded in ExPlus media (Stemcell Technologies) and then seeded in 0.4 µm pore 6.5 mm trans-well inserts (Costar, Corning). After air-lift, cells were maintained in PneumaCult ALI basal media (Stemcell Technologies) according to the manufacturer’s instructions, with 1:5 reduced hydrocortisone. Cells were cultured at air-liquid interface for 4 weeks for differentiation before they displayed beating cilia and mucus production.

extract_protocol:
To obtain single cells, 3 to 4 rounds of gentle trypsin (TrypLE, Gibco) treatment were performed disassociate ALI culture. Cells were passed though 70µ strainers and fixed according to Parse Biosciences protocol. Counting and viability check using trypan blue were performed before fixation and samples with >80% viability were selected to proceed to library preparation.
Parse Biosciences SPLiT-Seq Whole Transcriptomics v1, polyA-selection (currently Evercode(TM)).
8 samples are included in this library: MOCKDAY1, MOCKDAY2, MOCKDAY5, RV1ADAY1, RV1ADAY2, RV1ADAY5, RV+BX795DAY1, RV+BX795DAY2. According to split-seq protocol, 8 samples are pooled into 1 library for sequencing. The full library was sequenced as 8 sub-libraries (not corresponding to 8 samples, each sub-library will contain multiplexed data from all samples).

treatment_protocol: Cells were pretreated with media containing 6uM BX795 (Cayman Chemical). To infect, cells were washed from the apical surface 3 times by pipitting 200uL warm PBS. Inoculum with MOI = 0.25 (assuming 1 million cells each culture well) was then applied apically in 200uL PBS with 0.1% Bovine Serum Albumin and infect for 40min to 1h. Cells were washed again with warm PBS after infection to remove residual virus. The infected cells were then incubated at 35°C. 200uL additional media was added to the basolateral chamber on day 3 post infection, with or without the corresponding BX795 treatment. Samples were collected at day 1, 2 and 5 post infection.

tag: tissue

value: air-liquid interface organoid culture

tag: cell line

value: primary human nasal epithelial cells

value: Female

tag: treatment

value: control, BX795 6uM

tag: infection

value: mock, RV1A MOI=0.25

tag: batch


title: Brg1-AID_CnR_MyoD-ER_4OHT_0h_K4me1

description: Library name: Sample 3

value: Brg1AID/AID preadipocytes

tag: chip antibody

value: Anti-H3K4me1 (13-0040, Epicypher)


title: TBM, blood,  MPH038, D0

description: Library name: DAV1202A19

value: Blood

tag: patient id

tag: study

value: laser

tag: Sex

value: male

tag: antibiotics

value: intensified

value: definite

value: positive

value: negative


title: Brg1-AID_CnR_MyoD-ER_4OHT_0h_T7

description: Library name: Sample 4

value: Preadipocyte


title: TBM, blood,  MPH001, D14

description: Library name: DAV1202A17

tag: timepoint

tag: age

value: soc

tag: aspirin

tag: diagnosis


title: HNEC ALI mock rep 2

description:
Library name: BW02
raw counts in BW02_HTSeq_counts.txt

data_processing:
Fasta files passed quality control by FastQC and were trimmed by Trim Galore.
Alignment was done using HISAT2 on GRCh38.09 genome. For viral reads, alignment was done using BowTie2 to HRV-1A genome (KC894166.1).
Transcript counting was performed using HTSeq-count.
Analysis on gene expression level was performed in R with DESeq2. Normalized count matrix is generated with DESeq2.
Assembly: GRCh38.09, KC894166.1
Supplementary files format and content: Comma delimited file includes normalized counts for all sample. Tab delimited file includes viral read counts for all sample.
Supplementary files format and content: "HTSeq_counts" txt files contains raw counts for each sample.

extract_protocol:
Total RNA was extracted using the Aurum Total RNA Mini Kit (Bio- Rad) according to the manufacturer’s protocol.
poly-A selection

treatment_protocol: Cells were pretreated with media containing 6uM BX795 (Cayman Chemical), 25uM TPCA-1 or plain media 1 day before infection. To infect, cells were washed from the apical surface 3 times by pipitting 200uL warm PBS. Inoculum with MOI = 0.25 (assuming 1 million cells each culture well) was then applied apically in 200uL PBS with 0.1% Bovine Serum Albumin and infect for 40min to 1h. Cells were washed again with warm PBS after infection to remove residual virus. The infected cells were then incubated at 35°C. 200uL additional media was added to the basolateral chamber on day 3 post infection, with or without the corresponding drug treatment. Samples were collected 5 days post infection.

tag: cell type

value: 34 years old

value: female

value: mock


title: CIC02-DMSO R1

description: Library name: RNA-C7

value: sarcoma

value: DMSO


title: TBM, blood,  GSH004, D14

description: Library name: DAV1202A24

value: no

value: possible

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: HNEC ALI mock rep 1

description:
Library name: BW01
raw counts in BW01_HTSeq_counts.txt

tag: tissue

value: air-liquid interface organoid culture

value: primary human nasal epithelial cells


title: CIC02-DMSO R2

description: Library name: RNA-C8

tag: cell line

tag: treatment


title: TBM, blood,  MPH023, D0

description: Library name: DAV1202A18

value: Blood

value: laser

tag: blood neutrophils


title: Healthy Control 1_L1

description:
Library name: HC01_S39_L001
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

value: CD45+ Cells

tag: genotype

value: XX

value: Healthy Control


title: Brg1-AID_CnR_MyoD-ER_4OHT_0h_K27ac

description: Library name: Sample 2

value: Brg1AID/AID preadipocytes

value: Preadipocyte

tag: chip antibody

value: Anti-H3K27ac (ab4729, Abcam)


title: TBM, blood,  MPH001, D0

description: Library name: DAV1202A14

tag: patient id

tag: study

tag: Sex

value: male

value: soc

value: definite

value: positive

value: negative


title: Brg1-AID_CnR_MyoD-ER_4OHT_0h_IgG

description: Library name: Sample 1

value: Anti-IgG (13-0042K, Epicypher)


title: CIC01-Tagtociclib 200nM R3

description: Library name: RNA-C6

value: sarcoma

value: Tagtociclib 200nM


title: CIC01-Tagtociclib 200nM R2

description: Library name: RNA-C5


title: TBM, blood,  MPH002, D56

description: Library name: DAV1202A21

value: Blood

tag: timepoint

tag: age

value: female

tag: antibiotics

value: intensified

value: no

value: possible


title: Healthy Control 1_L2

description:
Library name: HC01_S39_L002
10x Genomics, GEX 5' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: Endometrium

tag: cell type

value: CD45+ Cells

value: XX

value: Healthy Control


title: PNH9_Linpositive_Wild-type_GEM

first: Shouguo

last: Gao

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the hg38 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
Assembly: hg38
Supplementary files format and content: Lineposicount.Rdata: read count matrix for BM
Supplementary files format and content: Lineposimeta.csv: cellannotationLineposicount
Supplementary files format and content: CD34count.Rdata: read count matrix for BM
Supplementary files format and content: CD34meta.csv: cellannotationCD34count

source_name: Human bone marrow

extract_protocol: Libraries of gene expression (Lineage+ mature cells and Lineage-CD34+HSPCs) for patients and healthy donors were generated using Genomics Chromium Single Cell 3' Solution Kit from 10XGenomics v3.1.

tag: subject

tag: disease state

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

value: FACS sorted Linjeage+ bone marrow

value: Female

tag: response at_primary_end_point


title: CIC01-Tagtociclib 200nM R1

description: Library name: RNA-C4


title: TBM, blood,  GSH005, D0

description: Library name: DAV1202A13

value: laser

value: male

tag: aspirin

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Y6 evolved isolate, 7-day-old colony, replicate B2

type: RNA

city: Paris

first: Claude

last: Saint-Ruf

address: 24 rue du faubourg Saint-Jacques

department: Institut Cochin

country: France

institute: Université paris Cité

description: Evolved isolate Y6 was originally isolated from a 3-week-old aging colony. For transcriptomic profiling, Y6 was regrown and RNA was extracted from a 7-day-old colony on LB agar

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) on NimbleGen E. coli K-12 MG1655 whole-genome ORF arrays (platform GPL9088), using standard NimbleGen gene-expression microarray protocols (v6.0). Hybridization, washing, and drying were carried out with the NimbleGen Hybridization System, including alignment oligos and Sample Tracking Controls.

scan_protocol: Arrays were scanned by Roche NimbleGen using the NimbleGen MS200 Microarray Scanner under one-color Cy3 settings. Image acquisition, grid alignment, feature extraction, and quality control were performed using standard NimbleGen procedures.

data_processing:
Raw intensity files (.pair files) were generated using NimbleGen DEVA software. Processed data were obtained using the Robust Multichip Average (RMA) algorithm, including background correction and quantile normalization. Normalized non-log₂ intensity values were used for all downstream analyses.
Processed data correspond to background-corrected, quantile-normalized RMA intensity values. For each sample, the reported value for every probe represents the arithmetic mean of five technical probe replicates present on the NimbleGen array.

organism: Escherichia coli

source_name: Escherichia coli colony (Y6)

label_protocol: Complementary DNA (cDNA) was synthesized from total RNA using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) and random hexamers. Cy3 labeling of cDNA was performed by Roche NimbleGen using their One-Color DNA Labeling Kit and standard manufacturer protocols.

growth_protocol: Escherichia coli strains were grown in Luria–Bertani (LB) broth or on LB agar at 37 °C with aeration. For colony growth, approximately 200 cells from overnight LB cultures were spotted onto sterile 0.22 µm polycarbonate membrane filters placed on fresh LB agar plates (15 g/L agar). Plates were incubated at 37 °C under controlled humidity (aluminium foil wrapping). After 7 days of growth, colonies were recovered by resuspending the filters in PBS.

extract_protocol: Total RNA was extracted from 7-day-old colonies using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion, following the manufacturer’s instructions. RNA concentration, purity, and integrity were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was applied. Samples correspond to spontaneous physiological states of 7-day-old colonies of the parental strain (pygYFP) and evolved isolates Y5 and Y6

tag: strain

tag: origin

value: isolated from 3-week-old aging colony

tag: genotype

value: evolved isolate

tag: colony age for transcriptome

value: 7 days

tag: bacterial cell


title: PNH9_CD34positive_Wild-type_GEM

description: 10x Genomics

tag: tissue

value: FACS sorted Linjeage-CD34+ bone marrow

tag: Sex

tag: age


title: TBM, blood,  MPH002, D7

description: Library name: DAV1202A12

value: Blood

tag: patient id

tag: study

tag: timepoint

value: female

tag: antibiotics

value: intensified

value: no

value: possible

tag: blood neutrophils


title: TBM, blood,  NSH010, D0

description: Library name: DAV1202A11

value: soc

tag: aspirin

tag: diagnosis

value: definite

tag: gxpu

value: positive


title: PNH9_CD34positive_PNH-type_GEM

description: 10x Genomics

tag: subject

tag: disease state

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

tag: cell type

value: Female

tag: response at_primary_end_point


title: CIC01-DMSO R2

description: Library name: RNA-C2

tag: cell line

value: sarcoma

tag: treatment

value: DMSO


title: Y5 evolved isolate, 7-day-old colony, replicate B2

description: Evolved isolate Y5 was originally isolated from a 3-week-old aging colony. For transcriptomic profiling, Y5 was regrown and RNA was extracted from a 7-day-old colony on LB agar

source_name: Escherichia coli colony (Y5)

tag: strain

tag: origin

value: isolated from 3-week-old aging colony

tag: genotype

tag: colony age for transcriptome

tag: bacterial cell


title: CIC01-DMSO R1

description: Library name: RNA-C1


title: TBM, blood,  NSH009, D56

description: Library name: DAV1202A10

tag: tissue

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: male

value: yes

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Y6 evolved isolate, 7-day-old colony, replicate B1

data_processing:
Processed data correspond to background-corrected, quantile-normalized signal intensities generated using the Robust Multichip Average (RMA) algorithm. Only processed values are available for this series.
Processed data correspond to background-corrected, quantile-normalized RMA intensity values. For each sample, the reported value for every probe represents the arithmetic mean of five technical probe replicates present on the NimbleGen array.

source_name: Escherichia coli Y6 colony

value: evolved isolate

value: 7 days

tag: cell type

value: bacterial cell


title: TBM, blood,  LH007, D56

description: Library name: DAV1202A8

value: Blood

tag: antibiotics

value: intensified

tag: aspirin

value: no

tag: diagnosis

tag: gxpu

tag: blood neutrophils


title: pygYFP strain, 7-day-old colony, replicate B2

description: RNA extracted from a 7-day-old colony of the parental pygYFP strain grown on LB agar

source_name: Escherichia coli colony (pygYFP)

tag: strain

value: pygYFP

tag: origin

value: ancestral control

tag: colony age for transcriptome


title: CIC01-DMSO R3

description: Library name: RNA-C3

tag: cell line

tag: treatment


title: LC25_FB_ZT24

city: Chicago

first: Marta

last: Iwanaszko

state: IL

address: 303 E. Superior Street, Simpson Querrey 7th Floor,

department: Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Diet Restriction 25C replicate 1 ZT24

data_processing:
Transcripts were quantified using kallisto ver.0.44.0
Quantified transcripts were summed to gene level using tximport (R library)
Quality control assessment was performed using FastQC
Genome_build: FlyBase_r6.14
Supplementary_files_format_and_content: Comma-delimited text file including TPMs for all samples
Supplementary_files_format_and_content: Comma-delimited text file including estimated counts for all samples

source_name: Abdominal Fat Body (including oenocytes and epidermis)

growth_protocol: All the flies used for experiments were raised on a standard yeast-cornmeal-molasses based diet under a light-dark (LD) 12:12h cycle

extract_protocol:
At every 2 hours, flies were directly dissected without dry ice to harvest fat tissues in the abdomen. Pinned flies were cut to remove organs in the abdomen (intestine, ovaries, malpighian tubules, etc). Fat tissues attached to epidermis was collected. Fat body from ~ 10 flies were harvested within 10 minutes for each time point of RNA-Seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Young mated female flies (~ 3 day old) were entrained under either DR diet (5SY) or control diet (15SY) for 5 days in 12L:12D cycles at 25°C.

tag: tissue

value: w1118 (iso31 / Bloomington stock #5905)

value: female

tag: mating status

value: mated

value: young flies (~8 d old)

tag: temperature

tag: diet condition

value: Diet Restriction

tag: zt

tag: replicate


title: PNH8_CD34positive_Wild-type_GEM

description: 10x Genomics

tag: subject

tag: disease state

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

tag: cell type

value: FACS sorted Linjeage-CD34+ bone marrow

tag: Sex

value: Female

tag: age

tag: response at_primary_end_point


title: PNH8_Linpositive_PNH-type_GEM

description: 10x Genomics

value: FACS sorted Linjeage+ bone marrow


title: FVFB

description:
Library name: FVFB
Amplicon sequencing of T0 primary library Replicate 2 to verify sgRNA representation
FVF_lib_counts.csv

source_name: plasmid library

value: plasmid library


title: TBM, blood,  MPH037, D0

description: Library name: DAV1202A7

tag: patient id

tag: study

value: laser

tag: timepoint

value: male

tag: antibiotics

tag: aspirin

value: yes

tag: diagnosis

value: definite

tag: gxpu

value: positive

tag: mtb culture

value: negative

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: TBM, blood,  NSH009, D7

description: Library name: DAV1202A9

tag: tissue

value: Blood

value: intensified

value: possible


title: TBM, blood,  NSH003, D7

description: Library name: DAV1202A5

value: female


title: KPC_K17_R3

first: Luisa

last: Escobar-Hoyos

state: CT

address: 15 York Street PO box 208040

department: Therapeutic Radiology

description: Library name: Sample 6

data_processing:
Sequence information was extracted in fastq format using bcl2fastq software 1.8.4
Reads were mapped using STAR (2.7.3a)
Reads per gene were counted using kallisto 0.46.2
Assembly: GRCh38.96, GRCm38.96
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: KPC

growth_protocol: Cells were cultured at 37°C with 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM, Gibco, #11995073), supplemented with 10% fetal bovine serum (FBS, Corning, #35010CV) and 1% penicillin and streptomycin (Gibco, #15140122). Cells were routinely screened for Mycoplasma using a PCR-based detection kit (ATCC, #30-1012K) and were used at fewer than 10 passages from thawing.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies, #10296010).
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit following the manufacterer's instructions.

tag: cell line

value: KPC

value: Pancreatic ductal adenocarcinoma

tag: treatment

value: K17 over-expression


title: PNH7_Linpositive_Wild-type_GEM

description: 10x Genomics

tag: subject

tag: disease state

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

tag: cell type

tag: Sex


title: KPC_K17_R2

description: Library name: Sample 5


title: PNH8_CD34positive_PNH-type_GEM

description: 10x Genomics

value: FACS sorted Linjeage-CD34+ bone marrow

value: Female

tag: age

tag: response at_primary_end_point


title: Y5 evolved isolate, 7-day-old colony, replicate B1

source_name: Escherichia coli Y5 colony

tag: strain

tag: origin

value: isolated from 3-week-old aging colony

tag: genotype

value: evolved isolate

tag: colony age for transcriptome

value: 7 days

value: bacterial cell


title: TBM, blood,  NSH003, D0

description: Library name: DAV1202A4

tag: patient id

tag: study

value: laser

tag: timepoint

tag: antibiotics

tag: aspirin

value: yes

tag: diagnosis

tag: gxpu

tag: mtb culture


title: FVFA

description:
Library name: FVFA
Amplicon sequencing of T0 primary library Replicate 1 to verify sgRNA representation
FVF_lib_counts.csv

value: plasmid library


title: PNH8_Linpositive_Wild-type_GEM

description: 10x Genomics

tag: subject

tag: disease state

tag: tissue

value: FACS sorted Linjeage+ bone marrow


title: LC25_FB_ZT20

description: Diet Restriction 25C replicate 1 ZT20

value: Abdominal Fat Body (including oenocytes and epidermis)

value: w1118 (iso31 / Bloomington stock #5905)

tag: Sex

tag: mating status

value: mated

tag: age

value: young flies (~8 d old)

tag: temperature

tag: diet condition

value: Diet Restriction

tag: zt

tag: replicate


title: KPC_K17_R1

description: Library name: Sample 4

tag: cell line

value: KPC

tag: cell type

value: Pancreatic ductal adenocarcinoma

tag: treatment

value: K17 over-expression


title: LC25_FB_ZT22

description: Diet Restriction 25C replicate 1 ZT22

tag: strain

value: female


title: KPC_EV_R3

description: Library name: Sample 3

value: Empty vector


title: PNH7_Linpositive_PNH-type_GEM

description: 10x Genomics

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

value: Female

tag: response at_primary_end_point


title: pygYFP strain, 7-day-old colony, replicate B1

source_name: Escherichia coli pygYFP colony

value: pygYFP

tag: origin

value: ancestral control

tag: colony age for transcriptome

value: 7 days

value: bacterial cell


title: TBM, blood,  MPH032, D0

description: Library name: DAV1202A2

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

value: male

tag: antibiotics

value: soc

tag: aspirin

value: no

tag: diagnosis

value: definite

tag: gxpu

value: positive

tag: mtb culture

value: negative

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: LC25_FB_ZT16

description: Diet Restriction 25C replicate 1 ZT16

tag: tissue

value: Abdominal Fat Body (including oenocytes and epidermis)

value: w1118 (iso31 / Bloomington stock #5905)

tag: Sex

value: female

tag: mating status

value: mated

tag: age

value: young flies (~8 d old)

tag: temperature

tag: diet condition

value: Diet Restriction

tag: zt

tag: replicate


title: LC25_FB_ZT18

description: Diet Restriction 25C replicate 1 ZT18

tag: strain


title: KPC_EV_R2

description: Library name: Sample 2

tag: cell line

value: KPC

tag: cell type

value: Pancreatic ductal adenocarcinoma

tag: treatment

value: Empty vector


title: LC25_FB_ZT14

description: Diet Restriction 25C replicate 1 ZT14


title: PNH7_CD34positive_Wild-type_GEM

description: 10x Genomics

tag: subject

tag: disease state

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

value: FACS sorted Linjeage-CD34+ bone marrow

value: Female

tag: response at_primary_end_point


title: PNH6-2_Linpositive_Wild-type_GEM

description: 10x Genomics

value: FACS sorted Linjeage+ bone marrow


title: M4

city: 吉林省长春市

first: Wang

last: Xu

address: 吉林省长春市净月开发区博硕路

department: college of traditional chinese medicine

country: China

institute: Changchun University of Chinese Medicine

description: Library name: M4

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: rn7
Supplementary files format and content: mRNA_Expression_Summary.xlsx

organism: Rattus norvegicus

source_name: Rat brain

extract_protocol:
The concentration of RNA samples was ≥ 100 ng/μL, the total amount was > 2 μg, the OD value was between 1.8~2.2, the OD was ≥ 2.0, and Agilent 2100 was required The Bioanalyzer assays RIN ≥ 6.5 to ensure the construction of downstream high-quality mRNA-seq libraries
Library concentration and fragment length distributions were measured using Qubit and Agilent 2100 Bioanalyzers, respectively. The concentration is required to be >5ng/μl and the fragment length is concentrated Between 300-400 bp

value: Rat brain

value: the model group (M group)


title: KPC_EV_R1

description: Library name: Sample 1


title: PNH7_CD34positive_PNH-type_GEM

description: 10x Genomics


title: HUVEC, 5% strain, replicate 6

first: Jessica

last: Shah

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description:
Library name: L6
Singular G4

data_processing:
Raw FASTQ files were processed using the nf-core/rnaseq pipeline (v3.17.0).
Reads were aligned to the human reference genome (GRCh38, GENCODE v47 annotation) using Salmon for transcript quantification. Transcript-level abundances were summarized to the gene level.
Differential expression analysis was performed in DESeq2 (v1.42.1) with log₂ fold-change shrinkage via the apeglm method. P values were adjusted for multiple testing using the Benjamini–Hochberg procedure.
Assembly: GRCh38 (GENCODE v47)
Supplementary files format and content: Gene-level raw counts and transcript per million (TPM) data generated by Salmon, tab-separated format

source_name: umbilical vein endothelium

growth_protocol: ImHUVECs expressing blue fluorescent protein (BFP, passages 12–20) were cultured in VascuLife VEGF-Mv Endothelial medium (Lifeline Cell Technology), with medium changes every 2 days. Cells were detached with TrypLE Express (Gibco) upon reaching ~80% confluency and seeded into a hollow cylindrical channel of a microfluidic device to form a 3D engineered vessel.

extract_protocol:
Endothelial cells were isolated from the collagen gel via liberase treatment. RNA was extracted from the cells using the Qiagen RNeasy Mini Kit. RNA quantity and integrity were assessed using Agilent Bioanalyzer prior to library preparation.
RNA-seq libraries were prepared using the Takara SMARTer Stranded Total RNA-Seq Kit v3 (Low Input, ZapR-based rRNA depletion; Takara Bio) following the manufacturer’s instructions. Library quality was assessed by Bioanalyzer prior to sequencing.

treatment_protocol: Cells were subjected to cyclic mechanical strain at 5% (low strain) or 15% (high strain) for 1 hour each day from days 3 to 7 using the Magnetic Matrix Actuation (MagMA) platform. Control cells were cultured under static conditions without strain.

value: umbilical vein endothelium

value: HUVEC

value: endothelial cell


title: HUVEC, 5% strain, replicate 5

description:
Library name: L5
Singular G4


title: PNH6-2_Linpositive_PNH-type_GEM

description: 10x Genomics


title: M1

address: 吉林省长春市净月开发区博硕路

description: Library name: M1


title: PNH6-2_CD34positive_Wild-type_GEM

description: 10x Genomics


title: LC25_FB_ZT08

description: Diet Restriction 25C replicate 1 ZT08

value: Abdominal Fat Body (including oenocytes and epidermis)

value: w1118 (iso31 / Bloomington stock #5905)

value: female


title: HUVEC, 5% strain, replicate 4

description:
Library name: L4
Singular G4


title: PNH6-2_CD34positive_PNH-type_GEM

description: 10x Genomics


title: LC25_FB_ZT06

description: Diet Restriction 25C replicate 1 ZT06

value: mated

value: young flies (~8 d old)

value: Diet Restriction


title: C5

address: 吉林省长春市净月开发区博硕路

description: Library name: C5

value: sham operation group (C group)


title: LC25_FB_ZT12

description: Diet Restriction 25C replicate 1 ZT12


title: LC25_FB_ZT10

description: Diet Restriction 25C replicate 1 ZT10


title: HUVEC, 5% strain, replicate 3

description:
Library name: L3
Singular G4


title: TBM, blood,  NSH002, D56

description: Library name: DAV1202A3

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: antibiotics

value: intensified

tag: aspirin

value: yes

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: TBM, blood,  GSH002, D0

description: Library name: DAV1202A1

tag: tissue

tag: age

tag: Sex

value: male

value: soc

value: no

value: possible

tag: blood neutrophils


title: PNH6-1_Linpositive_Wild-type_GEM

description: 10x Genomics

tag: subject

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

tag: cell type

value: FACS sorted Linjeage+ bone marrow

value: Female


title: PNH9_Linpositive_PNH-type_GEM

description: 10x Genomics

tag: disease state

tag: response at_primary_end_point


title: C3

address: 吉林省长春市净月开发区博硕路

description: Library name: C3

value: Rat brain

tag: treatment


title: LC25_FB_ZT04

description: Diet Restriction 25C replicate 1 ZT04

value: Abdominal Fat Body (including oenocytes and epidermis)

tag: strain

value: w1118 (iso31 / Bloomington stock #5905)

value: female

tag: mating status

value: mated

value: young flies (~8 d old)

tag: temperature

tag: diet condition

value: Diet Restriction

tag: zt

tag: replicate


title: LC25_FB_ZT02

description: Diet Restriction 25C replicate 1 ZT02


title: C1

address: 吉林省长春市净月开发区博硕路

description: Library name: C1

value: sham operation group (C group)


title: HUVEC, 5% strain, replicate 2

description:
Library name: L2
Singular G4

value: umbilical vein endothelium

tag: cell line

value: HUVEC

value: endothelial cell


title: M3

address: 吉林省长春市净月开发区博硕路

description: Library name: M3

value: the model group (M group)


title: HUVEC, 5% strain, replicate 1

description:
Library name: L1
Singular G4


title: PNH6-1_Linpositive_PNH-type_GEM

description: 10x Genomics


title: HUVEC, 15% strain, replicate 6

description:
Library name: H6
Singular G4


title: LC25_FB_2_ZT24

description: Diet Restriction 25C replicate 2 ZT24


title: PNH6-1_CD34positive_PNH-type_GEM

description: 10x Genomics

value: FACS sorted Linjeage-CD34+ bone marrow


title: LC25_FB_2_ZT20

description: Diet Restriction 25C replicate 2 ZT20


title: T2

address: 吉林省长春市净月开发区博硕路

description: Library name: T2

value: the medium dose group (45 mg/kg, T group)


title: HUVEC, 15% strain, replicate 5

description:
Library name: H5
Singular G4


title: T3

address: 吉林省长春市净月开发区博硕路

description: Library name: T3


title: PNH6-1_CD34positive_Wild-type_GEM

description: 10x Genomics

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow


title: HUVEC, 15% strain, replicate 3

description:
Library name: H3
Singular G4


title: T1

address: 吉林省长春市净月开发区博硕路

description: Library name: T1


title: LC25_FB_2_ZT16

description: Diet Restriction 25C replicate 2 ZT16


title: LC25_FB_2_ZT22

description: Diet Restriction 25C replicate 2 ZT22


title: PNH5_CD34positive_PNH-type_GEM

description: 10x Genomics

value: Female


title: HUVEC, 15% strain, replicate 4

description:
Library name: H4
Singular G4


title: Primary microglia, LPS, 4 h, replicate 3

city: Nantong

first: Xia

last: Li

state: Jiangsu

address: No. 9 Seyuan Road

institute: Nantong University

description:
Library name: LPS3
Column name in all_sample_raw_count.tsv: LPS3

data_processing:
Raw reads were firstly processed using fastp (v0.22.0) and the low  quality reads were removed to obtain the clean reads. The clean reads were mapped to the  reference genome Rnor_6.0.99 using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by featureCounts.
Assembly: Rnor_6.0.99
Supplementary files format and content: Processed counts of all samples are provided in the file all_sample_raw_count.tsv

source_name: brain

growth_protocol: DMEM/F12 complete medium

extract_protocol:
Total RNA was extracted from primary microglia, and its integrity was determined using agarose gel electrophoresis. The concentration of RNA was accurately determined with a NanoDrop spectrophotometer.
Magnetic beads coated with oligo-dT were employed to isolate mRNA from total RNA. The captured mRNA was fragmented, and the first and second strands of cDNA were then synthesized using reverse transcriptase. The cDNA fragments were processed using an end-repair reaction after the addition of a single “A” base, followed by adapter ligation. These ligation products were purified and then amplified by PCR to generate the final cDNA library, which was further purified with magnetic beads. After library preparation was complete, the concentration was detected with a Qubit instrument, and the length of the library fragments was detected with an Agilent fragment analyzer to ensure quality.

treatment_protocol: The primary cultured microglia were randominzed into three groups: 1) control: only the vehicle were added in the culture medium; 2) LPS: 100 ng/mL LPS was added in the culture medium for 4 hours. 3) LPS+Ar:  Argon mixed gas (74% Ar + 21% O₂ + 5% CO₂) was administered immediately after 100 ng/mL LPS was added to the culture medium, and the exposure was sustained for 3 h. Cells were collected for RNA isolation 4 hours after LPS administration.

value: brain

value: primary cultured microglia

tag: genotype

value: wildtype festus rat

value: 100 ng/mL LPS treated for 4 hours


title: Primary microglia, LPS+Argon treatment, 4 h, replicate 2

description:
Library name: ArLPS2
Column name in all_sample_raw_count.tsv: ArLPS2

tag: tissue

value: Argon mixed gas (74% Ar + 21% O₂ + 5% CO₂) was administered immediately after 100 ng/mL LPS was added to the culture medium, and the exposure was sustained for 3 h.


title: LC25_FB_2_ZT14

description: Diet Restriction 25C replicate 2 ZT14

value: Abdominal Fat Body (including oenocytes and epidermis)

value: w1118 (iso31 / Bloomington stock #5905)

value: female

value: mated

tag: age

value: young flies (~8 d old)


title: PNH5_CD34positive_Wild-type_GEM

description: 10x Genomics

tag: Sex


title: Primary microglia, LPS+Argon treatment, 4 h, replicate 1

description:
Library name: ArLPS1
Column name in all_sample_raw_count.tsv: ArLPS1


title: LC25_FB_2_ZT18

description: Diet Restriction 25C replicate 2 ZT18

value: Diet Restriction


title: PNH5_Linpositive_Wild-type_GEM

description: 10x Genomics

value: FACS sorted Linjeage+ bone marrow


title: PNH5_Linpositive_PNH-type_GEM

description: 10x Genomics


title: HUVEC, control, replicate 3

description:
Library name: C3
Singular G4

value: umbilical vein endothelium

value: HUVEC

value: endothelial cell


title: LC25_FB_2_ZT12

description: Diet Restriction 25C replicate 2 ZT12


title: Primary microglia, LPS, 4 h, replicate 2

description:
Library name: LPS2
Column name in all_sample_raw_count.tsv: LPS2


title: HUVEC, 15% strain, replicate 2

description:
Library name: H2
Singular G4


title: Primary microglia, LPS+Argon treatment, 4 h, replicate 3

description:
Library name: ArLPS3
Column name in all_sample_raw_count.tsv: ArLPS3


title: LC25_FB_2_ZT10

description: Diet Restriction 25C replicate 2 ZT10


title: PNH4_CD34positive_Wild-type_GEM

description: 10x Genomics

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: Human bone marrow

value: FACS sorted Linjeage-CD34+ bone marrow


title: PNH4_Linpositive_PNH-type_GEM

description: 10x Genomics

value: Female


title: PNH4_Linpositive_Wild-type_GEM

description: 10x Genomics


title: HUVEC, 15% strain, replicate 1

description:
Library name: H1
Singular G4


title: HUVEC, control, replicate 2

description:
Library name: C2
Singular G4


title: LC25_FB_2_ZT08

description: Diet Restriction 25C replicate 2 ZT08


title: HUVEC, control, replicate 1

description:
Library name: C1
Singular G4


title: Primary microglia, LPS, 4 h, replicate 1

description:
Library name: LPS1
Column name in all_sample_raw_count.tsv: LPS1

value: brain

value: primary cultured microglia

value: wildtype festus rat


title: LC25_FB_2_ZT06

description: Diet Restriction 25C replicate 2 ZT06

value: Abdominal Fat Body (including oenocytes and epidermis)


title: Primary microglia, vehicle, 4 h, replicate 3

description:
Library name: Con3
Column name in all_sample_raw_count.tsv: Con3

value: vehicle