title: Input, hMSC-TERT4-iCas9-4 E+102 KO clone 3 adipocyte diff d1

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

description: Library name: H89

data_processing:
For ChIP-seq, the quality of sequenced reads was estimated using FastQC. Sequencing reads were mapped to the human genome (hg19) using STAR (v. 2.5.3). Duplicated reads/fragments were removed using Picard (v2.5.0) from aligned reads.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: hMSC-TERT4-iCas9-4 E+102 KO

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells (hMSC-TERT4) and hMSC-TERT4 with inducible Cas9 expression (hMSC-TERT4-iCas9) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
Chromatin was prepared as described previously (Rauch A, et al. 2019. Nature Genetics 51(4):716-727). Briefly, only for MED1 ChIP cells were crosslinked in 2 mM disuccinimidyl glutarate (DSG) in PBS (100 µL of 0.5 M DSG (Proteochem) in DMSO per 25 ml of PBS) for 20 minutes. For H3K4me1, CTCF, C/EBPβ, C/EBPα and PPARγ ChIP, this step was omitted. Then, cells were crosslinked in 1% formaldehyde in PBS for 10 minutes followed by quenching with 0.125 M glycine for 10 minutes. Cells were harvested in cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH 8) and stored at -80°C prior to sonication. Samples were sonicated using ME220 Focused-ultrasonicator (Covaris) for 10 min, peak power 75, duty% factor 26.66, cycles/burst 500  using miliTUBE 1 ml AFA Fiber(100) (Covaris)).
ChIP-seq libraries were constructed from 7-20 ng of genomic DNA using NEBNext UltraExpress® DNA Library Prep Kit according to the manufacturer's instructions (New England Biolabs) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

treatment_protocol: Adipogenic differentiation was induced two days post confluence (day 0) by changing the growth medium to the differentiation medium: DMEM with 10% FBS, 1% P/S and 100nM freshly added dexamethasone in 96% ethanol, 0.5 mM 3-isobutyl-1-methylxanthine in 0.1 M KOH, 2 μM human insulin, and 1 μM rosiglitazone in DMSO. Differentiation medium was renewed every second day until cells were harvested.

value: hMSC-TERT4-iCas9-4 E+102 KO

value: human mesenchymal stromal progenitors

tag: differentation status

value: adipocyte

tag: timepoint


title: Input, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d1

status: Public on Feb 05 2026

type: SRA

country: Denmark

description: Library name: H88

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: Input, hMSC-TERT4-iCas9-4 E+2 KO clone 1 adipocyte diff d1

description: Library name: H86

source_name: hMSC-TERT4-iCas9-4 E+2 KO

value: hMSC-TERT4-iCas9-4 E+2 KO


title: Input, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d1

description: Library name: H82

source_name: hMSC-TERT4-iCas9-4 nogRNA

value: hMSC-TERT4-iCas9-4 nogRNA


title: Input, hMSC-TERT4-iCas9-4 nogRNA clone 3 adipocyte diff d1

description: Library name: H83


title: mRNA from uninfected clones from donor 5104

city: New York

first: Alberto

last: Herrera

state: New York

department: Medicine

country: USA

institute: Weill Cornell Medicine

description:
Library name: BJ-Clones-2_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv
Library strategy: CITE-seq

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: Memory CD4+ T-cells (mCD4) were isolated from the PBMCs  of people with HIV (PWH) by negative selection using EasySep™ Human Memory CD4+ T Cell Enrichment Kit (STEMCELL Technologies), plated (10 cells/well, 96-well plates), and stimulated with irradiated allogeneic HIV-negative PBMCs (1x106/mL) in R10-100 with ARVs (RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, 1% HEPES buffer, 1% L-Glutamine supplemented with 100 Units/mL of IL-2, 1 µM Nevirapine, 1 µM Emtricitabine, 1 µM Tenofovir, 10 µM Enfuvirtide, and 10 µg/mL 10-1074 bNAb) with CD3 and CD28 antibodies for 21 days. Feeder PBMCs were depleted of CD8+ T-cells and NK cells using EasySep™ Human CD8 Positive Selection Kit II and EasySep™ Human CD56 Positive Selection Kit II (STEMCELL Technologies) before being co-cultured with mCD4 T-cells from PWH. At the end of stimulation cycle, p24 ELISA was performed on all plates. Cells from p24 ELISA-positive wells were plated in serial 3-fold dilution (96-well plates), stimulated at the same condition as aforementioned, and subjected to p24 ELISA after 21 days. After the second round of plating and ELISA, cells from p24 ELISA-positive wells were expanded under the same stimulation condition. Clonal purity of isolated infected populations was determined using IPDA and further serial dilution subs were performed as needed.

extract_protocol:
Following 2 weeks of rest from stimulation with  CD3 and CD28 antibodies and feeders in R10-100 with ARVs, cells were stained with DNA oligo-barcoded antibodies and loaded onto the 10x Chromium single-cell workflow (10X Genomics) as previously described61 with a few modifications. Approximately 0.05-0.3 x 106 cells per sample were resuspended in R10 media and incubated with the TotalSeq™-C Human Universal Cocktail (Biolegend) for 30 minutes at 4°C. In some cases, TotalSeq™-C hashing antibodies #1, #3 and #4 (Biolegend) were spiked into individual samples, which allowed for multiplexing of ARCs and uninfected clone combinations into the same 10X lane. After staining, cells were washed 3 times in R10 media, followed by centrifugation (400 × g for 5 minutes at 4°C) and supernatant aspiration. After the final wash, cells were resuspended in PBS and filtered through 70-µm cell strainers
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions (CG000330, revision G)

tag: tissue

value: peripheral blood

value: CD4+ T cells


title: Input, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d1

description: Library name: H87


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d1 rep1

description: Library name: H71

tag: chip antibody

value: C/EBPβ (Santa Cruz #sc-7962)


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 3 adipocyte diff d1 rep1

description: Library name: H73


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 1 adipocyte diff d1 rep2

description: Library name: H78


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d1 rep2

description: Library name: H80


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 1 adipocyte diff d1 rep1

description: Library name: H70


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d1 rep2

description: Library name: H79


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d1 rep1

description: Library name: H72


title: Input, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d3 rep2

description: Library name: D362


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 3 adipocyte diff d1 rep2

description: Library name: H81


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d1 rep1

description: Library name: H66


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 3 adipocyte diff d1 rep1

description: Library name: H67


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 3 adipocyte diff d1 rep2

description: Library name: H75


title: Input, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d3 rep1

description: Library name: D358


title: Input, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d3 rep2

description: Library name: D361


title: CEBPbeta ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d1 rep2

description: Library name: H74


title: Input, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d3 rep1

description: Library name: D357


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d3 rep2

description: Library name: D346

value: MED1 (Bethyl Laboratories #A300-793A)


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d3 rep1

description: Library name: D342


title: Input, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d3 rep2

description: Library name: D359


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d3 rep1

description: Library name: D341


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+2 KO clone 3 adipocyte diff d3 rep2

description: Library name: D345


title: MED1 ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d3 rep1

description: Library name: D339


title: MED1 ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d3 rep2

description: Library name: D343


title: Input, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d10

description: Library name: I328


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d10 rep1

description: Library name: I325


title: Input, hMSC-TERT4 adipocyte diff d10 rep2

description: Library name: 9326


title: MED1 ChIP, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d10 rep2

description: Library name: I327


title: Input, hMSC-TERT4 adipocyte diff d10 rep1

description: Library name: 9321


title: Input, hMSC-TERT4 adipocyte diff d7 rep2

description: Library name: 9325


title: MED1 ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d10 rep1

description: Library name: I324


title: Input, hMSC-TERT4-iCas9-4 E+102 KO clone 1 adipocyte diff d10

description: Library name: I329


title: Input, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d3 rep1

description: Library name: D355


title: Input, hMSC-TERT4 adipocyte diff d1 rep2

description: Library name: 9323


title: Input, hMSC-TERT4 adipocyte diff d3 rep2

description: Library name: 9324


title: CEBPalpha ChIP, hMSC-TERT4 adipocyte d10 rep2

description: Library name: E877

value: C/EBPα (Cell Signaling #8178S)


title: Input, hMSC-TERT4 adipocyte diff d1 rep1

description: Library name: 9318


title: Input, hMSC-TERT4 adipocyte diff d3 rep1

description: Library name: 9319


title: Input, hMSC-TERT4 undifferentiated rep1

description: Library name: 9317

value: undifferentiated


title: CEBPalpha ChIP, hMSC-TERT4 adipocyte d10 rep1

description: Library name: C071


title: CEBPalpha ChIP, hMSC-TERT4 undifferentiated rep2

description: Library name: E876


title: CEBPalpha ChIP, hMSC-TERT4 undifferentiated rep1

description: Library name: C070


title: Input, hMSC-TERT4 undifferentiated rep2

description: Library name: 9322


title: Input, hMSC-TERT4 adipocyte diff d7 rep1

description:
Library name: 9220
9320


title: MED1 ChIP, hMSC-TERT4-iCas9-4 nogRNA clone 1 adipocyte diff d10 rep2

description: Library name: I326


title: CEBPbeta ChIP, hMSC-TERT4 adipocyte diff d1 rep1

description: Library name: C992


title: CEBPbeta ChIP, hMSC-TERT4 adipocyte diff d3 rep1

description: Library name: C993


title: CEBPbeta ChIP, hMSC-TERT4 undifferentiated rep1

description: Library name: C991


title: CEBPbeta ChIP, hMSC-TERT4 adipocyte diff d1 rep2

description: Library name: C996


title: CEBPbeta ChIP, hMSC-TERT4 undifferentiated rep2

description: Library name: C995


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d7 rep2

description: Library name: 9305

value: PPARγ (Cell Signaling #2443S)


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d10 rep2

description: Library name: B179


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d3 rep2

description: Library name: 9304


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d1 rep2

description: Library name: I323


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d3 rep1

description: Library name: 9299


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d10 rep1

description: Library name: 9301


title: CEBPbeta ChIP, hMSC-TERT4 adipocyte diff d3 rep2

description: Library name: C997


title: PPARgamma ChIP, hMSC-TERT4 undifferentiated rep1

description: Library name: 9297


title: PPARgamma ChIP, hMSC-TERT4 undifferentiated rep2

description: Library name: 9302


title: CTCF ChIP, hMSC-TERT4 adipocyte diff d10 rep1

description: Library name: 9311

value: CTCF (Active Motif #61311)


title: CTCF ChIP, hMSC-TERT4 adipocyte diff d10 rep2

description: Library name: 9316


title: CTCF ChIP, hMSC-TERT4 adipocyte diff d1 rep1

description: Library name: 9308


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d1 rep1

description: Library name: 9298


title: PPARgamma ChIP, hMSC-TERT4 adipocyte diff d7 rep1

description: Library name: 9300


title: H3K4me1 ChIP, hMSC-TERT4 adipocyte diff d3 rep2

description: Library name: D087

value: H3K4me1 (abcam #ab8895)


title: CTCF ChIP, hMSC-TERT4 undifferentiated rep2

description: Library name: 9312


title: H3K4me1 ChIP, hMSC-TERT4 adipocyte diff d3 rep1

description: Library name: D084


title: CTCF ChIP, hMSC-TERT4 undifferentiated rep1

description: Library name: 9307


title: H3K4me1 ChIP, hMSC-TERT4 undifferentiated rep2

description: Library name: D085


title: Capture-C hMSC-TERT4/iCas9-4 E+125 KO adipocyte d10 rep2

description: Library name: 44_E125_KO_D10_rep2

data_processing:
The raw sequencing reads were mapped to hg19 and quality-filtered using the CCseqBasicS pipeline (v1.0) in a version customized to handle reads produced with the restriction enzymes DraI and DdeI. Resulting unique interaction counts from chromosome 3 were normalized to 50,000 counts per sample and viewpoint. Analysis was restricted to chr3:12.1–12.6 Mb (PPARG locus), excluding ±2 kb from each viewpoint to minimize local signal artifacts. Normalized interaction counts were summarized in 1 kb or 5 kb bins. Expected interaction profiles per viewpoint were modeled via cubic polynomial fits to binned counts, using the geometric mean across intact viewpoints. Statistical significance was assessed using Student’s t-test with Benjamini–Hochberg correction (FDR ≤ 0.01), identifying 208 ROI-wide significant interactions. Differential interactions were called using unadjusted t-tests to retain power given sample size. Element-specific enhancer–enhancer interactions were computed from un-binned counts, averaging interactions from each viewpoint to RFs overlapping a second enhancer and summing bidirectionally. A total of 34 significant enhancer interactions were detected (FDR ≤ 0.01). Control conditions ('No gRNA' and 'PPP gRNA') were grouped based on replicate correlation.
Assembly: hg19
Supplementary files format and content: Capture-C_interaction_counts.txt all significant element-specific enhancer–enhancer interactions detected upon different enhancer deletions at day 0 and 10 of adipogenesis
Library strategy: Capture-C

source_name: hMSC-TERT4/iCas9-4 E+125 KO

growth_protocol: Enhancer and deletion telomerase-immortalized human mesenchymal stromal cells  with inducible Cas9 expression (hMSC-TERT4-iCas9-4) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal bovine serum (FBS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
hMSC-TERT4/iCas9-4 enhancer deletion and control cell lines (one clone for each condition) were harvested at day 0 and 10 of adipogenic differentiation. Capture-C was performed using a customized version of a previously published protocol (Oudelaar M, et al., 2018, Nature Genetics 50, 1744–1751). Briefly, cells were cross-linked for 10 minutes in 2% formaldehyde in PBS,  quenched with 0.125 M glycine, harvested in fresh cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, 1x Complete), incubated 20 minutes on ice and snap-frozen in liquid nitrogen before storage at -80°C.
3C libraries were generated by in-nucleus double digestion with 3x 150 U of each DdeI and DraI restriction enzymes added over approximately 24 hours (final buffer conditions after last addition of enzyme: 1x enzyme buffer, 0.06% sodium dodecyl sulfate, 1.5% Triton X-100). Restriction enzymes were chosen based on the distribution of restriction sites in the genomic region surrounding the PPARG locus, aiming for the regulatory elements of interest located on restriction fragments (RFs) of approximately 120-250 bp. Digestion overhangs were filled in with dNTP and blunt-end ligated. De-crosslinked chromatin was purified. Approximately 5 μg of purified 3C library was sheared to an average size of 450 bp by sonication on an ME220 Focused-ultrasonicator (Covaris) and cleaned up with 0.85:1 AMPure XP beads sample ratio to remove fragments <200 bp. For sequencing library preparation, sheared DNA was end-repaired, adenine-tailed and ligated to NEBNext hairpin adaptors (New England Biolabs), followed by U excision by USER Enzyme. Libraries were amplified using Q5 high-fidelity DNA polymerase (New England Biolabs), universal primer and 8-bp-index primers (New England Biolabs) in 7 cycles of PCR. For capture, 5’ biotinylated 116-120 bp DNA oligos were designed to target the middle of single RFs spanning, or located as close as possible to, the regulatory elements of interest, avoiding repetitive regions. From each sample, 1650 ng of amplified 3C library was used to generate one multiplexed library for capture (biological replicates were kept separate). Per sample in the multiplexed library, 13 fmol in total of pooled biotinylated DNA oligos targeting all 10 regulatory elements of interest was used for capture, i.e. 1.3 fmol of each oligo, and 130 fmol total oligo pool if the multiplexed library consisted of 10 samples. Sequencing adapters and indexes were blocked using a total of 2 nmol custom blockers per sample in the multiplexed library, and two rounds of capture were performed as previously described (Oudelaar M, et al., 2018, Nature Genetics 50, 1744–1751), using 10 cycles of amplification after each capture. According to the manufacturer's instructions, multiplexed and double-captured libraries were subjected to 150 bp paired-end sequencing (Illumina).

value: hMSC-TERT4/iCas9-4 E+125 KO


title: H3K4me1 ChIP, hMSC-TERT4 undifferentiated rep1

description: Library name: D081


title: Capture-C hMSC-TERT4/iCas9-4 E+107 KO adipocyte d10 rep2

description: Library name: 42_E107_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E+107 KO

value: hMSC-TERT4/iCas9-4 E+107 KO


title: Capture-C hMSC-TERT4/iCas9-4 E+111 KO adipocyte d10 rep2

description: Library name: 43_E111_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E+111 KO

value: hMSC-TERT4/iCas9-4 E+111 KO


title: Capture-C hMSC-TERT4/iCas9-4 E+102 KO adipocyte d10 rep2

description: Library name: 41_E102_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E+102 KO

value: hMSC-TERT4/iCas9-4 E+102 KO


title: Capture-C hMSC-TERT4/iCas9-4 E+2 KO adipocyte d10 rep2

description: Library name: 39_E2_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E+2 KO

value: hMSC-TERT4/iCas9-4 E+2 KO

value: human mesenchymal stromal progenitors


title: Capture-C hMSC-TERT4/iCas9-4 E-130 KO adipocyte d10 rep2

description: Library name: 36_E130_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E-130 KO

value: hMSC-TERT4/iCas9-4 E-130 KO

value: adipocyte


title: Capture-C hMSC-TERT4/iCas9-4 E-123 KO adipocyte d10 rep2

description: Library name: 37_E123_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E-123 KO

value: hMSC-TERT4/iCas9-4 E-123 KO


title: CTCF ChIP, hMSC-TERT4 adipocyte diff d1 rep2

description: Library name: 9313


title: Capture-C hMSC-TERT4/iCas9-4 E+89 KO adipocyte d10 rep2

description: Library name: 40_E89_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E+89 KO

value: hMSC-TERT4/iCas9-4 E+89 KO


title: Capture-C hMSC-TERT4/iCas9-4 E+125 KO undifferentiated rep2

description: Library name: 33_E125_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E+111 KO undifferentiated rep2

description: Library name: 32_E111_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E+2 KO undifferentiated rep2

description: Library name: 28_E2_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 nogRNA adipocyte d10 rep2

description: Library name: 34_nogRNA_D10_rep2

source_name: hMSC-TERT4/iCas9-4 nogRNA

value: hMSC-TERT4/iCas9-4 nogRNA


title: Capture-C hMSC-TERT4/iCas9-4 E+89 KO undifferentiated rep2

description: Library name: 29_E89_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E-1 KO adipocyte d10 rep2

description: Library name: 38_E1_KO_D10_rep2

source_name: hMSC-TERT4/iCas9-4 E-1 KO

value: hMSC-TERT4/iCas9-4 E-1 KO


title: Capture-C hMSC-TERT4/iCas9-4 E-123 KO undifferentiated rep2

description: Library name: 26_E123_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E-1 KO undifferentiated rep2

description: Library name: 27_E1_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 PPP1R12C intron KO undifferentiated rep2

description: Library name: 24_PPP_D0_rep2

source_name: hMSC-TERT4/iCas9-4 PPP1R12C intron KO

value: hMSC-TERT4/iCas9-4 PPP1R12C intron KO


title: Capture-C hMSC-TERT4/iCas9-4 E+102 KO undifferentiated rep2

description: Library name: 30_E102_KO_D0_rep2

value: undifferentiated


title: Capture-C hMSC-TERT4/iCas9-4 E+125 KO adipocyte d10 rep1

description: Library name: 22_E125_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 nogRNA undifferentiated rep2

description: Library name: 23_nogRNA_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E+107 KO adipocyte d10 rep1

description: Library name: 20_E107_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+102 KO adipocyte d10 rep1

description: Library name: 19_E102_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+107 KO undifferentiated rep2

description: Library name: 31_E107_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 PPP1R12C intron KO adipocyte d10 rep2

description: Library name: 35_PPP_D10_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E+89 KO adipocyte d10 rep1

description: Library name: 18_E89_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+111 KO adipocyte d10 rep1

description: Library name: 21_E111_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E-130 KO adipocyte d10 rep1

description: Library name: 14_E130_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 nogRNA adipocyte d10 rep1

description: Library name: 12_nogRNA_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 PPP1R12C intron KO adipocyte d10 rep1

description: Library name: 13_PPP_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E-123 KO adipocyte d10 rep1

description: Library name: 15_E123_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E-130 KO undifferentiated rep2

description: Library name: 25_E130_KO_D0_rep2


title: Capture-C hMSC-TERT4/iCas9-4 E+125 KO undifferentiated rep1

description: Library name: 11_E125_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+107 KO undifferentiated rep1

description: Library name: 9_E107_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+111 KO undifferentiated rep1

description: Library name: 10_E111_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+102 KO undifferentiated rep1

description: Library name: 8_E102_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+2 KO undifferentiated rep1

description: Library name: 6_E2_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+89 KO undifferentiated rep1

description: Library name: 7_E89_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E-1 KO adipocyte d10 rep1

description: Library name: 16_E1_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E+2 KO adipocyte d10 rep1

description: Library name: 17_E2_KO_D10_rep1


title: Capture-C hMSC-TERT4/iCas9-4 E-123 KO undifferentiated rep1

description: Library name: 4_E123_KO_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 nogRNA undifferentiated rep1

description: Library name: 1_nogRNA_D0_rep1


title: Capture-C hMSC-TERT4/iCas9-4 PPP1R12C intron KO undifferentiated rep1

description: Library name: 2_PPP_D0_rep1


city: Davos

first: Paola

middle: Andrey

last: Martinez Murillo

address: Herman-Burchard-Str 12

country: Switzerland

institute: CK-CARE

description:
Library name: n36
Co-culture infected Monocytes,replicate5

data_processing:
The pipeline was developed on Linux and includes Conda environment setup with tools like FASTQC, Trimmomatic, STAR, and MultiQC.
It loops through sample directories to process paired-end reads: renaming, compressing, quality control, and trimming.
STAR was used for genome indexing and alignment; MultiQC aggregated results across all tools for summary reporting.
Assembly: hg38
Supplementary files format and content: cvs file for  raw counts
Supplementary files format and content: csv files for normalized counts as Log2CPM

source_name: Monocytes

extract_protocol:
Cells were then harvested by centrifugation at 1500rpm for 5 minutes and resuspended in lysis buffer RLT buffer with β-mercaptoethanol (Qiagen) for RNA extraction. Total RNA was extracted from human monocytes, synoviocytes or co-culture using the Qiagen RNeasy Mini Kit, following the manufacturer's protocol. Cells were lysed, homogenized, and RNA was purified using spin columns.
50ng of total RNA were processed using Illumina Stranded mRNA Prep Ligation kit (Illumina) to prepare cdna dual-indexed libraries according to manufacturer's recommendations

value: Monocytes

tag: treatment

value: rVSVΔG-ZEBOV-GP MOI 1

tag: batch


title: Capture-C hMSC-TERT4/iCas9-4 E-130 KO undifferentiated rep1

description: Library name: 3_E130_KO_D0_rep1


description:
Library name: n35
Co-culture non-infected Monocytes,replicate5

value: Mock stimulated


title: Monocytes non-infect,replicate6

description:
Library name: n26
Monocytes non-infect,replicate6

source_name: Blood

value: Blood


description:
Library name: n37
Co-culture infected Monocytes,replicate6


title: Capture-C hMSC-TERT4/iCas9-4 E-1 KO undifferentiated rep1

description: Library name: 5_E1_KO_D0_rep1


title: Synoviocytes non-infected,replicate5

description:
Library name: n33
Synoviocytes non-infected,replicate5

source_name: human synoviocytes (HS) primary cells

value: human synoviocytes (HS) primary cells


title: CR BH Negative Experiment 2, CR BH Positive Slow

city: Leeds

first: Heiko

last: Wurdak

address: Worsley Building, University of Leeds, Woodhouse

country: United Kingdom

institute: Leeds Institute of Medical Research (LIMR)

description:
Library name: Parsed dataset 2
BCR_A2/B2 Raw FASTQs are pooled for samples "CR_BH_Neg Experiment 1", "CR_BH_Pos_Fast" and "FUCCI_GBM1_Line". PRR_A2/B2 Raw FASTQs are pooled for samples "CR_BH_Pos_Slow" and "CR_BH_Neg Experiment  2". More detailed explanation can be seen in the README file.

library_source: transcriptomic single cell

data_processing:
For bioinformatic analysis of the GB-FUCCI cells, FASTQ files were delivered via the sequencing provider (Novogene) cloud-based platform. Following data integrity verification using a Message-digest algorithm 5 (MD5) checker to ensure complete cloud delivery, sequencing data were concatenated and aligned to the human genome reference GRCh38 (Hg38) using the PARSE bioinformatics pipeline (https://www.biomage.net/blog/converting-parsebio-output-for-cellenics). The organoids were preprocessed and filtered using the following parameters: filtered to retain cells with more than 5000 UMIs, normalisation using LogNormalize and scale factor kept at 10000. The resulting outputs was formatted for compatibility with 10x Genomics analytical workflows and analysed using the BioTuring ‘BBrowser’ platform (https://bioturing.com/).
Assembly: Human/ Homo sapiens GRCh38 (Hg38)
Supplementary files format and content: tab-separated value files and matrix files

molecule: total RNA

source_name: FUCCI_GBM1 cells

extract_protocol:
GB-FUCCI (FUCCI_GBM1) cells were enzymatically dissociated from adherent cultures using TrypLE™ Express Enzyme (Thermo Fisher Scientific, Cat# 12604013). Cell suspensions were centrifuged at 300 × g and resuspended in NB medium. Samples were fixed using the Evercode™ Cell Fixation v2 kit (Parse Biosciences, ECF2001/ECF2101) following the manufacturer’s instructions. Fixed cells were stored at –80 °C for up to 1 month prior to barcoding. GB spheroids were co-cultured with either neural-like organoids, or foregut-like organoids. A few days were given for the GB cells to invade into the neigbouring organoid/ environment. The now “assembloid” was dissociated and the GB cells and environment cells separated by Fluorescence-Activated Cell Sorting through the means of GFP expressing GB cells. The cells were then pooled again at a 1:1 ratio.
Library preparation was performed for the GB-FUCCI cells according to manufacturer instructions using the EvercodeTM WT Mini v2 kit (Parse Biosciences, ECW02010/ECW02110). Fixed single-cell suspensions underwent a series of intracellular, instrument-free reverse transcription barcoding reactions. Resulting barcoded libraries were divided into sublibraries as required, with an additional sublibrary-specific barcode introduced. Final sublibraries were lysed, and barcoded cDNA was amplified by PCR and prepared for Illumina sequencing. Satisfactory sublibrary quality control was checked and confirmed on a Tapestation 4200 (Agilent). Sequencing was performed using the NovaSeq 6000 platform with a resultant 100% clean reads.Library preparation for the pooled assembloid cells was performed using the 10x Genomics GEM-X 3′ v4 assay, and the libraries were processed and sequenced on an Illumina NovaSeq X Plus at 50,000 reads per cell using the 10x Genomics 3′ Single Cell Gene Expression Service provided by Single Cell Discoveries.

value: FUCCI_GBM1 cells


title: Monocytes infect,replicate6

description:
Library name: n32
Monocytes infect,replicate6


title: CR BH Negative Experiment 1, CR BH Positive Fast, FUCCI GBM1 Line

description:
Library name: Parsed dataset 1
BCR_A2/B2 Raw FASTQs are pooled for samples "CR_BH_Neg Experiment 1", "CR_BH_Pos_Fast" and "FUCCI_GBM1_Line". PRR_A2/B2 Raw FASTQs are pooled for samples "CR_BH_Pos_Slow" and "CR_BH_Neg Experiment  2". More detailed explanation can be seen in the README file.


title: Monocytes infect,replicate4

description:
Library name: n24
Monocytes infect,replicate4


title: Monocytes non-infect,replicate5

description:
Library name: n25
Monocytes non-infect,replicate5


title: Monocytes infect,replicate3

description:
Library name: n23
Monocytes infect,replicate3


title: Monocytes infect,replicate1

description:
Library name: n21
Monocytes infect,replicate1


title: Monocytes infect,replicate2

description:
Library name: n22
Monocytes infect,replicate2


description:
Library name: n18
Co-culture infected Monocytes,replicate2


title: Monocytes infect,replicate5

description:
Library name: n31
Monocytes infect,replicate5


description:
Library name: n19
Co-culture infected Monocytes,replicate3


description:
Library name: n20
Co-culture infected Monocytes,replicate4


title: Synoviocytes infected,replicate3

description:
Library name: n15
Synoviocytes infected,replicate3


title: Synoviocytes infected,replicate2

description:
Library name: n14
Synoviocytes infected,replicate2


title: Monocytes non-infect,replicate4

description:
Library name: n12
Monocytes non-infect,replicate4


title: Monocytes non-infect,replicate3

description:
Library name: n11
Monocytes non-infect,replicate3


description:
Library name: n17
Co-culture infected Monocytes,replicate1


title: Monocytes non-infect,replicate1

description:
Library name: n9
Monocytes non-infect,replicate1


description:
Library name: n8
Co-culture non-infected Monocytes,replicate4


title: Monocytes non-infect,replicate2

description:
Library name: n10
Monocytes non-infect,replicate2


title: Synoviocytes infected,replicate4

description:
Library name: n16
Synoviocytes infected,replicate4


description:
Library name: n5
Co-culture non-infected Monocytes,replicate1


title: Synoviocytes infected,replicate1

description:
Library name: n13
Synoviocytes infected,replicate1


description:
Library name: n6
Co-culture non-infected Monocytes,replicate2


title: Synoviocytes non-infected,replicate4

description:
Library name: n4
Synoviocytes non-infected,replicate4


title: Synoviocytes non-infected,replicate2

description:
Library name: n2
Synoviocytes non-infected,replicate2


title: Synoviocytes non-infected,replicate3

description:
Library name: n3
Synoviocytes non-infected,replicate3


description:
Library name: n7
Co-culture non-infected Monocytes,replicate3


title: LYI_HS2_20240404 | 026 | Immune cell

city: Seoul

first: Seoyoon

last: Ham

address: Yonsei-ro 50-1, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: DSP-1001660024093-A-F02

data_processing:
Raw fastq files were converted to DCC files by the Nanostring geomxngspipeline software.
The DCC files were uploaded to the DSP software and the read counts file was exported for further analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files generated by the Nanostring geomxngspipeline software.
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
FFPE tissue sections (5 µm) were prepared on BOND Plus slides, followed by deparaffinization, rehydration, and antigen retrieval using Tris-EDTA and proteinase K treatment. The tissues were hybridized overnight with GeoMx WTA RNA probes (18,677 genes) and stained with morphology markers (panCK, CD45, CD31, and SYTO 13). ROIs were selected and categorized into four regions: epithelium epidermis (above dermis), epithelium dermis (sinus tracts), dermis superficial inflammation (immune cells near epidermis), and dermis deep inflammation (immune cells near epithelium dermis). Using the DSP instrument, ROIs were segmented into AOIs, and indexed oligonucleotides were UV-released and collected.
Spatial transcriptome libraries were prepared using NanoString's GeoMx Human Whole Transcriptome Atlas kit and Digital Spatial Profiler instrument, followed by library construction with Seq Code primers and AMPure XP bead purification. Sequencing was performed on Illumina NovaSeq 6000 (2 × 151 bp paired-end).

value: Skin

tag: disease


title: LYI_HS2_20240404 | 022 | Epithelial cell

description: Library name: DSP-1001660024093-A-E10


title: LYI_HS2_20240404 | 025 | Immune cell

description: Library name: DSP-1001660024093-A-F01


title: LYI_HS2_20240404 | 019 | Immune cell

description: Library name: DSP-1001660024093-A-E07


title: Synoviocytes non-infected,replicate1

description:
Library name: n1
Synoviocytes non-infected,replicate1


title: LYI_HS2_20240404 | 024 | Epithelial cell

description: Library name: DSP-1001660024093-A-E12


title: LYI_HS2_20240404 | 015 | Epithelial cell

description: Library name: DSP-1001660024093-A-E03


title: LYI_HS2_20240404 | 023 | Epithelial cell

description: Library name: DSP-1001660024093-A-E11


title: LYI_HS2_20240404 | 017 | Immune cell

description: Library name: DSP-1001660024093-A-E05


title: LYI_HS2_20240404 | 016 | Epithelial cell

description: Library name: DSP-1001660024093-A-E04


title: LYI_HS2_20240404 | 020 | Immune cell

description: Library name: DSP-1001660024093-A-E08


title: LYI_HS2_20240404 | 021 | Epithelial cell

description: Library name: DSP-1001660024093-A-E09


title: LYI_HS2_20240404 | 014 | Epithelial cell

description: Library name: DSP-1001660024093-A-E02


title: LYI_HS2_20240404 | 018 | Immune cell

description: Library name: DSP-1001660024093-A-E06


title: LYI_HS2_20240404 | 010 | Epithelial cell

description: Library name: DSP-1001660024093-A-D10


title: LYI_HS2_20240404 | 013 | Epithelial cell

description: Library name: DSP-1001660024093-A-E01


title: LYI_HS2_20240404 | 011 | Immune cell

description: Library name: DSP-1001660024093-A-D11


title: LYI_HS2_20240404 | 012 | Epithelial cell

description: Library name: DSP-1001660024093-A-D12


title: LYI_HS2_20240404 | 008 | Immune cell

description: Library name: DSP-1001660024093-A-D08


title: LYI_HS2_20240404 | 006 | Epithelial cell

description: Library name: DSP-1001660024093-A-D06


title: LYI_HS2_20240404 | 007 | Epithelial cell

description: Library name: DSP-1001660024093-A-D07


title: LYI_HS2_20240404 | 004 | Immune cell

description: Library name: DSP-1001660024093-A-D04


title: LYI_HS2_20240404 | 005 | Epithelial cell

description: Library name: DSP-1001660024093-A-D05


title: LYI_HS2_20240404 | 002 | Epithelial cell

description: Library name: DSP-1001660024093-A-D02


title: LYI_HS1_20240404 | 034 | Immune cell

description: Library name: DSP-1001660024093-A-C11


title: LYI_HS2_20240404 | 009 | Immune cell

description: Library name: DSP-1001660024093-A-D09


title: LYI_HS1_20240404 | 033 | Epithelial cell

description: Library name: DSP-1001660024093-A-C10


title: LYI_HS2_20240404 | 001 | Epithelial cell

description: Library name: DSP-1001660024093-A-D01


title: LYI_HS1_20240404 | 032 | Epithelial cell

description: Library name: DSP-1001660024093-A-C09


title: LYI_HS2_20240404 | 003 | Immune cell

description: Library name: DSP-1001660024093-A-D03


title: LYI_HS1_20240404 | 031 | Epithelial cell

description: Library name: DSP-1001660024093-A-C08


title: LYI_HS1_20240404 | 028 | Epithelial cell

description: Library name: DSP-1001660024093-A-C05


title: LYI_HS1_20240404 | 029 | Immune cell

description: Library name: DSP-1001660024093-A-C06


title: LYI_HS1_20240404 | 030 | Immune cell

description: Library name: DSP-1001660024093-A-C07


title: LYI_HS1_20240404 | 026 | Immune cell

description: Library name: DSP-1001660024093-A-C03


title: LYI_HS1_20240404 | 022 | Immune cell

description: Library name: DSP-1001660024093-A-B11


title: LYI_HS1_20240404 | 019 | Epithelial cell

description: Library name: DSP-1001660024093-A-B08


title: LYI_HS1_20240404 | 024 | Immune cell

description: Library name: DSP-1001660024093-A-C01


title: LYI_HS1_20240404 | 020 | Epithelial cell

description: Library name: DSP-1001660024093-A-B09


title: LYI_HS1_20240404 | 027 | Epithelial cell

description: Library name: DSP-1001660024093-A-C04


title: LYI_HS1_20240404 | 025 | Immune cell

description: Library name: DSP-1001660024093-A-C02


title: LYI_HS1_20240404 | 017 | Immune cell

description: Library name: DSP-1001660024093-A-B06


title: LYI_HS1_20240404 | 018 | Epithelial cell

description: Library name: DSP-1001660024093-A-B07


title: LYI_HS1_20240404 | 023 | Immune cell

description: Library name: DSP-1001660024093-A-B12


title: LYI_HS1_20240404 | 016 | Immune cell

description: Library name: DSP-1001660024093-A-B05


title: LYI_HS1_20240404 | 015 | Immune cell

description: Library name: DSP-1001660024093-A-B04


title: LYI_HS1_20240404 | 035 | Immune cell

description: Library name: DSP-1001660024093-A-C12


title: LYI_HS1_20240404 | 012 | Epithelial cell

description: Library name: DSP-1001660024093-A-B01


title: LYI_HS1_20240404 | 021 | Epithelial cell

description: Library name: DSP-1001660024093-A-B10


title: LYI_HS1_20240404 | 010 | Immune cell

description: Library name: DSP-1001660024093-A-A11


title: LYI_HS1_20240404 | 013 | Epithelial cell

description: Library name: DSP-1001660024093-A-B02


title: LYI_HS1_20240404 | 009 | Immune cell

description: Library name: DSP-1001660024093-A-A10


title: LYI_HS1_20240404 | 007 | Immune cell

description: Library name: DSP-1001660024093-A-A08


title: LYI_HS1_20240404 | 008 | Immune cell

description: Library name: DSP-1001660024093-A-A09


title: LYI_HS1_20240404 | 006 | Epithelial cell

description: Library name: DSP-1001660024093-A-A07


title: LYI_HS1_20240404 | 014 | Immune cell

description: Library name: DSP-1001660024093-A-B03


title: LYI_HS1_20240404 | 011 | Immune cell

description: Library name: DSP-1001660024093-A-A12


title: LYI_HS1_20240404 | 005 | Epithelial cell

description: Library name: DSP-1001660024093-A-A06


title: HS slide 2 plz | 09 | Epithelial cell

description: Library name: DSP-1001660021344-B-E01


title: LYI_HS1_20240404 | 004 | Epithelial cell

description: Library name: DSP-1001660024093-A-A05


title: LYI_HS1_20240404 | 003 | Epithelial cell

description: Library name: DSP-1001660024093-A-A04


title: HS slide 2 plz | 023 | Epithelial cell

description: Library name: DSP-1001660021344-B-D11


title: HS slide 2 plz | 024 | Epithelial cell

description: Library name: DSP-1001660021344-B-D12


title: LYI_HS1_20240404 | 001 | Epithelial cell

description: Library name: DSP-1001660024093-A-A02


title: HS slide 2 plz | 020 | Epithelial cell

description: Library name: DSP-1001660021344-B-D08


title: HS slide 2 plz | 017 | Epithelial cell

description: Library name: DSP-1001660021344-B-D05


title: HS slide 2 plz | 015 | Immune cell

description: Library name: DSP-1001660021344-B-D03


title: HS slide 2 plz | 022 | Epithelial cell

description: Library name: DSP-1001660021344-B-D10


title: HS slide 2 plz | 021 | Epithelial cell

description: Library name: DSP-1001660021344-B-D09


title: HS slide 2 plz | 016 | Epithelial cell

description: Library name: DSP-1001660021344-B-D04


title: HS slide 2 plz | 012 | Epithelial cell

description: Library name: DSP-1001660021344-B-C12


title: HS slide 2 plz | 019 | Epithelial cell

description: Library name: DSP-1001660021344-B-D07


title: HS slide 2 plz | 014 | Immune cell

description: Library name: DSP-1001660021344-B-D02


title: LYI_HS1_20240404 | 002 | Epithelial cell

description: Library name: DSP-1001660024093-A-A03


title: HS slide 2 plz | 008 | Epithelial cell

description: Library name: DSP-1001660021344-B-C10


title: HS slide 2 plz | 011 | Epithelial cell

description: Library name: DSP-1001660021344-B-C11


title: HS slide 2 plz | 005 | Epithelial cell

description: Library name: DSP-1001660021344-B-C07


title: HS slide 2 plz | 018 | Epithelial cell

description: Library name: DSP-1001660021344-B-D06


title: HS slide 2 plz | 003 | Epithelial cell

description: Library name: DSP-1001660021344-B-C05


title: HS slide 2 plz | 006 | Epithelial cell

description: Library name: DSP-1001660021344-B-C08


title: HS slide 2 plz | 002 | Epithelial cell

description: Library name: DSP-1001660021344-B-C04


title: HS slide 2 plz | 013 | Immune cell

description: Library name: DSP-1001660021344-B-D01


title: HS slide 2 plz | 004 | Epithelial cell

description: Library name: DSP-1001660021344-B-C06


title: HS slide 2 plz | 007 | Epithelial cell

description: Library name: DSP-1001660021344-B-C09


title: HS slide 1 | 023 | Epithelial cell

description: Library name: DSP-1001660021344-B-B12


title: HS slide 2 plz | 001 | Immune cell

description: Library name: DSP-1001660021344-B-C02


title: HS slide 1 | 022 | Epithelial cell

description: Library name: DSP-1001660021344-B-B11


title: HS slide 1 | 024 | Epithelial cell

description: Library name: DSP-1001660021344-B-C01


title: HS slide 1 | 020 | Epithelial cell

description: Library name: DSP-1001660021344-B-B09


title: HS slide 2 plz | 0010 | Immune cell

description: Library name: DSP-1001660021344-B-C03


title: HS slide 1 | 018 | Immune cell

description: Library name: DSP-1001660021344-B-B07


title: HS slide 1 | 017 | Epithelial cell

description: Library name: DSP-1001660021344-B-B06


title: HS slide 1 | 016 | Epithelial cell

description: Library name: DSP-1001660021344-B-B05


title: HS slide 1 | 013 | Epithelial cell

description: Library name: DSP-1001660021344-B-B02


title: HS slide 1 | 014 | Immune cell

description: Library name: DSP-1001660021344-B-B03


title: HS slide 1 | 010 | Epithelial cell

description: Library name: DSP-1001660021344-B-A11


title: HS slide 1 | 015 | Epithelial cell

description: Library name: DSP-1001660021344-B-B04


title: HS slide 1 | 008 | Epithelial cell

description: Library name: DSP-1001660021344-B-A09


title: HS slide 1 | 011 | Epithelial cell

description: Library name: DSP-1001660021344-B-A12


title: HS slide 1 | 019 | Immune cell

description: Library name: DSP-1001660021344-B-B08


title: HS slide 1 | 009 | Epithelial cell

description: Library name: DSP-1001660021344-B-A10


title: HS slide 1 | 021 | Epithelial cell

description: Library name: DSP-1001660021344-B-B10


title: HS slide 1 | 004 | Epithelial cell

description: Library name: DSP-1001660021344-B-A05


title: HS slide 1 | 003 | Epithelial cell

description: Library name: DSP-1001660021344-B-A04


title: HS slide 1 | 006 | Immune cell

description: Library name: DSP-1001660021344-B-A07


title: HS slide 1 | 002 | Epithelial cell

description: Library name: DSP-1001660021344-B-A03


title: KimJ_RNA035 | 021 | PANCK

description: Library name: DSP-1001660011091-D-H11


title: HS slide 1 | 005 | Epithelial cell

description: Library name: DSP-1001660021344-B-A06


title: HS slide 1 | 007 | Epithelial cell

description: Library name: DSP-1001660021344-B-A08


title: KimJ_RNA035 | 021 | CD45

description: Library name: DSP-1001660011091-D-H12


title: HS slide 1 | 001 | Epithelial cell

description: Library name: DSP-1001660021344-B-A02


title: HS slide 1 | 012 | Epithelial cell

description: Library name: DSP-1001660021344-B-B01


title: KimJ_RNA035 | 016 | PANCK

description: Library name: DSP-1001660011091-D-H05


title: KimJ_RNA035 | 018 | CD45

description: Library name: DSP-1001660011091-D-H07


title: KimJ_RNA035 | 015 | CD45

description: Library name: DSP-1001660011091-D-H04


title: KimJ_RNA035 | 014 | CD45

description: Library name: DSP-1001660011091-D-H03


title: KimJ_RNA035 | 012 | CD45

description: Library name: DSP-1001660011091-D-H01


title: KimJ_RNA035 | 019 | CD45

description: Library name: DSP-1001660011091-D-H08


title: KimJ_RNA035 | 013 | CD45

description: Library name: DSP-1001660011091-D-H02


title: KimJ_RNA035 | 017 | CD45

description: Library name: DSP-1001660011091-D-H06


title: KimJ_RNA035 | 020 | CD45

description: Library name: DSP-1001660011091-D-H10


title: KimJ_RNA035 | 009 | PANCK

description: Library name: DSP-1001660011091-D-G09


title: KimJ_RNA035 | 009 | CD45

description: Library name: DSP-1001660011091-D-G10


title: KimJ_RNA035 | 011 | CD45

description: Library name: DSP-1001660011091-D-G12


title: KimJ_RNA035 | 008 | PANCK

description: Library name: DSP-1001660011091-D-G07


title: KimJ_RNA035 | 007 | PANCK

description: Library name: DSP-1001660011091-D-G05


title: KimJ_RNA035 | 005 | PANCK

description: Library name: DSP-1001660011091-D-G03


title: KimJ_RNA035 | 020 | PANCK

description: Library name: DSP-1001660011091-D-H09


title: KimJ_RNA035 | 010 | CD45

description: Library name: DSP-1001660011091-D-G11


title: KimJ_RNA035 | 004 | PANCK

description: Library name: DSP-1001660011091-D-G02


title: KimJ_RNA035 | 006 | PANCK

description: Library name: DSP-1001660011091-D-G04


title: KimJ_RNA035 | 008 | CD45

description: Library name: DSP-1001660011091-D-G08


title: KimJ_RNA035 | 003 | PANCK

description: Library name: DSP-1001660011091-D-G01


title: KimJ_RNA036 | 022 | CD45

description: Library name: DSP-1001660011091-D-F10


title: WT-SID-rep2

city: Buffalo

first: Johnny

last: Cruz Corchado

state: NY

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

institute: Roswell Park Comprehensive Cancer Institue

description:
Library name: WT dauer starvation rep2
Column name in processed data : WT-SID-rep2

data_processing:
The quality of the RNA sequences was assessed with FastQC
Adapters sequences and reads with a quality lower than Q25 were trimmed by using Trimgalore version 0.67.
Sequencing reads were aligned to the C. elegans genome WBcel235  using the Star aligner v2.7.9a2
Alignments were quantified with Salmon using the annotation  (WBCel235 GTF release 113)
Assembly: WBCel235 ensembl release 113
Supplementary files format and content: tab-delimited file include rawcounts for each sample
Supplementary files format and content: tab-delimeted files include TPM values for each sample

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Populations of 250-300 gravid adults were generated by passaging L4s on NGM plates. These plates were used for obtaining synchronized embryos by bleach-induced solubilization of the adults to then obtain larvae for harvesting mRNA. Specifically, animals were washed off the plates with 1X PBS and pelleted by centrifuging at 2665Xg for 30s. The PBS was removed carefully, and worms were gently vortexed in the presence of bleaching solution [250µl 1N NaOH, 200µl standard (regular) bleach and 550µl sterile water] until all the worm bodies had dissolved (approximately 5-6 minutes), and only eggs were viable. The eggs were pelleted by centrifugation (2665Xg for 45s), bleaching solution was carefully removed and then embryos were washed with sterile water 4-5 times and counted under the microscope. The desired number of embryos were seeded on fresh OP50 plates and allowed to grow at 25°C or 27°C for specific time periods depending on the experimental need. If >5% of eggs remained unhatched, these plates were discarded.

extract_protocol:
Total RNA was extracted from biological triplicates (duplicates in the case of Pheromone and Starvation dauers) using either the Direct-zol RNA Miniprep kit (Zymo Research, R2050) following the manufacturer's protocol, including an on-column DNase I digestion step, or a standard Trizol extraction method for dauer larvae.
mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Pheromone: Briefly, ~1000 embryos were bleach hatched from Gravid Adults and grown in six-well plates with a mixture 3ml of M9 buffer, 10µl of OP50 bacteria, and 100µl of 20µM ascarosides (#2, #3, #5) mixture at 25°C for 10 days1. 1% SDS was used to select dauers; the dauers were washed and processed for RNA extraction. Starvation : Two day-1 adults that were moved onto seeded OP50 plated, and the population was allowed to exhaust food over 10-12 days. Plates were washed off with sterile water, 1% SDS was used to select dauers; the dauers were washed and processed for RNA extraction.

value: Whole Animal

tag: genotype

value: wild-type dauers (N2; Bristol)

value: Starvation


title: KimJ_RNA035 | 002 | PANCK

description: Library name: DSP-1001660011091-D-F12


title: KimJ_RNA035 | 007 | CD45

description: Library name: DSP-1001660011091-D-G06


title: WT-SID-rep1

description:
Library name: WT dauer starvation rep1
Column name in processed data : WT-SID-rep1


title: WT-PID-rep1

description:
Library name: WT Pheromone treated rep1
Column name in processed data : WT-PID-rep1

value: Pheromone treatment


title: KimJ_RNA036 | 019 | PanCK

description: Library name: DSP-1001660011091-D-F08


title: KimJ_RNA036 | 020 | PanCK

description: Library name: DSP-1001660011091-D-F09


title: KimJ_RNA035 | 001 | PANCK

description: Library name: DSP-1001660011091-D-F11


title: KimJ_RNA036 | 018 | PanCK

description: Library name: DSP-1001660011091-D-F07


title: con_3

city: Guangzhou

first: Haiyang

last: Sun

address: Zhongshan road

department: The first affiliated hosptial

country: China

institute: Sun Yat-sen university

data_processing:
*library strategy: 16S seq
OTU abundance was normalized using the least represented sequences. Alpha diversity was assessed using Chao and Shannon indices calculated with QIIME 1.8.0. Beta diversity, reflecting species complexity, was evaluated through principal coordinates analysis (PCoA) and cluster analysis using QIIME
Assembly: SILVA ribosomal RNA database
Supplementary files format and content: Excel file is the abundance of microbiota Family.  We analyzed the raw data and the results were obtained after comparison with the database.

organism: feces metagenome

source_name: fecal

extract_protocol:
collect mouse fecal and 16S seq
a PhiX Control library (v3) from   Illumina was mixed with the amplicon library

value: fecal

value: control; WT


title: con_2


title: KimJ_RNA036 | 016 | PanCK

description: Library name: DSP-1001660011091-D-F05

value: Late_HS_Dermis_Eccrine gland


title: KimJ_RNA036 | 017 | PanCK

description: Library name: DSP-1001660011091-D-F06


title: con_1


title: con_4


title: KimJ_RNA036 | 015 | CD45

description: Library name: DSP-1001660011091-D-F04


title: ko_4

value: Dectin-2 ko


title: KimJ_RNA036 | 014 | CD45

description: Library name: DSP-1001660011091-D-F03


title: ko_3


title: KimJ_RNA036 | 013 | CD45

description: Library name: DSP-1001660011091-D-F02


title: ko_2


title: KimJ_RNA036 | 012 | CD45

description: Library name: DSP-1001660011091-D-F01


title: KimJ_RNA036 | 011 | CD45

description: Library name: DSP-1001660011091-D-E12


title: WT-PID-rep2

description:
Library name: WT Pheromone treated rep2
Column name in processed data : WT-PID-rep2


title: Rep3_SegB

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

country: Japan

institute: National institute of infectious diseases

description: Library name: Sample 5

data_processing:
Paired-end SITE-seq reads were aligned to the T6 reference genome using bwa mem with sample-specific read groups. Alignments were converted to duplicate-marked BAM files using samtools (fixmate, coordinate sorting, and markdup), and basic statistics were obtained with samtools flagstat and idxstats. For 5′ end analysis, only first mates (R1) were retained, coordinate-sorted, and indexed. The genomic position of each R1 5′ end was defined as the read start for forward reads and read end −1 for reverse reads. Reads failing basic mapping filters or shorter than 40 nt were excluded. Per-base 5′ end counts were converted to CPM, summed within each condition, smoothed with a 5-bp moving average, and log₂ fold changes were calculated using a small pseudocount.
Assembly: Enterobacteria phage T6 (accession number NC_054907.1)
Supplementary files format and content: BigWig
Library strategy: SITE-seq

organism: Enterobacteria phage T6

source_name: bacteriophage

extract_protocol:
Phage suspensions were lysed with 10% (w/v) SDS and 0.5 M EDTA (pH 8.0) at 68°C for 10 min, followed by the addition of 3 M sodium acetate (pH 6.5). The lysate was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and centrifuged at 16,000 ×g for 3 min. The aqueous phase was re-extracted twice with chloroform:isoamyl alcohol, then precipitated with two volumes of ice-cold ethanol, 1/30 volume of 3 M sodium acetate (pH 6.5), and 1 μl GlycoBlue™ coprecipitant at −30°C for 20 min. The DNA pellet was washed with 75% ethanol, briefly air-dried, and resuspended in 50 μl of sterile water.
High-molecular-weight genomic DNA was isolated from PEG-precipitated T6 phage lysates and adjusted to 1 µg per SITE-seq reaction. Purified DNA was incubated with 50 ng purified SegB or mock control in 20 µL reactions containing 1× NEBuffer 2 and 2 mM MnCl₂ at 30°C for 1 h. Reactions were terminated with EDTA and Proteinase K, followed by incubation at 55°C for 30 min. DNA was purified using SPRISelect beads and subjected to end repair and dA-tailing using the NEBNext Ultra II kit. Biotinylated adapter 1 oligos were annealed and ligated to end-repaired DNA using NEB Quick Ligase, with incubation at 20°C for 30 min followed by overnight incubation at 16°C. Ligation products were purified with SPRISelect beads and fragmented using NEBNext dsDNA Fragmentase at 37°C for 1 h. Fragmented DNA was purified, end-repaired, and dA-tailed again before ligation of adapter 2 using the NEBNext Ultra II Ligation Module. Adapter-ligated DNA was captured with Dynabeads in B&W buffer, washed, and amplified by PCR using Q5 Hot-Start Master Mix and recovery primers. Following magnetic separation, recovered DNA was further amplified by indexing PCR using NEBNext Multiplex Oligos for Illumina.

value: bacteriophage

tag: strain

tag: treated with

value: SegB


title: KimJ_RNA036 | 009 | PanCK

description: Library name: DSP-1001660011091-D-E10


title: Rep3_Mock

description: Library name: Sample 6

value: Mock


title: ko_1


title: KimJ_RNA036 | 010 | CD45

description: Library name: DSP-1001660011091-D-E11


title: Rep1_SegB

description: Library name: Sample 1


title: KimJ_RNA036 | 006 | PanCK

description: Library name: DSP-1001660011091-D-E07


title: KimJ_RNA036 | 008 | PanCK

description: Library name: DSP-1001660011091-D-E09


title: Rep2_SegB

description: Library name: Sample 3


title: Rep1_Mock

description: Library name: Sample 2


title: KimJ_RNA036 | 005 | PanCK

description: Library name: DSP-1001660011091-D-E06


title: Rep2_Mock

description: Library name: Sample 4


title: Cbx2 knock-in mESCs treated with OHT for 2 days to generate Cbx2 KO, replicate2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: Cbx2_KO_day2_rep2

data_processing:
The raw fastq files were trimmed with trim-galore to obtain clean fastq files
The clean fastq fiels were mapping to transcriptome using Salmon to obtainTPM matrix
Assembly: GRCm38/mm10
Supplementary files format and content: CSV file containing a gene-level matrix with TPM values for each sample

organism: Mus musculus

source_name: mESC CBX2fl/fl-HaloTag

growth_protocol: Female mouse embryonic stem cells (PGK12.1 provided by Dr. Neil Brockdoff from University of Oxford, UK) were cultured at 37°C and 5% CO2 on 0.2% gelatin, in mESC medium which consists of Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 15% Fetal Bovine Serum (VWR), 0.1 mM β-mercaptoethanol (Gibco), 2.0 mM L-Glutamine (Gibco), 100 Units/mL Penicillin-Streptomycin (Gibco), 1× MEM Non-Essential Amino Acids (Gibco), 10 µg/mL Ciprofloxacin (Sigma), and 10^3 units/mL leukemia inhibitor factor (LIF).

extract_protocol:
RNA was extracted using QIAGEN® RNeasy Mini Kit
Library was generated using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with 1ug total RNA as input

treatment_protocol: To conditionally deplete CBX2, CBX2 fl/fl-HT mESCs were treated with 1.0 µM 4-Hydroxytamoxifen (4-OHT, Sigma) for 48 hours

value: mESC CBX2fl/fl-HaloTag

value: mESC

value: Knockout

value: OHT


title: KimJ_RNA036 | 004 | PanCK

description: Library name: DSP-1001660011091-D-E05


title: KimJ_RNA036 | 003 | PanCK

description: Library name: DSP-1001660011091-D-E04


title: Cbx2 knock-in mESCs treated with OHT for 2 days to generate Cbx2 KO, replicate1

description: Library name: Cbx2_KO_day2_rep1


title: Cbx2 knock-in mESCs treated with EtOH as day 0 control, replicate1

description: Library name: Cbx2_WT_day0_rep1

value: Wildtype

value: EtOH


title: Cbx2 knock-in mESCs treated with EtOH as day 0 control, replicate2

description: Library name: Cbx2_WT_day0_rep2


title: KimJ_RNA036 | 007 | PanCK

description: Library name: DSP-1001660011091-D-E08

value: Skin


title: KPPC-Vehicle replicate_3

city: ST LOUIS

first: SAPANA

middle: PRAKASHRAO

last: BANSOD

state: MO

address: 4482 LINDELL BLVD, 608

department: INTERNAL MEDICINE

institute: WASHINGTON UNIVERSITY, ST LOUIS

description:
Library name: Sample 3
KPPC_Vehicle_replicate_3.LIB076661.gene_counts.txt

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Purelink RNA Mini isolation kit. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells treated with vehicle replicate 3


title: KPPC_EPHA2i-5nM_replicate_3

description:
Library name: Sample 6
KPPC_EPHA2i-5nM_replicate_3.LIB076664.gene_counts.txt

value: KPPC cells treated with EphA2 inhibitor replicate 3


title: KPPC_EPHA2i-5nM_replicate_1

description:
Library name: Sample 4
KPPC_EPHA2i-5nM_replicate_1.LIB076662.gene_counts.txt

value: KPPC cells treated with EphA2 inhibitor replicate 1


title: KimJ_RNA036 | 002 | PanCK

description: Library name: DSP-1001660011091-D-E03


title: KPPC-Vehicle replicate_2

description:
Library name: Sample 2
KPPC_Vehicle_replicate_2.LIB076660.gene_counts.txt

value: KPPC cells treated with vehicle replicate 2


title: KPPC_EPHA2i-5nM_replicate_2

description:
Library name: Sample 5
KPPC_EPHA2i-5nM_replicate_2.LIB076663.gene_counts.txt

value: KPPC cells treated with EphA2 inhibitor replicate 2


title: KimJ_RNA036 | 001 | PanCK

description: Library name: DSP-1001660011091-D-E02


title: Torin Treated Pooled Polysomal RNA 3

city: Philadelphia

first: Montana

last: Knight

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

description: Library name: F3_Poly

data_processing:
Reads underwent quality assessment and control using fastqc, multiqc, and fastp. Reads were aligned to the mouse genome using STAR. Gene counts obtained and compared between sample groups using htseq-count and edgeR.
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts from htseq-count

source_name: Macrophages

extract_protocol:
Cells were washed with PBS containing cycloheximide and lysed in polysome extraction buffer with triton. Incubated for 30 minutes on ice, vortexing every 5 to 10 minute and centrifuged for 15 minutes. Lysate was frozen as input or loaded onto a sucrose gradient to collect polysomal information.
mRNA was isolated using oligo(dT)-attached magnetic beads. First-strand cDNA was synthesized with random hexamer primers, second-strand by incorporating dUTP instead of DTTP. Directional libraries prepared through end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification.

value: Macrophages

value: Torin Treated LPS Stimulated Complete Media


title: KPPC-Vehicle replicate_1

description:
Library name: Sample 1
KPPC_Vehicle_replicate_1.LIB076659.gene_counts.txt

value: KPPC cells treated with vehicle replicate 1


title: KimJ_RNA037 | 024 | CD45

description: Library name: DSP-1001660011091-D-E01


title: wt_total_S2

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

description:
Library name: wt_total_S2
wttotal2

data_processing:
kallisto tpm estimation, splicing analyses using rMATSv4.1.2 , DESeq2v1.44.0 in Rv4.4.0
Assembly: GENCODE Release 49 (GRCh38.p14)
Supplementary files format and content: kallisto tpm estimation

growth_protocol: High-glucose DMEM media (Gibco, 11995-065) supplemented with 10% Fetal Bovine Serum (Gibco, A52567-01) and 100 units/ml Pen/Strep antibiotics (Sigma-Aldrich, A5955) at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using Trizol (Invitrogen, #15596026).
Total RNA extracts assessed by Bioanalyzer with a RIN value > 6.0 and were sent to Azenta for Illumina library preparation with PolyA selection for paired-end, 150bp sequencing at a minimum of 100 million reads per sample.

treatment_protocol: An OnTarget Plus SMARTpool (Dharmacon, #SO-3019437G) siRNA targeting TAOK2 (9344) was used for TAOK2 knockdown. A549 cells raised in media were reverse transfected in triplicate with siRNAs using Lipofectamine RNAiMAX transfection reagent (Invitrogen, 13778150) according to the manufacturer’s instructions. siCON control pool #2 (Dharmacon, #D-001206-14-20) was used in parallel for control samples. siRNAs were used at a final concentration of 30 nM.

value: Lung epithelial

value: WT

value: non-targeting pool siRNA


title: Torin Treated Total RNA 3

description: Library name: F3_In


title: KimJ_RNA037 | 023 | CD45

description: Library name: DSP-1001660011091-D-D12


title: wt_total_S1

description:
Library name: wt_total_S1
wttotal1


title: wt_nuc_S2

description:
Library name: wt_nuc_S2
wtnuc2

molecule: nuclear RNA


title: wt_nuc_S1

description:
Library name: wt_nuc_S1
wtnuc1


title: wt_cyto_S2

description:
Library name: wt_cyto_S2
wtcyto2

molecule: cytoplasmic RNA


title: KimJ_RNA037 | 022 | CD45

description: Library name: DSP-1001660011091-D-D11


title: wt_cyto_S1

description:
Library name: wt_cyto_S1
wtcyto1


title: KimJ_RNA037 | 021 | CD45

description: Library name: DSP-1001660011091-D-D10


title: taok2kd_total_S2

description:
Library name: taok2kd_total_S2
kdtotal2

value: TAOK2 siRNA


title: Torin Treated Total RNA 2

description: Library name: F2_In


title: Torin Treated Pooled Polysomal RNA 1

description: Library name: F1_Poly


title: KimJ_RNA037 | 020 | CD45

description: Library name: DSP-1001660011091-D-D09


title: Torin Treated Pooled Polysomal RNA 2

description: Library name: F2_Poly


title: taok2kd_nuc_S1

description:
Library name: taok2kd_nuc_S1
kdnuc1


title: taok2kd_nuc_S2

description:
Library name: taok2kd_nuc_S2
kdnuc2


title: taok2kd_total_S1

description:
Library name: taok2kd_total_S1
kdtotal1


title: Torin Treated Total RNA 1

description: Library name: F1_In


title: taok2kd_cyto_S2

description:
Library name: taok2kd_cyto_S2
kdcyto2


title: KimJ_RNA037 | 019 | CD45

description: Library name: DSP-1001660011091-D-D08


title: scRNA_seq_submerged_differentiated_HNEC_donor3

city: Utrecht

first: Gimano

last: Amatngalim

address: Heidelberglaan 100

department: Pediatrics

country: Netherlands

institute: University Medical Center Utrecht

description: Library name: UMC-HR-s003_scRNAseq.

data_processing:
Samples were sequenced with 75.000 reads per cell on a Illumina NextSeq. For the analysis of the scRNA-seq data, paired-end reads were aligned to the human transcriptome using Burrows-Wheeler Alignment tool 40. Read 1 was used to assign reads to map reads to the correct cells and read 2 was mapped to gene models. Only uniquely mapped reads were used for further analysis. Reads duplicated were removed by excluding reads with identical library, cellular and molecular barcodes. Transcript counts were adjusted to the number of expected molecules based on counts, possible UMI’s and Poissonian counting statistics.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts of all samples

source_name: Nasal epithelium

growth_protocol: Cells were  expanded as previously described (Rodenburg et al., 2023; https://doi.org/10.1016/j.xpro.2023.102337)

extract_protocol:
Cells were dissociated using TrypLE express enzyme and resuspended to a single cell suspension. Samples were pelleted, washed with PBS, resuspended in FACS buffer (PBS0, 1% FBS, 0.5 mM EDTA and DAPI) and strained (35 µm). 376 cells per donor were immediately sorted into 384-well cell-capture plates containing ERCC spike-ins (Agilent), RT primers and dNTP (Promega) using a BD FACSJazz. ScRNA-seq was performed according to the SORT-seq protocol Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst. 3, 385-394.e3 (2016).
Sequencing libraries were prepared with the Illumina Truseq small RNA library preparation kit.

treatment_protocol: HNEC where differentiated for 21 days in submerged (sub) cultures

value: Nasal epithelium

value: Human Nasal Epithelial Cells


title: scRNA_seq_submerged_differentiated_HNEC_donor2

description: Library name: UMC-HR-s002_scRNAseq.


title: scRNA_seq_submerged_differentiated_HNEC_donor1

description: Library name: UMC-HR-s001_scRNAseq.


title: KimJ_RNA037 | 018 | Panck

description: Library name: DSP-1001660011091-D-D07

value: Skin


title: taok2kd_cyto_S1

description:
Library name: taok2kd_cyto_S1
kdcyto1


title: Donor9_submerged_differentiated

description: Library name: 9_sub

data_processing:
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles), and a sequencing depth of 12 million reads per sample.
Read 1 was used to identify the Illumina library index and to check for valid CEL-seq sample barcodes that have a maximum Hamming distance of 1. Read 2 was trimmed and aligned to the human GRCh38 reference transcriptome using BWA (version 0.7.15) MEM -t 8 and other parameters were set to default51.
Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was automated and carried out using the MapAndGo (version 3.0) script
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts of all samples

extract_protocol:
Total RNA was extracted from ALI-differentiated nasal and bronchial airway epithelial cells using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol
Sequencing libraries were prepared with the Illumina Truseq small RNA library preparation kit.

treatment_protocol: Cells remained undifferentiated (BCs), or where differentiated for 21 days in submerged (sub) org air-liquid interface cultures

value: Nasal epithelial cells


title: KimJ_RNA037 | 017 | Panck

description: Library name: DSP-1001660011091-D-D06


title: Stimulated Control Total RNA 2

description: Library name: C2_In

value: LPS Stimulated Complete Media


title: KimJ_RNA037 | 016 | Panck

description: Library name: DSP-1001660011091-D-D05


title: Donor9_basal_cells

description: Library name: 9_BC


title: Donor8_submerged_differentiated

description: Library name: 8_sub


title: KimJ_RNA037 | 015 | CD45

description: Library name: DSP-1001660011091-D-D04


title: Stimulated Control Pooled Polysomal RNA 3

description: Library name: C3_Poly


title: Donor9_ALI_differentiated

description: Library name: 9_ALI


title: Stimulated Control Pooled Polysomal RNA 2

description: Library name: C2_Poly


title: Donor8_ALI_differentiated

description: Library name: 8_ALI


title: Stimulated Control Total RNA 1

description: Library name: C1_In


title: KimJ_RNA037 | 014 | CD45

description: Library name: DSP-1001660011091-D-D03


title: Donor7_basal_cells

description: Library name: 7_BC


title: Stimulated Control Total RNA 3

description: Library name: C3_In_Redo


title: Donor7_submerged_differentiated

description: Library name: 7_sub


title: Donor8_basal_cells

description: Library name: 8_BC


title: Stimulated Control Pooled Polysomal RNA 1

description: Library name: C1_Poly


title: Rat, 14 days post lesion, Rep3

city: Cambridge

first: Ragnhildur

middle: Thora

last: Karadottir

address: Puddicombe Way

institute: Cambridge Stem Cell Institute

description:
Library name: DBIT_RNA_14DLP_03
DBiT-seq

data_processing:
A total of 15 transcriptomes were sequenced from CCP and IO after saline injection or 7, 14 and 28 days after lesion. Unfortunately, the 28 days post lesion samples were discarded due to low quality samples.Fastq files from the same sample sequenced on multiple lanes were merged prior PCR primers and spatial linkers assessement using bbduk (v39.01). Spatial barcodes were extracted from sequencing reads using a custom Python script. A custom made whitelist of barcodes was designed and supplied to cellranger count (v.7.1.0) to align remaining reads from each sample to the rat genome.
Assembly: mRatBN7.2, RefSeq annotation, NCBI
Supplementary files format and content: raw_feature_bc_matrix.h5 : Raw count matrix from cellranger outputs in h5 format
Supplementary files format and content: seruat objects in the .rds format: contains the pixels of the selected regions (healthy, Inferior olive and lesion site (ccp)). Sample metadata is stored in "orig.ident"
Supplementary files format and content: image_coordinate.csv: coordinates of each DBiT pixel
Supplementary files format and content: grid.tiff: high resolution image of the sample
Supplementary files format and content: image_grid_only_grid.png: low resolution image of the grid only, for plotting

organism: Rattus norvegicus

source_name: Caudal cerebellar preduncle (ccp) and Inferior Olive

extract_protocol:
Reverse crosslinking buffer was applied to tissue section (50 mM of Tris-HCl, 1 mM EDTA, 1% (wt/vol) of SDS, 200 mM NaCl, 0.4 mg-mL Proteinase K, nuclease-free H2O) was added to each well, then incubated at 58˚C for two hours. Each lysate was further incubated overnight at 65˚C with agitation.
Nextera XT Library Prep Kit was used and the Tagment Mix (1ng of purified cDNA in RNase-free water to a volume of 5 µL, 10 µL of Tagment DNA buffer, 5 µL of Amplicon Tagment Mix) was incubated at 55˚C for 5 minutes. NT Buffer (5 µL) was added then incubated at room temperature for 5 minutes. The final PCR mix was added (15 µL PCR master mix, 1 µL of 10 µM Ad1.X primer, 1 µL of 10 µM N70x primer, 8 µL of RNase-free water) and thermocycling was completed (Stage 1 – 1 cycle: 95˚C for 30 seconds, Stage 2 – 12 cycles: 95˚C for 10 seconds – 55˚C for 30 seconds – 72˚C for 30 seconds, Stage 3 – 1 cycle: 72˚C for 4 minute – 4˚C hold). Next Generation Sequencing was completed at NGI (National Genomics Infrastructure) using IllµMina NovaSeq X Plus 25B in paired-end 150bp mode with a total of 6 million reads for each sample and a 15% PhiX sequencing step.

tag: age

value: 9-12 week old

tag: Sex

value: Female

value: Sprague Dawley

tag: sections

value: coronal

value: lesion at caudal cerebellar peduncle (ccp)

tag: library name_(orig.ident)


title: Rat, 14 days post lesion, Rep4

description:
Library name: DBIT_RNA_14DLP_04
DBiT-seq

value: Caudal cerebellar preduncle (ccp) and Inferior Olive


title: KimJ_RNA037 | 011 | CD45

description: Library name: DSP-1001660011091-D-C12


title: Donor6_ALI_differentiated

description: Library name: 6_ALI


title: Donor6_basal_cells

description: Library name: 6_BC


title: Rat, 14 days post lesion, Rep2

description:
Library name: DBIT_RNA_14DLP_02
DBiT-seq


title: Donor5_submerged_differentiated

description: Library name: 5_sub


title: KimJ_RNA037 | 013 | CD45

description: Library name: DSP-1001660011091-D-D02


title: Donor5_basal_cells

description: Library name: 5_BC


title: Rat, 14 days post lesion, Rep1

description:
Library name: DBIT_RNA_14DLP_01
DBiT-seq


title: KimJ_RNA037 | 010 | CD45

description: Library name: DSP-1001660011091-D-C11


title: KimJ_RNA037 | 012 | CD45

description: Library name: DSP-1001660011091-D-D01


title: Donor6_submerged_differentiated

description: Library name: 6_sub


title: Donor7_ALI_differentiated

description: Library name: 7_ALI


title: KimJ_RNA037 | 009 | Panck

description: Library name: DSP-1001660011091-D-C10


title: Donor5_ALI_differentiated

description: Library name: 5_ALI


title: Donor4_basal_cells

description: Library name: 4_BC


title: Donor4_submerged_differentiated

description: Library name: 4_sub


title: Rat, 7 days post lesion, Rep4

description:
Library name: DBIT_RNA_7DLP_04
DBiT-seq


title: Rat, 7 days post lesion, Rep3

description:
Library name: DBIT_RNA_7DLP_03
DBiT-seq


title: Donor4_ALI_differentiated

description: Library name: 4_ALI


title: Donor3_basal_cells

description: Library name: 3_BC


title: Donor3_submerged_differentiated

description: Library name: 3_sub


title: KimJ_RNA037 | 008 | Panck

description: Library name: DSP-1001660011091-D-C09


title: Donor3_ALI_differentiated

description: Library name: 3_ALI


title: Donor2_submerged_differentiated

description: Library name: 2_sub


title: Rat, 7 days post lesion, Rep2

description:
Library name: DBIT_RNA_7DLP_02
DBiT-seq


title: Donor2_ALI_differentiated

description: Library name: 2_ALI


title: Rat, 7 days post lesion, Rep1

description:
Library name: DBIT_RNA_7DLP_01
DBiT-seq


title: KimJ_RNA037 | 005 | Panck

description: Library name: DSP-1001660011091-D-C06


title: KimJ_RNA037 | 006 | Panck

description: Library name: DSP-1001660011091-D-C07


title: KimJ_RNA037 | 007 | Panck

description: Library name: DSP-1001660011091-D-C08


title: KimJ_RNA037 | 004 | Panck

description: Library name: DSP-1001660011091-D-C05


title: Donor1_submerged_differentiated

description: Library name: 1_sub


title: Donor1_ALI_differentiated

description: Library name: 1_ALI


title: Rat, Control, Rep3

description:
Library name: DBIT_RNA_0DLP_03
DBiT-seq

value: Saline injection in the caudal cerebellar peduncle (ccp)


title: KimJ_RNA037 | 003 | Panck

description: Library name: DSP-1001660011091-D-C04


title: Rat, Control, Rep2

description:
Library name: DBIT_RNA_0DLP_02
DBiT-seq


title: SR184

city: Gainesville

first: Leslie

middle: Anne

last: Smith

state: Fl

address: 1889 Museum Rd

department: Computer Information Science and Engineering

institute: University of Florida

description: Library name: SR184

data_processing:
After sequencing, the RNA-seq aligner STAR was used to align reads using GRCh38 reference genome. fastqc was used to perform quality control on bam files. Multiqc was used to create report of qc results. Transcripts for each gene are counted using featureCounts from the subread package. Subsequent processing of the expression matrix mimicked refine.bio's RNA-seq processing pipeline for consistent processing across datasets: First duplicate HUGO symbol gene names were summarized by taking the mean, then expression values were quantile normalized using the homo sapien reference quantiles provided by refine.bio (https://api.refine.bio/v1/qn_targets/).
Assembly: GRCh38 reference genome
Supplementary files format and content: Processed samples are included in the ExpressionAllSamples.tsv gene expression matrix tsv file and MetadataAllSamplesAfterAddedSurvival.xlsx along with all other samples used in study. New samples can be identified in MetadataAllSamplesAfterAddedSurvival.xlsx file under dataset Guirgisetal

source_name: Whole blood

extract_protocol:
The preparation and subsequent sequencing (using the Illumina NextSeq 550 instrument) followed exactly the protocol described in the Illumina Stranded mRNA Prep Ligation Reference Guide. Quickly summarized, this involved 8 steps - (1) purifying and fragmenting the messenger RNA by capturing mRNAs with polyA tails using oligo(dT) magnetic beads and then fragmenting and priming the RNA , (2) synthesizing the first strand cDNA (complimentary DNA) by reverse transcribing the hexamer-primed RNA-fragments, (3) synthesizing the second strand cDNA to generate blunt-ended and doubled-stranded cDNA fragments, (4) adenylating 3-inch ends by adding an adenine nucleotide and a thymine nucleotide to the ends of the blunt fragments to prevent them from ligating to each other and for providing overhang for ligating the adaptors, (5) ligating anchors to the ends of the cDNA fragments in preparation for dual indexing, (6) cleaning up fragments with magnetic beads
(Numbered steps continued from extraction protocol): (7) amplifying the library using PCR to selectively amplify fragments and add indexes and primer sequences for cluster generation, and (8) cleaning up the library using magnetic beads to purify the dual-indexed libraries. The final libraries were checked using the Agilent 2100 Bioanalyzer and DNA 1000 kit and were then diluted to the starting concentration for the NextSeq550 model. Each of our samples required four lanes on the flow cells that went into the sequencing machine and each lane was run twice.

value: Whole blood

tag: outcome

value: RAP

tag: gender

tag: race

value: Caucasian

tag: shock

value: Yes

tag: sofa

tag: respsofa

tag: inhospdeath

value: No

tag: phenotype

value: Hypo

tag: ards


title: Donor1_basal_cells

description: Library name: 1_BC

tag: tissue

value: Nasal epithelium

tag: cell type

tag: treatment


title: SR182

description: Library name: SR182

value: Male

value: Normo


title: KimJ_RNA037 | 002 | Panck

description: Library name: DSP-1001660011091-D-C03

value: Skin

tag: disease


title: Donor2_basal_cells

description: Library name: 2_BC

value: Nasal epithelial cells


title: SR177

description: Library name: SR177

tag: age

value: Female

value: African American


title: Rat, Control, Rep1

description:
Library name: DBIT_RNA_0DLP_01
DBiT-seq

value: 9-12 week old

tag: Sex

tag: strain

value: Sprague Dawley

value: coronal


title: SR180

description: Library name: SR180


title: IgG

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

description: Library name: IgG

data_processing:
The raw data (raw reads) generated in high-throughput sequencing are in fastq format sequences. To obtain high-quality reads for subsequent analysis, further quality filtering of the raw reads is required. First, adapters are removed using the fatsp software, and on this basis, low-quality bases and N-base or low-quality reads are filtered out, ultimately yielding high-quality clean reads. Sequence alignment is a fundamental component and important basis of bioinformatics. For the analysis of data from second-generation sequencing platforms, the most crucial step is to align the generated reads to genomic positions. Bowtie2 is a commonly used sequence alignment software that can perform high-speed alignment of complex reference genomes. Ouyi Biotech uses Bowtie2 to align clean reads to the reference genome of the experimental species, and evaluates the sample status through the genome and gene alignment rates, using default parameters. To evaluate the quality of IP (Immunoprecipitation and Sequencing) experiments, we employ strand cross-correlation (SCC) analysis. Theoretically, the reads obtained from sequencing will eventually be approximately evenly distributed across the positive and negative strands. Therefore, by calculating the number of reads allocated to the positive and negative strands, not only can the correlation coefficient between the positive and negative strands be obtained, but also the quality of the IP experiment can be evaluated. In IP experiments, the SCC curve has a peak at the fragment length size, and the ratio of the cross correlation (CC) value at this point to the minimum CC value of the entire SCC curve (NSC) should be no less than 1.05. At the same time, a phantom peak also forms at the read length size, and the CC value at this point is obtained, and the relative strand cross-correlation (RSC) is calculated. The ideal value of RSC is no less than 0.8. Additionally, we use deeptools software to draw FingerPrint plots, which show the distinction between the enriched signals of CUT&Tag and background signals, and can also determine the type of ChIP signals (narrow peaks or broad peaks).
Processed data files include: (1) peak calls in BED (SEACR “stringent”) representing EGR1-enriched binding regions on mm10; (2) optional normalized signal tracks in bigWig for genome browser visualization; (3) optional differential binding results tables from DiffBind.
BED files contain genomic coordinates of EGR1 peaks (chr, start, end; plus peak score/statistics as output by SEACR). bigWig files contain genome-wide normalized coverage for visualization (e.g., IGV). DiffBind output tables contain differential binding statistics with thresholds p < 0.05 and |log2FC| > 1.
Assembly: mm10
Supplementary files format and content: BED files contain genomic coordinates of EGR1 peaks (chr, start, end; plus peak score/statistics as output by SEACR).
Library strategy: CUT&Tag

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from wild-type C57BL/6J mice and differentiated into bone-marrow–derived macrophages (BMDMs) in vitro using GM-CSF for 7 days under standard humidified culture conditions (37 °C, 5% CO₂). Cells were harvested at the end of differentiation for CUT-taq.

extract_protocol:
Cells (4.0 × 10^5 per sample) were processed using the Hyperactive™ In-Situ ChIP Library Prep Kit for Illumina (Vazyme TD901–TD902) following the manufacturer’s instructions. Briefly, cells were immobilized on concanavalin A beads, permeabilized with digitonin, and sequentially incubated with anti-EGR1 primary antibody and secondary antibody (Thermo). Hyperactive pA-Tn5 (Vazyme) was then applied to bind antibody-targeted chromatin, followed by in situ tagmentation to generate sequencing-ready DNA fragments.
After tagmentation, DNA fragments were PCR-amplified using P5/P7 indexed primers (as provided in the kit). Libraries were assessed for size distribution and quality using an Agilent 2100 Bioanalyzer, quantified per standard Illumina-compatible procedures, and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads (PE150).

treatment_protocol: BMDMs were differentiated with GM-CSF for 7 days and collected without additional stimulation prior to CUT-taq.

value: bone marrow

value: bone-marrow-derived macrophage

tag: genotype

value: WT (C57BL/6J)

value: GM-CSF differentiation for 7 days (in vitro)

tag: batch


title: KimJ_RNA038 | 021 | CD45

description: Library name: DSP-1001660011091-D-C01


title: SR179

description: Library name: SR179

value: Whole blood

tag: outcome

value: RAP

tag: gender

value: Caucasian

value: Yes


title: SR174

description: Library name: SR174

value: Male

tag: race

tag: shock

value: No


title: EGR1-siRNA3

description: Library name: EGR1-siRNA3


title: SR170

description: Library name: SR170

value: CCI

tag: sofa

tag: respsofa

value: Hypo


title: KimJ_RNA038 | 020 | CD45

description: Library name: DSP-1001660011091-D-B12

value: Skin


title: SR172

description: Library name: SR172

tag: inhospdeath

tag: phenotype

value: Normo


title: SR171

description: Library name: SR171

tag: tissue

value: African American

tag: ards

value: yes


title: Rat, Control, Rep4

description:
Library name: DBIT_RNA_0DLP_04
DBiT-seq

value: Caudal cerebellar preduncle (ccp) and Inferior Olive

value: 9-12 week old

value: Female

value: Sprague Dawley

tag: sections

value: coronal

tag: treatment

value: Saline injection in the caudal cerebellar peduncle (ccp)

tag: library name_(orig.ident)


title: KimJ_RNA037 | 001 | Panck

description: Library name: DSP-1001660011091-D-C02

tag: disease


title: SR141

description: Library name: SR141

value: Whole blood

value: RAP

tag: age


title: EGR1-siRNA1

description: Library name: EGR1-siRNA1

value: bone marrow

tag: cell type

value: bone-marrow-derived macrophage

tag: genotype

value: WT (C57BL/6J)

value: GM-CSF differentiation for 7 days (in vitro)


title: SR165

description: Library name: SR165

tag: outcome

value: Male

value: No


title: KimJ_RNA038 | 018 | CD45

description: Library name: DSP-1001660011091-D-B10

value: Skin


title: Micro-C, CBX2_KO_rep3

description:
Library name: X2_KO_rep3
Micro-C

data_processing:
Micro-C data processing and analysis: Micro-C datasets were processed using the ENCODE Hi-C data processing pipeline, aligning to the mm10 reference genome (UCSC notation) without specifying a restriction enzyme map. Each condition was processed independently. Finally, hic files were produced using the Juicer software suite. 68 The resultant interaction maps were normalized using the Knight-Ruiz (KR) matrix balancing algorithm, and all downstream analyses were performed on a 5 kb resolution. Pile-up analysis and contact intensity distribution: Micro-C data with a 5-kb resolution were used as input for the analyses. These analyses were performed using the coolpup.py package (version 0.9.5) running on Python version 3.10.12. 53 This package was employed under default settings to generate interaction profiles that quantitatively assess the average interaction strength between designated pairs of genomic intervals within each identified cluster. Interaction profiles were visualized using the plot_coolpup.py module. Subsequently, the distribution of interaction profile values was analyzed to detect significant differences between the two experimental conditions. Outliers in interaction values were removed, retaining data within the 20th and 80th percentiles. A two-sided Mann-Whitney U test was applied to the distribution data, where a p-value of less than 0.0001 was annotated with three asterisks (***), denoting statistical significance.
Assembly: mm10
Supplementary files format and content: .cool file with 5000bp Bin

extract_protocol:
Micro-C experiments were performed using a Dovetail® Micro-C Kit (Cantata Bio). 1.0 × 10⁶ cells were frozen at -80°C for at least 30 minutes and then thawed at room temperature for 5 minutes. The thawed pellet was resuspended in 200 µL of the freshly prepared DSG solution and nutated for 10 minutes at room temperature. Following nutation, 5.4 µL of 37% formaldehyde was added to a final concentration of 1%, and the mixture was nutated for an additional 10 minutes. After washing with 1× Wash buffer, the cells were resuspended in 50 µL of a MNase digest master mix (50 µL 1× Nuclease Digest Buffer + 0.5 µL MNase Enzyme Mix). The tube was then incubated in an agitating thermal mixer at 37°C at 1250 RPM for 18 minutes for in situ MNase digestion. After digestion, the reaction was stopped by adding 5 μL of 0.5 M EGTA, and QC was performed to confirm a 50-90% mono-nucleosome digestion profile. 3 μL of 20% SDS was added to the digested samples. The mixture was then incubated at 22°C for 5 minutes in the thermal mixer at 1250 RPM. Up to 1500 ng of lysate per sample was mixed with Chromatin Capture Beads. Once mixed, samples were incubated at room temperature for 10 minutes. The beads were collected on the magnetic rack and then washed 3 times with 1× Wash buffer. 53 μL of an End Polishing Master Mix (50 μL End Polishing Buffer + 3 μL End Polishing Enzyme Mix) was added to the washed sample. After the end polishing, 50 µl Bridge Ligation Mix was added to the beads, followed by 1 µl Bridge Ligase. Once thoroughly mixed, the reactions were incubated at 22°C for 30 minutes in an agitating thermal mixer set at 1,250 rpm. Following the bridge ligation, 50 μL Intra-Aggregate Ligation Mix was added to each sample. The samples were mixed and incubated at 22°C for 4 hours in an agitating thermal mixer at 1,250 rpm. After intra-aggregate ligation, samples were resuspended with 51.5 µL of Crosslink Reversal Solution (55 µL Crosslink Reversal Buffer + 1.7 µL Proteinase K) and incubated at 55°C for 10 minutes, then the temperature was increased to 65°C for overnight. DNAs were purified using SPRIselect beads and eluted with 95 μL TE Buffer pH 8.0. The eluted DNAs were quantified using a Qubit fluorometer and dsDNA HS kit.
For Micro-C 150 ng of purified DNA was used to prepare a library for each replicate using the NEBNext Ultra II kit. 25 μL of Streptavidin beads was washed and mixed with 95 μL of purified and adaptor-ligated DNA. The beads were then washed with LWB, NWB, and 1× Wash buffer. 45 µL Index PCR Master Mix (25 µL Hot Start PCR Ready Mix + 20 µL water per sample) was added to the beads, followed by 5 µL of a unique UDI Primer Pair. The PCR reactions were performed with the following settings: Enzyme activation at 98°C for 3 minutes, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 65°C for 30 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 1 minute. After amplification, 47 μL of the supernatant was collected, and 53 µL of TE Buffer (pH 8.0) was added to the solution, followed by 50 μL of SPRIselect beads. 145 µl of the supernatant was collected and mixed with 30 μL of SPRIselect beads. After washing, the beads were air-dried, and the DNA fragments were eluted with 30 μL TE Buffer (pH 8.0). The final elution was quantified with a Qubit fluorometer and a dsDNA HS kit, and the fragments were analyzed on a Tapestation to confirm a size distribution of 350-1,000 bp. NSG was performed to obtain a total of 300 million to 800 million reads between the replicates for each condition

tag: cell line

value: mESC CBX2fl/fl-HaloTag

value: mESC

value: 48 hours of 1.0 µM 4-Hydroxytamoxifen


title: SR138

description: Library name: SR138

tag: gender

tag: race

value: Caucasian

value: Yes

value: Hypo


title: SR127

description: Library name: SR127

value: CCI

value: Female

value: African American

tag: shock

tag: sofa

value: Normo


title: KimJ_RNA038 | 019 | CD45

description: Library name: DSP-1001660011091-D-B11


title: SR139

description: Library name: SR139

value: Whole blood

value: RAP

tag: respsofa

tag: inhospdeath


title: EGR1-siRNA2

description: Library name: EGR1-siRNA2

tag: tissue

value: bone marrow

value: bone-marrow-derived macrophage

value: WT (C57BL/6J)

tag: batch


title: Micro-C, CBX2_KO_rep2

description:
Library name: X2_KO_rep2
Micro-C


title: KimJ_RNA038 | 017 | CD45

description: Library name: DSP-1001660011091-D-B09


title: SR118

description: Library name: SR118

value: Male

value: No

tag: phenotype

tag: ards


title: SR116

description: Library name: SR116


title: SR119

description: Library name: SR119

value: Other


title: KimJ_RNA038 | 015 | CD45

description: Library name: DSP-1001660011091-D-B07

value: Skin


title: SR114

description: Library name: SR114

value: yes


title: SR124

description: Library name: SR124


title: SR117

description: Library name: SR117


title: SR111

description: Library name: SR111

value: CON

value: Caucasian


title: Micro-C, CBX2_WT_rep2

description:
Library name: X2_WT_rep2
Micro-C

value: mESC CBX2fl/fl-HaloTag

value: mESC


title: SR112

description: Library name: SR112

value: Female

value: Hypo


title: Micro-C, CBX2_WT_rep1

description:
Library name: X2_WT_rep1
Micro-C


title: KimJ_RNA038 | 013 | CD45

description: Library name: DSP-1001660011091-D-B05


title: SR104

description: Library name: SR104

value: ED

value: Yes


title: KimJ_RNA038 | 012 | CD45

description: Library name: DSP-1001660011091-D-B04


title: SR130

description: Library name: SR130

value: Whole blood

value: CCI

value: African American

value: Normo