title: SHSY5Y treated with FHD-286 rep1

description: Library name: 34_SHSY5Y_FHD286_R1

value: Neuronal

value: WT


title: SHSY5Y treated with FHD-286 rep2

status: Public on Apr 06 2026

type: SRA

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

country: USA

institute: Weill Cornell

description: Library name: 35_SHSY5Y_FHD286_R2

library_source: genomic

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

treatment_protocol: Inhibitor or DMSO treatment for 24h.

tag: tissue

value: cell line

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 8_5_Liver_KO_NK

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

institute: Washington University School of Medicine

description: Library name: sample.8_5_Liv_KO_NK

library_source: transcriptomic

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq X Plus.  Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Assembly: Ensembl release 101 primary assembly with STAR version 2.7.9a
Supplementary files format and content: The count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights and is supplied in a tsv file format.

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Qiagen RNA easy micro kit was used to extract RNA of cells directly sorted into Buffer RLT + β-mercaptoethanol, following manufacturer’s protocol.
Sequencing library was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) and sequenced on Illumina NovaSeq X Plus.

value: liver

value: NK

tag: batch


title: ASC_N10_1

city: Beijing

first: wuhan

last: wei

address: No. 33, Badachu Road, Shijingshan District

department: Plastic Surgery Hospital

country: China

institute: Chinese Academy of Medical Sciences

description:
Library name: ASC_N10_1
N10 oversxpression

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: TPM value for each Sample

molecule: total RNA

source_name: adipose-derived stem cells (ADSCs)

extract_protocol:
RNA was extracted from cell using TRIzol reagent. Briefly, cell were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: adipose-derived stem cells (ADSCs)

value: N10 overexpression


title: ASC_N10_2

description:
Library name: ASC_N10_2
N10 oversxpression


title: SUM-159 treated with DMSO rep3

description: Library name: 57_SUM-159_DMSO_R3

value: Breast

value: DMSO


title: SUM-159 treated with DMSO rep1

description: Library name: 55_SUM-159_DMSO_R1


title: ASC_NC_2

description:
Library name: ASC_NC_2
N10 WT

value: N10 WT


title: H1299, shFTO_1

city: Stanford

first: Erinn

last: Rankin

state: California

address: 269 Campus Dr

department: Rad Onc

institute: Stanford University

description:
Library name: Sample-4
NovaSeq X Plus Series (PE150)

data_processing:
Performed by the Novogene. Methods pdf attached. RNAseq_methods
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: Compiled in a single spreadsheet

source_name: Lung cancer

growth_protocol: RPMI-1640 + 10% FBS + pen/strep (37 degree + 5% CO2

extract_protocol:
RNA was extracted using Rnesay mini kit (Qiagen) and 1ug total Rna was sent it to the Novogene for library prep.
Performed by the Novogene. Methods pdf attached. RNAseq_methods

treatment_protocol: stable FTO KD vs WT cell ine

value: Lung cancer

value: NSCLC, epithelial


title: H1299, shFTO_2

description:
Library name: Sample-5
NovaSeq X Plus Series (PE150)


title: ASC_N10_3

description:
Library name: ASC_N10_3
N10 oversxpression


title: 8_5_Liver_KO_ILC

description: Library name: sample.8_5_Liv_KO_ILC

value: ILC


title: H1299, shCtrl_3

description:
Library name: Sample-3
NovaSeq X Plus Series (PE150)


title: H1299, shFTO_3

description:
Library name: Sample-6
NovaSeq X Plus Series (PE150)


title: ASC_NC_1

description:
Library name: ASC_NC_1
N10 WT


title: H1299, shCtrl_2

description:
Library name: Sample-2
NovaSeq X Plus Series (PE150)


title: 8_4_Liver_KO_NK

description: Library name: sample.8_4_Liv_KO_NK


title: 8_2_Liver_WT_NK

description: Library name: sample.8_2_Liv_WT_NK


title: 8_4_Liver_KO_ILC

description: Library name: sample.8_4_Liv_KO_ILC


title: SUM-159 treated with DMSO rep2

description: Library name: 56_SUM-159_DMSO_R2


title: 8_2_Liver_WT_ILC

description: Library name: sample.8_2_Liv_WT_ILC


title: SUM-159 treated with FHD-286 rep3

description: Library name: 60_SUM-159_FHD_R3


title: H1299, shCtrl_1

description:
Library name: Sample-1
NovaSeq X Plus Series (PE150)


title: dTAGV-1 4sUDRB-seq 20 min rep2

city: Shanghai

first: tian

last: tian

address: Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: dTAGV-1 4sUDRB-seq 20 min rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1.
Normalized abundancy in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: hg19
Supplementary files format and content: BigWig files contain normalized read counts (CPM, in 50-bp bins).
Library strategy: 4sUDRB-seq

growth_protocol: Jurkat-PAF1-dTAG cells were cultured in RPMI-1640 + 10% FBS + 2% Penicillin-Streptomycin + 2 mM L-Glutamine.

extract_protocol:
Total RNA was extracted using TRNzol according to the manufacturer’s instructions.
The total RNA was fragmented by treatment with NaOH at a final concentration of 0.2 M for 15 minutes, followed by neutralization with Tris-HCl (pH 6.8) at a final concentration of 0.5 M. Fragmented RNA was purified by isopropanol precipitation. After biotinylation of 4sU-labeled RNA, purification of biotinylated RNA with Dynabeads M-280 streptavidin and rRNA depletion, strand-specific RNA-seq libraries were constructed as previously described (Zhong et al., 2011). Libraries were sequenced on Illumina NovaSeq X Plus.

treatment_protocol: The cells were transferred to fresh antibiotics-free medium for 4 hours before initiating the experimental procedures. After DRB, DMSO, dTAGV-1 treatment and 4sU incorporation, total RNA was extracted.

value: Human T lymphocyte

tag: treatment 1

value: DRB

tag: time 1

value: 3 h

tag: treatment 2

tag: time 2

value: 2 h

tag: treatment 3

tag: time 3

value: 20 min


title: SUM-159 treated with FHD-286 rep2

description: Library name: 59_SUM-159_FHD_R2

value: WT


title: dTAGV-1 4sUDRB-seq 10 min rep2

description: Library name: dTAGV-1 4sUDRB-seq 10 min rep2

value: 10 min


title: dTAGV-1 4sUDRB-seq 0 min rep2

description: Library name: dTAGV-1 4sUDRB-seq 0 min rep2

value: 0 min


title: 8_1_Liver_WT_NK

description: Library name: sample.8_1_Liv_WT_NK

value: liver

value: NK


title: SUM-159 treated with FHD-286 rep1

description: Library name: 58_SUM-159_FHD_R1

value: cell line


title: dTAGV-1 4sUDRB-seq 20 min rep1

description: Library name: dTAGV-1 4sUDRB-seq 20 min rep1


title: K562 treated with DMSO rep3

description: Library name: 51_K562_DMSO_R3

value: Lymphoblastic


title: 8_1_Liver_WT_ILC

description: Library name: sample.8_1_Liv_WT_ILC


title: KLF4_FLAG_Plagl1ko_rep3_CUTtagseq

first: Jiahui

last: Du

address: Zhizaoju Road 639

description: Library name: KLF4_FLAG_Plagl1ko_rep3

data_processing:
Raw reads were ﬁltered using trim_galore (v0.6.10). Clean reads were aligned to the mm39 mouse genome using Bowtie 2 (v2.5.4).
Primary aligned reads were processed through duplicate marking using GATK4 (v4.5.5.0), followed by duplicate removal, unmapped and multimapped reads exclusion, and quality filtering (MAPQ > 20) with samtools (v1.21).
Tn5 transposase-mediated sequence offset correction was subsequently performed using the alignmentSieve function in deepTools (v3.5.5). Then the processed aligned reads were called for peaks using MACS3(v3.0.2)
For KLF4-FLAG CUT&Tag-seq data, differential binding analysis was performed using DiffBind (v3.16.0) and edgeR(v4.2.0) to identify differentially enriched peaks between samples from control and Ctsk-iCre;Plagl1fl/fl mice.
The peaks were annotated using HOMER (v4.11.1) and visualized with deepTools (v3.5.5).
Assembly: Mus_musculus.mm39.
Supplementary files format and content: Processed data outputs were systematically compiled in Excel spreadsheets, containing: peak annotation files and differential binding analysis result.
Library strategy: CUT&Tag

growth_protocol: Mandibular angle blocks were micro-dissected  at eight weeks old, digested with collagenase, type 1 (2 mg/mL), dispase II (2 mg/mL) in HBSS for 20 min at 37°C. The digestion solution was then filtered through a 70 μm filter, and resulting cells were cultured in α-minimum essential medium (α-MEM) containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
For each single CUT＆Tag-seq experiment: 0.1 millions PSPCs were processed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme Biotech, TD904), following the manufacturer’s protocol.
CUT＆Tag-seq libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme Biotech, TD904). Adapters were selected from the matching TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202).

treatment_protocol: For lentivirus transfection,  periosteal stem/progenitor cells (PSPCs) were infected with lentivirus expressing at a multiplicity of 10. For osteogenic induction, PSPCs were cultured in a complete medium supplemented with 50 μg/ml ascorbic acid (Sigma-Aldrich, A4544), 5 mM β-glycerophosphate (Sigma-Aldrich, G9422), and 10-7 M dexamethasone (Sigma-Aldrich, D4902) for 3 days.

value: Klf4-overexpression lentivirus (LV-Klf9-OE-Flag) transfection and osteogenic induction

tag: chip antibody

value: anti-Flag antibody (Cell signaling, 14793)


title: DMSO 4sUDRB-seq 20 min rep2

description: Library name: DMSO 4sUDRB-seq 20 min rep2

value: DMSO


title: K562 treated with DMSO rep2

description: Library name: 50_K562_DMSO_R2


title: dTAGV-1 4sUDRB-seq 10 min rep1

description: Library name: dTAGV-1 4sUDRB-seq 10 min rep1


title: DMSO 4sUDRB-seq 10 min rep2

description: Library name: DMSO 4sUDRB-seq 10 min rep2


title: dTAGV-1 4sUDRB-seq 0 min rep1

description: Library name: dTAGV-1 4sUDRB-seq 0 min rep1


title: DMSO 4sUDRB-seq 20 min rep1

description: Library name: DMSO 4sUDRB-seq 20 min rep1


title: K562 treated with DMSO rep1

description: Library name: 49_K562_DMSO_R1


title: KLF4_FLAG_Plagl1ko_rep2_CUTtagseq

description: Library name: KLF4_FLAG_Plagl1ko_rep2

source_name: periosteal stem/progenitor cells (PSPCs)

value: Klf4-overexpression lentivirus (LV-Klf8-OE-Flag) transfection and osteogenic induction


title: DMSO 4sUDRB-seq 10 min rep1

description: Library name: DMSO 4sUDRB-seq 10 min rep1


title: KLF4_FLAG_Plagl1ko_rep1_CUTtagseq

description: Library name: KLF4_FLAG_Plagl1ko_rep1

value: periosteal stem/progenitor cells (PSPCs)

value: Klf4-overexpression lentivirus (LV-Klf7-OE-Flag) transfection and osteogenic induction


title: DMSO 4sUDRB-seq 0 min rep2

description: Library name: DMSO 4sUDRB-seq 0 min rep2

value: Human T lymphocyte

value: DRB


title: KLF4_FLAG_Control_rep3_CUTtagseq

description: Library name: KLF4_FLAG_Control_rep3

value: Klf4-overexpression lentivirus (LV-Klf6-OE-Flag) transfection and osteogenic induction


title: K562 treated with FHD-286 rep3

description: Library name: 54_K562_FHD_R3


title: Input to PBRM1 ChIP in RIVA ARID1A HET clone 2 batch 3 rep2

description: Library name: 18_RIVA_ChIP_Arid1aHet_TQ2_input_R2

data_processing:
Processed through nfcore ChIPseq analysis pipeline.
Trimmed by TrimGalore, aligned with BWA, sequences filtered and duplicates marked.
Peak calling by macs2
Assembly: hg38
Supplementary files format and content: macs2 narrowPeak bed file

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min in 37 C. The reaction was quenched with glycine. Nuclei were isolated with a Triton-X-100-containing buffer, and chromatin was subject to sonication with BioRuptor Pico (Diagenode). After immunoprecipitation and reversal of crosslinking, the DNA was isolated with the phenol-chloroform method, and subject to library preparation.
Ultra II DNA Library Prep Kit for Illumina, with dual indexes. Size distribution of the libarries was assessed by Agilent Bioanalyzer.

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: Arid1a HET


title: K562 treated with FHD-286 rep2

description: Library name: 53_K562_FHD_R2

value: WT


title: KLF4_FLAG_Control_rep1_CUTtagseq

description: Library name: KLF4_FLAG_Control_rep1

value: Klf4-overexpression lentivirus (LV-Klf4-OE-Flag) transfection and osteogenic induction


title: DMSO 4sUDRB-seq 0 min rep1

description: Library name: DMSO 4sUDRB-seq 0 min rep1

value: 3 h

value: 2 h

value: 0 min


title: BRD7 to ChIP in RIVA ARID1A HET clone 2 batch 2

description: Library name: 06_RIVA_ChIP_Arid1aHet _TQ2_BRD7

value: cell line


title: H3K4me3_CUTtagseq

description: Library name: H3K4me3

value: osteogenic induction

value: anti-H3K4me3 antibody (Cell signaling, 9751)


title: KLF4_FLAG_Control_rep2_CUTtagseq

description: Library name: KLF4_FLAG_Control_rep2

value: Klf4-overexpression lentivirus (LV-Klf5-OE-Flag) transfection and osteogenic induction

value: anti-Flag antibody (Cell signaling, 14793)


title: Input to PBRM1 ChIP in RIVA ARID1A WT clone 2 batch 3 rep2

description: Library name: 16_RIVA_ChIP_Arid1aWt _DQ2_input_R1

value: Arid1a WT


title: AML3 treated with DMSO rep2

description: Library name: 05_AML3_ATAC_DMSO_R2

value: Bone Marrow

value: DMSO


title: BRD7 ChIP in RIVA ARID1A WT clone 1 batch 2

description: Library name: 03_RIVA_ChIP_Arid1aWt _DQ1_BRD7


title: Input to PBRM1 ChIP in RIVA ARID1A HET clone 1 batch 3 rep1

description: Library name: 13_RIVA_ChIP_Arid1aHet_TQ1_input_R1


title: K562 treated with FHD-286 rep1

description: Library name: 52_K562_FHD_R1

value: Lymphoblastic


title: AML3 treated with DMSO rep3

description: Library name: 06_AML3_ATAC_DMSO_R3


title: PLAGL1_igG_CUTtagseq

description: Library name: PLAGL1_igG

value: periosteal stem/progenitor cells (PSPCs)

value: Plagl1-overexpression lentivirus (LV-Plagl1-OE-HA) transfection and osteogenic induction

value: Normal Rabbit IgG antibody (Cell signaling, 2729)


title: Input to PBRM1 ChIP in RIVA ARID1A HET clone 2 batch 3 rep1

description: Library name: 17_RIVA_ChIP_Arid1aHet_TQ2_input_R1

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: Arid1a HET


title: Input to PBRM1 ChIP in RIVA ARID1A WT clone 2 batch 3 rep1

description: Library name: 15_RIVA_ChIP_Arid1aWt _DQ2_input_R1


title: Input to PBRM1 ChIP in RIVA ARID1A HET clone 1 batch 3 rep2

description: Library name: 14_RIVA_ChIP_Arid1aHet_TQ1_input_R2


title: AML3 treated with DMSO rep1

description: Library name: 04_AML3_ATAC_DMSO_R1

value: WT


title: PLAGL1_HA_CUTtagseq

description: Library name: PLAGL1_HA

value: anti-HA antibody (Cell signaling, 3724)


title: PBRM1 ChIP in RIVA ARID1A HET clone 2 batch 3 rep1

description: Library name: 07_RIVA_ChIP_Arid1aHet _TQ2_PBRM1_R1

value: cell line


title: Plagl1ko_ATACseq_rep2

description: Library name: Plagl1ko_rep2

data_processing:
Raw reads were ﬁltered using trim_galore (v0.6.10). Clean reads were aligned to the mm39 mouse genome using Bowtie 2 (v2.5.4).
Primary aligned reads were processed through duplicate marking using GATK4 (v4.5.5.0), followed by duplicate removal, unmapped and multimapped reads exclusion, and quality filtering (MAPQ > 20) with samtools (v1.21).
Tn5 transposase-mediated sequence offset correction was subsequently performed using the alignmentSieve function in deepTools (v3.5.5).
Differential binding analysis was performed using DiffBind (v3.16.0) to identify differentially accessible regions between samples from control and Ctsk-iCre;Plagl1fl/fl mice. All differentially accessible regions were then annotated using HOMER and visualized with deepTools (v3.5.5).
Motif enrichment analysis on differential accessiblity regions was performed by AME (v5.0.2) with default settings.
Assembly: Mus_musculus.mm39.
Supplementary files format and content: Processed data outputs were systematically compiled in Excel spreadsheets, containing: differential binding analysis result and  peak annotation files .

growth_protocol: Mandibular angle blocks from control and Ctsk-iCre;Plagl1fl/fl mice were micro-dissected  at eight weeks old, digested with collagenase, type 1 (2 mg/mL), dispase II (2 mg/mL) in HBSS for 20 min at 37°C. The digestion solution was then filtered through a 70 μm filter, and resulting cells were cultured in α-minimum essential medium (α-MEM) containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
For each single ATAC-seq experiment: 0.1 millions PSPCs after osteogenic induction were processed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711), following the manufacturer’s protocol.
ATAC-seq libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711). Adapters were selected from the matching TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202).

treatment_protocol: For osteogenic induction, PSPCs were cultured in a complete medium supplemented with 50 μg/ml ascorbic acid (Sigma-Aldrich, A4544), 5 mM β-glycerophosphate (Sigma-Aldrich, G9422), and 10-7 M dexamethasone (Sigma-Aldrich, D4902) for 3 days.

value: osteogenic induction for 3 days


title: Input to PBRM1 ChIP in RIVA ARID1A WT clone 1 batch 3 rep1

description: Library name: 11_RIVA_ChIP_Arid1aWt _DQ1_input_R1


title: Input to PBRM1 ChIP in RIVA ARID1A WT clone 1 batch 3 rep2

description: Library name: 12_RIVA_ChIP_Arid1aWt _DQ1_input_R2


title: PBRM1 ChIP in RIVA ARID1A HET clone 2 batch 3 rep2

description: Library name: 08_RIVA_ChIP_Arid1aHet _TQ2_PBRM1_R2


title: PBRM1 ChIP in RIVA ARID1A HET clone 1 batch 3  rep1

description: Library name: 03_RIVA_ChIP_Arid1aHet _TQ1_PBRM1_R1


title: RIVA Arid1a_Het_CTCF_WT clone 2

description: Library name: 08_TQ2_N1

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38
Supplementary files format and content: bed files of MACS2 narrowPeaks

value: ARID1A HET

value: non-treated


title: PBRM1 ChIP in RIVA ARID1A HET clone 1 batch 3 rep2

description: Library name: 04_RIVA_ChIP_Arid1aHet_TQ1_PBRM1_R2


title: Control_ATACseq_rep2

description: Library name: Control_rep2


title: AML3 treated with FHD-286 rep3

description: Library name: 03_AML3_ATAC_FHD286_R3


title: Control_ATACseq_rep1

description: Library name: Control_rep1


title: Plagl1ko_ATACseq_rep1

description: Library name: Plagl1ko_rep1


title: PBRM1 ChIP in RIVA ARID1A WT clone 2 batch 3 rep1

description: Library name: 05_RIVA_ChIP_Arid1aWt _DQ2_PBRM1_R1


title: PBRM1 ChIP in RIVA ARID1A WT clone 2 batch 3 rep2

description: Library name: 06_RIVA_ChIP_Arid1aWt _DQ2_PBRM1_R2


title: AML3 treated with FHD-286 rep1

description: Library name: 01_AML3_ATAC_FHD286_R1


title: RIVA Arid1a_Het_CTCF_WT clone 1

description: Library name: 07_TQ1_N1


title: AML3 treated with FHD-286 rep2

description: Library name: 02_AML3_ATAC_FHD286_R2


title: PBRM1 ChIP in RIVA ARID1A WT clone 1 batch 3 rep1

description: Library name: 01_RIVA_ChIP_Arid1aWt _DQ1_PBRM1_R1


title: SV-HUC treated with FHD-286 rep3

description: Library name: 24_SV-HUC_FHD_R3

value: SVHUC

value: Epithelial


title: Micro-C of RIVA ARID1A WT clone 2

description:
Library name: 03_RIVA_MicroC_Arid1aWt _DQ2_R1
WT_DQ.10kb.cool
hitad_dq_20kb.txt

data_processing:
*library strategy: Micro-C
Paired-end reads were aligned to the human genome (hg38) using BWA-MEM v0.7.18 for Novaseq output. Valid read pairs were retained using the parse module from pairtools v0.3.0. The pairtools split module was then used to generate a .bam and .pairs file, from which conact matrices (cool format) where generated using cooler cload pairix v0.9.3 and KR-normalized at 10kb resolution.
TADs were called using HiTAD v0.4.5 on 20kb cool matrices
Assembly: hg38
Supplementary files format and content: cool (raw and normalized contact matrices); bed (TAD calls)
the files generated from both clone samples are linked to the corresponding 'clone 1' sample records

source_name: RIVA

extract_protocol:
Two ARID1A wild-type and two heterozygous clones were used. Cells were crosslinked with 1% formaldehyde at room temperature for 10 min and quenched with 750 mM Tris-HCl (pH 7.4). Chromatin was digested with micrococcal nuclease. Digested DNA ends were repaired using biotinylated oligos and subjected to proximity ligation. For library preparation, biotynilated DNA was purified with streptavidin beads.
For library preparation, the DNA was bound to MyOne Streptavidin C1 beads from Invitrogen, washed with TBW, and processed using the NEB Ultra II DNA Library Prep Kit. Libraries were amplified using 10 PCR cycles, quantified via BioAnalyzer and Tapestation, and then sequenced on the NovoSeq X Plus platform using the PE150 SP Kit.

value: ARID1A WT


title: Micro-C of RIVA ARID1A Het clone 2

description:
Library name: 04_RIVA_MicroC_Arid1aHet_TQ2_R1
HET_TQ.10kb.cool
hitad_tq_20kb.txt


title: Micro-C of RIVA ARID1A Het clone 1

description:
Library name: 02_RIVA_MicroC_Arid1aHet _TQ1_R1
HET_TQ.10kb.cool
hitad_tq_20kb.txt


title: PBRM1 ChIP in RIVA ARID1A WT clone 1 batch 3 rep2

description: Library name: 02_RIVA_ChIP_Arid1aWt _DQ1_PBRM1_R2

value: Arid1a WT


city: Palo Alto

first: Basak

last: Eraslan

state: CA

address: 2360 Saint Francis Drive

institute: Genentech

description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch6_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad

library_source: other

data_processing:
scRNA files were demultiplexed using Cellranger mkfastq
Assembly: mm10
Supplementary files format and content: H5AD file containing raw counts matrix

molecule: other

source_name: Blood cells

extract_protocol:
BMDCs derived from mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a Chromium Single Cell 3' GEM Library and Gel Bead kit.
Hashtag (HTO) and guide dial out (GDO) libraries were generated as described (Geiger-Schuller and Eraslan et al., 2020)

value: Blood cells

value: BMDCs

tag: library type

value: GDO


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch5_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad

library_source: transcriptomic single cell

value: mRNA


title: Micro-C of RIVA ARID1A WT clone 1

description:
Library name: 01_RIVA_MicroC_Arid1aWt _DQ1_R1
WT_DQ.10kb.cool
hitad_dq_20kb.txt

value: RIVA


title: PBMC, HUVEC and LPS and Adalimumab, Donor 3

city: Aachen

middle: Thomas

last: Neullens

address: Pauwelsstraße 30, 52074

country: Germany

institute: RWTH Aachen University Medical Faculty

description:
Library name: Sample 40
CN208_D2_P7_S40

data_processing:
nextflow run nf-core/rnaseq
Assembly: GENCODE_GRCh38_v46
Supplementary files format and content: tsv data, mapped reads

source_name: blood

growth_protocol: 1x10^6 cells of HUVEC were seeded into 6-well plates and incubated for 24 hours at 37°C.

extract_protocol:
PBMCs from the supernatant were harvested. HUVECs were trysinised from the well plates. RNA from each sample was isolated using the RNeasy Mini Kit (Qiagen).
RNA libraries for RNA Seq were prepared using QuantSeq 3'mRNA-Seq Library Prep Kit v2 with Unique Dual Indices (UDIs) FWD for Illumina following manufacturor's protocol.

treatment_protocol: 4.8x10^6 cells of PBMCs were added to the HUVECs per 6-well plate, along with other stimuli, and incubated for another 24 hours. (10 ng/ml TNF, 50 µg/ml Abatacept, 10 µg/ml Adalimumab, 100 ng/ml LPS)

value: blood

value: mononuclear cells

value: HUVEC and LPS and Adalimumab


title: HUVEC, static, Donor 3

description:
Library name: Sample 36
CN208_D2_Hstatic_S36

source_name: umbilical vein

value: umbilical vein

value: endothelial cells

value: static culture control


title: PBMC, HUVEC, Donor 3

description:
Library name: Sample 37
CN208_D2_P3_S37

value: HUVEC


title: HUVEC, PBMC and LPS and Abatacept, Donor 3

description:
Library name: Sample 34
CN208_D2_H6_S34

value: PBMC and LPS and Abatacept


title: RIVA Arid1a_Het_CTCF_KO clone 2

description: Library name: 06_TQ2_BN

value: cell line

value: B-cell lymphoma ABC-DLBCL

value: ARID1A HET

value: non-treated


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch4_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad

value: Blood cells


title: RIVA Arid1a_Het_CTCF_KO clone 1

description: Library name: 05_TQ1_BN


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch6_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad

value: BMDCs


title: HUVEC, PBMC and LPS and Adalimumab, Donor 3

description:
Library name: Sample 35
CN208_D2_H7_S35

value: PBMC and LPS and Adalimumab


title: HUVEC, TNF, Donor 3

description:
Library name: Sample 33
CN208_D2_H5_S33

value: TNF


title: PBMC, HUVEC and LPS and Abatacept, Donor 3

description:
Library name: Sample 39
CN208_D2_P6_S39

value: HUVEC and LPS and Abatacept


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch3_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad

value: mRNA


title: RIVA Arid1a_WT_CTCF_WT clone 1

description: Library name: 03_DQ1_N1

value: RIVA

value: ARID1A WT


title: PBMC, HUVEC and LPS, Donor 3

description:
Library name: Sample 38
CN208_D2_P4_S38

value: blood

value: mononuclear cells

value: HUVEC and LPS


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch4_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad


title: PBMC, Control, Donor 3

description:
Library name: Sample 41
CN208_D2_P8_S41

value: Control


title: RIVA Arid1a_WT_CTCF_WT clone 2

description: Library name: 04_DQ2_N1


title: PBMC, LPS, Donor 3

description:
Library name: Sample 42
CN208_D2_P9_S42

value: LPS


title: Gene expression of MOCK, scRNAseq

city: Taipei City

first: Nai-Wen

last: Chang

address: 2F., No.7, Zhongshan S. Rd., Zhongzheng Dist.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
Library name: PL_Mock
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.0.0(https://support.10xgenomics.com/)
Assembly: Homo sapiens
Supplementary files format and content: Tab-seprated values files and matrix files

source_name: Immune cell

extract_protocol:
MPE CD3+ T cells were treated with or without 500 nM JQ1 for 3 days (D3R3, n=3). Multiplex single-cell sequencing analysis was performed using TotalSeq™-B antibodies (394645, 394647, 394635, and 394637, BioLegend) as per the manufacturer’s instructions. Briefly, 2 × 10^6 cells were resuspended in Cell Staining Buffer (BioLegend) and incubated with Human TruStain FcX™ Fc Blocking Reagent (BioLegend) for 10 minutes at 4°C. TotalSeq™-B antibodies were then added to each cell suspension and incubated for 30 minutes at 4°C. After antibody labeling, the samples were pooled, filtered through a 40 µm Flowmi™ Cell Strainer (BAH136800040, Sigma), and the cell concentration and viability were assessed using a Countess II FL Automated Cell Counter (Invitrogen™). Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, CG000206 Rev D), incorporating Feature Barcoding technology for cell surface protein analysis. To target a recovery of 10,000 cells, the cell suspension was adjusted to 700–1,200 viable cells per microliter before generating single628 cell gel beads in emulsion (GEM). Libraries were sequenced on a NovaSeq 6000 System (Illumina) using paired-end 150 bp reads, generating at least 80 GB of data per sample for gene transcriptome sequencing and 20 GB for hashing tags.
Single-cell gene expression library was prepared by the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer’s instructions.

value: Immune cell


title: HUVEC, PBMC, Donor 3

description:
Library name: Sample 31
CN208_D2_H3_S31

value: umbilical vein

value: endothelial cells

value: PBMC


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch5_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad

value: Blood cells

value: GDO


title: RIVA Arid1a_WT_CTCF_KO clone 1

description: Library name: 01_DQ1_BN

value: cell line

value: B-cell lymphoma ABC-DLBCL

value: non-treated


title: RIVA Arid1a_WT_CTCF_KO clone 2

description: Library name: 02_DQ2_BN


title: HUVEC, PBMC and LPS, Donor 3

description:
Library name: Sample 32
CN208_D2_H4_S32

value: PBMC and LPS


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch3_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad

value: BMDCs


title: Gene expression of JQ1, scRNAseq

description:
Library name: PL_JQ1
10x Genomics


title: HUVEC, Control, Donor 3

description:
Library name: Sample 29
CN208_D2_H1_S29


title: Hepatoblastoma, tumor cultured in DMSO [1-81-T2-DMSO]

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Analyses were performed on two paired-end samples using raw (>15 Gb) and trimmed data (>12 Gb), and the Q30 percentages of raw and trimmed data were >90% and >95%, respectively.
Trimmed reads were mapped to the reference genome (hg19) with HISAT2 resulting in >76% mapping ratio and transcripts were assembled by StringTie.
Assembly: Hg19
Supplementary files format and content: tab-delimited file with gene symbol and transcripts per million

extract_protocol:
Total RNA was extracted from fresh (immediately after surgery) tissues using the Trizol/chloroform extraction. Total RNA was isolated from cells of passages 1 and 2 using RiboZol (VWR).
PolyA stranded RNA-Seq was performed using NovaSeq6000 according to manufacturers protocols.

value: liver

value: cultured hepatoblastoma

value: Cultured


title: PBMC, HUVEC and LPS and Adalimumab, Donor 2

description:
Library name: Sample 26
CN201_P7_S26

value: blood

value: mononuclear cells

value: HUVEC and LPS and Adalimumab


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch1_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad

value: mRNA


title: PBMC, HUVEC and LPS and Abatacept, Donor 2

description:
Library name: Sample 25
CN201_P6_S25

value: HUVEC and LPS and Abatacept


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch2_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R1_raw.h5ad


title: Hepatoblastoma, tumor cultured in DMSO [LungMet86-DMSO]


title: HUVEC, TNF, Donor 2

description:
Library name: Sample 19
CN201_H5_S19

value: umbilical vein

value: endothelial cells

value: TNF


title: HUVEC, static, Donor 2

description:
Library name: Sample 22
CN201_Hstatic_S22

value: static culture control


title: Dual RNA-seq of mus_musculus RAW_qychJ_3

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description:
Library name: RAW_qychJ_3
Column name in gene_count_raw.xls: RAW_qychJ_3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: txt file includes gene counts for all Sample

source_name: RAW264.7 cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: RAW264.7 cells

value: murine macrophage


title: HUVEC, PBMC and LPS and Adalimumab, Donor 2

description:
Library name: Sample 21
CN201_H7_S21

value: PBMC and LPS and Adalimumab


title: Hepatoblastoma, fresh tumor [81T-original]

value: hepatoblastoma

value: Fresh


title: PBMC, HUVEC and LPS, Donor 2

description:
Library name: Sample 24
CN201_P4_S24

value: HUVEC and LPS


title: PBMC, Control, Donor 2

description:
Library name: Sample 27
CN201_P8_S27

value: Control


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch2_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad

value: Blood cells

value: BMDCs

value: GDO


description:
Library name: BMDC E3 screen, Combo Validation Round 1, ch1_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R1_raw.h5ad


title: HUVEC, PBMC and LPS, Donor 2

description:
Library name: Sample 18
CN201_H4_S18

value: PBMC and LPS


title: Hepatoblastoma, tumor cultured in DMSO [74T1-DMSO]

value: liver

value: cultured hepatoblastoma

value: Cultured


title: HUVEC, PBMC and LPS and Abatacept, Donor 2

description:
Library name: Sample 20
CN201_H6_S20

value: umbilical vein

value: endothelial cells

value: PBMC and LPS and Abatacept


title: HUVEC, PBMC, Donor 2

description:
Library name: Sample 17
CN201_H3_S17

value: PBMC


title: Hepatoblastoma, fresh tumor [LungMet86-OG-tumor]


title: PBMC, LPS, Donor 2

description:
Library name: Sample 28
CN201_P9_S28

value: blood

value: mononuclear cells

value: LPS


title: Dual RNA-seq of mus_musculus RAW_qychJ_1

description:
Library name: RAW_qychJ_1
Column name in gene_count_raw.xls: RAW_qychJ_1

value: RAW264.7 cells

value: murine macrophage


title: Dual RNA-seq of mus_musculus RAW_qychJ_2

description:
Library name: RAW_qychJ_2
Column name in gene_count_raw.xls: RAW_qychJ_2


title: PBMC, HUVEC, Donor 2

description:
Library name: Sample 23
CN201_P3_S23

value: HUVEC


title: HUVEC, LPS, Donor 3

description:
Library name: Sample 30
CN208_D2_H2_S30


title: Hepatoblastoma, tumor cultured in DMSO [75T2-DMSO]


title: HUVEC, Control, Donor 2

description:
Library name: Sample 15
CN201_H1_S15

value: Control


title: Hepatoblastoma, fresh tumor [75T-OG]

value: hepatoblastoma

value: Fresh


title: HUVEC, LPS, Donor 2

description:
Library name: Sample 16
CN201_H2_S16


title: Dual RNA-seq of mus_musculus RAW_WT_2

description:
Library name: RAW_WT_2
Column name in gene_count_raw.xls: RAW_WT_2


title: PBMC, Control, Donor 1

description:
Library name: Sample 13
CN198_P8_S13


title: PBMC, HUVEC and LPS and Adalimumab, Donor 1

description:
Library name: Sample 12
CN198_P7_S12

value: HUVEC and LPS and Adalimumab


title: Dual RNA-seq of mus_musculus RAW_WT_3

description:
Library name: RAW_WT_3
Column name in gene_count_raw.xls: RAW_WT_3


title: PBMC, HUVEC and LPS, Donor 1

description:
Library name: Sample 10
CN198_P4_S10

value: HUVEC and LPS


title: PBMC, HUVEC, Donor 1

description:
Library name: Sample 9
CN198_P3_S9


title: Dual RNA-seq of mus_musculus RAW_WT_1

description:
Library name: RAW_WT_1
Column name in gene_count_raw.xls: RAW_WT_1


title: ABE OT 3 Rep 2

city: Urbana

first: Pablo

last: Perez-Pinera

state: il

address: 1406 West Green Street

institute: University of Illinois Urbana-Champaign

description:
Library name: OT3_ABE_S2
Processed_GEO_Data_Sheet.xlsx

data_processing:
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing rates and figure number

extract_protocol:
For mouse tissues only striatum extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: epitheleal

value: Lipofectamine 2000 transfected

tag: sample group

value: ABE OT 3


title: ABE OT 3 Rep 3

description:
Library name: OT3_ABE_S3
Processed_GEO_Data_Sheet.xlsx


title: PBMC, HUVEC and LPS and Abatacept, Donor 1

description:
Library name: Sample 11
CN198_P6_S11

value: HUVEC and LPS and Abatacept


title: TNFR1ko-STmwtd1pi_4_S31

first: Kaiyi

last: Zhang

address: Pauwelsstraße 30

department: Medicine Microbiology

institute: Uniklinik RWTH Aachen

description: Library name: S15

data_processing:
Sequence reads were trimmed for adapter/low quality reads using Cutadapt v4.9 (-j 16 -a "poly A=A{20}" --quality-cutoff 20 -m 20 -u 12)
Trimmed sequences were mapped to the reference genome GRCm39_112 using STAR v2.7.11b (genomeGenerate with --sjdbOverhang 63 on GRCm39.112; then alignment with --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts)
Read count matrix creation was performed using featureCounts function from Rsubread v2.14.2
Assembly: mm39
Supplementary files format and content: countmatrix file is the matrix table for all the samples

source_name: Neonatal intestinal epithelial cells

growth_protocol: C57BL/6 and Tnfr1 knockout are bred locally at University Hospital RWTH Aachen under SPF conditions.

extract_protocol:
RNA was isolated from the epithelial cell pellet or homogenized intestinal tissue using TRIzol® according to manufacturer’s recommendations. 125 ng is used for library preparation
QuantSeq 3'mRNA-Seq v2 Library Prep Kit FWD with UDIs (Lexogen)

treatment_protocol: Overnight culture of wildtype (wt) S. Typhimurium (ATCC14028) or an isogenic ΔsopB mutant strain are diluted 1:10 and incubated at 37°C until reaching the logarithmic phase (OD600: 0.5). Bacteria are diluted to obtain the appropriate inoculum in PBS. One-day-old pups were orally infected with 100 CFU wt or ΔsopB S. Typhimurium.

value: Neonatal intestinal epithelial cells

value: Tnfr1 knockout

value: Salmonella wildtype infected for 1 day


title: HUVEC, static, Donor 1

description:
Library name: Sample 8
CN198_Hstatic_S8

value: umbilical vein

value: endothelial cells

value: static culture control


title: HUVEC, PBMC and LPS and Adalimumab, Donor 1

description:
Library name: Sample 7
CN198_H7_S7

value: PBMC and LPS and Adalimumab


title: Hepatoblastoma, fresh tumor [74T-OG]

value: liver


title: TNFR1ko-STmwtd1pi_3_S23

description: Library name: S14


title: HUVEC, PBMC and LPS and Abatacept, Donor 1

description:
Library name: Sample 6
CN198_H6_S6

value: PBMC and LPS and Abatacept


title: ABE OT 1 Rep 3

description:
Library name: OT1_ABE_S3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 1


title: PBMC, LPS, Donor 1

description:
Library name: Sample 14
CN198_P9_S14

value: blood

value: mononuclear cells

value: LPS


title: TNFR1ko-STmwtd1pi_2_S38

description: Library name: S13


title: HUVEC, PBMC and LPS, Donor 1

description:
Library name: Sample 4
CN198_H4_S4

value: PBMC and LPS


title: TNFR1ko-STmwtd1pi_1_S30

description: Library name: S12


title: ABE OT 1 Rep 2

description:
Library name: OT1_ABE_S2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected


title: HUVEC, PBMC, Donor 1

description:
Library name: Sample 3
CN198_H3_S3

value: PBMC


title: HUVEC, LPS, Donor 1

description:
Library name: Sample 2
CN198_H2_S2


title: BMDC E3 screen, Round 2, Ch24_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch24_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: Blood cells

value: BMDCs

value: mRNA


title: CBE OT 8C Rep 3

description:
Library name: HTTCBEOT8C_3
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 8C


title: CBE OT 7C Rep 3

description:
Library name: HTTCBEOT7C_3
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 7C


title: HUVEC, Control, Donor 1

description:
Library name: Sample 1
CN198_H1_S1

value: umbilical vein

value: endothelial cells

value: Control


title: ABE OT 1 Rep 1

description:
Library name: OT1_ABE_S1
Processed_GEO_Data_Sheet.xlsx


title: BMDC, 3hr +LPS

description:
Library name: BMDC, 3hr +LPS
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
stim_baseline_data_raw.h5ad


title: BMDC E3 screen, Round 2, Ch24_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch24_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: ABE OT 3 Rep 1

description:
Library name: OT3_ABE_S1
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 3


title: BMDC, baseline

description:
Library name: BMDC, baseline
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
stim_baseline_data_raw.h5ad


title: TNFR1ko-STmdsopBd1pi_4_S40

description: Library name: S11

value: Neonatal intestinal epithelial cells

value: Tnfr1 knockout

value: Salmonella delta sopB infected for 1 day


title: BMDC E3 screen, Round 2, Ch24_hash

description:
Library name: BMDC E3 screen, Round 2, Ch24_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

molecule: protein

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: BMDC E3 screen, Round 2, Ch22_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch22_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: CBE OT 7C Rep 2

description:
Library name: HTTCBEOT7C_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected


title: TNFR1ko-STmdsopBd1pi_3_S32

description: Library name: S10


title: TNFR1ko-STmdsopBd1pi_1_S39

description: Library name: S8


title: TNFR1ko-STmdsopBd1pi_2_S24

description: Library name: S9


title: BMDC E3 screen, Round 2, Ch22_hash

description:
Library name: BMDC E3 screen, Round 2, Ch22_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: Blood cells


title: CBE OT 7C Rep 1

description:
Library name: HTTCBEOT7C_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch21_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch21_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: BMDCs


title: BMDC E3 screen, Round 2, Ch22_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch22_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: TNFR1ko-co2d_4_S22

description: Library name: S7

value: no treatment


title: CBE OT 3 Rep 7

description:
Library name: HTTCBEOT3_7
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 3


title: BMDC E3 screen, Round 2, Ch20_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch20_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: BMDC E3 screen, Round 2, Ch21_hash

description:
Library name: BMDC E3 screen, Round 2, Ch21_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: TNFR1ko-co2d_1_S21

description: Library name: S4


title: BMDC E3 screen, Round 2, Ch19_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch19_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch19_hash

description:
Library name: BMDC E3 screen, Round 2, Ch19_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 3 Rep 5

description:
Library name: HTTCBEOT3_5
Processed_GEO_Data_Sheet.xlsx


title: B6-STmwtd1pi_S33

description: Library name: S3

value: C57BL/6 wildtype

value: Salmonella wildtype infected for 1 day


title: CBE OT 3 Rep 6

description:
Library name: HTTCBEOT3_6
Processed_GEO_Data_Sheet.xlsx


title: CBE OT 3 Rep 4

description:
Library name: HTTCBEOT3_4
Processed_GEO_Data_Sheet.xlsx


title: TNFR1ko-co2d_2_S29

description: Library name: S5


title: BMDC E3 screen, Round 2, Ch17_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch17_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch21_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch21_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: TNFR1ko-co2d_3_S37

description: Library name: S6


title: BMDC E3 screen, Round 2, Ch17_hash

description:
Library name: BMDC E3 screen, Round 2, Ch17_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: B6-STmdsopBd1pi_S41

description: Library name: S2


title: BMDC E3 screen, Round 2, Ch20_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch20_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: CBE OT 2 Rep 7

description:
Library name: HTTCBEOT2_7
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 2


title: CBE OT 2 Rep 6

description:
Library name: HTTCBEOT2_6
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch17_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch17_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: BMDC E3 screen, Round 2, Ch19_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch19_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch20_hash

description:
Library name: BMDC E3 screen, Round 2, Ch20_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch16_hash

description:
Library name: BMDC E3 screen, Round 2, Ch16_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: B6-co2d_S25

description: Library name: S1


title: HUVEC, TNF, Donor 1

description:
Library name: Sample 5
CN198_H5_S5

value: umbilical vein

value: endothelial cells

value: TNF


title: CBE OT 2 Rep 5

description:
Library name: HTTCBEOT2_5
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch15_hash

description:
Library name: BMDC E3 screen, Round 2, Ch15_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch15_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch15_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch14_hash

description:
Library name: BMDC E3 screen, Round 2, Ch14_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 1 Rep 7

description:
Library name: HTTCBEOT1_7
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 1


title: WT-1

city: Nanjing

first: Shuya

last: Sun

state: Jiangsu

address: No.12 Jiangwangmiao Street, Xuanwu District, Nanjing, Jiangsu Province, China

institute: Hospital for Skin Diseases, Institute of Dermatology, PUMC

description:
Library name: sample5
WT-1

data_processing:
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: HISAT2
Supplementary files format and content: FPKM

source_name: Epidermis

extract_protocol:
Total RNA from mouse epidermises was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
RNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Epidermis

value: Keratinocytes

value: WT

value: Imiquimod

value: same


title: WT-4

description:
Library name: sample8
WT-4


title: BMDC E3 screen, Round 2, Ch16_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch16_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: Blood cells

value: BMDCs


title: WT-3

description:
Library name: sample7
WT-3


title: BMDC E3 screen, Round 2, Ch13_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch13_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch14_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch14_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch15_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch15_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: CBE OT 2 Rep 4

description:
Library name: HTTCBEOT2_4
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected


title: CBE OT 1 Rep 6

description:
Library name: HTTCBEOT1_6
Processed_GEO_Data_Sheet.xlsx


title: WT-2

description:
Library name: sample6
WT-2


title: hnrnpu-cKO-4

description:
Library name: sample4
hnrnpu-cKO-4

value: Hnrnp-u knockout


title: BMDC E3 screen, Round 2, Ch13_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch13_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch13_hash

description:
Library name: BMDC E3 screen, Round 2, Ch13_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: BMDC E3 screen, Round 2, Ch14_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch14_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: CBE OT 1 Rep 5

description:
Library name: HTTCBEOT1_5
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 5 Rep 3

description:
Library name: HTTABEOT5_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 5


title: BMDC E3 screen, Round 2, Ch12_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch12_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch12_hash

description:
Library name: BMDC E3 screen, Round 2, Ch12_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch12_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch12_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: hnrnpu-cKO-2

description:
Library name: sample2
hnrnpu-cKO-2


title: CBE OT 1 Rep 4

description:
Library name: HTTCBEOT1_4
Processed_GEO_Data_Sheet.xlsx


title: hnrnpu-cKO-1

description:
Library name: sample1
hnrnpu-cKO-1


title: BMDC E3 screen, Round 2, Ch11_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch11_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: hnrnpu-cKO-3

description:
Library name: sample3
hnrnpu-cKO-3


title: ABE OT 5 Rep 1

description:
Library name: HTTABEOT5_1
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 5 Rep 2

description:
Library name: HTTABEOT5_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch11_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch11_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch11_hash

description:
Library name: BMDC E3 screen, Round 2, Ch11_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: Lung, infected, no antibiotics

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

description: Library name: ES3_INF_NT

data_processing:
Reads with read quality less than 30 were filtered out and CellRanger Count v6.0.2 (10X Genomics) was used to align reads onto mm10-2020-A reference genome.
Ambient background RNA were cleaned from the scRNA-seq data with “SoupX” (version 1.6.1). We utilized the following genes to estimate the non-expressing cells, calculate the contamination fraction, and adjust the gene expression counts: Dcn, Bgn, Aspn, Ecm2, Fos, Hbb-bs, Hbb-bt, Hba-a1, Hba-a2, Lyz1, Lyz2, Mgp, Postn, Scgb1a1.
Data integration and clustering was performed using a standard Seurat (v4.1.1) / SCTransform (v0.3.3.0) workflow. Individual SoupX “cleaned” libraries were concatenated and analyzed jointly. After quality filtering (removal of cells with <700 genes detected, or >10% or < 0.5% mitochondrial gene expression), data were normalized, highly-variable genes were identified, and percent mitochondrial gene expression and sequencing batch were regressed. Following PCA, Harmony v1.2.0 was run using a theta = 1 for batch correction.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrix in HDF5 format of counts for each cell.
Supplementary files format and content: Annotation and metadata for immune cells in csv format.

source_name: Lung

extract_protocol:
At the indicated timepoints, lung lobes were harvested, minced, and incubated for 30 minutes at 37°C in dissociation media (RPMI-1640 with 0.7 mg/ml collagenase XI and 30 mg/ml type IV bovine pancreatic DNase). After incubation, lobes were passed through a wide bore pipet tip and filtered through a 40 μm filter. Single cell lung suspension was then counted, aliquoted, and blocked with CD-32 Fc block (BD cat #553142) for 20 minutes on ice. After 2% FBS staining buffer wash, cells were incubated with the conjugated primary antibodies anti-CD45 (BioLegend cat # 103106) and anti-Ter119 (BioLegend cat# 116211). In the same manner, fluorescence minus one controls were blocked and stained with the appropriate antibody controls. Cells from individual mice were then incubated with identifiable hashtags, resuspended in staining buffer, and treated with PI viability dye. 2500 CD45 positive, 5000 CD45 negative, Ter119 negative, viable cells were collected by fluorescence associated cell sorting using a 70 μm nozzle on a 4-laser FACSAria III Cell Sorter. Both single and fluorescence-minus-one controls were used for compensation.
ScRNA-seq libraries were generated using the 10X Chromium platform 5’ library preparation kits (10X Genomics) following the manufacturer's recommendations and targeting 10,000 - 20,000 cells per sample.

value: Lung

value: infected, no antibiotics


title: ABE OT 4 Rep 3

description:
Library name: HTTABEOT4_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 4


title: Lung, infected, antibiotic prophylaxis

description: Library name: ES4_INF_VANC

value: infected, antibiotic prophylaxis


title: BMDC E3 screen, Round 2, Ch9_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch9_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch9_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch9_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch10_hash

description:
Library name: BMDC E3 screen, Round 2, Ch10_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch10_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch10_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: Lung, non-infected, no antibiotics

description: Library name: ES1_CTRL_NT

value: non-infected, no antibiotics


title: ABE OT 4 Rep 2

description:
Library name: HTTABEOT4_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch10_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch10_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch9_hash

description:
Library name: BMDC E3 screen, Round 2, Ch9_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: Lung, non-infected, antibiotic prophylaxis

description: Library name: ES2_CTRL_VANC

value: non-infected, antibiotic prophylaxis


title: ABE OT 4 Rep 1

description:
Library name: HTTABEOT4_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch8_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch8_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch8_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch8_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch8_hash

description:
Library name: BMDC E3 screen, Round 2, Ch8_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: ABE OT 2 Rep 3

description:
Library name: HTTABEOT2_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 2


title: 129CAS_MN_3

city: Berkeley

first: Rachel

middle: B

last: Brem

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

description: Library name: 129CAS_MN_3

data_processing:
Reads were mapped to either the CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

extract_protocol:
motor neurons were processed using Rneasy Micro Kit (Qiagen); samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: strain

value: motor neuron


title: ABE OT 2C Rep 3

description:
Library name: HTTABEOT2C_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 2C


title: BMDC E3 screen, Round 2, Ch7_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch7_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

tag: tissue

value: Blood cells

value: BMDCs


title: BMDC E3 screen, Round 2, Ch5_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch5_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch7_hash

description:
Library name: BMDC E3 screen, Round 2, Ch7_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: ABE OT 2 Rep 2

description:
Library name: HTTABEOT2_2
Processed_GEO_Data_Sheet.xlsx

tag: cell line

value: epitheleal

value: Lipofectamine 2000 transfected


title: ABE OT 2C Rep 2

description:
Library name: HTTABEOT2C_2
Processed_GEO_Data_Sheet.xlsx

tag: cell type


title: BMDC E3 screen, Round 2, Ch6_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch6_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: ABE OT 2 Rep 1

description:
Library name: HTTABEOT2_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 2, Ch6_hash

description:
Library name: BMDC E3 screen, Round 2, Ch6_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: BMDC E3 screen, Round 2, Ch7_FeatBarc and Ch16_mRNA (shared index SI-GA-D8)

description:
Library name: BMDC E3 screen, Round 2, Ch7_FeatBarc_Ch16_mRNA
R4_Ch7 CRISPR guide capture (GDO) and R4_Ch16 gene expression (3' mRNA) were sequenced with the same sample index (SI-GA-D8) on lanes 2-6 of flowcell H72G3CCX2. The shared FASTQs contain both library types and were computationally separated during cellranger count. Read1 contains cell barcode and UMI; Read2 contains either transcript or Guide Derived Oligo reads depending on library type.
BMDC_E3_screen_raw.h5ad

value: GDO+mRNA


title: 129CAS_MN_2

description: Library name: 129CAS_MN_2


title: BMDC E3 screen, Round 2, Ch5_hash

description:
Library name: BMDC E3 screen, Round 2, Ch5_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: 129CAS_MN_1

description: Library name: 129CAS_MN_1


title: BMDC E3 screen, Round 2, Ch4_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch4_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: BMDC E3 screen, Round 2, Ch6_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch6_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: RTX tumor – CMO library

city: New York

first: Daniel

last: Kutsovsky

address: 1300 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

description:
Library name: RTX_CMO_L003
Same cells as row 3; hash‑tag reads only

data_processing:
The RNA sequencing of the 12 tumors (n=3 per condition) itself was performed together to minimize batch effects between cohorts. Libraries were diluted to 10nM, pooled at a 4:1 ratio (gene expression:CMO) and clustered on an Illumina NovaSeq 6000 on a pair end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs), followed by 10 cycles of I7 Index (sample Index), and 91 bases on R2 (transcript), with a coverage around 400M reads per sample. Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA).  10x Genomics Cell Ranger Single Cell Software suite v7.1.0  was used to perform sample de-multiplexing, alignment (mm10), filtering, UMI counting,  single-cell 3’end gene counting, CMO mapping and performing quality control using the manufacturer parameters
Assembly: mm10
Supplementary files format and content: fastq: raw read data
Supplementary files format and content: .h5: CellRanger outs

source_name: skin

extract_protocol:
Tumors were acutely dissected out, washed with 10ml PBS(Gibco), and then cut into small pieces with scissors. The tissues were dissociated with Tumor Dissociation Kit (Miltenyi Biotech). Briefly, tissues were digested at 37°C for 30 minutes in 2.35ml RPMI (Corning) with 100ml Enzyme D, 50 ml enzyme R, 12.5 ml  enzyme A, then passed through 70mm cell strainer. The cell suspension was centrifuged at 300g for 7 minutes at room temperature and supernatants were removed. The cell pellet was resuspended with 1mL Red Blood Cell Lysis Solution (Miltenyi Biotech) and incubated for 10 minutes at 4°C. 10mL DPBS with 1% BSA was used to stop the red blood cell lysis. Cells were centrifuged and resuspended in 5mL DPBS with 1% BSA. Dead cells were then removed by Dead Cell Removal Kit (Miltenyi Biotech) using MS columns (Miltenyi Biotech) and the MiniMACS magnetic separator. After that, live cells were isolated via centrifuging, incubated with 100ml unique Cell Multiplexing Oligo (CMO) mixture (10x Genomics) for 5 minutes at room temperature, and washed several times to remove excess CMOs. Cell viability was assessed via staining with Trypan Blue and a hemocytometer, and then diluted to achieve target concentration for 10X sequencing.
Single-cell RNA-seq libraries were prepared according to 10x Genomics specifications (Single Cell 3′ Reagent Kits v3.1 User Guide CG000388, 10x Genomics, Pleasanton, CA, USA). Cellular suspensions (96% viable) at a concentration of 800 cells/µl, were loaded onto to the Chromium Controller to generate barcoded single-cell GEMs, targeting about 15000 single cells per sample. Barcoded and UMI labeled cDNA from poly A mRNA and DNA from the Cell Multiplexing Oligo tags (CMO) were generated simultaneously from the same cells inside the GEMs by incubation at 53 °C for 45 min, 85 °C for 5 min; held at 4 °C in a C1000 Touch Thermal cycler (Bio-Rad, Hercules). GEMs were broken, and cDNA and DNA from CMOs were amplified 11 cycles (98 °C for 3 min; 98 °C for 15 s, 63°C for 20 s) and the products separated by size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN). Gene expression libraries and CMOs libraries were generated independently. The fraction containing the cDNA was enzymatically fragmented, end repaired, A-tailed, and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through 12 cycles of PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s). To obtain the CMO libraries, the fraction containing the CMO was PCR amplified with unique Indexes for 6 cycles using the same conditions as above. Quality and quantity of the libraries was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Average cDNA size was 1600bp, average gene expression library 549bp and CMO library 212bp.

value: skin

value: cell multiplexing oligos

tag: genotype

value: DMSO or RTX

value: lane L003


title: BMDC E3 screen, Round 2, Ch5_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch5_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: ABE OT 2C Rep 1

description:
Library name: HTTABEOT2C_1
Processed_GEO_Data_Sheet.xlsx

tag: treatment


title: RTX tumor – gene‑expression library

description:
Library name: RTX_GEX_L003
10x Chromium 3′ v3.1; hashed sample S2

value: tumor+TME

tag: batch


title: 6‑OHDA tumor – cell‑multiplex (CMO) library

description:
Library name: 6OHDA_CMO_L003
Same cells as row 1; hash‑tag reads only

value: VC or 6OHDA


title: ABE OT 20C Rep 2

description:
Library name: HTTABEOT20C_2
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 20C


title: 6‑OHDA tumor – gene‑expression library

description:
Library name: 6OHDA_GEX_L003
10x Chromium 3′ v3.1; hashed sample S1


title: ABE OT 12C Rep 1

description:
Library name: HTTABEOT12C_1
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 12C


title: BMDC E3 screen, Round 2, Ch4_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch4_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: Blood cells


title: BMDC E3 screen, Round 2, Ch3_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch3_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: BMDCs


title: BMDC E3 screen, Round 2, Ch3_hash

description:
Library name: BMDC E3 screen, Round 2, Ch3_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch4_hash

description:
Library name: BMDC E3 screen, Round 2, Ch4_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 8C Rep 1

description:
Library name: CHTTCBEOT8_1
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: CBE OT 8C


title: RPE_null_spleen

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: Library name: RPE_null_spleen

data_processing:
All RNA-seq reads were processed using the 10x Cell Ranger pipeline v5.0.1. Fragments were aligned to the mm10 genome assembly using STAR aligner v2.7.2a.
Reads within coding regions were counted and normalized using Cell Ranger v5.0.1
Assembly: mm10
Supplementary files format and content: Expression values in binary HDF5 format

source_name: Spleen PBMCs following RPE-null treatment

growth_protocol: C57BL/6 mice that were implanted with encapsulated engineered cells that secrete IL10 or IL12 cytokines (RPE-IL10 or RPE-IL12), encapsulated non-engineered cells (RPE-null), or microcapsules alone (sham).

extract_protocol:
Cells surrounding implants in the intraperitoneal cavity or spleens were harvested. All samples are pooled from 6 independent mice in the same condition.
Libraries were processed using 10x Chromium NextGEM Single Cell Immune Profiling Solution 5’v2 according to the manufacturer's instructions.

treatment_protocol: Following implantation, mice received no additional treatment.

value: Spleen

value: PBMC


title: BMDC E3 screen, Round 2, Ch2_hash

description:
Library name: BMDC E3 screen, Round 2, Ch2_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: BMDC E3 screen, Round 2, Ch2_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch2_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: BMDC E3 screen, Round 2, Ch3_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch3_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: sham_null_IP

description: Library name: sham_null_IP

source_name: Intraperitoneal PBMCs following sham treatment

value: Intraperitoneal


title: RPE_null_IP

description: Library name: RPE_null_IP

source_name: Intraperitoneal PBMCs following RPE-null treatment


title: BMDC E3 screen, Round 2, Ch2_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch2_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch1_hash

description:
Library name: BMDC E3 screen, Round 2, Ch1_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 8C Rep 2

description:
Library name: CHTTCBEOT8_2
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected


title: RPE_IL12_spleen

description: Library name: RPE_IL12_spleen

source_name: Spleen PBMCs following treatment with RPE-IL12


title: CBE OT 6C Rep 3

description:
Library name: CHTTCBEOT6C_3
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 6C


title: BMDC E3 screen, Round 2, Ch1_mRNA

description:
Library name: BMDC E3 screen, Round 2, Ch1_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: CBE OT 6C Rep 2

description:
Library name: CHTTCBEOT6C_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch24_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch24_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: CBE OT 6C Rep 1

description:
Library name: CHTTCBEOT6C_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch24_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch24_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 2, Ch1_FeatBarc

description:
Library name: BMDC E3 screen, Round 2, Ch1_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch24_hash

description:
Library name: BMDC E3 screen, Round 1, Ch24_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 5C Rep 3

description:
Library name: CHTTCBEOT5C_3
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 5C


title: BMDC E3 screen, Round 1, Ch23_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch23_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: RPE_IL12_IP

description: Library name: RPE_IL12_IP

source_name: Intraperitoneal PBMCs following treatment with RPE-IL12


title: RPE_IL10_spleen

description: Library name: RPE_IL10_spleen

source_name: Spleen PBMCs following treatment with RPE-IL10


title: BMDC E3 screen, Round 1, Ch23_hash

description:
Library name: BMDC E3 screen, Round 1, Ch23_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch23_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch23_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: CBE OT 5C Rep 2

description:
Library name: CHTTCBEOT5C_2
Processed_GEO_Data_Sheet.xlsx


title: RPE_IL10_IP

description: Library name: RPE_IL10_IP

source_name: Intraperitoneal PBMCs following treatment with RPE-IL10


title: BMDC E3 screen, Round 1, Ch22_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch22_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: CBE OT 5C Rep 1

description:
Library name: CHTTCBEOT5C_1
Processed_GEO_Data_Sheet.xlsx


title: mES treated with DMSO rep2

first: Christopher

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: 08_mES_ATAC_DMSO_R2

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

source_name: cell line

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

value: cell line

value: mES

value: mouse embryonic stem cells

value: WT

value: DMSO


title: BMDC E3 screen, Round 1, Ch21_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch21_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

source_name: Blood cells

value: Blood cells

value: BMDCs


title: CBE OT 4C Rep 2

description:
Library name: CHTTCBEOT4C_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: CBE OT 4C


title: BMDC E3 screen, Round 1, Ch22_hash

description:
Library name: BMDC E3 screen, Round 1, Ch22_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO


title: BMDC E3 screen, Round 1, Ch22_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch22_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch20_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch20_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch21_hash

description:
Library name: BMDC E3 screen, Round 1, Ch21_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: BMDC E3 screen, Round 1, Ch20_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch20_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch21_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch21_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: mES treated with DMSO rep3

description: Library name: 09_mES_ATAC_DMSO_R3


title: CBE OT 4C Rep 3

description:
Library name: CHTTCBEOT4C_3
Processed_GEO_Data_Sheet.xlsx


title: mES treated with DMSO rep1

description: Library name: 07_mES_ATAC_DMSO_R1


title: BMDC E3 screen, Round 1, Ch20_hash

description:
Library name: BMDC E3 screen, Round 1, Ch20_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: mES treated with FHD-286 rep3

description: Library name: 12_mES_ATAC_FHD_100nM_R3


title: CBE OT 4C Rep 1

description:
Library name: CHTTCBEOT4C_1
Processed_GEO_Data_Sheet.xlsx


title: mES treated with FHD-286 rep2

description: Library name: 11_mES_ATAC_FHD_100nM_R2


title: BMDC E3 screen, Round 1, Ch19_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch19_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: CBE OT 3C Rep 3

description:
Library name: CHTTCBEOT3_3
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 3C


title: BMDC E3 screen, Round 1, Ch19_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch19_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: BMDC E3 screen, Round 1, Ch18_hash

description:
Library name: BMDC E3 screen, Round 1, Ch18_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch18_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch18_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: mES treated with FHD-286 rep1

description: Library name: 10_mES_ATAC_FHD_100nM_R1


title: ID8 treated with DMSO rep3

description: Library name: 09_ID8_DMSO_R3

value: Ovaries


title: BMDC E3 screen, Round 1, Ch17_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch17_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch19_hash

description:
Library name: BMDC E3 screen, Round 1, Ch19_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 3C Rep 2

description:
Library name: CHTTCBEOT3_2
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected


title: BMDC E3 screen, Round 1, Ch17_hash

description:
Library name: BMDC E3 screen, Round 1, Ch17_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 2C Rep 2

description:
Library name: CHTTCBEOT2_2
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 2C


title: CBE OT 3C Rep 1

description:
Library name: CHTTCBEOT3_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch16_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch16_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: ID8 treated with DMSO rep1

description: Library name: 07_ID8_DMSO_R1

value: cell line


title: BMDC E3 screen, Round 1, Ch18_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch18_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch17_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch17_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: CBE OT 2C Rep 3

description:
Library name: CHTTCBEOT2_3
Processed_GEO_Data_Sheet.xlsx


title: ID8 treated with FHD-286 rep3

description: Library name: 12_ID8_FHD_R3


title: ID8 treated with DMSO rep2

description: Library name: 08_ID8_DMSO_R2


title: BMDC E3 screen, Round 1, Ch16_hash

description:
Library name: BMDC E3 screen, Round 1, Ch16_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch16_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch16_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: CBE OT 2C Rep 1

description:
Library name: CHTTCBEOT2_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch15_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch15_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: ID8 treated with FHD-286 rep1

description: Library name: 10_ID8_FHD_R1


title: BMDC E3 screen, Round 1, Ch15_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch15_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch15_hash

description:
Library name: BMDC E3 screen, Round 1, Ch15_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: CBE OT 1C Rep 1

description:
Library name: CHTTCBEOT1_1
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 1C


title: BMDC E3 screen, Round 1, Ch14_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch14_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: GCB_CtcfHet_D10_ATAC

description:
Library name: 2_CTCF-30_ATAC
Single cell ATAC data of CtcfHet processed and sequenced with GSE237987

library_source: genomic single cell

data_processing:
Cellranger Arc 2.0.0
Signac 1.5.0 Processing
MACS2 peak calling
Harmony correction of PCA and LSI
Label transfer from reference dataset
Slingshot 2.8.0 pseudotime
Assembly: mm10
Supplementary files format and content: ctcf.gc.multiome.sobj.chromvar.rds (Signac object), corresponds to both the scRNA and scATAC

source_name: spleen

extract_protocol:
Germinal Center B cells were sorted from the spleen and underwent the manufacturer's nuclear preparation procedure
20000 nuclei were loaded into the 10x Chromium Instrument and prepared according to the manufacturer's protocol for 10x multiome

treatment_protocol: Mice were immunized with SRBC 10 days prior to the experiment

value: spleen

value: primary cells

value: Germinal Center B Cells

value: Ctcf+/-

value: SRBC Immunization


title: CBE OT 1C Rep 3

description:
Library name: CHTTCBEOT1_3
Processed_GEO_Data_Sheet.xlsx

value: epitheleal


title: ABE OT 9C Rep 3

description:
Library name: CHTTABEOT9_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 9C


title: BMDC E3 screen, Round 1, Ch14_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch14_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: Blood cells

value: BMDCs


title: ID8 treated with FHD-286 rep2

description: Library name: 11_ID8_FHD_R2

value: WT


title: CBE OT 1C Rep 2

description:
Library name: CHTTCBEOT1_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch12_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch12_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: BMDC E3 screen, Round 1, Ch14_hash

description:
Library name: BMDC E3 screen, Round 1, Ch14_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: ABE OT 9C Rep 2

description:
Library name: CHTTABEOT9_2
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected


title: GCB_CtcfHet_D10_RNA

description:
Library name: 2_CTCF-30_RNA
Single cell RNA data of CtcfHet processed and sequenced with GSE237987


title: BMDC E3 screen, Round 1, Ch13_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch13_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: Wild-type, hypothalamus, rep2, batch 2019

city: Los Angeles

first: Xia

last: Yang

email: xyang123@ucla.edu, jading@ucla.edu

address: 610 Charles E Young Dr S

institute: University of California Los Angeles

description:
Library name: WT-2-19-Hyp
10x Genomics

data_processing:
Reads were aligned to the mm10 genome and gene counts were calculated using CellRanger software (v 3.0.2) (10X Genomics).
CellBender remove-background was used on raw feature-barcode matrices to remove ambient RNA contamination.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hypothalamus

extract_protocol:
Papain was used to digest freshly dissected hippocampus and hypothalamus tissues. The cells were suspended to a final concentration of 1000 cells/μl in 0.04% BSA-PBS.
Libraries were prepared according to the manufacturer's protocol (3' single cell RNAseq V3 kit, 10x Genomics).

treatment_protocol: High fructose (F), DHA, NR, DHA+F, NR+F

value: hypothalamus

value: Wild-type


title: Wild-type, hypothalamus, rep3, batch 2019

description:
Library name: WT-3-19-Hyp
10x Genomics


title: BMDC E3 screen, Round 1, Ch12_hash

description:
Library name: BMDC E3 screen, Round 1, Ch12_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch13_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch13_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: Wild-type, hypothalamus, rep1, batch 2019

description:
Library name: WT-1-19-Hyp
10x Genomics


title: ABE OT 9C Rep 1

description:
Library name: CHTTABEOT9_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch13_hash

description:
Library name: BMDC E3 screen, Round 1, Ch13_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch11_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch11_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: ABE OT 8C Rep 2

description:
Library name: CHTTABEOT8_2
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 8C


title: ABE OT 8C Rep 3

description:
Library name: CHTTABEOT8_3
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch10_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch10_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch11_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch11_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch12_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch12_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch9_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch9_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch10_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch10_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch10_hash

description:
Library name: BMDC E3 screen, Round 1, Ch10_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: ABE OT 7C Rep 3

description:
Library name: CHTTABEOT7_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 7C


title: BMDC E3 screen, Round 1, Ch11_hash

description:
Library name: BMDC E3 screen, Round 1, Ch11_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: 5xFAD, hypothalamus, rep2, batch 2019

description:
Library name: AD-5-19-Hyp
10x Genomics


title: 5xFAD, hypothalamus, NR and fructose, rep3, batch 2019

description:
Library name: AD-NRF-3-19-Hyp
10x Genomics

value: NR and fructose


title: BMDC E3 screen, Round 1, Ch8_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch8_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: 5xFAD, hypothalamus, rep1, batch 2019

description:
Library name: AD-3-19-Hyp
10x Genomics


title: ABE OT 7C Rep 2

description:
Library name: CHTTABEOT7_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch9_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch9_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: ABE OT 8C Rep 1

description:
Library name: CHTTABEOT8_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch8_hash

description:
Library name: BMDC E3 screen, Round 1, Ch8_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: 5xFAD, hypothalamus, rep3, batch 2019

description:
Library name: AD-6-19-Hyp
10x Genomics