title: 12b-SR-RA_F02_SR_RA

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

institute: Queen Mary University of London

hyb_protocol: Array hibridisation was carried out at the QMUL Genome Centre following manufacturer specifications with Infinium MethylationEPIC v2.0 Kit.

scan_protocol: Array scanning was carried out at the QMUL Genome Centre following manufacturer specifications for Infinium MethylationEPIC v2.0 (GPL33022)

data_processing:
Methylation array data was processed to quantify methylation levels for a total of 930,698 CpG sites using the R Bioconductor package meffil (v1.3.6) (Min et al., 2018). Briefly, functional normalisation was applied to array intensity data (“.idat” files) to correct for between-array technical variation. As a quality control, sex of the individuals was properly assigned based on X and Y chromosome probes measurements and multidimensional scaling visualisation displayed clear grouping of anatomical side pairs per individual, confirming the expected inter-individual variability in DNAm signals. Low-quality and sex chromosome probes were removed.
*processed value definition: Methylation status was reported for all measured CpG sites as β-values ranging from 0 to 1 representing the fraction of DNAm signal compared to the total locus signal intensity.

label: biotin (ddCTP and ddGTP) and DNP (ddATP and ddUTP)

source_name: heart right atrium

label_protocol: Bisulfite treatment and subsequent amplification and hybridisation to methylation profiling microarray was performed by the QMUL Genome Centre. The Infinium MethylationEPIC v2.0 kit was used, providing coverage of approximately 930K CpGs, including RefSeq annotated genes, CpG islands and enhancer regions. Even and random distribution of biological groups across two chips of 8 samples each was assigned using the OSAT R Bioconductor package (Yan et al., 2012).

extract_protocol: Genomic DNA was isolated from 16 heart atrial biopsies (AF-LA, n=6; AF-RA, n=5; SR-LA, n=4; SR-RA, n=4) using the DNeasy Blood & Tissue Kit (Qiagen). DNA quality was determined with a NanoDrop Spectrophotometer.

value: heart right atrium

tag: disease state

value: synus rhythm


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 5

status: Public on Feb 16 2026

type: SRA

city: Darmstadt

first: Daniel

last: Kelvin

address: Merckstrasse 25

department: Centre for Synthetic Biology

country: Germany

institute: Technical University of Darmstadt

description: Library name: TcNeo5

library_source: other

data_processing:
Initial data processing performed by Azenta/GENEWIZ.
Assembly: TNNAND1: TGCCTAAAACATACTAGCTTGTCCTTTAATGGTCCTAGAGAGGTGAAGAATACGACCACCTAGGCA; TNNAND8: TGCCTAAAACATACTCGCTTGTCCTTTAATGGTCCTTGAGAGGTGAAGAATACGACCACCTAGGCA
Supplementary files format and content: csv files include the readcount of each sequence discovered in a sample.

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
Plasmid DNA was extracted from yeast using the Yeast Plasmid Miniprep II kit from Zymo Research. The randomized region on the plasmid was amplified via PCR and the product was purified using the Wizard SV Gel and PCR Clean-Up System from Promega.
Yeast libraries were created through homologous recombination by amplifying each sequence pool with primers homologous to the linearized (AgeI+NheI) backbone pCBB06 (Boussebayle et al., 2019) and transforming S. cerevisiae RS453 with with linearized backbone and amplified pool DNA using a high efficiency electroporation protocol (Benatuil et al., 2010).

tag: cell line

tag: sample group


title: Whole Stool 16S Sample S21B

city: Jacksonville

first: John

last: Gubatan

state: FL

address: Mayo Clinic Mangurian Building 5220, 4500 San Pablo Rd

country: USA

institute: Mayo Clinic Florida

description:
Library name: S21B
Novogene

library_source: genomic

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged VD16Seq2.rds Phyloseq object
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: human feces metagenome

source_name: Stool

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.

treatment_protocol: Patients with established inflammatory bowel disease (ulcerative colitis or Crohn’s disease) were screened and invited to participate in vitamin D prospective study at Stanford University (IRB 60958) and the University of Copenhagen (IRB 2021-1696). Patients who met inclusion criteria (adult patients (18 years or older) with inflammatory bowel disease (ulcerative colitis or Crohn's disease), low serum vitamin D (25(OH)D ≤ 25 ng/mL, not on vitamin D supplementation at time of recruitment, no prior bowel resections, no antibiotic use in past 3 months) were enrolled. Patients who had prior bowel surgeries (colectomy, small bowel resections), renal dysfunction, history of hypercalcemia, history of HIV (human immunodeficiency virus), history of IgA deficiency, history of common variable immunodeficiency (CVID), or current or recent C. diff infection were excluded from study. All patients provided consent in accordance with Institutional Review Board guidance for each institution as noted above. At the time of enrollment (week 0), patients had blood and stool samples collected. Patients were then treated with 50,000 units of oral vitamin D (ergocalciferol) once per week for 12 weeks. Blood and stool samples were collected at the end of study (week 12). C-reactive protein and fecal calprotectin were measured from week 0 and week 12 blood and stool samples, respectively. Disease activity scores (partial Mayo score for ulcerative colitis, Harvey Bradshaw Index for Crohn’s disease), quality of life scores (short inflammatory bowel disease questionnaire/SIBDQ) were collected at week 0 and week 12.

tag: tissue

value: Stool

tag: patient id

tag: treatment

value: Post-vitamin D


title: Whole Stool 16S Sample S20B

description:
Library name: S20B
Novogene


title: LS-WFPM0.1 somatic cells 6

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description:
Library name: T6
Column name in RawCounts2.csv: T6

library_source: transcriptomic

data_processing:
High-quality, trimmed paired-end reads were processed using Partek Flow software. Potential ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) contaminants were removed using Bowtie 2. The cleaned reads were aligned to the mouse reference genome (mm10) using the HISAT 2 aligner. Raw read counts were generated by mapping aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm, and normalization was performed using the Transcripts Per Million (TPM) method.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: primary cell

extract_protocol:
Arcturus PicoPure RNA Isolation Kit
Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems), following the manufacturer’s protocol. Library preparation and low-input RNA-seq were conducted on the Illumina NovaSeq PE150 platform by Novogene (Novogene Corporation, Sacramento, CA).

tag: cell type

value: primary cell

tag: genotype

value: WT

tag: batch


title: LS-WFPM0.1 somatic cells 5

description:
Library name: T5
Column name in RawCounts2.csv: T5


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 4

description: Library name: TcNeo4


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 3

description: Library name: TcNeo3


title: IgG-Seq Sample IgG24A

description:
Library name: IgG24A
Novogene
IGGSEQ.rds

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

organism: Homo sapiens

value: Pre-vitamin D


title: Whole Stool 16S Sample S19B

description:
Library name: S19B
Novogene


title: LS-WFPM0.1 somatic cells 4

description:
Library name: T4
Column name in RawCounts2.csv: T4


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 2

description: Library name: TcNeo2


title: IgG-Seq Sample IgG23A

description:
Library name: IgG23A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 1

description: Library name: TcNeo1


title: LS-WFPM0.1 somatic cells 2

description:
Library name: T2
Column name in RawCounts2.csv: T2


title: Whole Stool 16S Sample S17B

description:
Library name: S17B
Novogene


title: IgG-Seq Sample IgG22A

description:
Library name: IgG22A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S18B

description:
Library name: S18B
Novogene


title: LS-WFPM0.1 somatic cells 3

description:
Library name: T3
Column name in RawCounts2.csv: T3


title: Whole Stool 16S Sample S16B

description:
Library name: S16B
Novogene


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation positive control

description: Library name: Neo-plus

value: TNNAND1_N6 sequence pool, condition Neo


title: IgG-Seq Sample IgG21A

description:
Library name: IgG21A
Novogene
IGGSEQ.rds


title: LS-WFPM0.1 somatic cells 1

description:
Library name: T1
Column name in RawCounts2.csv: T1


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation negative control

description: Library name: Neo-minus


title: Whole Stool 16S Sample S15B

description:
Library name: S15B
Novogene


title: IgG-Seq Sample IgG20A

description:
Library name: IgG20A
Novogene
IGGSEQ.rds


title: Control somatic cells 5

description:
Library name: C5
Column name in RawCounts2.csv: C5

value: Vehicle


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 8

description: Library name: Neo8


title: Whole Stool 16S Sample S14B

description:
Library name: S14B
Novogene


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 7

description: Library name: Neo7


title: IgG-Seq Sample IgG19A

description:
Library name: IgG19A
Novogene
IGGSEQ.rds


title: Control somatic cells 4

description:
Library name: C4
Column name in RawCounts2.csv: C4


title: IgG-Seq Sample IgG18A

description:
Library name: IgG18A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S13B

description:
Library name: S13B
Novogene


title: Control somatic cells 3

description:
Library name: C3
Column name in RawCounts2.csv: C3


title: Control somatic cells 2

description:
Library name: C2
Column name in RawCounts2.csv: C2


title: Whole Stool 16S Sample S12B

description:
Library name: S12B
Novogene


title: IgG-Seq Sample IgG17A

description:
Library name: IgG17A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 6

description: Library name: Neo6


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 5

description: Library name: Neo5


title: IgG-Seq Sample IgG16A

description:
Library name: IgG16A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S11B

description:
Library name: S11B
Novogene


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 4

description: Library name: Neo4


title: IgG-Seq Sample IgG15A

description:
Library name: IgG15A
Novogene
IGGSEQ.rds


title: C-WFPM0.1 somatic cells 6

description:
Library name: T6
Column name in RawCounts4.csv: T6


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 3

description: Library name: Neo3


title: Whole Stool 16S Sample S10B

description:
Library name: S10B
Novogene


title: Control somatic cells 1

description:
Library name: C1
Column name in RawCounts2.csv: C1


title: Whole Stool 16S Sample S9B

description:
Library name: S9B
Novogene


title: IgG-Seq Sample IgG14A

description:
Library name: IgG14A
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG13A

description:
Library name: IgG13A
Novogene
IGGSEQ.rds


title: C-WFPM0.1 somatic cells 5

description:
Library name: T5
Column name in RawCounts4.csv: T5


title: Whole Stool 16S Sample S8B

description:
Library name: S8B
Novogene


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 2

description: Library name: Neo2


title: C-WFPM0.1 somatic cells 4

description:
Library name: T4
Column name in RawCounts4.csv: T4


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 1

description: Library name: Neo1


title: IgG-Seq Sample IgG12A

description:
Library name: IgG12A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S7B

description:
Library name: S7B
Novogene


title: C-WFPM0.1 somatic cells 3

description:
Library name: T3
Column name in RawCounts4.csv: T3


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation positive control

description: Library name: Tc-plus

value: TNNAND1_N6 sequence pool, condition Tc


title: IgG-Seq Sample IgG11A

description:
Library name: IgG11A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S6B

description:
Library name: S6B
Novogene


title: C-WFPM0.1 somatic cells 2

description:
Library name: T2
Column name in RawCounts4.csv: T2


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation negative control

description: Library name: Tc-minus


title: C-WFPM0.1 somatic cells 1

description:
Library name: T1
Column name in RawCounts4.csv: T1


title: IgG-Seq Sample IgG10A

description:
Library name: IgG10A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S5B

description:
Library name: S5B
Novogene


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 8

description: Library name: Tc8


title: IgG-Seq Sample IgG9A

description:
Library name: IgG9A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S4B

description:
Library name: S4B
Novogene


title: Control somatic cells 5

description:
Library name: C5
Column name in RawCounts4.csv: C5


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 7

description: Library name: Tc7


title: IgG-Seq Sample IgG8A

description:
Library name: IgG8A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S3B

description:
Library name: S3B
Novogene


title: Control somatic cells 4

description:
Library name: C4
Column name in RawCounts4.csv: C4


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 6

description: Library name: Tc6


title: IgG-Seq Sample IgG7A

description:
Library name: IgG7A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S2B

description:
Library name: S2B
Novogene


title: Control somatic cells 3

description:
Library name: C3
Column name in RawCounts4.csv: C3


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 5

description: Library name: Tc5


title: IgG-Seq Sample IgG6A

description:
Library name: IgG6A
Novogene
IGGSEQ.rds


title: Control somatic cells 2

description:
Library name: C2
Column name in RawCounts4.csv: C2


title: Whole Stool 16S Sample S1B

description:
Library name: S1B
Novogene


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 4

description: Library name: Tc4


title: IgG-Seq Sample IgG5A

description:
Library name: IgG5A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S48A

description:
Library name: S48A
Novogene


title: Control somatic cells 1

description:
Library name: C1
Column name in RawCounts4.csv: C1


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 3

description: Library name: Tc3


title: IgG-Seq Sample IgG4A

description:
Library name: IgG4A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S47A

description:
Library name: S47A
Novogene


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 2

description: Library name: Tc2


title: LS-WFPM0.1 somatic cells 2

description:
Library name: H2
Column name in RawCounts1.csv: H2

data_processing:
After sequencing, fastq files were imported into Galaxy (version 24.2.rc1) for downstream analysis. RNA-seq reads were aligned to the whole mouse genome assembly-mm10 by HISAT2, quantified by featureCounts, and normalized using the Transcripts Per Million (TPM) method.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 1

description: Library name: Tc1


title: Whole Stool 16S Sample S46A

description:
Library name: S46A
Novogene


title: Whole Stool 16S Sample S45A

description:
Library name: S45A
Novogene


title: LS-WFPM0.1 somatic cells 1

description:
Library name: H1
Column name in RawCounts1.csv: H1


title: LS-WFPM0.1 somatic cells 3

description:
Library name: H3
Column name in RawCounts1.csv: H3


title: IgG-Seq Sample IgG3A

description:
Library name: IgG3A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation positive control

description: Library name: wo-plus

value: TNNAND1_N6 sequence pool, condition wo


title: IgG-Seq Sample IgG1A

description:
Library name: IgG1A
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG2A

description:
Library name: IgG2A
Novogene
IGGSEQ.rds


title: Control somatic cells 3

description:
Library name: C3
Column name in RawCounts1.csv: C3


title: Whole Stool 16S Sample S44A

description:
Library name: S44A
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation negative control

description: Library name: wo-minus


title: Whole Stool 16S Sample S43A

description:
Library name: S43A
Novogene


title: IgA-Seq Sample IgA48B

description:
Library name: IgA48B
Novogene
IGASEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 8

description: Library name: wo8


title: Control somatic cells 2

description:
Library name: C2
Column name in RawCounts1.csv: C2


title: Whole Stool 16S Sample S42A

description:
Library name: S42A
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 7

description: Library name: wo7


title: IgA-Seq Sample IgA46B

description:
Library name: IgA46B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S41A

description:
Library name: S41A
Novogene


title: IgA-Seq Sample IgA47B

description:
Library name: IgA47B
Novogene
IGASEQ.rds


title: LS-WFPM0.1 oocyte 4

description:
Library name: W4
Column name in RawCounts3.csv: W4

data_processing:
After sequencing, fastq files were imported into Galaxy (version 24.2.rc1) for downstream analysis. RNA-seq reads were aligned to the whole mouse genome assembly-mm10 by HISAT2, quantified by featureCounts, and normalized using the Transcripts Per Million (TPM) method
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

extract_protocol:
SMART-seq v4 Ultra-low input RNA kit
The single-cell SMART-seq2 RNA-seq libraries were constructed using a modified single-cell tagged reverse transcription sequencing protocol. Briefly, mRNA from each single cell was extracted into the lysis buffer provided by the SMART-seq v4 Ultra-low input RNA kit (634891, TaKaRa, San Jose, CA, USA). mRNAs were then reversed transcribed into complementary DNA（cDNA), which was then pre-amplified and purified. High-quality cDNA products were subjected to tagmentation and library preparation, with multiplexing by Nextera XT Indexes (Illumina). Pooled indexed libraries were sequenced on the NovaSeq X Plus platform with 150 bp pair-end reads by Novogene.


title: IgA-Seq Sample IgA45B

description:
Library name: IgA45B
Novogene
IGASEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 6

description: Library name: wo6


title: Whole Stool 16S Sample S40A

description:
Library name: S40A
Novogene


title: Control somatic cells 1

description:
Library name: C1
Column name in RawCounts1.csv: C1


title: Whole Stool 16S Sample S39A

description:
Library name: S39A
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 5

description: Library name: wo5


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 4

description: Library name: wo4


title: IgA-Seq Sample IgA44B

description:
Library name: IgA44B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S38A

description:
Library name: S38A
Novogene


title: IgA-Seq Sample IgA43B

description:
Library name: IgA43B
Novogene
IGASEQ.rds


title: LS-WFPM0.1 oocyte 3

description:
Library name: W3
Column name in RawCounts3.csv: W3


title: LS-WFPM0.1 oocyte 2

description:
Library name: W2
Column name in RawCounts3.csv: W2


title: Control oocyte 4

description:
Library name: C4
Column name in RawCounts3.csv: C4


title: Whole Stool 16S Sample S37A

description:
Library name: S37A
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 2

description: Library name: wo2


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 3

description: Library name: wo3


title: LS-WFPM0.1 oocyte 1

description:
Library name: W1
Column name in RawCounts3.csv: W1


title: Whole Stool 16S Sample S36A

description:
Library name: S36A
Novogene


title: Control oocyte 3

description:
Library name: C3
Column name in RawCounts3.csv: C3


title: IgA-Seq Sample IgA42B

description:
Library name: IgA42B
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA41B

description:
Library name: IgA41B
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA40B

description:
Library name: IgA40B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S35A

description:
Library name: S35A
Novogene


title: Control oocyte 2

description:
Library name: C2
Column name in RawCounts3.csv: C2


title: DNA_lib_3

city: guangzhou

first: wang

last: xing

address: No. 382, Outer Ring East Road, Guangzhou University Town, Panyu District

country: China

institute: South China University of Technology

description: Library name: Sample6

data_processing:
Raw sequencing reads were demultiplexed and quality filtered according to standard Illumina procedures. Sequencing libraries consisted of PCR-amplified barcode-containing fragments; therefore, barcode sequences were directly counted by matching reads to the reference barcode list. Barcode read counts from RNA-derived libraries were used to quantify promoter-driven transcriptional output, while barcode read counts from DNA-derived libraries were used to assess construct abundance in the input library. RNA and DNA barcode counts were independently normalized by library size, and promoter strength was calculated as the ratio of normalized RNA to DNA barcode counts. Promoter activity values were averaged across three independent biological replicates.
Assembly: ASM98243v1
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: This file reports barcode-level promoter activity. Each row represents a promoter–barcode pair with RNA and DNA barcode read counts from multiple libraries, and normalized promoter activity values (FPKM) calculated by RNA/DNA normalization.

organism: Escherichia coli DH5[alpha]

source_name: E. coli DH5[alpha] cells carrying the pooled barcoded promoter plasmid library

growth_protocol: Escherichia coli DH5[alpha] cells carrying the pooled barcoded promoter plasmid library were cultured in LB medium supplemented with 50 µg/mL kanamycin at 37 C with shaking at 200 rpm. After overnight growth on selective plates, approximately 20,000 monoclonal colonies were pooled and inoculated into liquid LB medium at a 1:1000 dilution. Cultures were grown for 4 h under the same conditions prior to sample collection.

extract_protocol:
Cells were harvested from the pooled cultures at a defined time point. Total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit according to the manufacturer’s instructions. In parallel, plasmid DNA was extracted from the same cultures to assess construct abundance in the library.
For RNA-derived samples, total RNA was reverse transcribed into cDNA using the HiScript IV 1st Strand cDNA Synthesis Kit. Barcode-containing regions were selectively amplified by PCR using the primers Test-bar-F/R. For DNA-derived samples, barcode regions were directly amplified from plasmid DNA using the same primer pair. Sequencing libraries were constructed from the amplified products following standard Illumina protocols.


title: IgA-Seq Sample IgA39B

description:
Library name: IgA39B
Novogene
IGASEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 1

description: Library name: wo1


title: Whole Stool 16S Sample S34A

description:
Library name: S34A
Novogene


title: DNA_lib_2

description: Library name: Sample5

value: E. coli DH5[alpha] cells carrying the pooled barcoded promoter plasmid library


title: IgA-Seq Sample IgA38B

description:
Library name: IgA38B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S33A

description:
Library name: S33A
Novogene


title: BK-BL-LRC-1

city: Kumamoto City

first: Yen

middle: Xuan

last: Ngo

state: Kumamoto

address: Honjo 2-1-1, Chuo-ku

department: International Research Center for Medical Sciences

country: Japan

institute: Kumamoto University

data_processing:
Sequencing was done in Illumina NextSeq500 generating 8 gz fastq files per samples
Fastq files were imported to CLC GW as paired-end reads and mapped to mouse mm10 genome (ENSEMBL but provided by CLC)
Mapped reads exported, converted into bedgraph for visualization in UCSC browser
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Differentially expressed genes were filtered using fold change and p value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and RPKM values for each gene in every sample

source_name: Back skin epidermis

extract_protocol:
Tissue was incubated overnight at 4 °C in 0.25% trypsin/EDTA and the next day at 37 °C for 30 minutes. Single-cell suspensions were then filtered, stained with antibodies and sorted by flow cytometry directly into Trizol (Ambion, 10296028) for RNA extraction. RNA quality was measured by Agilent Bioanalyzer RNA 6000 pico kit (5067-1513) and quantity using nanodrop.
Library was synthesized using low input protocol (≤50ng RNA) by SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara) and the library quality was checked by Agilent Bioanalyzer DNA high-sensitivity kit (5067-4626).

treatment_protocol: Doxycycline was mixed in the chow (cat no) for 10 days for oral tissues and 2 weeks for skin, fresh chow was given every week.

value: Back skin epidermis

value: slow-cycling epidermal stem cells

tag: other name

value: Basal layer cells (BL), Label retaining cells (LRCs)

value: K5-tTA/pTRE H2B-GFP

tag: age

value: 2 months old

tag: strain

value: doxycycline 2 weeks


title: IgA-Seq Sample IgA37B

description:
Library name: IgA37B
Novogene
IGASEQ.rds


title: DNA_lib_1

description: Library name: Sample4


title: Control oocyte 1

description:
Library name: C1
Column name in RawCounts3.csv: C1


title: RNA_pool_3

description: Library name: Sample3


title: IgA-Seq Sample IgA36B

description:
Library name: IgA36B
Novogene
IGASEQ.rds


title: SRF floxed WT, snRNA-seq, iWAT

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: Sample 29

library_source: transcriptomic single cell

data_processing:
For Samples 1-2 (ChIP-seq): Sequence reads were trimmed with fastp and aligned to the mm10 genome using Bowtie2. PCR duplicates and low-quality reads were removed with Samtools. Peak were called with MACS2, merged using Bedops across samples, and quantified with featureCounts. For Samples 3-26 (RNA-seq): Sequence reads were trimmed with fastp and aligned to the mm10 genome using STAR. Filtered reads were assigned to transcriptome and quantified by featureCounts. For Samples 27-30 (snRNA-seq): Sequence reads were processed with Cell Ranger v7.1.0 for demultiplexing, alignment, read filtering, and barcode and UMI counting. Ambient RNA was removed using CellBender v0.3.0.
Assembly: mm10
Supplementary files format and content: txt (raw counts for each sample of ChIP-seq or bulk RNA-seq); tsv (lists of cell barcodes and genes for each sample of snRNA-seq); mtx (expression count matrix for each sample of snRNA-seq)

source_name: adipose

growth_protocol: For Samples 1-2: 3T3-L1 preadipocytes were maintained in DMEM supplemented with 10% bovine calf serum and 1% penicillin–streptomycin, and differentiated upon confluence with DMEM containing 10% fetal bovine serum (FBS), 5 μg/mL insulin, 500 μM isobutylmethylxanthine, and 1 μM dexamethasone for 48 hours. Cells were then maintained in DMEM supplemented with 10% FBS and 5 μg/mL insulin for another 2 days, followed by maintenance in DMEM with 10% FBS alone for the remainder of the culture period.

extract_protocol:
For Samples 1-2 (ChIP-seq): Cells were homogenized in chilled Douncers and immediatelly cross-linked  with 1% PFA (and quenched with glycine). Chromatin was sheared using a Covaris E220 sonicator, and the fragmented chromatin was incubated with SRF antibody (Santa Cruz, sc-335X) overnight at 4C and immunoprecipitated using protein A/G dynabeads. Following elution, chromatin was reverse cross-linked and purified using AMPure XP beads. For Samples 3-26 (RNA-seq): RNA was extracted from adipose tissue using TRIzol and then purified by on-column DNA digestion. For Samples 27-30 (snRNA-seq): Nuclei were isolated from frozen adipose tissue by pulverizing in liquid nitrogen and homogenizing in chilled Douncers. Next, Hoechst-stained nucleus suspension was subject to sorting to remove debris and multiplets. The nucleus suspension was loaded onto the 10x Genomics Chromium Controller.
For Samples 1-2 (ChIP-seq): Purified DNA was subject to end repair and phosphorylation using the End-It DNA End-Repair Kit, followed by A-tailing with Klenow Fragment and adaptor ligation with Quick Ligase. Then, the libraries were PCR amplified with PfuUltra II Hotstart PCR Master Mix. The DNA fragments were selected based on size using E-Gel EX Agarose Gels and then extracted with MinElute Gel Extraction Kit. For Samples 3-26 (RNA-seq): Extracted RNA (100ng) was processed by NEBNext rRNA Depletion Kit for removing ribosomal RNA. Then, RNA was converted to cDNA using Maxima Reverse Transcriptas and NEBNext mRNA Second Strand Synthesis Kit following manufacturer's protocols. After purification of cDNA based on size, sequencing libraries were generated using Nextera XT DNA Library Preparation Kit and subsequent PCR amplification. For Samples 27-30 (snRNA-seq): Libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3.3, indexed with sample barcodes.

treatment_protocol: For Samples 1-2: For TGFβ1 treatment, differentiated 3T3-L1 cells were treated with 1 ng/mL of TGFβ1.

value: adipose

value: Adipoq-CreERT2-/-; Srfflox/flox

value: High-fat diet (HFD)


title: SRF-AKO, snRNA-seq, iWAT

description: Library name: Sample 30

value: Adipoq-CreERT2+/-; Srfflox/flox


title: Whole Stool 16S Sample S31A

description:
Library name: S31A
Novogene

value: Stool


title: SRF-AKO, snRNA-seq, eWAT

description: Library name: Sample 28


title: RNA_pool_2

description: Library name: Sample2

value: WT


title: Whole Stool 16S Sample S32A

description:
Library name: S32A
Novogene

value: Pre-vitamin D


title: IgA-Seq Sample IgA35B

description:
Library name: IgA35B
Novogene
IGASEQ.rds

value: Post-vitamin D


title: IgA-Seq Sample IgA34B

description:
Library name: IgA34B
Novogene
IGASEQ.rds


title: RNA_pool_1

description: Library name: Sample1


title: SRF floxed WT, snRNA-seq, eWAT

description: Library name: Sample 27


title: Stool_N12_NIK^CX3CR1

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

description: Library name: N.12

data_processing:
Raw paired-end sequencing reads were demultiplexed and quality filtered to remove low-quality reads and adapter contamination.
Paired-end reads were merged and chimeric sequences were identified and removed.
High-quality sequences were clustered into operational taxonomic units (OTUs) at 97% sequence similarity
Representative sequences were taxonomically classified using a reference database.
An OTU abundance table was generated for downstream statistical and diversity analyses.
Supplementary files format and content: alpha diversity (Shannon index) and beta diversity (weighted UniFrac principal coordinates analysis (PCoA); relative abundance of dominant bacterial taxa at the genus_level for samples N.1 to N.12 in one .txt file
Supplementary files format and content: .txt
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: Mus musculus stool

extract_protocol:
Microbial genomic DNA was extracted from stool samples using a commercial DNA extraction kit following the manufacturer’s instructions. DNA quality and concentration were checked with Qubit and real-time PCR for quantification, while a bioanalyzer was used for size distribution detection.
The V3–V4 region of the bacterial 16S rRNA gene was amplified using region-specific primers. Sequencing libraries were prepared according to Illumina standard protocols and sequenced using paired-end reads.

treatment_protocol: Faecal samples were collected from age-matched mice and stored at −80 °C until processing. No additional treatment was applied prior to DNA extraction

value: Mus musculus stool


title: Whole Stool 16S Sample S29A

description:
Library name: S29A
Novogene


title: Whole Stool 16S Sample S30A

description:
Library name: S30A
Novogene


title: Whole Stool 16S Sample S28A

description:
Library name: S28A
Novogene


title: Stool_N11_Control

description: Library name: N.11

value: NIKfl/fl


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 5

description: Library name: Sample 25


title: IgA-Seq Sample IgA33B

description:
Library name: IgA33B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S27A

description:
Library name: S27A
Novogene


title: IgA-Seq Sample IgA32B

description:
Library name: IgA32B
Novogene
IGASEQ.rds


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 4

description: Library name: Sample 24


title: Stool_N10_Control

description: Library name: N.10


title: IgA-Seq Sample IgA31B

description:
Library name: IgA31B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S26A

description:
Library name: S26A
Novogene


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 3

description: Library name: Sample 23


title: Stool_N9_NIK^CX3CR1

description: Library name: N.9


title: IgA-Seq Sample IgA30B

description:
Library name: IgA30B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S25A

description:
Library name: S25A
Novogene


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 2

description: Library name: Sample 22


title: Whole Stool 16S Sample S24A

description:
Library name: S24A
Novogene


title: Stool_N8_NIK^CX3CR1

description: Library name: N.8


title: Stool_N7_Control

description: Library name: N.7


title: IgA-Seq Sample IgA28B

description:
Library name: IgA28B
Novogene
IGASEQ.rds


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 6

description: Library name: Sample 20


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 1

description: Library name: Sample 21


title: Stool_N6_Control

description: Library name: N.6


title: IgA-Seq Sample IgA27B

description:
Library name: IgA27B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S23A

description:
Library name: S23A
Novogene


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 5

description: Library name: Sample 19


title: IgA-Seq Sample IgA26B

description:
Library name: IgA26B
Novogene
IGASEQ.rds


title: Stool_N5_Control

description: Library name: N.5


title: Whole Stool 16S Sample S22A

description:
Library name: S22A
Novogene


title: Whole Stool 16S Sample S21A

description:
Library name: S21A
Novogene


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 4

description: Library name: Sample 18


title: IgA-Seq Sample IgA25B

description:
Library name: IgA25B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S20A

description:
Library name: S20A
Novogene


title: Stool_N4_NIK^CX3CR1

description: Library name: N.4


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 3

description: Library name: Sample 17


title: Stool_N3_NIK^CX3CR1

description: Library name: N.3


title: IgA-Seq Sample IgA24B

description:
Library name: IgA24B
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA29B

description:
Library name: IgA29B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S19A

description:
Library name: S19A
Novogene


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 2

description: Library name: Sample 16


title: Stool_N2_NIK^CX3CR1

description: Library name: N.2


title: Whole Stool 16S Sample S18A

description:
Library name: S18A
Novogene


title: IgA-Seq Sample IgA23B

description:
Library name: IgA23B
Novogene
IGASEQ.rds


title: SRF floxed WT, bulk RNA-seq, iWAT, replicate 1

description: Library name: Sample 15


title: Stool_N1_Control

description: Library name: N.1


title: Whole Stool 16S Sample S17A

description:
Library name: S17A
Novogene


title: IgA-Seq Sample IgA22B

description:
Library name: IgA22B
Novogene
IGASEQ.rds


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 6

description: Library name: Sample 14


title: Whole Stool 16S Sample S16A

description:
Library name: S16A
Novogene


title: IgA-Seq Sample IgA21B

description:
Library name: IgA21B
Novogene
IGASEQ.rds


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 5

description: Library name: Sample 13


title: Mouse sacral spinal cord snATAC-seq_biol_rep3_tech_rep3

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

description:
Library name: AS03C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

library_source: genomic single cell

data_processing:
Raw sequencing reads were demultiplexed, aligned, and a count matrix was generated using CellRanger Arc (v2.0.2) using the Mouse mm10 (GENCODE vM23/Ensembl98) reference transcriptome with – include introns parameter specified.
Assembly: GENCODE vM23/Ensembl98
Supplementary files format and content: Summary RDS files containing gene expression data were generated with Seurat v5

source_name: Mouse sacral spinal cord

extract_protocol:
8-week old male and female mice were anesthetized with isoflurane and decapitated. Vertebral column was rapidly dissected out and transferred to ice-cold carbogenated (95% O2 and 5% CO2) NMDG-HEPES-ACSF (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 1 mM CaCl2, 1 mM kynurenic-acid Na salt, 5 mM Na-ascorbate, 2 mM thiourea and 3 mM Na-pyruvate, pH adjusted to 7.4, osmolarity ranging 300–310 mOsm). Cervical, thoracic, lumbar or sacral segments of the spinal cord were microdissected out and cut into small 1 mm2 size pieces. Microdissected spinal cord pieces were transferred to a Kimble Dounce tissue-grinder containing 750 microL of Lysis Buffer (0.1% Triton-X100, 320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Tissue was homogenized with 5 strokes with loose pestle and 15 strokes with tight pestle and resulting nuclear suspension was strained with a 40 micron cell strainer and washed with 1.25 mL of Nuclear Buffer (320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Cell suspension is layered onto 12 mL of 1M sucrose cushion (1M sucrose, 10 mM pH=7.4, Tris-HCl (pH=7.4), 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O) in a 5 mL Oakridge tube. The latter are centrifuged at 500g for 5 min at 4C in a spin-out-rotor. The sucrose cushion is decanted and pure nuclei are resuspended in 300 µL of nuclear buffer containing 10 µg/mL 7-AAD and 1:100 custom conjugated anti-NeuN-Alexa647 antibody (Biolegend #608452). The nuclei are incubated for 15 min at 4C. Thereafter, nuclei are spun down at 500g for 5 minutes and washed twice with 3 mL of nucleus buffer and resuspended in 1 mL of nucleus buffer. The resulting nucleus suspension is FACS sorted to enrich for NeuN/7-AAD double positive cells (neurons). The neuronal nuclei are concentrated with CUTANA ConA beads per manufacturer’s protocol and resuspended in 1x Nucleus Buffer from 10x Genomics with resulting nuclear suspension loaded to the 10x Genomics microfluidic chip and processed per manufacturer’s protocol.
Single-nucleus suspensions were processed on a 10X Chromium Xi instrument using the Chromium Next GEM Single Cell Multiome Reagent Bundle (#100028) following the manufacturers protocol. The resulting sequencing libraries were sequenced on a Novaseq X platform (PE 150 bp). Libraries were sequenced to a minimum depth of 50,000 reads per nucleus.

value: Mouse sacral spinal cord


title: IgA-Seq Sample IgA20B

description:
Library name: IgA20B
Novogene
IGASEQ.rds


title: Mouse sacral spinal cord snRNA-seq_biol_rep3_tech_rep3

description:
Library name: AS03C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

molecule: nuclear RNA


title: IgA-Seq Sample IgA19B

description:
Library name: IgA19B
Novogene
IGASEQ.rds


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 4

description: Library name: Sample 12


title: Whole Stool 16S Sample S15A

description:
Library name: S15A
Novogene


title: Mouse sacral spinal cord snATAC-seq_biol_rep3_tech_rep2

description:
Library name: AS03B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Whole Stool 16S Sample S14A

description:
Library name: S14A
Novogene


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 3

description: Library name: Sample 11


title: IgA-Seq Sample IgA18B

description:
Library name: IgA18B
Novogene
IGASEQ.rds


title: Mouse sacral spinal cord snRNA-seq_biol_rep3_tech_rep2

description:
Library name: AS03B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Whole Stool 16S Sample S13A

description:
Library name: S13A
Novogene


title: Mouse sacral spinal cord snATAC-seq_biol_rep3_tech_rep1

description:
Library name: AS03A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 2

description: Library name: Sample 10


title: IgA-Seq Sample IgA17B

description:
Library name: IgA17B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S12A

description:
Library name: S12A
Novogene


title: Mouse sacral spinal cord snRNA-seq_biol_rep3_tech_rep1

description:
Library name: AS03A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: SRF-AKO, bulk RNA-seq, eWAT, replicate 1

description: Library name: Sample 9


title: Mouse sacral spinal cord snATAC-seq_biol_rep2_tech_rep3

description:
Library name: AS02C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA16B

description:
Library name: IgA16B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S11A

description:
Library name: S11A
Novogene


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 6

description: Library name: Sample 8


title: IgA-Seq Sample IgA15B

description:
Library name: IgA15B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S10A

description:
Library name: S10A
Novogene


title: Mouse sacral spinal cord snRNA-seq_biol_rep2_tech_rep3

description:
Library name: AS02C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 5

description: Library name: Sample 7


title: IgA-Seq Sample IgA14B

description:
Library name: IgA14B
Novogene
IGASEQ.rds


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 4

description: Library name: Sample 6


title: Whole Stool 16S Sample S9A

description:
Library name: S9A
Novogene


title: Mouse sacral spinal cord snATAC-seq_biol_rep2_tech_rep2

description:
Library name: AS02B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA13B

description:
Library name: IgA13B
Novogene
IGASEQ.rds


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 3

description: Library name: Sample 5


title: Mouse sacral spinal cord snRNA-seq_biol_rep2_tech_rep2

description:
Library name: AS02B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse sacral spinal cord snATAC-seq_biol_rep2_tech_rep1

description:
Library name: AS02A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Whole Stool 16S Sample S8A

description:
Library name: S8A
Novogene


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 2

description: Library name: Sample 4


title: IgA-Seq Sample IgA12B

description:
Library name: IgA12B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S7A

description:
Library name: S7A
Novogene


title: IgA-Seq Sample IgA11B

description:
Library name: IgA11B
Novogene
IGASEQ.rds


title: Whole Stool 16S Sample S32B

description:
Library name: S32B
Novogene


title: SRF floxed WT, bulk RNA-seq, eWAT, replicate 1

description: Library name: Sample 3


title: Whole Stool 16S Sample S5A

description:
Library name: S5A
Novogene


title: Whole Stool 16S Sample S6A

description:
Library name: S6A
Novogene


title: Mouse sacral spinal cord snRNA-seq_biol_rep2_tech_rep1

description:
Library name: AS02A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Whole Stool 16S Sample S4A

description:
Library name: S4A
Novogene


title: IgA-Seq Sample IgA10B

description:
Library name: IgA10B
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA9B

description:
Library name: IgA9B
Novogene
IGASEQ.rds


title: Mouse sacral spinal cord snRNA-seq_biol_rep1_tech_rep3

description:
Library name: AS01C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA8B

description:
Library name: IgA8B
Novogene
IGASEQ.rds


title: SC_PP_Count

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA36860

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0, 10x Genomics) for UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene and cell (barcode) combination

molecule: polyA RNA

source_name: Skull

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: Skull

value: Mesenchymal cells

value: Prx1Cre Tomato


title: Mouse sacral spinal cord snATAC-seq_biol_rep1_tech_rep3

description:
Library name: AS01C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA7B

description:
Library name: IgA7B
Novogene
IGASEQ.rds


title: Mouse sacral spinal cord snATAC-seq_biol_rep1_tech_rep2

description:
Library name: AS01B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: G1-ESC-p300_ESC_A485_rep2-batch1

city: New York

first: UkJin

last: Lee

state: NY

address: 413 E 69th St

department: Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: G1-ESC-p300_ESC_A485_rep2-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESC-p300_rawCounts.csv
G1-ESC-p300_DESeqNormCounts.csv

data_processing:
FASTQ files were aligned to the mouse genome (mm10) using Star aligner (v2.7.11a) with the default setting for paired-end reads. Samtools (v1.20) was used to process the aligned data, including transforming file formats, filtering low-quality reads, and sorting paired reads.
FeatureCounts from subread (v2.0.6) was used to count fragments that have both ends successfully aligned. Normalization of read counts was done in R using RPM and TPM methods. Genes with RPM > 1 in at least 2 samples were considered expressed.
Assembly: mm10
Supplementary files format and content: ".csv" for raw read counts and DESeq2-normalized read counts with batch correction.

source_name: RAD21-dTAG cell line (Bruce-4 derived)

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C.

extract_protocol:
Total RNA was extracted from 500,000 cells per sample using RNeasy Mini Kit (Qiagen, 74104), following the manufacturer’s instructions.
For M-to-G1 experiments, RNA-seq libraries were generated by Weill Cornell Medicine Genomics Resources Core Facility using NEBNext Ultra II Directional RNA library kit (New England Biolabs, E7760) and TruSeq Stranded mRNA library kit (Illumina, 20020595). For asynchronous experiments, RNA-seq libraries were generated by Novogene using their mRNA library preparation service with poly A enrichment.

treatment_protocol: 0.05% v/v DMSO, 500 nM dTAG, or 20 µM A485.

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell


title: sc_PP_Mut

description: Library name: GA37151

value: Prx1Cre Tomato Pth1r


title: Whole Stool 16S Sample S2A

description:
Library name: S2A
Novogene


title: G1-ESC-p300_ESC_A485_rep1-batch1

description:
Library name: G1-ESC-p300_ESC_A485_rep1-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESC-p300_rawCounts.csv
G1-ESC-p300_DESeqNormCounts.csv


title: Whole Stool 16S Sample S3A

description:
Library name: S3A
Novogene


title: Mouse sacral spinal cord snRNA-seq_biol_rep1_tech_rep2

description:
Library name: AS01B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA6B

description:
Library name: IgA6B
Novogene
IGASEQ.rds


title: G1-ESC-p300_ESC_DMSO_rep2-batch1

description:
Library name: G1-ESC-p300_ESC_DMSO_rep2-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESC-p300_rawCounts.csv
G1-ESC-p300_DESeqNormCounts.csv

value: DMSO


title: Whole Stool 16S Sample S1A

description:
Library name: S1A
Novogene


title: Mouse sacral spinal cord snATAC-seq_biol_rep1_tech_rep1

description:
Library name: AS01A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA5B

description:
Library name: IgA5B
Novogene
IGASEQ.rds


title: G1-ESC-p300_ESC_DMSO_rep1-batch1

description:
Library name: G1-ESC-p300_ESC_DMSO_rep1-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESC-p300_rawCounts.csv
G1-ESC-p300_DESeqNormCounts.csv


title: mouse_NM53_IFNg_CM272_3

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

description:
Library name: NM12_S47
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt

data_processing:
Low-quality reads and adapter sequences were removed using TrimGalore (v0.6.0) with Cutadapt (v1.18) using default parameters. For mouse NM53 samples, trimmed reads were aligned to the GRCm39 reference genome using STAR (v2.7.9a) with the GENCODE vM37 gene annotation. Gene-level quantification was obtained using the STAR --quantMode GeneCounts option. Transposable element (TE) family counts were generated using TEtranscripts (v2.1.4) in multimapping mode with the GENCODE vM37 GTF and a GRCm39 RepeatMasker-derived TE annotation (GTF format). For human PLC/PRF/5 samples, trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.9a) with the MANE gene annotation (v1.4), and gene-level quantification was obtained using the STAR --quantMode GeneCounts option.
Assembly: GRCm39 (mouse); GRCh38 (human)
Supplementary files format and content: Tab-delimited text files containing raw read counts per gene for mouse NM53 and human PLC/PRF/5 samples, and transposable element (TE) family-level counts for mouse NM53 samples.

growth_protocol: NM53 mouse HCC cells and PLC/PRF/5 human HCC cells were cultured in DMEM supplemented with 10% fetal bovine serum, glutamine, and antibiotics under standard culture conditions.

extract_protocol:
Automated Maxwell System (Promega)
Illumina Stranded mRNA Prep Ligation kit

treatment_protocol: NM53 mouse HCC cells were treated with CM272 (400 nM for 48 h) or vehicle control (0.0001% DMSO), followed by interferon gamma (IFN-gamma, 75 U/mL for 24 h) or vehicle control (H2O). PLC/PRF/5 human HCC cells were treated with EZM8266 (5 uM for 48 h) or vehicle control.


title: IgA-Seq Sample IgA4B

description:
Library name: IgA4B
Novogene
IGASEQ.rds


title: mouse_NM53_IFNg_CM272_2

description:
Library name: NM11_S46
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: Mouse lumbar spinal cord snATAC-seq_biol_rep3_tech_rep3

description:
Library name: AL03C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

source_name: Mouse lumbar spinal cord

value: Mouse lumbar spinal cord


description:
Library name: G1-ESCtoEpiLC-RAD21_EpiLC_dTAG_rep2-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv

value: Mouse epiblast-like cell

value: dTAG


title: mouse_NM53_IFNg_CM272_1

description:
Library name: NM10_S45
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


description:
Library name: G1-ESCtoEpiLC-RAD21_EpiLC_dTAG_rep1-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: Mouse sacral spinal cord snRNA-seq_biol_rep1_tech_rep1

description:
Library name: AS01A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse lumbar spinal cord snATAC-seq_biol_rep3_tech_rep2

description:
Library name: AL03B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: mouse_NM53_IFNg_3

description:
Library name: NM9_S44
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt

value: IFNg


description:
Library name: G1-ESCtoEpiLC-RAD21_EpiLC_DMSO_rep2-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: IgA-Seq Sample IgA3B

description:
Library name: IgA3B
Novogene
IGASEQ.rds

value: Stool


title: IgA-Seq Sample IgA1B

description:
Library name: IgA1B
Novogene
IGASEQ.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_EpiLC_DMSO_rep1-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: mouse_NM53_IFNg_2

description:
Library name: NM8_S43
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: IgA-Seq Sample IgA2B

description:
Library name: IgA2B
Novogene
IGASEQ.rds


title: Mouse lumbar spinal cord snRNA-seq_biol_rep3_tech_rep3

description:
Library name: AL03C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse lumbar spinal cord snRNA-seq_biol_rep3_tech_rep2

description:
Library name: AL03B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA48A

description:
Library name: IgA48A
Novogene
IGASEQ.rds

value: Pre-vitamin D


title: mouse_NM53_IFNg_1

description:
Library name: NM7_S42
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: mouse_NM53_CM272_3

description:
Library name: NM6_S41
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: Mouse lumbar spinal cord snATAC-seq_biol_rep3_tech_rep1

description:
Library name: AL03A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse lumbar spinal cord snRNA-seq_biol_rep3_tech_rep1

description:
Library name: AL03A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: mouse_NM53_CM272_2

description:
Library name: NM5_S40
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_dTAG_rep1-batch3
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_dTAG_rep2-batch3
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: IgA-Seq Sample IgA47A

description:
Library name: IgA47A
Novogene
IGASEQ.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_dTAG_rep2-batch2
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: IgA-Seq Sample IgA46A

description:
Library name: IgA46A
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA45A

description:
Library name: IgA45A
Novogene
IGASEQ.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_dTAG_rep1-batch2
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: mouse_NM53_CM272_1

description:
Library name: NM4_S39
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: Mouse lumbar spinal cord snRNA-seq_biol_rep2_tech_rep3

description:
Library name: AL02C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse lumbar spinal cord snATAC-seq_biol_rep2_tech_rep3

description:
Library name: AL02C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: mouse_NM53_Control_3

description:
Library name: NM3_S38
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt

value: Control


title: IgA-Seq Sample IgA44A

description:
Library name: IgA44A
Novogene
IGASEQ.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_DMSO_rep2-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: Mouse lumbar spinal cord snATAC-seq_biol_rep2_tech_rep2

description:
Library name: AL02B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_DMSO_rep1-batch3
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: IgA-Seq Sample IgA42A

description:
Library name: IgA42A
Novogene
IGASEQ.rds


title: Mouse lumbar spinal cord snRNA-seq_biol_rep2_tech_rep2

description:
Library name: AL02B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: mouse_NM53_Control_2

description:
Library name: NM2_S37
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: mouse_NM53_Control_1

description:
Library name: NM1_S36
NM_CM272_IFNg_RAW_Counts_Gene_Symbol.txt
NM_CM272_IFNg_RAW_Counts_TE.txt


title: Mouse lumbar spinal cord snATAC-seq_biol_rep2_tech_rep1

description:
Library name: AL02A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


description:
Library name: G1-ESCtoEpiLC-RAD21_ESC_DMSO_rep1-batch1
Weill Cornell Medicine Genomics Resources Core Facility
G1-ESCtoEpiLC-RAD21_rawCounts.csv
G1-ESCtoEpiLC-RAD21_DESeqNormCounts.csv


title: IgA-Seq Sample IgA43A

description:
Library name: IgA43A
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA41A

description:
Library name: IgA41A
Novogene
IGASEQ.rds


title: Mm-HAR1984 (del/del) - rep3

city: Durham

first: Federica

last: Mosti

state: NC

address: 213 Research Dr

institute: Duke University

description: Library name: sample9

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt
Trimmed sequence reads were mapped to rRNA using bowtie2  v2.4.4, and remaining reads were maped to mm10 supplied with GENCODE22 annotation using STAR v2.7.9a (Dobin, 2013).
Assembly: mm9
Supplementary files format and content: Supplementary files format and content: excel files include average log2FC and average CPM for control, CRISPR KI and CRISPR KO

source_name: Embryonic cortices E16.6

extract_protocol:
RNA-seq: RNA was harvested using the RNAeasy kit (Qiagen, 74034). 50 ng of total RNA was used for the construction of sequencing libraries.
RNAseq: cDNA libraries for RNA-seq were prepared using the Kapa mRNA HyperPrep kit with mRNA capture (KapaBiosystems, KR1352)

value: Embryonic cortices E16.6

value: Neural progenitors

value: Mm-HAR1984 (del/del)

value: CRISPR KO


title: GEX + HTO (Sample tags 8, 9, 10, 11)

description:
Library name: Cartridge 2 BD Rhapsody
SampleTag08_mm_RSEC_MolsPerCell_MEX.zip
SampleTag09_mm_RSEC_MolsPerCell_MEX.zip
SampleTag10_mm_RSEC_MolsPerCell_MEX.zip
SampleTag11_mm_RSEC_MolsPerCell_MEX.zip

data_processing:
Raw fastq-sequencing reads were loaded into BD Rhapsody WTA Analysis Pipeline hosted by SevenBridgesGenomics and analyzed using version 1.9 of the pipeline.
Single Cell RNA data have been processed using the software R studio and the Seurat package. Cells that contained less than 200 detected genes and a percentage of mitochondrial counts higher than 12% were removed from subsequent analysis. Single-cell counts were normalised by scaling each cell's expression values by its total expression, multiplying by a factor of 10,000, and then applying a log transformation. Dimensionality reduction was performed using Principal Component Analysis (PCA) to identify the principal components that capture the most significant variance in the gene expression data. The first 15 principal components were selected for downstream analysis. A graph-based approach was employed for clustering. First, a shared nearest neighbour (SNN) graph was constructed using the identified principal components. Then, the Louvain algorithm was applied to this graph to identify clusters of cells with similar expression profiles. A resolution parameter of 0.5 was used to determine the granularity of the clustering. Clusters were visualised using the UMAP technique and annotated according to ImmGen‘s (www.immgen.org) data browser.
Sampletag assignment: Sampletag5=NIKfl/fl; Sampletag6=NIK^CX3CR1; Sampletag7=NIK^CX3CR1; Sampletag12=NIKfl/fl; Sampletag8=NIK^CX3CR1; Sampletag9=NIKfl/fl; Sampletag10=NIKfl/fl; Sampletag11=NIK^CX3CR1
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw molecule counts for every cell, gene and sample

source_name: inguinal lymph nodes

extract_protocol:
at day 4 single cell suspensions were prepared from isolated inguinal lymph nodes by digestion using  Collagenase Type II (1mg/ml) and DNase Type I (0,1 mg/ml) in PBS with calcium and magnesium while shaking at 37 °C for 30 minutes. Myeloid cells were enriched by depletion of T and B cells with CD19 microbeads and CD90.2 microbeads (Milteny) using MACS technology
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). For multiplexing samples, cells were conjugated with unique oligos as indicated in the processed data file section. Sequence of sample tags can be found under BD; Doc ID 210970. Cells were loaded on BD Rhapsody cartridge. Capture of single RNA molecules on barcoded magnetic Oligo-dT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). mRNA and Sample Tag Libraries were prepared following the manual (mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol; 23--21712-00). Upon purifying WTA and Sample tag library, concentration of libraries was assessed by Qubit Flex using the DNA high sensitivity kit and average library size was determined on a bioanalyzer 2100 using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling of mRNA and Sample tag library following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on Illumina's NovaSeq 6000 at Novogene (Cambridge, UK). For processing of the sequencing raw data BD Rhapsody WTA analysis pipeline version 2.0 was used.

treatment_protocol: Mice were subcutaneously injected with an emulsion of 50 µg MOG35-55 peptide and CFA supplemented with heat‐inactivated Mycobacterium tuberculosis H37RA. 150 ng of pertussis toxin in PBS was injected i.p. on the same day as the MOG immunisation and again two days later.

value: inguinal lymph nodes

tag: sampletag assignment

value: CD45 positive immune cells

tag: library type

value: mRNA and HTO Cartridge 2

value: MOG-immunised

value: Rhapsody cartridge 2


title: IgA-Seq Sample IgA40A

description:
Library name: IgA40A
Novogene
IGASEQ.rds


title: Mouse lumbar spinal cord snRNA-seq_biol_rep2_tech_rep1

description:
Library name: AL02A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: GEX + HTO (Sample tags: 5, 6, 7, 12)

description:
Library name: Cartridge 1 BD Rhapsody
SampleTag05_mm_RSEC_MolsPerCell_MEX.zip
SampleTag06_mm_RSEC_MolsPerCell_MEX.zip
SampleTag07_mm_RSEC_MolsPerCell_MEX.zip
SampleTag12_mm_RSEC_MolsPerCell_MEX.zip

value: Sampletag5=NIKfl/fl; Sampletag6=NIK^CX3CR1; Sampletag7=NIK^CX3CR1; Sampletag12=NIKfl/fl;

value: mRNA and HTO Cartridge 1

value: MOG immunised

value: Rhapsody cartridge 1


title: Mm-HAR1984 (del/del) - rep1

description: Library name: sample7

source_name: Embryonic cortices E16.5

value: Embryonic cortices E16.5


title: Mouse lumbar spinal cord snRNA-seq_biol_rep1_tech_rep3

description:
Library name: AL01C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

value: Mouse lumbar spinal cord


title: Mouse lumbar spinal cord snATAC-seq_biol_rep1_tech_rep3

description:
Library name: AL01C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mm-HAR1984 (del/del) - rep2

description: Library name: sample8


title: SRF-AKO, bulk RNA-seq, iWAT, replicate 6

description: Library name: Sample 26

value: adipose

value: Adipoq-CreERT2+/-; Srfflox/flox

value: High-fat diet (HFD)


title: Mm-HAR1984 (Hs/Mm) - rep3

description: Library name: sample6

value: Neural progenitors

value: Mm-HAR1984 (Hs/Mm)

value: CRISPR KI


title: IgA-Seq Sample IgA38A

description:
Library name: IgA38A
Novogene
IGASEQ.rds

value: Stool

value: Pre-vitamin D


title: P21_lib6_cre_pos_tom

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

country: Sweden

institute: Stockholm University

description: 10x Genomics

data_processing:
For the analysis of P21 single cell, cell suspension from two mice were pooled as Cre negative control sample (Scgb1a1CREERT2 -/- ; FGFR2 flox/flox ; Rosa26R-Ai14/Ai9) and from three mice as Cre positive mutant sample (Scgb1a1CREERT2 +/- ; FGFR2 flox/flox ; Rosa26R-Ai14/Ai9). For time point P7, the single cell suspension from three mice were pooled as Cre negative control sample and thress as Cre positive mutant sample.
Cells were washed two times more by resuspending in HBSS++ and spinning down. Cells were counted with Biorad cell counter, blocked, stained by PE/Cyanine7 anti-mouse CD326(Ep-CAM) antibody and washed according to standard protocol (Biolegend). From the Cre negative samples, we sorted EpCam+ cells and from the Cre positive mutant samples we sorted EpCam+/Tomato- and EpCAM+/Tomato+ cells for further analysis.
After sorting, the cell suspensions were spun down, counted with Biorad cell counter and diluted according to manufacturer's protocol to obtain not less than 7000 single cell data points per sample. Each sample was run seperately on a lane in Chromium controller with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics).
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Lungs from all experiments were perfused with ice cold HBSS (Hanks' Balanced Salt Solution), were removed and the whole lung was cut in small pieces and was placed in the enzyme solution (5ml Elastase 4U/ml in HBSS + 200ul DNaseI 2.5mg/ml). Suspension is incubated for 1-1,5 hour in 37 C with gentle rotation. The digestion reaction was terminated by adding 20ml HBSS++ (with 10mM HEPES, 2mM EGTA, 1000 U/ml Penicilin, 0.1 mg/ml Streptomycin, 1% BSA). Cells were filtered through a 70μm filter coated with HBSS++, spun down at 400g for 10 min at 4C and resuspended in 10 ml HBSS++.
Library was performed according to the manufacter’s instructions (single cell 3’ v1 protocol, 10x Genomics). Single cell RNAseq library preparatio was done using standard protocol (10x Genomics). Libraries were sequenced together by time point (3 libraries/NovaSeq 6000 SP flowcell).

value: lung

value: lung epithelial cells

tag: condition

value: Mutant cells in mutant animals

tag: developmental stage

value: Postnatal day 21

value: Conditional inactivation of FGFR in secretory cells by administration of tamoxifen at P1,P2,P3 stages


title: Br5588

type: RNA

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

hyb_protocol: The next day, hybridization reactions were washed 2x in 0.05% 1xPBS-Tween-20 (Thermo Fisher Scientific, 28320)  and  incubated in 500mL Xenium Post Hybridization Wash Buffer at 37℃ for 30 minutes. After 3 washes of 0.05% 1xPBS-Tween-20, probes were ligated at 37℃ for 2 hours in a reaction consisting of 87.5% Xenium Ligation Buffer, 2.5% Xenium Ligation Enzyme A and 10% Xenium Ligation Enzyme B. After 3 washes of 0.05% 1xPBS-Tween-20, rolling circle products were amplified in a reaction consisting of 90% Xenium Amplification Mix  and 10% Xenium Amplification Enzyme for 2 hours at 30℃. After amplification was completed, slides were washed 2x in TE buffer, 3x in 1xPBS (1mL/wash) and quenched for autofluorescence with 1% Reducing Agent B (10x Genomics) diluted in 1xPBS for 10 minutes at room temperature. Following 3 rinses of 100% Ethanol (Millipore Sigma), slides were dehydrated for 5 minutes at 37℃ and then rehydrated in 1xPBS followed by a 2-minute incubation of 0.05% 1xPBS-Tween-20. Nuclei were then stained in Nuclei Staining Buffer (10x Genomics)and washed 3x in 0.05% 1xPBS-Tween-20. Slides were then stored overnight in the dark at 4℃ and imaged the following day.

scan_protocol: The Xenium instrument was used for automated imaging and onboard processing of the data.

data_processing: Data processed using Xenium Ranger software.

source_name: dorsolateral prefrontal cortex - dlpfc

label_protocol: For probe hybridization, ligation, and amplification, the 10X Genomics protocol: Xenium In Situ Gene Expression was followed (CG000582, Rev E). The probe hybridization solution was then prepared. A custom panel of 300 genes was designed using the 10x Genomics Xenium platform (10X Genomics; Xenium Custom Gene Expression Panel, Part No. 1000563). Details of the custom probe panel design are described in the manuscript. Probe mix was applied to each slide, a cassette lid was applied to each slide cassette and the slides were incubated at 50 ℃ overnight.

growth_protocol: Human dorsolateral prefrontal cortex (dlPFC) was dissected from frozen (-80℃), unfixed postmortem human tissue. 10-micron coronal sections were obtained by cryosectioning. RNAscope smFISH was performed on tissue sections to confirm the inclusion of full laminar organization spanning layer 1 though white matter. Tissue blocks containing these full laminar organization were then cryosectioned to collect 10-micron coronal sections onto microscopy slides for Xenium.

extract_protocol: Xenium slides were fixed and permeabilized according to 10X Genomics’ Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization Protocol (CG000581, Rev C).

value: dorsolateral prefrontal cortex


title: IgA-Seq Sample IgA37A

description:
Library name: IgA37A
Novogene
IGASEQ.rds


title: Mouse lumbar spinal cord snATAC-seq_biol_rep1_tech_rep2

description:
Library name: AL01B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mm-HAR1984 (Hs/Mm) - rep2

description: Library name: sample5


title: P21_lib4_cre_neg_epcam

description: 10x Genomics

value: Scgb1a1CREERT2 -/- ; FGFR2 flox/flox ; Rosa26R-Ai14/Ai9

value: WT cells in control animals

value: Conditional inactivation of FGFR in secretory cells by administration of tamoxifen at P1,P2,P3 stages - litter mate control


title: P21_lib5_cre_pos_epcam

description: 10x Genomics

value: Scgb1a1CREERT2 +/- ; FGFR2 flox/flox ; Rosa26R-Ai14/Ai9

value: WT cells in mutant animals


title: Mouse lumbar spinal cord snRNA-seq_biol_rep1_tech_rep2

description:
Library name: AL01B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

value: Mouse lumbar spinal cord


title: IgA-Seq Sample IgA39A

description:
Library name: IgA39A
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA36A

description:
Library name: IgA36A
Novogene
IGASEQ.rds


title: Mm-HAR1984 (Hs/Mm) - rep1

description: Library name: sample4

value: Embryonic cortices E16.5

value: Neural progenitors


title: Mouse lumbar spinal cord snATAC-seq_biol_rep1_tech_rep1

description:
Library name: AL01A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mm-HAR1984 (Mm/Mm) - rep3

description: Library name: sample3

value: Mm-HAR1984 (Mm/Mm)

value: control


title: P7_lib3_cre_pos_tom

description: 10x Genomics

value: Postnatal day 7


title: IgA-Seq Sample IgA35A

description:
Library name: IgA35A
Novogene
IGASEQ.rds

value: Stool

value: Pre-vitamin D


title: Mouse lumbar spinal cord snRNA-seq_biol_rep1_tech_rep1

description:
Library name: AL01A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Patient BL1045; H3K4me2 ChIP

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: BL1045_H3K4me2

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated

source_name: Primary; Cystectomy; Muscle invasive; T4aN1

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

tag: antibody

value: H3K4me2 antibody, Millipore C07030


title: Mm-HAR1984 (Mm/Mm) - rep2

description: Library name: sample2


title: IgA-Seq Sample IgA34A

description:
Library name: IgA34A
Novogene
IGASEQ.rds


title: P7_lib2_cre_pos_epcam

description: 10x Genomics

value: lung

value: lung epithelial cells


title: Mm-HAR1984 (Mm/Mm) - rep1

description: Library name: sample1


title: P7_lib1_cre_neg_epcam

description: 10x Genomics


title: Mouse thoracic spinal cord snRNA-seq_biol_rep3_tech_rep3

description:
Library name: AT03C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

source_name: Mouse thoracic spinal cord

value: Mouse thoracic spinal cord


title: IgA-Seq Sample IgA32A

description:
Library name: IgA32A
Novogene
IGASEQ.rds

source_name: Stool


title: P16358_4005

description: 10x Genomics

data_processing:
Cells were washed two times more by resuspending in HBSS++ and spinning down. Cells were counted with Biorad cell counter, blocked, stained by anti-mouse podoplanin (Pdpn) antibody and washed according to standard protocol (Biolegend). From the Tomato positive cells Pdpn+ (Tomato+/Pdpn+) cells and Pdpn- (Tomato+/Pdpn-) cells.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Lungs from all experiments were perfused with ice cold HBSS (Hanks' Balanced Salt Solution), were removed and the whole lung was cut in small pieces and was placed in the enzyme solution (5ml Elastase 4U/ml in HBSS + 200ul DNaseI 2.5mg/ml). Suspension is incubated for 1-1,5 hour in 37 C with gentle rotation. The digestion reaction was terminated by adding 20ml HBSS++ (with 10mM HEPES, 2mM EGTA, 1000 U/ml Penicilin, 0.1 mg/ml Streptomycin, 1% BSA). Cells were filtered through a 70μm filter coated with HBSS++, spun down at 400g for 10 min at 4C and resuspended in 10 ml HBSS++.
Droplet based scRNA-seq was carried out with Chromium Next Gen Single Cell 3' Kit version3 (10X Genomics). Single cell RNAseq library preparation was done using standard protocol (10x Genomics).

value: WT

value: Postnatal day 63

value: Oral administration of tamoxifen (100ug/gr of body weight) via gavage at stage P60 - cell collection at P63


title: 10xMulti_Pomc_2_HTO

first: Li

last: Li

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: Library name: Pomc_2_HTO

data_processing:
Raw Fastq files were precessed using 10x Cellranger-ARC.
Assembly: mm10
Supplementary files format and content: Pomc.Joint.v2.rds : Merged data after QC in R format
Supplementary files format and content: feature_ref.csv : HTO&ADT barcode
Library strategy: CITE-seq

molecule: protein

source_name: Mediobasal Hypothalamus

extract_protocol:
Tissue preparation, dissociation, and nuclei extraction were described in a STAR Protocol (https://doi.org/10.1016/j.xpro.2023.102595). In this study, the ARH regions were dissected from four-week-old for Pomc-Cre; Sun1/sfGFP and Pomc-Cre; Otpfl/fl; Sun1/sfGFP mice, under a fluorescent dissecting microscope and stored at -80°C. Different genotype samples were separately homogenized with 1 ml homogenization buffer using a Dounce grinder pestle. The homogenate solutions were centrifuged at 500 g for 5 min in a swing bucket rotor, and the supernatants were removed. The nuclei were resuspended with 100 μl of wash buffer and incubated with different TotalSeq Hashtag antibodies against the nuclear pore complex (0.5 μl, MAb414; BioLegend) for 10 min. The nuclei suspensions were washed thrice with 1 ml wash buffer and spun down at 500 g for 5 min. After hashtagging each sample with the antibody, all samples were pooled together, and GFP-positive nuclei were sorted during FACS at the Flow Cytometry Core of UTSW Medical Center.
After sorting, the nuclei solution was adjusted to the desired concentration at 500–2,000 nuclei/μl, then proceeded with the 10× Multiome kit at the UTSW Next Generation Sequencing Core.

value: Mediobasal Hypothalamus

value: Pomc-Cre; R26LSL-Sun1-sfGFP

value: Ctrl

value: mixed sample


title: IgA-Seq Sample IgA33A

description:
Library name: IgA33A
Novogene
IGASEQ.rds

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.


title: Mouse thoracic spinal cord snATAC-seq_biol_rep3_tech_rep3

description:
Library name: AT03C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse thoracic spinal cord snATAC-seq_biol_rep3_tech_rep2

description:
Library name: AT03B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA31A

description:
Library name: IgA31A
Novogene
IGASEQ.rds


title: P16358_4004

description: 10x Genomics


title: 10xMulti_Pomc_2_ATAC

description: Library name: Pomc_2_ATAC

data_processing:
Raw Fastq files were precessed using 10x Cellranger-ARC.
Assembly: mm10
Supplementary files format and content: Pomc.Joint.v2.rds : Merged data after QC in R format
Supplementary files format and content: feature_ref.csv : HTO&ADT barcode


title: Mouse thoracic spinal cord snRNA-seq_biol_rep3_tech_rep2

description:
Library name: AT03B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: P16358_4003

description: 10x Genomics


title: IgA-Seq Sample IgA30A

description:
Library name: IgA30A
Novogene
IGASEQ.rds


title: 10xMulti_Pomc_2_GEX

description: Library name: Pomc_2_GEX


title: Mouse thoracic spinal cord snATAC-seq_biol_rep3_tech_rep1

description:
Library name: AT03A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA29A

description:
Library name: IgA29A
Novogene
IGASEQ.rds


title: P16358_4002

description: 10x Genomics


title: human_PLC_PRF_5_EZM8266_3

description:
Library name: PLC_EZM3_S17
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt


title: CCseq_MJ907_sae2Drec114-8D_6h_rep2

city: Brighton

first: Jon

middle: Alexander

last: Harper

address: School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX6/’, rec114-8D::hphMX4/’ rep2

data_processing:
FASTQ reads were aligned to the reference genome (SacCer3H4L2; which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 S. cerevisiae genome build as described in Gittens 2019) via Bowtie2, using TermMapper as previously described in Gittens 2019 (https://github.com/Neale-Lab/terminalMapper) Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build Supplementary files format and content: Sparse table of positions (Pos) of read frequencies of 5' ends of Read 1 molecules mapping to the top (Watson) and bottom (Crick) strand of each chromosome (Chrom) of the reference genome Library strategy: CC-seq
Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build
Supplementary files format and content: FASTQ paired reads

growth_protocol: For meiosis induction, a single colony was inoculated in 4mL of YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) and incubated at 30 °C, 250 rpm for a day to reach saturation, then diluted to OD600 of 0.2 in a volume of 200 mL of either YPA (1% yeast extract, 2% peptone, 1% potassium acetate) or SPS (0.5% yeast extract, 1% peptone, 0.67% Yeast Nitrogen Base without amino acids, 1% potassium acetate, 0.05M Potassium Hydrogen phthalate, 0.001% Antifoam 204) pre-sporulation medium. Cultures were incubated at 30 °C, 250 rpm for 14–16 hours, then washed and resuspended in 200 mL pre-warmed SPM sporulation medium (2% potassium acetate supplemented with diluted amino acids) and incubated at 30°C, 250rpm for the duration of the time course.

extract_protocol:
Protein-DNA Covalent-Complex Mapping (CC-seq) in yeast followed a method previously described (Gittens 2019). Briefly, meiotic cell samples are chilled and frozen at -20˚C for at least 8 hours, then thawed and spheroplasted (in 1 M sorbitol, 50 mM NaHPO4, 10 mM EDTA, 30 min at 37˚C), fixed in 70% ice-cold ethanol, collected by centrifugation, dried briefly, then lysed in STE (2% SDS, 0.5 M Tris, 10 mM EDTA). Genomic DNA was extracted via Phenol/Chloroform/IAA extraction (25:24:1 ratio) at room temperature, with aqueous material carefully collected, precipitated with ethanol, washed, dried, then resuspended in 1xTE buffer (10 mM Tris/1 mM EDTA). Total genomic DNA was sonicated to <500 bp average length using a Covaris M220 before equilibrating to a final concentration of 0.3 M NaCl, 0.1% TritonX100, 0.05% Sarkosyl. Covalent complexes were enriched on silica columns (Qiagen) via centrifugation, washed with TEN solution (10 mM Tris / 1 mM EDTA / 0.3 M NaCl), before eluted with TES buffer (10 mM Tris / 1 mM EDTA / 1% SDS). Samples were treated with Proteinase K at 50˚C, and purified by ethanol precipitation.
DNA ends were filled and repaired using NEB Ultra II end-repair module (NEB #E7645), with adapters ligated sequentially to the sonicated, then blocked, ends with recombinant TDP2 treatment in between these steps to remove the 5-phosphotyrosyl-linked Spo11 peptide. Ampure bead cleanups were used to facilitate sequential reactions. PCR-amplified libraries were quantified on a Bioanalyser and appropriately diluted and multiplexed for deep sequencing (Illumina MiSeq 2x75 bp).

treatment_protocol: 50 mL of culture was taken at t = 6 hours. Samples were centrifuged at 3000 x g for 5 minutes, supernatant discarded and pellet frozen at -20 °C until use.

value: Meiotic

value: 6 hour


title: IgA-Seq Sample IgA28A

description:
Library name: IgA28A
Novogene
IGASEQ.rds


title: human_PLC_PRF_5_EZM8266_2

description:
Library name: PLC_EZM2_S16
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt


title: CCseq_MJ907_sae2Drec114-8D_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX6/’, rec114-8D::hphMX4/’ rep1


title: IgA-Seq Sample IgA27A

description:
Library name: IgA27A
Novogene
IGASEQ.rds


title: Mouse thoracic spinal cord snATAC-seq_biol_rep2_tech_rep3

description:
Library name: AT02C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse thoracic spinal cord snRNA-seq_biol_rep3_tech_rep1

description:
Library name: AT03A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: human_PLC_PRF_5_EZM8266_1

description:
Library name: PLC_EZM1_S15
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt


title: Mouse thoracic spinal cord snRNA-seq_biol_rep2_tech_rep3

description:
Library name: AT02C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA26A

description:
Library name: IgA26A
Novogene
IGASEQ.rds


title: CCseq_MJ906D_sae2Drec114-8A_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX6/’, rec114-8A::hphMX4/’ rep2


title: Mouse thoracic spinal cord snATAC-seq_biol_rep2_tech_rep2

description:
Library name: AT02B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: CCseq_MJ906_sae2Drec114-8A_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX6/’, rec114-8A::hphMX4/’ rep1


title: IgA-Seq Sample IgA25A

description:
Library name: IgA25A
Novogene
IGASEQ.rds


title: human_PLC_PRF_5_Control_2

description:
Library name: PLC_C2_S13
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt

value: Control


title: human_PLC_PRF_5_Control_3

description:
Library name: PLC_C3_S14
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt


title: CCseq_LLR40_sae2Dndt80Drec114-8Dtel1D_6h_rep2

description: Library name: MATa/alpha ho::LYS2/_, lys2/_, ura3/_, arg4-nsp/_, leu2::hisG/_, his4X::LEU2/_, nuc1::LEU2/_, sae2∆::KanMX4/_, ndt80∆::LEU2/_, rec114-8D::hphMX4/_, tel1∆::HphMX4/_ rep2


title: Mouse thoracic spinal cord snRNA-seq_biol_rep2_tech_rep2

description:
Library name: AT02B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA24A

description:
Library name: IgA24A
Novogene
IGASEQ.rds


title: human_PLC_PRF_5_Control_1

description:
Library name: PLC_C1_S12
PLC_EZM8266_RAW_Counts_Gene_Symbol.txt


title: CCseq_LLR40_sae2Dndt80Drec114-8Dtel1D_6h_rep1

description: Library name: MATa/alpha ho::LYS2/_, lys2/_, ura3/_, arg4-nsp/_, leu2::hisG/_, his4X::LEU2/_, nuc1::LEU2/_, sae2∆::KanMX4/_, ndt80∆::LEU2/_, rec114-8D::hphMX4/_, tel1∆::HphMX4/_ rep1


title: Mouse thoracic spinal cord snATAC-seq_biol_rep2_tech_rep1

description:
Library name: AT02A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: CCseq_LLR36_sae2Dndt80Drec114-8D_6h_rep2

description: Library name: MATa/alpha ho::LYS2/_, lys2/_, ura3/_, arg4-nsp/_, leu2::hisG/_, his4X::LEU2/_, nuc1::LEU2/_, sae2∆::KanMX4/_, ndt80∆::LEU2/_, rec114-8D::hphMX4/_ rep2


title: IgA-Seq Sample IgA23A

description:
Library name: IgA23A
Novogene
IGASEQ.rds


title: Mouse thoracic spinal cord snRNA-seq_biol_rep2_tech_rep1

description:
Library name: AT02A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA22A

description:
Library name: IgA22A
Novogene
IGASEQ.rds