title: PBS Sirpa+ DC Sample 2

city: Chiba

first: YANGSONG

last: WANG

state: Chiba

address: 1-8-1, Inohana,

department: Experimental Immunology

country: Japan

institute: Chiba University

description: Library name: PBS Sirpa+ DC Sample 2

data_processing:
Sequencing was performed on an illumina NextSeq 500 system
The resulting sequencing data were converted to fastq format using Bcl2fastq v2.17.
Assembly: mm10
Supplementary files format and content: count.txt

source_name: Thymus

extract_protocol:
Thymic pDC and Sirpa+ DC sorted using BD FACS Aria III. As CD11c low B220+ for pDC, and CD11c high Sirpa+ for Sirpa+ DC. Total RNA of sorted cells was extracted with TRIzol (Invitrogen).
For cDNA library construction, Ovation SoLo RNA-Seq Mouse (TECAN) was utilized according to the manufacturer's protocol, with 5 ng of total RNA used per sample.

value: Thymus

value: Thymic DC

value: Sirpa+ DC (CD11c high Sirpa+)

value: Wild Type

value: PBS_2 weeks


title: PBS Sirpa+ DC Sample 1

status: Public on Feb 03 2026

type: SRA

description: Library name: PBS Sirpa+ DC Sample 1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: batch


title: hBMSC-TERT4 cells, Ob 7 days, rep 1

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description:
Library name: RNA_7dOb_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 7dOb_1

data_processing:
Bulk RNA-seq reads were aligned to GRCh37 (hg19) genome using STAR (Dobin A, et al., Bioinformatics 29:15-21) and default settings. Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing all time points and including Replicate information in the model.
Raw base calls of 10x libraries were demultiplexed into fastq files and then aligned and quantified at the exon and intron level using zUMI (Parekh S, et al., Gigascience 7:giy059) and STAR (Dobin A, et al., Bioinformatics 29:15-21) with genome GRCh38. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411) to yield a gene count matrix for 29939 cells.
Raw base calls of Parse libraries were demultiplexed into fastq files, which contain sequencing information of several libraries. Spliting of reads according to  loading scheme of a WTmini and alignment to genome GRCh38 as well as quantification of gene counts were done using the Parse Trailmaker pipeline, with the libraries of interest being distributed in wells A7 to A9 (Ob-Ad-Ob-Ad-Ob-Ad-Ob-Ad) and A10 to A12 (Ad-Ob-Ad-Ob-Ad-Ob-Ad-Ob). Due to low recovery of sample Ad-Ob-Ad-Ob-Ad-Ob-Ad-Ob, we later only analyzed the Ob-Ad-Ob-Ad-Ob-Ad-Ob-Ad sample. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411).
Assembly: GRCh38 for scRNA-seq and snRNA-seq, GRCh37 for bulk RNA-seq
Supplementary files format and content: Counts_normalDiff_TERT.txt, tab delimited file with Homer derrived raw gene counts of bulk RNA-seq data for normal differentiation (derrived from Rauch A, et al., Nature Genetics 51:716-727).
Supplementary files format and content: Counts_Media_Change.txt, tab delimited file with Homer derrived raw gene counts of bulk RNA-seq data for cells with media change.
Supplementary files format and content: TERT_MSC.dgecounts.rds, TERT_7dOb.dgecounts.rds, TERT_7dAd.dgecounts.rds, TERT_7dOb_4dAd.dgecounts.rds, and TERT_7dAd_4dOb.dgecounts.rds, tab delimited files to retrieve zUMI derrived raw gene count matrices of the individual 10x scRNA-seq libraries.
Supplementary files format and content: Parse_transdiff.mtx, all_genes_parse.csv, and cell_metadata_parse.csv, tab delimited files to retrieve Parse trailmaker derrived raw gene count matrices of Parse snRNA-seq data.

molecule: polyA RNA

organism: Homo sapiens

source_name: immortalized human stromal cells from bone marrow

growth_protocol: hBMSC-TERT4 cells (Simonsen JL, et al. 2002. Nat Biotechnol. 20(6):592-6.) were seeded in tissue culture flasks and expanded in culture medium consisting of minimum essential medium (MEM, 32561-094, Invitrogen) supplemented with 10% fetal bovine serum (FBS, 16000044, Life Technologies) and 1% penicillin/streptomycin (P/S, 15140-130, Invitrogen). They were incubated at 37 °C with 5% CO2 and 95% humidity. The culture medium was changed three times a week, and the cells were either passaged or set out for differentiation when reaching 80-90% confluency.

extract_protocol:
Bulk RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
For Parse snRNA-seq, cells have been trypsinized and spun down at 200 g cells. Supernatant was carefully removed without touching the upper layer. Cells were subjected to nuclei isolation following a protocol adjusted from Hauwaert et al. (STAR Protocols 2:100612). Briefly, cells were dounced 5 times in nuclei isolation buffer consisting of 250 mM Sucrose (84097, Sigma-Aldrich), 10 mM HEPES (22320022, Thermo Fisher Scientific), 1.5 mM MgCl2 (M2670, Sigma-Aldrich), 10 mM KCl (P9541, Sigma-Aldrich), 0.001% IGEPAL CA-630 (I8896, Sigma-Aldrich), 0.2 mM DL-Dithiothreitol (43819, Sigma-Aldrich) and 0.5 U/mL RNase inhibitor (40,000 U/mL, M0314L, Bionordika) in DEPC-treated water. Nuclei were passed through a 30 µm cell strainer, centrifugated at 200 g for 10 min at 4C and resuspended in nuclei resuspension buffer consisting of 1% BSA (A9418, Sigma-Aldrich) in PBS, 2 mM MgCl2 and 0.04 U/µL RNase inhibitor in PBS followed by a final transfer through a 30 µm cell strainer. Nuclei fixation was carried out according to manufacturer’s instructions (Parse Biosciences Evercode WT, version 2).
For 10x scRNA-seq, cells have been trypsinized and spun down at 200 g and washed twice in culture media. Cells were separated using a 40 µm mesh, washed 3 times in PBS with 0.04% non-acetylated BSA, and cell numbers were adjusted to 0.7 million cells per ml followed by a final transfer through a 40 µm mesh.
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.
scRNA-seq: Libraries were prepared according to manufactures instructions (10x Genomics). snRNA-seq: Libraries were prepared using a WTmini loading scheme according to manufactures instructions (Parse).

treatment_protocol: hBMSC-TERT4 cells were stimulated with osteogenic (MEM (32561-094, Invitrogen)  supplemented with 10% FBS, 1% P/S, 5mM ß-glycerophosphate (50020-100, Sigma-Aldrich), 10nM dexamethasone (D4902, Sigma-Aldrich), 50µg/mL 2-phosphate ascorbic acid (A4544, Sigma-Aldrich) and 10nM 1,25-vitamin D3 (D1530, Sigma-Aldrich)) or adipogenic (DMEM (41965062, Thermo Fisher Scientific) supplemented with 10% FBS, 1% P/S, 100nM dexamethasone, 3µg/mL insulin (I9278, Sigma-Aldrich), 1µM rosiglitazone (BRL, 71740, Cayman Chemicals) and 225µM 3-isobutyl-1-methylxanthine (IBMX, I5879-5G, Sigma-Aldrich)) media according to the time points indicated.

value: osteogenic diff 7 days

tag: time point

value: 7 days


title: E. coli mono-colonized, male, rep4

city: Atlanta

first: Timothy

middle: R

last: Sampson

state: Georgia

address: 615 Michael St

country: USA

institute: Emory University

description: Library name: 21173FL-01-06

data_processing:
Sequencing quality control was performed using FastQC (version 0.11.9) and reads were pseudoaligned to the mouse reference genome (GRCm39) using Kallisto (version 0.44.0)
Assembly: GRCm39
Supplementary files format and content: Kallisto abundance.h5 files

source_name: Brain

extract_protocol:
Brains were perfused with PBS then homogenized using a Wheaton dounce tissue grinder (with 0.114 ±0.025mm pestle clearance) in culture media comprised of HBBS with 1.5% HEPES, and 0.5% glucose. Cells were then transferred to a 35% isotonic percoll gradient solution and spun 20 minutes at 700 x g to remove the myelin layer. Transcription (Actinomycin D, Sigma #A1410) and translation (Anisomycin, Sigma #A9789) inhibitors were added to every solution throughout both procedures to prevent transcriptional changes that could impact downstream results. The remaining cells were washed several times in HBBS culture media before undergoing immunopanning. Cells were resuspended in 0.02% BSA in PBS and incubated at room temperature on a 10cm petri dish with anti-CD11b and secondary antibody already adhered to the dish (Thermo Scientific, 14-0112-82 and Jackson 112-005-167) for 10-15 minutes. After incubation the unadhered cells were washed away and remaining cells scraped off the plate directly into Trizol (Zymo Research R2050-1-200) and stored at -80 C until later use.
RNA was extracted from isolated brain myeloid cells using the Qiagen RNeasy Kit (#74106) according to the manufacturer’s guidelines. Bulk RNA-sequencing libraries were created for each sample using the Takara SMART-Seq mRNA HT LP kit (#634792) according to the manufacturer’s protocol and recommendations.

treatment_protocol: Germ-free 3-4 month old DBA/2NTac mice were mono-colonized with either Bacteroides thetaiotaomicron, Clostridium celatum, Lactobacillus johnsonii, or Escherichia coli for 2 weeks.

value: Brain

value: CD11b+ brain myeloid cells

value: E. coli mono-colonized

tag: Sex

value: male

tag: bacterial strain

value: Escherichia coli str. K12 MC4100


title: E. coli mono-colonized, male, rep3

description: Library name: 21173FL-01-05


title: PBS pDC Sample 1

description: Library name: PBS pDC Sample 1

value: pDC (CD11c low B220+)


title: PBS pDC Sample 2

description: Library name: PBS pDC Sample 2


title: E. coli mono-colonized, male, rep2

description: Library name: 21173FL-01-04


title: P0hetF1KO_300mM_biol_rep3

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

description:
Library name: P0hetF1KO_300mM_biol_rep3
small RNAs from L1 larvae

data_processing:
For all of the library, normalized bigwig files were generated from the mapping results using millions of non-structural mappers as a normalization factor. This normalized coverage information was computed for 10 bp bins using the bedtools and bedops v.2.4.26 packages. For the 2-cell embryo small RNA sequencing, counts were normalized in each sample using spike-ins counts (scaling factor per sample = 10^3 x total_nb_spikes_counted / total_nb_reads_aligned) in a dataset. Scaling factors were then generally "minimized" : all scaling factors of the dataset were divided by the smallest scaling factor in the dataset).
Assembly: ce11 C. elegans Sequencing Consortium WBcel235
Supplementary files format and content: normalized big wig files will be provided for each libraries

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching or L1 larvae. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. For the 2-cell embryo RNA extraction, precisely staged 2-cell embryos were obtained by alkaline hypochlorite treatment of synchronized gravid adult hermaphrodites, and fifty 2-cell embryos were collected using a mouth pipet. Embryos were lysed for 10min at 65˚C and 1min at 85˚C in a lysis solution containing Tris pH8 5mM final, EDTA 0.25mM final, Triton 100X 0.5%, Tween 20 0.5%, Proteinase K 0.5% and Water. The lysates were subjected to RNA purification using the Quick-RNA MicroPrep kit (ZymoResearch, R1051), and small RNAs (RNA fraction from 17 to 200 nucleotides) and mRNAs (RNA fraction >200 nucleotides) were collected separately. A small RNA spike-in was added before embryo lysis.
The small RNA library preparation was performed essentially as described previously by Barucci et al., 2020.

treatment_protocol: In all experiments using AID strains, 250 mM auxin stock solution was prepared in ethanol and stored at 4 °C. Auxin plates or ethanol plates were prepared by the addition of auxin or only ethanol to NGM plates (final concentration: 500 µM auxin, 0.2% ethanol for auxin plates and 0.2% ethanol for ethanol plates). Plates were seeded with OP50 Escherichia coli. Synchronized worms were placed on auxin or ethanol plates from L3 stage. To collect embryos from day 3 adult AID strains the auxin treatment was initiated at day 1 of adulthood. For experiments using the AID2 system, 10mM stock solution of 5-Ph-IAA was prepared in ethanol and stored at -20 ˚C for not more than a month. 5-Ph-IAA plates were prepared at a final concentration of 1µM. For osmotic stress treatment, synchronized populations of L1 larvae, obtained by hypochlorite treatment of gravid adults, were grown on NGM plates for 48 hours. After 48 hours, worms were washed from the NGM plates and divided on two NGM plates seeded with OP-50 E. coli and containing 50mM NaCl (control treatment) or 300mM NaCl (mild osmotic stress). After 24 hours of exposure, adults were collected and washed from the plates. Adults were pelleted by sedimentation rather than centrifugation to avoid collecting laid eggs derived from not fully exposed worms. Eggs from adults were collected by hypochlorite treatment and 2-cell stage embryos were manually picked or let them developed until L1 for small RNA sequencing.

value: L1 larvae

value: whole worm

value: mothers exposed to 300mM NaCl


title: hBMSC-TERT4 cells, Ad 3 days, rep 2

description:
Library name: RNA_3dAd_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 3dAd_2

value: immortalized human stromal cells from bone marrow

value: adipogenic diff 3 days

value: 3 days


title: hBMSC-TERT4 cells, Ad 3 days, rep 3

description:
Library name: RNA_3dAd_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 3dAd_3


title: YG+ pDC Sample 2

description: Library name: YG+ pDC Sample 2

value: Thymus

value: Thymic DC

value: YG+ pDC (CD11c low B220+)

value: MC38_2 weeks with YG


title: P0hetF1KO_300mM_biol_rep2

description:
Library name: P0hetF1KO_300mM_biol_rep2
small RNAs from L1 larvae


title: hBMSC-TERT4 cells, Ob 3 days, rep 3

description:
Library name: RNA_3dOb_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 3dOb_3

value: osteogenic diff 3 days


title: YG+ pDC Sample 1

description: Library name: YG+ pDC Sample 1

value: Wild Type


title: L. johnsonii mono-colonized, female, rep2

description: Library name: 21173FL-01-02

value: Brain

value: CD11b+ brain myeloid cells

value: L. johnsonii mono-colonized

value: female

value: Lactobacillus johnsonii str. VPI 7960


title: P0hetF1KO_300mM_biol_rep1

description:
Library name: P0hetF1KO_300mM_biol_rep1
small RNAs from L1 larvae

value: L1 larvae


title: hBMSC-TERT4 cells, Ad 3 days, rep 1

description:
Library name: RNA_3dAd_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 3dAd_1


title: hBMSC-TERT4 cells, Ob 3 days, rep 2

description:
Library name: RNA_3dOb_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 3dOb_2


title: P0hetF1het_300mM_biol_rep3

description:
Library name: P0hetF1het_300mM_biol_rep3
small RNAs from L1 larvae

value: whole worm


title: L. johnsonii mono-colonized, female, rep1

description: Library name: 21173FL-01-01


title: PH_4mOVX_replicate6

city: Boston

first: Victor

last: Navarro

state: MA

address: 221 Longwood Ave

department: Division of Endocrinology

institute: Brigham and Women's Hospital

description: Library name: L534_9_S9

data_processing:
Reads were aligned using kallisto and the resulting count data was imported into R using tximport for analysis with DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text file with library size adjusted gene-level counts for each sample

source_name: posterior hypothalamus

extract_protocol:
RNA was extracted using Zymo Quick RNA micropreo kit following the manufacturer's instructions
RNA sequencing libraries were prepared using the KAPA mRNA HyperPrep-Stranded Kit following the manufacturer's protocol

value: posterior hypothalamus

value: 4 months post-OVX

value: batch 2


title: Kat6a homozygous, E12.5 dorsal telencephalon, litter 3782, sample 5

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: Kat6a_homo_E125_3782_5

data_processing:
Reads were aligned to a combined genome comprising mouse mm10 and Drosophila melanogaster R6.35 using Rsubread version 2.2.6.
Read counts were summarized using the Rsubread featureCounts function, with GENCODE annotation version M25 for mouse and Drosophila chromosomes from release R6.35.
Gene expression counts were normalized using the TMM (Trimmed Mean of M-values) method in edgeR. Spike-in normalization using Drosophila melanogaster was explored but not used in the final analysis.
Assembly: mm10, R6.35 (Drosophila melanogaster, FlyBase release)
Supplementary files format and content: tab-delimited text files; columns represent Ensembl ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Dorsal telencephalon

growth_protocol: The dorsal telencephalon was dissected from E12.5 embryos, frozen and used for RNA extraction. For E16.5 cortical neurons, the dorsal forebrain was dissected from E16.5 foetuses, incubated in trypsin/EDTA (Sigma, 1006132) on ice for 30 min, then at 37˚C for 5 min, rinsed in 2% BSA in PBS and dissociated with gentle pipetting. Samples were centrifuged 10 min at 200 g 4˚C, the supernatant was removed, and the cell pellet was resuspended in 2% BSA in PBS and the suspension was centrifuged 10 min at 200 g 4˚C. Cells were resuspended in Neurobasal medium (21103049, Life Technologies) supplemented with 2% B27 supplement (17504044, Life Technologies), 500 μM GlutaMAX supplement (35050061, Life Technologies), then passed through a 40 μM sieve. Cell preparations from each foetus were plated on one 6 cm dish previously coated with Poly-D-Lysine (Sigma Aldrich, P6407-5MG) and grown at 37˚C in 5% CO2. Cells were cultured overnight and then used for RNA extraction.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions including the optional DNase I digestion step. RNA concentration and quality were determined with an Agilent 2200 TapeStation (Agilent).
Stranded mRNA libraries were generated with a TruSeq Stranded mRNA (100ng plus) kit (Illumina) according to the manufacturer’s instructions.

value: Dorsal telencephalon

value: Kat6a homozygous

tag: Stage

value: M


title: Kat6a homozygous, E12.5 dorsal telencephalon, litter 3684, sample 9

description: Library name: Kat6a_homo_E125_3684_9

value: F


title: hBMSC-TERT4 cells, Ob 3 days, rep 1

description:
Library name: RNA_3dOb_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 3dOb_1

value: immortalized human stromal cells from bone marrow

value: 3 days


title: Kat6a homozygous, E12.5 dorsal telencephalon, litter 3781, sample 4

description: Library name: Kat6a_homo_E125_3781_4


title: E. coli mono-colonized, male, rep1

description: Library name: 21173FL-01-03

value: E. coli mono-colonized

value: male

value: Escherichia coli str. K12 MC4100


title: PH_4mOVX_replicate4

description: Library name: L534_7_S7


title: P0hetF1het_300mM_biol_rep2

description:
Library name: P0hetF1het_300mM_biol_rep2
small RNAs from L1 larvae

value: mothers exposed to 300mM NaCl


title: PH_4mOVX_replicate5

description: Library name: L534_8_S8

value: female


title: hBMSC-TERT4 cells, Ad 1 day, rep 3

description:
Library name: RNA_1dAd_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 1dAd_3

value: adipogenic diff 1 day

value: 1 day


title: Kat6a homozygous, E12.5 dorsal telencephalon, litter 3684, sample 8

description: Library name: Kat6a_homo_E125_3684_8


title: P0hetF1het_300mM_biol_rep1

description:
Library name: P0hetF1het_300mM_biol_rep1
small RNAs from L1 larvae

value: L1 larvae

value: whole worm


title: Kat6a heterozygous, E16.5 cortical neurons, litter 3715, sample 7

description: Library name: Kat6a_het_E165_3715_7

source_name: Cortex

value: Cortex

value: Kat6a heterozygous


title: hBMSC-TERT4 cells, Ad 1 day, rep 2

description:
Library name: RNA_1dAd_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 1dAd_2


title: PH_14dOVX_replicate6

description: Library name: L534_6_S6

value: posterior hypothalamus

value: 14 days post-OVX

value: batch 2


title: Kat6a heterozygous, E16.5 cortical neurons, litter 3715, sample 5

description: Library name: Kat6a_het_E165_3715_5

value: M


title: Starved_N2_Day1_biol_rep3

description:
Library name: Starved_N2_Day1_biol_rep3
small RNAs from 2-cell embryos

source_name: embryo

value: embryo

value: 2-cell embryos

value: Wild-type

value: mother exposed to starvation


title: hBMSC-TERT4 cells, Ad 1 day, rep 1

description:
Library name: RNA_1dAd_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 1dAd_1

value: immortalized human stromal cells from bone marrow


title: Starved_N2_Day1_biol_rep2

description:
Library name: Starved_N2_Day1_biol_rep2
small RNAs from 2-cell embryos


title: Kat6a heterozygous, E16.5 cortical neurons, litter 3715, sample 3

description: Library name: Kat6a_het_E165_3715_3

value: F


title: Kat6a heterozygous, E16.5 cortical neurons, litter 3675, sample 1

description: Library name: Kat6a_het_E165_3675_1


title: Starved_N2_Day1_biol_rep1

description:
Library name: Starved_N2_Day1_biol_rep1
small RNAs from 2-cell embryos


title: PH_14dOVX_replicate4

description: Library name: L534_4_S4

value: female


title: PH_sham_replicate3

description: Library name: L534_1_S1

value: intact


title: PH_sham_replicate4

description: Library name: L534_2_S2


title: hBMSC-TERT4 cells, Ob 1 day, rep 2

description:
Library name: RNA_1dOb_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 1dOb_2

value: osteogenic diff 1 day

value: 1 day


title: hBMSC-TERT4 cells, Ob 1 day, rep 1

description:
Library name: RNA_1dOb_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 1dOb_1


title: hBMSC-TERT4 cells, Ob 1 day, rep 3

description:
Library name: RNA_1dOb_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 1dOb_3


title: Kat6a heterozygous, E12.5 dorsal telencephalon, litter 3782, sample 4

description: Library name: Kat6a_het_E125_3782_4

value: Dorsal telencephalon


title: POA_4mOVX_replicate6

description: Library name: L534_18_S18

source_name: preoptic area

value: preoptic area

value: 4 months post-OVX


title: Ctrl_N2_Day1_biol_rep3

description:
Library name: Ctrl_N2_Day1_biol_rep3
small RNAs from 2-cell embryos


title: Ctrl_N2_Day1_biol_rep1

description:
Library name: Ctrl_N2_Day1_biol_rep1
small RNAs from 2-cell embryos


title: hBMSC-TERT4 cells, Ad 4  hrs, rep 3

description:
Library name: RNA_4hAd_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 4hAd_3

value: adipogenic diff 4 hrs

value: 4 hours


title: Kat6a heterozygous, E12.5 dorsal telencephalon, litter 3781, sample 3

description: Library name: Kat6a_het_E125_3781_3

value: Kat6a heterozygous


title: PH_14dOVX_replicate5

description: Library name: L534_5_S5

value: posterior hypothalamus

value: 14 days post-OVX

value: batch 2


title: hBMSC-TERT4 cells, Ad 4 hrs, rep 2

description:
Library name: RNA_4hAd_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 4hAd_2


title: DP_AID_Auxin_Adult_biol_rep3

description:
Library name: DP_AID_Auxin_Adult_biol_rep3
small RNAs from whole worms

source_name: Young adult worms

value: Young adult worms

value: MHE229 (Drosha Pasha intestinal degron)

value: whole worm

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc]) pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: Auxin


title: Kat6a heterozygous, E12.5 dorsal telencephalon, litter 3684, sample 4

description: Library name: Kat6a_het_E125_3684_4

value: M


title: Kat6a heterozygous, E12.5 dorsal telencephalon, litter 3684, sample 5

description: Library name: Kat6a_het_E125_3684_5

value: F


title: Ctrl_N2_Day1_biol_rep2

description:
Library name: Ctrl_N2_Day1_biol_rep2
small RNAs from 2-cell embryos

value: embryo

value: 2-cell embryos

value: Wild-type


title: POA_4mOVX_replicate5

description: Library name: L534_17_S17

value: preoptic area

value: female

value: 4 months post-OVX


title: hBMSC-TERT4 cells, Ob 4 hrs, rep 3

description:
Library name: RNA_4hOb_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 4hOb_3

value: immortalized human stromal cells from bone marrow

value: osteogenic diff 4 hrs

value: 4 hours


title: DP_AID_Auxin_Adult_biol_rep1

description:
Library name: DP_AID_Auxin_Adult_biol_rep1
small RNAs from whole worms


title: POA_4mOVX_replicate4

description: Library name: L534_16_S16

value: batch 2


title: Wild Type, E16.5 cortical neurons, litter 3715, sample 2

description: Library name: WT_E165_3715_2

value: Cortex

value: Wild type


title: DP_AID_Auxin_Adult_biol_rep2

description:
Library name: DP_AID_Auxin_Adult_biol_rep2
small RNAs from whole worms

value: Young adult worms

value: MHE229 (Drosha Pasha intestinal degron)

value: whole worm


title: hBMSC-TERT4 cells, Ad 4 hrs, rep 1

description:
Library name: RNA_4hAd_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 4hAd_1

value: adipogenic diff 4 hrs


title: Wild Type, E16.5 cortical neurons, litter 3715, sample 1

description: Library name: WT_E165_3715_1

value: M


title: POA_14dOVX_replicate6

description: Library name: L534_15_S15

value: 14 days post-OVX


title: hBMSC-TERT4 cells, Ob 4 hrs, rep 2

description:
Library name: RNA_4hOb_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 4hOb_2


title: hBMSC-TERT4 cells, Ob 4 hrs, rep 1

description:
Library name: RNA_4hOb_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 4hOb_1


title: POA_14dOVX_replicate4

description: Library name: L534_13_S13


title: POA_14dOVX_replicate5

description: Library name: L534_14_S14


title: Wild Type, E16.5 cortical neurons, litter 3675, sample 3

description: Library name: WT_E165_3675_3

value: F


title: Wild Type, E16.5 cortical neurons, litter 3675, sample 7

description: Library name: WT_E165_3675_7


title: DP_AID_EtOH_Adult_biol_rep2

description:
Library name: DP_AID_EtOH_Adult_biol_rep2
small RNAs from whole worms

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc]) pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: EtOH


title: DP_AID_EtOH_Adult_biol_rep1

description:
Library name: DP_AID_EtOH_Adult_biol_rep1
small RNAs from whole worms


title: Wild Type, E12.5 dorsal telencephalon, litter 3782, sample 3

description: Library name: WT_E125_3782_3

value: Dorsal telencephalon


title: hBMSC-TERT4 cells, day 0, rep 3

description:
Library name: RNA_Msc_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: Msc_3

value: undifferentiated

value: day 0


title: VRC01 engineered ImmunoCult culutres B cells on D13 of culture-2

city: La Jolla

first: Morgan

last: Bravo

state: CA

address: 10466 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

description: Library name: M11093

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode analysis and gene counts were done using Cellranger v8
Assembly: mMul_10
Supplementary files format and content: H5

organism: Macaca mulatta

source_name: primary B cells

extract_protocol:
B cells were enriched via FACs or directly removed from culture,washed with cold PBS, and resuspended at the appropriate concentration for the sequencing pipeline.
Library preparation was performed according to manufacturer's instructions (10x Genomics, V2 Chromium Next GEM Single Cell 5')

value: primary B cells


title: POA_sham_replicate5

description: Library name: L534_12_S12

value: preoptic area

value: female

value: intact


title: VRC01 engineered ImmunoCult culutres B cells on D13 of culture-1

description: Library name: M3052


title: DP_AID_EtOH_Adult_biol_rep3

description:
Library name: DP_AID_EtOH_Adult_biol_rep3
small RNAs from whole worms


title: Wild Type, E12.5 dorsal telencephalon, litter 3684, sample 7

description: Library name: WT_E125_3684_7

value: Wild type


title: POA_sham_replicate4

description: Library name: L534_11_S11

value: batch 2


title: POA_sham_replicate3

description: Library name: L534_10_S10


title: hBMSC-TERT4 cells, day 0, rep 2

description:
Library name: RNA_Msc_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: Msc_2

value: immortalized human stromal cells from bone marrow


title: Wild Type, E12.5 dorsal telencephalon, litter 3781, sample 1

description: Library name: WT_E125_3781_1


title: hBMSC-TERT4 cells, day 0, rep 1

description:
Library name: RNA_Msc_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: Msc_1


title: VRC01 engineered primary B cells at the time of engraftment (D6)-1

description: Library name: J3029


title: VRC01 engineered primary B cells at the time of engraftment (D6)-2

description: Library name: J3052


title: Primary tumor, patient #5

city: Beijing

first: Pengfei

last: Zhao

address: No.17, Panjiayuan Nanli, South Huawei Road

country: China

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using
the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). After the insert size met the expectation, the Bio-RAD CFX 96 fluorescence quantitative PCR
instrument was used to accurately quantify the library effective concentration (Library effective concentration > 10nm), and the reagent used was Bio-RAD KIT iQ SYBR GRN.
the software used for read alignment is HISAT (Version:2.0.5) and for read quantification is HTSeq (Version: 0.6.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: ovarian tumor

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. A total amount of 1-3μg RNA per sample was used as input material for the RNA  sample preparations.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® ( NR604-01/02) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: ovarian tumor


title: Wild Type, E12.5 dorsal telencephalon, litter 3684, sample 1

description: Library name: WT_E125_3684_1


title: POA_4mOVX_replicate3

description: Library name: L16_5460_S18

value: 4 months post-OVX

value: batch 1


title: Metastasis tumor, patient #5

source_name: peritoneal tumor

value: peritoneal tumor


title: POA_4mOVX_replicate2

description: Library name: L16_5459_S17


title: H3K115ac_seChIP_NPC-day7_INPUT

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

description: INPUT library

library_source: genomic

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings
For single-end ChIP libraries: Filtered and trimmed reads were aligned to the mm10 assembly of mouse genome using bowtie and uniquely mapped reads were kept. Alignments were converted to BAM format and sorted using SAMtools and PCR duplicates removed using Picard. Bedtools was used to create BED files followed by conversion into HOMER tag directory format (makeTagDirectory) using default parameters. We called peaks using HOMERs findPeaks command with options -F 2 -localSize 50000 -size 150 -minDist 300 -fdr 0.01 –region. UCSC compatible bigwig files normalized to sequencing depth were generated using makeUCSCfile with parameters: -bigWig -style chipseq –fragLength 150.
Paired-end ChIP libraries: Filtered and trimmed reads were aligned to mm10 genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates as above. Read pairs were converted into ChIP fragments using bedtools bamtobed –bedpe and fractionated into sub-nucleosomes (<150 bp) and mono-nucleosomes (150-225 bp). Fragment coverage was computed at base-pair resolution with bedtools genomeCoverageBed and coverage normalized to sequencing depth and scaled to 107. Coverage data was converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: Read density in bigwig format

molecule: genomic DNA

source_name: mESC (46C)

growth_protocol: 46C cells were maintained in GMEM supplemented with 10% Serum and LIF.

extract_protocol:
Native MNase ChIP (detailed protocol: PMID: 27089178)
NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB catalogue # E7645)

treatment_protocol: For differentiation, three million 46C Cells were seeded 24 hours (h) prior to differentiation on 0.1% gelatine coated T75 Corning flasks in the maintenance medium. On Day-0, one flask of ESCs were harvested and rest of the cells were supplied with differentiation media ((1:1DMEM/F12: Neuro basal medium (GIBCO, #31330-032 and 21103-049 respectively) supplemented with 0.5x B27 (Invitrogen, #17504044), 0.5x N2 (Invitrogen, #17502048), L-Glutamine and 50mM 2--mercaptoethanol (GIBCO, #31350010)). Cells were then cultured for 7 days with daily media changes after day-2 NPC differentiation was monitored visually through expression of the Sox1-GFP reporter.

value: mESC (46C)

tag: chip antibody

value: NPC differentiation Day-7


title: Metastasis tumor, patient #4

source_name: omentum tumor

value: omentum tumor


title: POA_4mOVX_replicate1

description: Library name: L16_5458_S16


title: U_6_vasectomized

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

description: Library name: U_6

data_processing:
QC of raw sequencing reads and trimming were performed using FastQC and Trim Galore! 0.6.7 (Brabraham Bioinformatics) using a Phred score cutoff of 30 and minimum sequence length of 100 after trimming. In order to separate out reads derived from semen (C57/Bl6 strain) we obtained the lists of all 129S1/SvImJ SNPs compared to the mouse genome (GRCm38) from the Ensembl database (ftp://ftp.ensembl.org). Based on this SNP database we generated a pseudo-hybrid genome using the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). Briefly, 129S1/SvImJ SNPs relative to the mouse genome were then N-masked to allow mapping of both FRT and semen-derived reads. The trimmed read files were then mapped to this pseudo-hybrid genome using HISAT2 2.2.1. Alignment rate ranged from 89.28% to 96.85%. This was followed by splitting the mapped files into reads originating from FRT or semen. Splitting was performed using the program SNPsplit (Brabraham Bioinformatics). We retained the mapped reads assigned to the FRT and discarded the reads determined to be semen derived.
StringTie 2.2.1 was used for transcript quantification and annotation. Gene annotation was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org)(GRCm38.89).
Assembly: GRCm38
Supplementary files format and content: tab delimited table including raw read counts for each sample

source_name: uterus

extract_protocol:
Plug-positive females were euthanized by cervical dislocation and tissue was dissected. Unpaired control females were euthanized and dissected in the morning, when determined to be in estrus. For each female the FRT was dissected, collecting tissue from both uterine horns (Us), both uterotubal junctions (UTJs) using precise microdissection and both oviducts (OVDs) (Fig. 1). For each female one of each U, UTJ and OVD was placed in RNAlater for RNA extraction. RNA was extracted from tissues stored in RNAlater using the RNeasy Plus Mini (uterine horn samples) or the RNeasy Plus Micro (for UTJ and OVD) kits (Qiagen) following the manufacturers recommendations. Samples were stored at -80º until sequencing.
Samples were sequenced on a Illumina NovaSeq X platform, producing ~30 M, 150bp, paired-end reads per sample. Sample quality control and library preparation was performed by the sequencing facility (Novogene Europe). RNA integrity ranged from 6.3 to 9.8.

treatment_protocol: Female 129SV/S2 mice were either paired 1-to-1 with intact (COP; n=4) or vasectomized (VAS; n=4) C57/Bl6 males or unpaired in estrus (CTR; n=5). Mice were maintained under standard laboratory conditions in environmentally controlled rooms (20–24ºC) on a 12L:12D photoperiod with nesting material and ad libitum food and water. All animal handling was conducted according to German law of animal protection and in agreement with the approval of the local institutional animal care committees (Landesamt für Natur, Umwelt und Verbraucherschutz, North Rhine-Westphalia, Germany, AZ81-02.04.2018.A369). Females were paired in the evening and checked for seminal plugs early the next morning ~6-8h post-copulation.

value: uterus

value: WT

value: post-copulation with vasectomized male


title: U_15_vasectomized

description: Library name: U_15


title: POA_14dOVX_replicate3

description: Library name: L16_5457_S15


title: Metastasis tumor, patient #3


title: H3K115ac_seChIP_NPC-day7_rep1

description: ChIP library


title: U_14_vasectomized

description: Library name: U_14


title: POA_14dOVX_replicate2

description: Library name: L16_5456_S14

value: 14 days post-OVX


title: POA_sham_replicate2

description: Library name: L16_5454_S12

value: preoptic area


title: H3K115ac_seChIP_mESC_rep1

description: ChIP library

value: NPC differentiation Day-0


title: Primary tumor, patient #3


title: Primary tumor, patient #2


title: H3K115ac_seChIP_NPC-day7_rep2

description: ChIP library


title: U_13_vasectomized

description: Library name: U_13


title: Metastasis tumor, patient #2


title: Primary tumor, patient #4


title: H3K115ac_seChIP_mESC_rep2

description: ChIP library


title: Metastasis tumor, patient #1


title: POA_sham_replicate1

description: Library name: L16_5453_S11

value: female

value: intact


title: H3K115ac_seChIP_mESC_INPUT

description: INPUT library


title: U_8_copulated

description: Library name: U_8

value: post-copulation with intact male


title: Primary tumor, patient #1


title: Bromocriptine-feded forager bees

city: Changchun

first: Miaoran

last: Zhang

state: Jilin

address: Xinmin Street

institute: Department of Physiology, College of Basic Medical Sciences, Jilin University

description:
Library name: sample1
10x Genomics

data_processing:
The CellRanger tool (v7.0.1) was utilized to map the sequenced reads onto the Amel_HAv3.1 reference genome. The resulting gene count matrices were then imported into Seurat (v5.1.0) to generate a Seurat object for each group. Through this step, the gene expression data was arranged and organized, enabling comprehensive downstream analysis and investigation via the Seurat framework. Prior to integrating cells across different groups, a filtering process was conducted using the criteria of log10GenesPerUMI>0.85, nFeature_RNA > 200 and nFeature_RNA <5000. log10GenesPerUMI is determined by calculating the log10(nFeature_RNA) / log10(nCount_RNA) and represents cell complexity. To identify potential cell doublets that might arise when multiple cells entered the same microfluid droplet and were assigned identical barcodes, the R package 'scDblFinder' (1.11.4) was employed (dbr.sd = 1). This particular package enabled the detection and removal of putative cell doublets, ensuring the integrity and reliability of subsequent analysis. In order to eliminate batch effects, we opted for the CCAIntegration algorithm available in Seurat (v5.1.0). Through unsupervised clustering using the first 50 principal components, the results were represented in a uniform manifold approximation and projection (UMAP) plot. The cell types were annotated manually by referring to marker genes. Notably, photoreceptors were excluded from further analysis. Details of the specific analysis can be found in the provided code. All data analysis was performed in R (v4.4.0).
Assembly: Amel_HAv3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apis mellifera

source_name: brain

extract_protocol:
Honeybee were anesthetized in a dissection dish on ice and washed with ethanol and phosphate buffer saline (PBS) twice, after which brains were dissected in PBS on ice under a stereomicroscope (OLYMPUS EP50). The surrounding trachea, ocelli, and compound eye (absent in drones) were carefully removed, after which honeybee brains were washed with 1ml PBS. The single nuclei were prepared by mechanical extraction.
snRNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) strategy.

treatment_protocol: Full-body spray

value: brain


title: POA_14dOVX_replicate1

description: Library name: L16_5455_S13


title: Water-feded forager bees

description:
Library name: sample2
10x Genomics


title: U_9_copulated

description: Library name: U_9


title: PH_4mOVX_replicate2

description: Library name: L16_5450_S8

value: posterior hypothalamus


title: U_7_copulated

description: Library name: U_7


title: tho5ab_Nuc_HS_7

city: Regensburg

first: Leo

last: Schmutterer

address: Universitätsstraße 31

department: Plant Cell Biology, Biochemistry, and Biotechnology

country: Germany

institute: University of Regensburg

description:
Library name: Sample48
UMIs in header

data_processing:
Reads were mapped to the TAIR10 genome (Lamesch et al., 2012)  STAR (v2.7.8a, ‘--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000  --outFilterMismatchNoverReadLmax 0.04 --outSAMmultNmax 1 –outMultimapperOrder Random’).
After tagging duplicated sequences using Picard MarkDuplicates (v2.21.8) (https://broadinstitute.github.io/picard/) the UMIs were used to remove technical duplicates using umi_tools dedup (v1.0.1).
For the differential gene expression analysis, the resulting reads from the pipeline outlined above were used to create a count table using the featureCounts function of the rsubread package (v1.6.3) (Liao et al., 2019)
Assembly: TAIR10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds of Arabidopsis thaliana (Col-0) were stratified in darkness for 48 h at 4°C and plants were grown and propagated at 21°C on soil in a phytochamber or on MS medium in plant incubators (PolyKlima) under long-day conditions (16h light at 21°C and 8h darkness at 18°C).

extract_protocol:
Nuclear and cytoplasmic fractions were prepared from rosettes of 14-d plants adapting a previously described protocol based on differential centrifugation (Park et al., 2005). RNA was isolated from nuclear and cytoplasmic fractions using the RNeasy Plant Mini Kit (Qiagen). Additionally, the ERCC RNA Spike-In Mix (ambion) was added
RNA-seq libraries were prepared using NuGEN Universal Plus RNA-Seq with NuQuant User Guide v3 (Tecan Genomics) in combination with Arabidopsis rRNA AnyDeplete module

treatment_protocol: For heat shock plants were transferred to 37 °C for 3hrs and plants were harvested without recovery period.

value: Seedling

tag: age

tag: compartment

value: Nuc

tag: condition


title: U_3_control

description: Library name: U_3

value: control


title: PH_4mOVX_replicate3

description: Library name: L16_5451_S9

value: 4 months post-OVX

value: batch 1


title: 4797-030-3-60

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: 4797-030-3-60

data_processing:
A Nextflow pipeline (https://github.com/compbiomed/RNA_Seq) was used to process the sequencing data to obtain the expression levels for each gene.
Both gene and transcript level counts were calculated using RSEM with Ensembl build 75 annotation.
Assembly: GRCh37
Supplementary files format and content: DECAMP2_mucus_plugging_filtered_counts.tsv: tab-separated values file containing 24599 x 48 matrix of counts for all Ensembl Gene IDs that passed filtering

source_name: Nasal brushing

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA). RNA integrity was quantified by Agilent Bioanalyzer, and RNA purity was confirmed using a NanoDrop spectrophotometer.
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol.

value: Nasal brushing

tag: mp score

tag: copd status

value: No

tag: smoking status

value: Former Smoker (not even a puff for >= 1 month)

value: Male


title: tho5ab_Nuc_6

description:
Library name: Sample46
UMIs in header

tag: tissue


title: 4797-021-3-60

description: Library name: 4797-021-3-60

value: Current Smoker (one puff in the last month)


title: PH_14dOVX_replicate3

description: Library name: L16_5448_S6

value: 14 days post-OVX


title: U_2_control

description: Library name: U_2

value: uterus

value: WT


title: tho5ab_Nuc_7

description:
Library name: Sample47
UMIs in header


title: U_12_control

description: Library name: U_12


title: 4797-017-3-60

description: Library name: 4797-017-3-60

value: Yes

value: Female


title: U_10_control

description: Library name: U_10


title: PH_14dOVX_replicate2

description: Library name: L16_5447_S5

value: female


title: 4796-026-3-60

description: Library name: 4796-026-3-60


title: PH_14dOVX_replicate1

description: Library name: L16_5446_S4

value: posterior hypothalamus


title: tho5ab_Nuc_4

description:
Library name: Sample45
UMIs in header

value: Seedling


title: PH_4mOVX_replicate1

description: Library name: L16_5449_S7


title: 4797-037-3-60

description: Library name: 4797-037-3-60


title: tho5ab_Nuc_2

description:
Library name: Sample44
UMIs in header

value: Nuc


title: PH_sham_replicate1

description: Library name: L16_5444_S2

value: intact


title: tho5ab_Nuc_1

description:
Library name: Sample43
UMIs in header


title: U_1_control

description: Library name: U_1

value: control


title: tho5ab_Nuc_HS_6

description:
Library name: Sample42
UMIs in header


title: UTJ_15_vasectomized

description: Library name: UTJ_15

source_name: uterotubal junction

value: uterotubal junction

value: post-copulation with vasectomized male


title: UTJ_6_vasectomized

description: Library name: UTJ_6


title: Fmr1KO-PolyIC-4

city: Nanjing

first: Jun-Yi

last: Chen

state: Jiangsu

address: Xianlin Campus, Nanjing University, No.163 Xianlin Avenue, Qixia District

institute: Nanjing University

description:
Library name: Sample 12
FMR1_P4

data_processing:
The raw paired end reads were trimmed and quality controlled by trim-galore(https://github.com/FelixKrueger/TrimGalore/) with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The read counts of each gene were obtained by featureCounts.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file include raw counts for all samples

source_name: Cerebellum

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The library was constructed using a TruseqTM RNA sample prep Kit (Illumina) according to the manufacturer’s protocol.Library quality was verified using the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA kit.

treatment_protocol: poly(I:C) is administered via intraperitoneal injection.

value: Cerebellum

value: Fmr1 knock out


title: 4792-008-3-60

description: Library name: 4792-008-3-60

value: Nasal brushing

value: No

value: Former Smoker (not even a puff for >= 1 month)

value: Male


title: PH_sham_replicate2

description: Library name: L16_5445_S3

source_name: posterior hypothalamus

value: batch 1


title: 4793-040-60

description: Library name: 4793-040-60


title: tho5ab_Nuc_HS_5

description:
Library name: Sample41
UMIs in header


title: Fmr1KO-PolyIC-3

description:
Library name: Sample 11
FMR1_P3


title: 4438-044-3-60

description: Library name: 4438-044-3-60

value: Yes


title: UTJ_13_vasectomized

description: Library name: UTJ_13

value: WT


title: Fmr1KO-PolyIC-2

description:
Library name: Sample 10
FMR1_P2


title: tho5ab_Nuc_HS_2

description:
Library name: Sample39
UMIs in header


title: UTJ_9_copulated

description: Library name: UTJ_9

value: post-copulation with intact male


title: 4792-025-60

description: Library name: 4792-025-60

value: Current Smoker (one puff in the last month)


title: UTJ_14_vasectomized

description: Library name: UTJ_14


title: 4438-039-3-60

description: Library name: 4438-039-3-60


title: UTJ_8_copulated

description: Library name: UTJ_8


title: 4438-043-3-60

description: Library name: 4438-043-3-60

value: Female


title: tho5ab_Nuc_HS_4

description:
Library name: Sample40
UMIs in header

value: Seedling

value: Nuc


title: tho5ab_Cyt_HS_7

description:
Library name: Sample37
UMIs in header

value: Cyt


title: 4797-049-3-60

description: Library name: 4797-049-3-60


title: Fmr1KO-sham-4

description:
Library name: Sample 8
FMR1_S4

value: Saline


title: tho5ab_Nuc_HS_1

description:
Library name: Sample38
UMIs in header


title: 4792-006-3-60

description: Library name: 4792-006-3-60


title: UTJ_7_copulated

description: Library name: UTJ_7

value: uterotubal junction


title: Fmr1KO-sham-3

description:
Library name: Sample 7
FMR1_S3

value: Cerebellum


title: UTJ_5_copulated

description: Library name: UTJ_5


title: Fmr1KO-sham-2

description:
Library name: Sample 6
FMR1_S2

value: Fmr1 knock out


title: tho5ab_Cyt_HS_6

description:
Library name: Sample36
UMIs in header


title: 4797-047-3-60

description: Library name: 4797-047-3-60

value: Nasal brushing


title: Fmr1KO-sham-1

description:
Library name: Sample 5
FMR1_S1


title: Fmr1KO-PolyIC-1

description:
Library name: Sample 9
FMR1_P1


title: tho5ab_Cyt_HS_5

description:
Library name: Sample35
UMIs in header


title: UTJ_3_control

description: Library name: UTJ_3

value: control


title: 4797-032-60

description: Library name: 4797-032-60

value: No


title: FVB-4

description:
Library name: Sample 4
FVB_S4

value: FVB


title: tho5ab_Cyt_HS_4

description:
Library name: Sample34
UMIs in header


title: 4796-086-63

description: Library name: 4796-086-63

value: Former Smoker (not even a puff for >= 1 month)

value: Male


title: UTJ_12_control

description: Library name: UTJ_12

value: WT


title: UTJ_2_control

description: Library name: UTJ_2


title: tho5ab_Cyt_HS_2

description:
Library name: Sample33
UMIs in header


title: 4796-083-3-60

description: Library name: 4796-083-3-60

value: Yes


title: tho5ab_Cyt_HS_1

description:
Library name: Sample32
UMIs in header


title: UTJ_10_control

description: Library name: UTJ_10


title: FVB-1

description:
Library name: Sample 1
FVB_S1


title: tho5ab_Nuc_5

description:
Library name: Sample31
UMIs in header


title: UTJ_1_control

description: Library name: UTJ_1


title: 4797-019-3-60

description: Library name: 4797-019-3-60

value: Current Smoker (one puff in the last month)


title: FVB-2

description:
Library name: Sample 2
FVB_S2


title: tho5ab_Cyt_7

description:
Library name: Sample30
UMIs in header


title: 4796-011-3-60

description: Library name: 4796-011-3-60


title: OVD_15_vasectomized

description: Library name: OVD_15

source_name: oviduct

value: oviduct

value: post-copulation with vasectomized male


title: OVD_6_vasectomized

description: Library name: OVD_6


title: OVD_14_vasectomized

description: Library name: OVD_14


title: 4796-049-63

description: Library name: 4796-049-63


title: FVB-3

description:
Library name: Sample 3
FVB_S3


title: tho5ab_Cyt_6

description:
Library name: Sample29
UMIs in header

value: Seedling


title: Fmr1KO-MG-PolyIC-3

description:
Library name: Sample 6
P3

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file include raw counts for all samples

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The mRNA was transcribed into full-length cDNA using a Smarter Amplification Kit from OE Biotech Co., Ltd. (Shanghai, China). Full-length cDNA (150 pg) was processed using a Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol.Library quality was verified using the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA kit.

treatment_protocol: poly(I:C) is administered via intraperitoneal injection. Mice were transcardially perfused with ice-cold PBS and cerebellums were rapidly dissected and placed into ice-cold PBS. Cerebellum was minced and homogenized with ice-cold PBS containing 200 μl of 0.4% DNaseI per 50 ml of PBS. Percoll was added during centrifugation to separate myelin from cells. The cell suspension volume was adjusted to 21 ml with PBS and 9 ml of 100% isotonic Percoll (8.1 ml of Percoll (cytiva) (30% isotonic Percoll final). Suspensions were centrifuged (15 min, 500g, 4 °C) and the supernatant and top layer of myelin were discarded. Rat CD11b MicroBeads (Miltenyi) were used to enrich cerebellar microglia using MACS columns according to manufacturer’s instructions.

value: Microglia


title: Fmr1KO-MG-PolyIC-2

description:
Library name: Sample 5
P2


title: Fmr1KO-MG-PolyIC-1

description:
Library name: Sample 4
P1


title: tho5ab_Cyt_5

description:
Library name: Sample28
UMIs in header

value: Cyt


title: tho5ab_Cyt_4

description:
Library name: Sample27
UMIs in header


title: 4795-047-3-60

description: Library name: 4795-047-3-60


title: Fmr1KO-MG-sham-3

description:
Library name: Sample 3
F3

value: Saline


title: 4795-075-3-60

description: Library name: 4795-075-3-60


title: OVD_13_vasectomized

description: Library name: OVD_13


title: tho5ab_Cyt_2

description:
Library name: Sample26
UMIs in header


title: Fmr1KO-MG-sham-2

description:
Library name: Sample 2
F2

value: Cerebellum


title: OVD_9_copulated

description: Library name: OVD_9

value: post-copulation with intact male


title: tho5ab_Cyt_1

description:
Library name: Sample25
UMIs in header


title: 4793-043-3-60

description: Library name: 4793-043-3-60

value: Nasal brushing


title: Fmr1KO-MG-sham-1

description:
Library name: Sample 1
F1

value: Fmr1 knock out


title: OVD_8_copulated

description: Library name: OVD_8


title: Col_0_Nuc_HS_6

description:
Library name: Sample24
UMIs in header

value: Nuc


title: 4792-022-3-60

description: Library name: 4792-022-3-60

value: No


title: 4793-029-63

description: Library name: 4793-029-63

value: Former Smoker (not even a puff for >= 1 month)


title: 4T1 cells shEtv5-4

city: guangzhou

first: mengxing

last: huang

address: huangpu

institute: guangdong

description: Library name: 4T1-sh2-4

data_processing:
Sequencing libraries were prepared using the Illumina TruseqTM RNA sample prep Kit v2 (Illumina, CA, USA). Sequencing was performed on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA).
Raw sequene data were processed on STAR_2.7.10a
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA from cultured cells was isolated using either TRIzol Reagent (15596018, Invitrogen) or Universal RNA Purification Kit (EZB-RN4)
Sequencing libraries were prepared using the Illumina TruseqTM RNA sample prep Kit v2 (Illumina, CA, USA). Sequencing was performed on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

tag: cell line

value: murine mammary tumor cell

value: Etv5 knockdown


title: 4T1 cells shEtv5-3

description: Library name: 4T1-sh2-3

tag: cell type


title: OVD_7_copulated

description: Library name: OVD_7

tag: genotype

value: WT


title: 4793-045-63

description: Library name: 4793-045-63

value: Yes

value: Current Smoker (one puff in the last month)

value: Male


title: Col_0_Nuc_HS_5

description:
Library name: Sample23
UMIs in header

value: Seedling


title: OVD_3_control

description: Library name: OVD_3

value: oviduct

tag: treatment

value: control


title: OVD_5_copulated

description: Library name: OVD_5


title: Col_0_Nuc_HS_4

description:
Library name: Sample22
UMIs in header


title: Col_0_Nuc_HS_3

description:
Library name: Sample21
UMIs in header


title: 4T1 cells shEtv5-2

description: Library name: 4T1-sh2-2


title: OVD_2_control

description: Library name: OVD_2


title: 4438-033-3-60

description: Library name: 4438-033-3-60


title: OVD_12_control

description: Library name: OVD_12


title: 4T1 cells shEtv5-1

description: Library name: 4T1-sh2-1


title: Col_0_Nuc_HS_2

description:
Library name: Sample20
UMIs in header


title: Col_0_Nuc_HS_1

description:
Library name: Sample19
UMIs in header


title: 4T1 cells shcontrol-4

description: Library name: 4T1-NT-4


title: 4792-004-60

description: Library name: 4792-004-60

value: Female


title: OVD_10_control

description: Library name: OVD_10


title: 4796-022-3-60

description: Library name: 4796-022-3-60


title: PA1 DGCR8  KO2 clon replicate 3

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

institute: Universitat Jaume I

description: Library name: KO2_3

library_source: other

data_processing:
BBDuk from the BBMap toolkit for sequencing adapter removal and read trimming.
RNA paired-end reads were aligned to GRCh38.p14 human genome assembly with STAR v2.7.6a
Reads were quantified with featureCounts v2.0.125 using NCBI Annotation Release 102 and with option ‘--extraAttributes "gene_biotype"’ for annotating sequence type
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes featureCounts output with counts.

molecule: other

source_name: Cultured cell line

growth_protocol: All cell lines were grown at 37 °C and 5% CO2. Human PA-1 cells were cultured in Gibco™ MEM, 20% heat-inactivated foetal bovine serum, 100 U/mL penicillin-streptomycin and 0.1 mM Non-Essential Amino Acids (Gibco™).

extract_protocol:
Cell pellets from WT, KO1 and KO2 were lysed in lysis buffer (10mM Tris pH 7.4, 150 mM NaCl, 0.075% IGEPAL, supplemented with RNAse inhibitors (40U), RQ1 DNase, 0.5 mM DTT, 0.2 mM PMSF, and Roche cOmplete EDTA-free protease inhibitors (4693159001, Merck) on ice for 5 min, followed by centrifugation at 3,500 x g for 5 min. Supernatant was centrifuged again for 5 min at 13,000 rpms to get rid of any debris, and saved as cytoplasmic fraction. 50 ul of slurry Protein G Dynabeads (10003D, ThermoFisher) were washed 3 times with IP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100), and coupled to 5 ug of anti-dsRNA monoclonal antibody (J2, RNT-SCI-10010200 Scicons) for 1 h at RT, followed by 3 washes with IP buffer to get rid of unbound antibody. Cytoplasmic supernatant was diluted in IP buffer, supplemented with 0.5 mM, 0.2 mM PMSF and Roche cOmplete EDTA-free protease inhibitors, and incubated with antibody-coupled beads for 4 hours at 4°C. Beads were washed 3 times with IP buffer, changing tubes after each wash. RNA was extracted from beads using Trizol L/S and precipitated O/N with isopropanol.
5 ng of each IP-RNA sample (3 biological replicates for each cell line; WT, KO1 and KO2) was used for library preparation using the NEBNEXT Ultra II Directional RNA Library Prep Kit (NEB #E7760) and the NEBNext rRNA Depletion kit (Human/Mouse/Rat) (NEB #E6310).

value: Human ovarian teratocarcinoma

value: DGCR8 KO


title: 4T1 cells shcontrol-3

description: Library name: 4T1-NT-3


title: 4T1 cells shcontrol-2

description: Library name: 4T1-NT-2


title: PA1 DGCR8  KO2 clon replicate 2

description: Library name: KO2_2


title: PA1 DGCR8  KO1 clon replicate 3

description: Library name: KO1_3


title: Col_0_Cyt_HS_4

description:
Library name: Sample17
UMIs in header

value: Cyt


title: Col_0_Cyt_HS_6

description:
Library name: Sample18
UMIs in header


title: PA1 DGCR8  KO1 clon replicate 2

description: Library name: KO1_2


title: Col_0_Cyt_5

description:
Library name: Sample14
UMIs in header


title: p130-WT, biol rep 3, Stag2-WT mouse urothelium, 1 week after TMX induction

first: Jaime

last: Martinez de Villarreal

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

description: Library name: WT-p130-3

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Cut&Run sequencing data was analysed using the Cut&Run Nextflow pipeline
reads were trimmed and aligned to mm10 reference genome and to S. cerevisiae as spike-in genome using Bowtie2
Peak calling was performed using MACS2 with pMNase-treated chromatin as control samples
Assembly: mm10
Supplementary files format and content: narrowpeak files and bigwigs
Library strategy: CUT&Run

source_name: peeled urothelium

extract_protocol:
Urothelial cells (approx. 500,000 cells for each experimental condition) were used for CUT&RUN experiments (2-3 replicates per experimental condition). Cut&Run was performed as described by Skene et al. 2018.
DNA samples were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB ref.E7645). Adapter-ligated libraries were completed by a limited-cycle PCR, with 63º T(ann/ext) for 10s, and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 320 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.

value: peeled urothelium

value: 1 week after TMX induction

tag: batch


title: OVD_1_control

description: Library name: OVD_1


title: Col_0_Cyt_7

description:
Library name: Sample15
UMIs in header


title: Col_0_Cyt_HS_3

description:
Library name: Sample16
UMIs in header


title: rNLS sample 5

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

data_processing:
Data were demultiplexed, barcode processing, gene counting, and aggregation according to the BBI pipeline available at https://github.com/bbi-lab/bbi-sci
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: whole brain

extract_protocol:
Mice were euthanized with CO2, and whole brains removed. Brains were split down the midline, snap frozen in liquid nitrogen, and stored at -80C until snRNAseq protocol was initiated. snRNAseq was performed as a fee-for-service by the Brotman Baty Advanced Technology Lab (BAT-Lab) at the University of Washington.
Libraries were constructed as described for sci-RNA-seq3 in Martin et al, DOI: 10.1038/s41596-022-00752-0

value: whole brain


title: p130-KO, biol rep 3, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-p130-3


title: rNLS sample 4


title: Col_0_Cyt_3

description:
Library name: Sample13
UMIs in header


title: control sample 5


title: PA1 wildtype replicate 3

description: Library name: WT_3

value: wildtype


title: PA1 DGCR8  KO2 clon replicate 1

description: Library name: KO2_1


title: Col_0_Cyt_HS_5

description:
Library name: Sample12
UMIs in header


title: PA1 DGCR8  KO1 clon replicate 1

description: Library name: KO1_1


title: p130-KO, biol rep 2, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-p130-2


title: rNLS sample 3


title: PA1 wildtype replicate 2

description: Library name: WT_2


title: control sample 4


title: p130-WT, biol rep 2, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-p130-2


title: p130-WT, biol rep 1, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-p130-1


title: PA1 wildtype replicate 1

description: Library name: WT_1


title: p130-KO, biol rep 1, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-p130-1


title: Col_0_Cyt_HS_2

description:
Library name: Sample11
UMIs in header


title: control sample 3


title: LIN54-KO, biol rep 2, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-LIN54-2


title: LIN54-KO, biol rep 1, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-LIN54-1


title: Col_0_Cyt_HS_1

description:
Library name: Sample10
UMIs in header


title: control sample 2


title: TVWB31

city: ILLKIRCH

first: Nicolas

last: Charlet-Berguerand

address: 1 rue Laurent Fries

institute: IGBMC

description:
Library name: Sample7
library construction protocol: P3250

data_processing:
Image analysis and base calling were performed using RTA 4.12.2 and bclconvert 4.2.7.
Sample demultiplexing, barcode processing, gene counting and feature barcode analysis were performed using Cell Ranger multi 8.0.1.
QC, exploration of the data and analysis were performed using Seurat 5.1.0.
Assembly: mm10
Supplementary files format and content: h5 file containing the matrix associating the number of UMI with a feature and a barcode.

source_name: myonuclei

extract_protocol:
Tibialis Anterior (TA), gastrocnemius and quadriceps muscles of 7 months post-AAV injection of two individuals per genotype (NaCl-, GFP-, ATG polyG-GFP-, uGIPpolyG-GFP-, uN2CpolyG-GFP- or LOC6polyG-GFP- injected mice) were isolated and dissociated with scissor in hypotonic buffer (250 mM sucrose, 10 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl pH8, 25 mM HEPES, 0,2 mM PMSF, 0,1 mM DTT, 0,3% Triton X-100, 0,2 U/µL RNase inhibitor). The muscles were homogenized with Precellys 24 Touch (Bertin) for 25 sec at 5000 rpm. Samples were filtered through 100 µm and 20 µm filters and centrifuged 10 min at 400 x g at 4°C. Pellets were washed in PBS, 2% BSA, 0,2 U/µL RNase inhibitor, centrifuged 10 min at 400 x g at 4°C, resuspended in PBS, 2% BSA, 0,2 U/µL RNase inhibitor, 200 nM DAPI to sort nuclei with FACSAria Fusion or FACSAria II. More than 3 million of isolated nuclei were centrifuged 12 min at 400 x g at 4°C and fixed with formaldehyde using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN 1000414) following 10X genomics procedure (CG000478).
P3250 : Single nuclei libraries were generated using the Chromium Next GEM Single Cell Fixed RNA reagent set (10x Genomics, Leiden, The Netherlands), according to the manufacturer's recommendations. During this process, cell (or nucleus) counting was performed using an ADAM MC Plus Fluorescence cell counter (NanoEntek, Seoul, Korea) with a mixed solution of Acridine Orange and 4',6-diamidino-2-phénylindole (DAPI) or by a Trypan Blue exclusion assay on a Buerker Chamber. For each of the 8 samples, from 133000 to 1060000 starting nuclei were hybridized with an unique Mouse WTA Probe Barcode (10x Genomics, PN-1000492). Hybridizations were completed in 80 µL of hybridization mixture plus 20 µL of WTA probes at 42oC for 21h. Following cell re-counting, an equal number of nuclei from each hybridization reaction was combined in a single pool before washing. After re-counting, nuclei were then loaded onto the Chromium iX using a Next GEM Chip Q, targeting 5000 nuclei per hybridization reaction for a total of 96000 nuclei loaded per library (8-plex). Full-length cDNA amplification was completed using 8 cycles of PCR. Dual-index library construction was performed with 10 cycles during sample index PCR. Final library quantification and quality control were performed using the Bioanalyzer 2100 (Agilent Technologies, Les Ulis, France).

value: myonuclei

tag: strain

value: male

value: OPDM4 asRILpolyG

tag: barcode


title: Col_0_Nuc_7

description:
Library name: Sample09
UMIs in header

value: Nuc


title: TVWB30

description:
Library name: Sample6
library construction protocol: P3250

tag: Sex

value: WT

value: OPDM3 uN2CpolyG


title: Col_0_Nuc_4

description:
Library name: Sample07
UMIs in header

value: Seedling


title: Col_0_Nuc_5

description:
Library name: Sample08
UMIs in header


title: rNLS sample 2


title: control sample 1


title: LIN54-WT, biol rep 2, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-LIN54-2


title: LIN54-WT, biol rep 3, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-LIN54-3


title: TVWB32

description:
Library name: Sample8
library construction protocol: P3250

value: OPML LOC6polyG


title: TVWB28

description:
Library name: Sample4
library construction protocol: P3250

value: OPDM2 uGIPex2polyG


title: LIN54-WT, biol rep 1, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-LIN54-1


title: TVWB29

description:
Library name: Sample5
library construction protocol: P3250

value: OPDM2 uGIPex4polyG


title: STAG2-KO, biol rep 2, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-STAG2-2


title: Col_0_Nuc_3

description:
Library name: Sample06
UMIs in header


title: TVWB27

description:
Library name: Sample3
library construction protocol: P3250

value: ATG-polyGly


title: rNLS sample 1


title: BALF from Influenza patient 9

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

description: Library name: FLU9_BALF

data_processing:
Quality Control: Raw reads were quality-filtered to remove low-quality data and adapters.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: A tab-delimited text file (matrix) containing the raw read counts for each sample.

source_name: Bronchoalveolar lavage fluid

extract_protocol:
PBMCs were isolated via density gradient centrifugation. BALF cells were obtained after DTT digestion and filtration. All samples were resuspended in TRIzol and stored at -80°C for RNA extraction.
Libraries were prepared using BGI/MGI standard protocols. This included mRNA enrichment, fragmentation, double-stranded cDNA synthesis, and adapter ligation for DNBSEQ sequencing.

treatment_protocol: Samples were collected from hospitalized patients diagnosed with COVID-19 or Influenza.All procedures were approved by the Ethics Committee.

value: Bronchoalveolar lavage fluid

value: Mixed


title: TVWB26

description:
Library name: Sample2
library construction protocol: P3250

value: Ctl GFP


title: BALF from Influenza patient 10

description: Library name: FLU10_BALF


title: STAG2-KO, biol rep 1, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-STAG2-1

value: peeled urothelium

value: 1 week after TMX induction


title: Col_0_Nuc_1

description:
Library name: Sample04
UMIs in header


title: 4T1 cells shcontrol-1

description: Library name: 4T1-NT-1

value: murine mammary tumor cell


title: Col_0_Nuc_2

description:
Library name: Sample05
UMIs in header


title: BALF from Influenza patient 8

description: Library name: FLU8_BALF


description: Library name: Sucrose_Gradient_Fractions_12-13_H3K115ac_INPUT

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings. A hybrid genome index for mouse (mm10) and human (hg38) was created with bowtie-build with default parameters. Filtered and trimmed reads were aligned to the hybrid genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates using Picard. Mouse and human reads were counted using samtools. A spike-in normalization factor was calculated (scaling factor= 10e6/Number of human reads). Read pairs aligned to mouse genome were converted into ChIP fragments using bedtools bamtobed –bedpe and Fragment coverage was computed at base-pair resolution with bedtools genomeCoverageBed and coverage was multiplied by the scaling facotor calculated above. Coverage data was converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: SpikeIn normalized signal tracks in bigwig format

growth_protocol: E14 mouse ESCs were maintained in GMEM supplemented with 10% Serum and LIF

extract_protocol:
Sucrose gradient sedimentation of MNase digested chromatin described in detail (PMID: 38956169) followed by Native MNase ChIP described earlier (PMID: 27089178).
NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB catalogue # E7645)


title: TVWB25

description:
Library name: Sample1
library construction protocol: P3250

value: myonuclei

value: Ctl NaCl


title: Col_0_Cyt_2

description:
Library name: Sample02
UMIs in header

value: Cyt


title: BALF from Influenza patient 7

description: Library name: FLU7_BALF


title: Col_0_Cyt_4

description:
Library name: Sample03
UMIs in header


title: STAG2-WT, biol rep 1, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-STAG2-1


title: STAG2-WT, biol rep 2, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-STAG2-3


title: Col_0_Cyt_1

description:
Library name: Sample01
UMIs in header


description: Library name: Sucrose_Gradient_Fractions_9-10_H3K115ac_INPUT


title: pMNase-WT, biol rep 1, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT-pMNase


title: BALF from Influenza patient 6

description: Library name: FLU6_BALF


description: Library name: Sucrose_Gradient_Fractions_12-13_H3K115ac_ChIP


title: pMNase-KO, biol rep 1, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO-pMNase


title: Brassica_napus_shoot_BnaROS1.A05-Flag_Flag_Repeat_1

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

organism: Brassica napus

source_name: shoot

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photoperiod. Shoots and roots of two-week-old plants and stems of four-week-old plants were collected for the indicated genotypes.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp reads, Annoroad Gene Technology).

value: shoot

value: Flag


title: Brassica_napus_shoot_BnaROS1.C04-Flag_Flag_Repeat_1


title: BALF from Influenza patient 5

description: Library name: FLU5_BALF


title: G2

first: Kerui

last: Ye

address: Courtyard 20, East Street

department: Disinfection and Infection Control

institute: Chinese PLA Center for Disease Control and Prevention

description:
Library name: G2
CEAΔku80, shc3 KO, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Af293_A_fumigatus_Af293
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

organism: Aspergillus fumigatus

source_name: cell culture

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

value: cell culture

value: shc3 ko

value: CEAΔku80, shc3 KO


title: G3

description:
Library name: G3
CEAΔku80, shc3 KO, replicate biosample 3


description: Library name: Sucrose_Gradient_Fractions_9-10_H3K115ac_ChIP


title: BALF from Influenza patient 4

description: Library name: FLU4_BALF


description: Library name: Sucrose_Gradient_Fractions_7-8_H3K115ac_INPUT


title: BALF from Influenza patient 3

description: Library name: FLU3_BALF


title: G1

description:
Library name: G1
CEAΔku80, shc3 KO, replicate biosample 1


title: F3

description:
Library name: F3
CEAΔku80, shc2 KO, replicate biosample3

value: shc2 ko

value: CEAΔku80, shc2 KO


description: Library name: Sucrose_Gradient_Fractions_7-8_H3K115ac_ChIP


title: Brassica_napus_shoot_BnaROS1.A05-Flag_Flag_Repeat_2


title: BALF from Influenza patient 2

description: Library name: FLU2_BALF


title: Brassica_napus_shoot_BnaROS1.C04-Flag_Flag_Repeat_2


title: BALF from Influenza patient 1

description: Library name: FLU1_BALF


description: Library name: Sucrose_Gradient_Fractions_5-6_H3K115ac_INPUT


title: KO, biol rep 2, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO2

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Paired-end sequencing data was analyzed using the ENCODE ATAC-Seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) with default parameters
differentially accessible regions (DARs) between experimental conditions were identified with DiffBind in R studio.
Assembly: mm10
Supplementary files format and content: narrowpeak files

source_name: sorted urothelial cells from peeled urothelium: GFP+, DAPI-

extract_protocol:
ATAC-Seq was conducted as described by Alonso-Curbelo et al 2021 using 50,000 viable GFP+ urothelial cells (per condition) isolated by FACS.
ATAC-Seq libraries were prepared using the NEBNext 2 X PCR Master Mix (NEB) as described (Corces et al. 2017) and purified using 1.8 X AMPure XP beads (Beckman Coulter).

treatment_protocol: Mice were fed a TMX-containing diet for a week at sacrificed one week or one month after treatment initiation. GFP+, DAPI- cells were sorted for analysis.

value: sorted urothelial cells from peeled urothelium:GFP+, DAPI-


title: KO, biol rep 3, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO4


title: BALF from COVID-19 patient 5

description: Library name: COVID5_BALF

value: Bronchoalveolar lavage fluid


title: F1

description:
Library name: F1
CEAΔku80, shc2 KO, replicate biosample1


title: BALF from COVID-19 patient 4

description: Library name: COVID4_BALF

value: Mixed


title: SGF_1_Fractions_12-13_H3K115ac_INPUT

description: Library name: SGF_1_Fractions_12-13_H3K115ac_INPUT

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings. Filtered and trimmed reads were aligned to mm10 genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates using Picard. Read pairs were converted into ChIP fragments using bedtools bamtobed –bedpe and Fragment coverage was computed at base-pair resolution with bedtools genomeCoverageBed and coverage normalized to sequencing depth and scaled to 107. Coverage data was converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: RPKM normalized signal tracks in bigwig format


title: KO, biol rep 1, Stag2-KO mouse urothelium, 1 week after TMX induction

description: Library name: KO1


title: SGF_1_Fractions_9-10_H3K115ac_INPUT

description: Library name: SGF_1_Fractions_9-10_H3K115ac_INPUT


title: SGF_1_Fractions_12-13_H3K115ac_ChIP

description: Library name: SGF_1_Fractions_12-13_H3K115ac_ChIP


title: BALF from COVID-19 patient 3

description: Library name: COVID3_BALF


title: SGF_1_Fractions_9-10_H3K115ac_ChIP

description: Library name: SGF_1_Fractions_9-10_H3K115ac_ChIP


title: E3

description:
Library name: E3
CEAΔku80, shc1 KO, replicate biosample 3

value: shc1 ko

value: CEAΔku80, shc1 KO


title: WT, biol rep 3, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT4

value: 1 week after TMX induction


title: E2

description:
Library name: E2
CEAΔku80, shc1 KO, replicate biosample 2


title: BALF from COVID-19 patient 2

description: Library name: COVID2_BALF


title: 4793-006-60

description: Library name: 4793-006-60

value: Nasal brushing

value: No

value: Former Smoker (not even a puff for >= 1 month)

value: Male


title: D3

description:
Library name: D3
CEAΔku80 group, replicate biosample 3

value: wt


title: F2

description:
Library name: F2
CEAΔku80, shc2 KO, replicate biosample2


title: PJH1224, Stag2-KO mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1224_ko
gene_expression_htseqcount_1month.txt

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Analyses were performed using Nextpresso RNA-seq pipeline.
Raw files were aligned to mm10 reference genome using Bowtie and TopHat aligners.
Raw counts were generated using htseq
Differential expression analysis was performed using DEseq2.
Assembly: mm10
Supplementary files format and content: text file with gene expression raw counts

extract_protocol:
Total RNA was extracted using a ReliaPrepTM System Kit (Promega), according to manufacturer’s instructions.
Total RNA samples (400ng; RQS average 9.0, range 8.7-9.3) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

treatment_protocol: Mice were fed a TMX-containing diet for a week at sacrificed one week or one month after treatment initiation.

value: peeled urothelium

value: 1 month after TMX induction


description: Library name: Sucrose_Gradient_Fractions_5-6_H3K115ac_ChIP


title: E1

description:
Library name: E1
CEAΔku80, shc1 KO, replicate biosample 1

value: cell culture


title: WT, biol rep 2, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT3


title: 4438-023-60

description: Library name: 4438-023-60

value: Yes

value: Female


title: BALF from COVID-19 patient 1

description: Library name: COVID1_BALF


title: PJH1221, Stag2-KO mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1221_ko
gene_expression_htseqcount_1month.txt


title: PJH1220, Stag2-KO mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1220_ko
gene_expression_htseqcount_1month.txt


title: WT, biol rep 1, Stag2-WT mouse urothelium, 1 week after TMX induction

description: Library name: WT1


title: N2 C elegans, tunicamycin treated, L4 stage, rep4

city: Galway City

first: Jose

middle: Carlos

last: Casas-Martinez

state: Galway County

address: Human Biology Building, University Road

department: Physiology

country: Ireland

institute: University of Galway

description: Library name: D4

data_processing:
Data Quality Control. Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality.
Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis. (For DESeq2[5] with biological replicates) Differential expression[6] analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR[7] without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: Mapping reads to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and generate a better mapping result than other non-splice mapping tools.
Supplementary files format and content: gene_fpkm_group.txt

source_name: Whole organism

growth_protocol: C. elegans were maintained in Nematode Growth Medium (NGM) at 20 ºC in the laboratory

extract_protocol:
Age-synchronised worms from a single NGM plate were incubated with TRIZol (500 ml per NGM plate), samples were mixed by vortexing for 30 sec. Chloroform was added to each tube (100 μL for a 12-well plate and 1 ml for a C. elegans 60 mm Ø plate), and the tube shaken vigorously by hand for 15 sec before incubation for 5 min at room temperature. RNA precipitation was achieved by adding 100% isopropanol to the aqueous phase (250 μL for a 12-well plate) and incubating at -20ºC overnight. RNA pellet was washed by adding 100 μL of 80% ethanol, supernatant was discarded and the tubes were allowed to air dry for 5-10 min at room temperature. The RNA was reconstituted in 10 μL of RNase-free H2O. Samples were analysed using the NanoDrop2000 spectrophotometer to quantify nucleic acid content and purity.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Tunicamycin treatment of C. elegans on a worm population synchronized by bleaching. Several plates of adult worms carrying embryos were subjected to a chemical (bleach-NaOH solution) and mechanical (by vortexing) procedure. The resulting embryos, for the embryonic stage, were treated with TM diluted in S Medium, for 24 h on a rocker at 20 °C. The resulting embryos, for the L4 stage, were transferred to NGM plates until they reached the L4 developmental stage and then treated with TM diluted in S Medium, for 24 h on a rocker at 20 °C. After treatment worms were transferred to NGM plates and allow to grow until adulthood.

value: Whole organism

value: wildtype

value: tunicamycin 1.25 μg/ml

tag: Stage

value: L4 Stage


title: SGF_1_Fractions_7-8_H3K115ac_ChIP

description: Library name: SGF_1_Fractions_7-8_H3K115ac_ChIP

tag: chip antibody


title: SGF_1_Fractions_7-8_H3K115ac_INPUT

description: Library name: SGF_1_Fractions_7-8_H3K115ac_INPUT


title: PJH1247, Stag2-WT mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1225_wt
gene_expression_htseqcount_1month.txt


title: D2

description:
Library name: D2
CEAΔku80 group, replicate biosample 2


title: 4796-013-60

description: Library name: 4796-013-60

value: Current Smoker (one puff in the last month)


title: D1

description:
Library name: D1
CEAΔku80 group, replicate biosample 1


title: H3K115ac_peChIP_mESC_Rep2_INPUT

description: INPUT library

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings
For single-end ChIP libraries: Filtered and trimmed reads were aligned to the mm10 assembly of mouse genome using bowtie and uniquely mapped reads were kept. Alignments were converted to BAM format and sorted using SAMtools and PCR duplicates removed using Picard. Bedtools was used to create BED files followed by conversion into HOMER tag directory format (makeTagDirectory) using default parameters. We called peaks using HOMERs findPeaks command with options -F 2 -localSize 50000 -size 150 -minDist 300 -fdr 0.01 –region. UCSC compatible bigwig files normalized to sequencing depth were generated using makeUCSCfile with parameters: -bigWig -style chipseq –fragLength 150.
Paired-end ChIP libraries: Filtered and trimmed reads were aligned to mm10 genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates as above. Read pairs were converted into ChIP fragments using bedtools bamtobed –bedpe and fractionated into sub-nucleosomes (<150 bp) and mono-nucleosomes (150-225 bp). Fragment coverage was computed at base-pair resolution with bedtools genomeCoverageBed and coverage normalized to sequencing depth and scaled to 107. Coverage data was converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: Read density in bigwig format

source_name: mESC (46C)

extract_protocol:
Native MNase ChIP (detailed protocol: PMID: 27089178)
NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB catalogue # E7645)

value: mESC (46C)


title: SGF_1_Fractions_5-6_H3K115ac_ChIP

description: Library name: SGF_1_Fractions_5-6_H3K115ac_ChIP


title: SGF_1_Fractions_5-6_H3K115ac_INPUT

description: Library name: SGF_1_Fractions_5-6_H3K115ac_INPUT


title: N2 C elegans, tunicamycin treated, L4 stage, rep2

description: Library name: D2


title: N2 C elegans, control, L4 stage, rep4

description: Library name: C4

value: control


title: 4796-024-60

description: Library name: 4796-024-60

data_processing:
A Nextflow pipeline (https://github.com/compbiomed/RNA_Seq) was used to process the sequencing data to obtain the expression levels for each gene.
Both gene and transcript level counts were calculated using RSEM with Ensembl build 75 annotation.
Assembly: GRCh37
Supplementary files format and content: DECAMP2_mucus_plugging_filtered_counts.tsv: tab-separated values file containing 24599 x 48 matrix of counts for all Ensembl Gene IDs that passed filtering

value: Nasal brushing


title: 4792-007-60

description: Library name: 4792-007-60

value: No


title: 4796-014-60

description: Library name: 4796-014-60

value: Former Smoker (not even a puff for >= 1 month)


title: N2 C elegans, tunicamycin treated, L4 stage, rep3

description: Library name: D3


title: H3K115ac_peChIP_mESC_Rep2

description: ChIP library


title: PJH1227, Stag2-WT mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1227_wt
gene_expression_htseqcount_1month.txt


title: 4796-018-60

description: Library name: 4796-018-60

value: Male


title: 4796-016-60

description: Library name: 4796-016-60


title: H3K27ac_peChIP_mESC_Rep2_INPUT

description: INPUT library


title: PJH1226, Stag2-WT mouse urothelium, 1 month after TMX induction

description:
Library name: PJH1226_wt
gene_expression_htseqcount_1month.txt


title: N2 C elegans, tunicamycin treated, L4 stage, rep1

description: Library name: D1