title: MCM control mouse heart spatial RNA-seq

description: 10X Visium Spatial Transcriptomics on control heart section

data_processing:
library strategy: Visium Spatial RNA-seq
Visium Spatial RNA-seq: H&E images were manually aligned to spots selected by Loupe Browser 4.0.0 (10X Genomics). The Space Ranger 1.0.0 pipeline (10X Genomics) was then used to generate feature-spot matrices from the sequencing data aligned to the mm10 mouse reference genome.
Visium Spatial RNA-seq: Sequencing data and images were aligned by using the Space Ranger 1.0.0 pipeline to derive a feature spot-barcode expression matrix (10X Genomics). Seurat toolkit version v.4.0 in R v.3.8 was used to perform downstream analyses. Spots were filtered for UMI counts (5000 < UMI counts < 30,000), genes (no genes > 500) and mitochondrial genes (mitochondrial % < 40%). The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Visium Spatial RNA-seq: Atrial spots were identified based on the H&E images and were manulally removed from the expression matrices before subsequent analyses
Assembly: mm10
Supplementary files format and content: Visium Spatial RNA-seq: H&E image, comma-separated metadata files and matrix files
scRNA-seq: After sequencing, preprocessing steps were performed by using CellRanger 3.0.1, without including intronic reads. Matrices were postprocessed with CellBender v0.1.
scRNA-seq: Single nuclei were filtered for unique molecular identifier (UMI) counts (500 < UMI Counts < 25,000), genes (no genes > 500), mitochondrial genes (mitochondrial % < 5%), and scrublet score (doublet score < 0.25). Seurat Toolkit version v.4.0 4 in R v.3.8 was used to perform downstream analyses. The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Supplementary files format and content: scRNA-seq: comma-separated metadata files and matrix files

value: Cardiac cells

value: Tamoxifen


title: Subject 100257, B+1D

status: Public on Jan 11 2024

type: SRA

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

description: Column name in processed data file: 49

library_source: transcriptomic

data_processing:
raw counts were normalized as Log2 counts per million
Assembly: hg18
Supplementary files format and content: normalized_counts_050523.csv, corresponding to 59 subjects

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the NEBNext single cell/low input RNA library prep kit for Illumina. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform

tag: subject

tag: timepoint

tag: tissue

value: Blood

tag: treatment

value: MVA-BN-Filo

tag: group

value: Boost


title: Control-AAV mouse heart CD45-enriched scRNA-seq

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description:
10X 3' scRNA-seq profiling immune cells in control AAV injected heart
scRNA_integrated.meta_data.csv.gz
scRNA_integrated.normalized_count.csv.gz
scRNA_integrated.raw_count.csv.gz

library_source: transcriptomic single cell

data_processing:
Visium Spatial RNA-seq: H&E images were manually aligned to spots selected by Loupe Browser 4.0.0 (10X Genomics). The Space Ranger 1.0.0 pipeline (10X Genomics) was then used to generate feature-spot matrices from the sequencing data aligned to the mm10 mouse reference genome.
Visium Spatial RNA-seq: Sequencing data and images were aligned by using the Space Ranger 1.0.0 pipeline to derive a feature spot-barcode expression matrix (10X Genomics). Seurat toolkit version v.4.0 in R v.3.8 was used to perform downstream analyses. Spots were filtered for UMI counts (5000 < UMI counts < 30,000), genes (no genes > 500) and mitochondrial genes (mitochondrial % < 40%). The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Visium Spatial RNA-seq: Atrial spots were identified based on the H&E images and were manulally removed from the expression matrices before subsequent analyses
Assembly: mm10
Supplementary files format and content: Visium Spatial RNA-seq: H&E image, comma-separated metadata files and matrix files
scRNA-seq: After sequencing, preprocessing steps were performed by using CellRanger 3.0.1, without including intronic reads. Matrices were postprocessed with CellBender v0.1.
scRNA-seq: Single nuclei were filtered for unique molecular identifier (UMI) counts (500 < UMI Counts < 25,000), genes (no genes > 500), mitochondrial genes (mitochondrial % < 5%), and scrublet score (doublet score < 0.25). Seurat Toolkit version v.4.0 4 in R v.3.8 was used to perform downstream analyses. The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Supplementary files format and content: scRNA-seq: comma-separated metadata files and matrix files

organism: Mus musculus

source_name: Heart

extract_protocol:
Visium Spatial RNA-seq: Frozen tissue sections from control (MCM) and Yap5SA (MCM Yap5SA) hearts were mounted on 10X Visium slide capture areas, each with 5000 barcoded RNA capture spots. Hematoxylin and eosin (H&E)-stained images of whole tissue sections were obtained by using the BioTek Cytation 5 with image stitching. Optimal permeabilization time for the release of mRNA from 10-μm thick tissue sections for both genotypes was 12 minutes, determined by using the Visium Tissue Optimization Kit.
Visium Spatial RNA-seq: Spatially barcoded cDNA libraries were generated from mRNA released from each tissue section by using the Visium Spatial Gene Expression Reagent Kit, before being sequenced on an Illumina NovaSeq 6000 with 150 cycle paired-end setting (read 1 = 28 cycles, read 2 = 90 cycles, index 1 = 10 cycles, index 2 = 10 cycles).
scRNA-seq: Control (n=3) and YAP5SA (n=3) mouse hearts were explanted and perfused with cold PBS (20 mM KCl). The hearts were then minced with a razor blade and digested using 30 ml of HBSS with type II collagenase (100 U/ul, Worthington LS004177) at 37 degrees C for 30 minutes. The samples were then filtered through 40 um strainers and centrifuged at 500g for 10 minutes. Red blood cells in the pellet were lysed by ACK lysing buffer (Thermo Fisher, A1049201). The samples were suspended in 1% BSA/PBS, with dead cells removed by using a dead cell removal kit (Miltenyi Biotec, 130-052-301).
scRNA-seq: Samples were diluted to obtain 15,000 – 18,000 live cells for single cell library construction according to the 10x single cell gene expression workflow (10x Genomics, Chromium Next GEM Single Cell 3’ Kit v3.1, 1000269). The libraries were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Visium Spatial RNA-seq: TAM injection 40 ug/g weight daily for 4 days

value: Heart

tag: cell type

value: Cardiac immune cells

tag: age

value: 8-10 weeks old adult

tag: strain background

tag: genotype

value: WT


title: shNC-1

city: Guangzhou

first: Xinyue

last: Zhang

state: guangdong

address: zhongshan road 2

country: China

institute: Sun Yat-sen University First Affiliated Hospital

description: RNA-seq

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp(version 0.18.0).
Assembly: GRCh38
Supplementary files format and content: Supplementary_files_format_and content_processed_data.xls

source_name: Liver cancer

growth_protocol: MHCC97H cells were matained in 10%FBS DMEM

extract_protocol:
Total RNAs were isolated using Trizol RNA extraction reagent (Ambion).
The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters.

value: Liver cancer

tag: cell line

value: Human liver cancer cells

value: shNC


title: shNC-2

description: RNA-seq


title: YTHDF1-RIP-IP


title: MCM-YAP5SA mouse heart spatial RNA-seq

description: 10X Visium Spatial Transcriptomics on YAP5SA heart section

value: Yap5SA+/tg; Myh6-MCM


title: Subject 100339, P+1D

description: Column name in processed data file: 48

value: Prime


title: Subject 100257, B+3H

description: Column name in processed data file: 47


title: YTHDF1-sh2-1

description: RNA-seq


title: YTHDF1-RIP-Input


title: Subject 100339, P+7D

description: Column name in processed data file: 46


title: 39hpi_CHX-treated_rep3

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
RNA-seq reads were mapped to the mm9 genome by STAR v2.5.0a
stacc-seq reads were mapped to mm10 whole genome using bowtie v1.3.0 with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33   --no-unal  -I 10 -X 700
replicates of same stage were pooled together and RPKM in wiggle files were counted by the number of reads falling into 100bp bin in the genome
FPKM_count.py is used to calculate the reads FPKM of each exon
Assembly: mm10
Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM

molecule: polyA RNA

source_name: 39hpi_late 2 cells

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
For RNA-seq, the collected embryos were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor);For Stacc-seq, embryos were   collected and transferred into a 200-μl low-binding tube (total volume with buffer less than 1 μl). Six microlitres of DB-1  (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor, 0.005% digitonin (Sigma, D141)) buffer was added.
For RNA-seq, samples were taken out from -80℃ freezer, and thawed on ice, 1μl of 10μM oligo-dT primer, 1μl of 10 mM dNTP mix were added to the lysis buffer. cDNA synthesis and amplification were performed following the Smart-seq2 ; Stacc-seq was performed following the previously reported protocol designed by Bofeng Liu etc. pG–Tn5 (Vazyme,TD901) and RNA pol ll antibody (Active motif,39097,lot102660) was used. The precipitated DNA was processed into sequencing libraries using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme,TD903 )following the manufacturer's instructions.

treatment_protocol: Embryos in this study were derived from IVF( In Vitro Fertilization). Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. COCs were isolated. Embryos at different stages were collected after adding the sperm of wild type male mice at different time periods.

value: 39hpi_late 2 cells

tag: strain

value: ICR

tag: developmental stage

value: embryo

value: wild type


title: 39hpi_CHX-treated_rep1


title: 39hpi_CHX-treated_rep2


title: m6A meRIP-NC-IP

description: m6A meRIP


title: Subject 100257, D0

description: Column name in processed data file: 45

value: Control


title: m6A meRIP-NC-INPUT

description: m6A meRIP


title: Tuft_untreated_Rep4

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

description:
wt_4_a
Bulk Mars-Seq (3' end-RNA-seq)

data_processing:
Data was processed using UTAP transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts, normalized abundance measurements and DESeq2 analysis.

source_name: Thymus

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. Tuft cells were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were treated with sublethal irradiation (425rad) 3 days before sacrificed, or left untreated.

value: Thymus

value: Tuft cells

tag: Sex

value: Female

value: Untreated


title: Tuft_3d irr_Rep2

description:
3d_2_a
Bulk Mars-Seq (3' end-RNA-seq)

value: Sublethal irradiation

tag: time


title: Tuft_3d irr_Rep3

description:
3d_3_a
Bulk Mars-Seq (3' end-RNA-seq)


title: Tuft_3d irr_Rep4

description:
3d_4_a
Bulk Mars-Seq (3' end-RNA-seq)


title: 39hpi_control_rep3


title: Tuft_untreated_Rep5

description:
wt_5_a
Bulk Mars-Seq (3' end-RNA-seq)


title: Tuft_untreated_Rep3

description:
wt_3_a
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100339, P+3H

description: Column name in processed data file: 44

value: Blood


title: Tuft_3d irr_Rep1

description:
3d_1_a
Bulk Mars-Seq (3' end-RNA-seq)

value: WT


title: 39hpi_control_rep2


title: Tuft_untreated_Rep2

description:
wt_2_a
Bulk Mars-Seq (3' end-RNA-seq)


title: Tuft_untreated_Rep1

description:
wt_1_a
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100257, P+1D

description: Column name in processed data file: 43


title: 39hpi_control_rep1


title: Subject 100339, D0

description: Column name in processed data file: 42


title: 33hpi_CHX-treated_rep2

source_name: 33hpi_late 2 cells

value: 33hpi_late 2 cells


title: Fibroblasts_Untreated_Rep3

description:
Fibro_ut4
Bulk Mars-Seq (3' end-RNA-seq)

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. Fibroblasts were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were injected I.P. with dexamethasone (200ug/10gr body weight) 4 days or 18 hours before sacrificed, or left untreated.

value: Male


title: Fibroblasts_Untreated_Rep2

description:
Fibro_ut3
Bulk Mars-Seq (3' end-RNA-seq)


title: 33hpi_control_rep3


title: Fibroblasts_Untreated_Rep1

description:
Fibro_ut1
Bulk Mars-Seq (3' end-RNA-seq)


title: 33hpi_control_rep2


title: Subject 100320, P+1D

description: Column name in processed data file: 39


title: Subject 100257, P+3H

description: Column name in processed data file: 41


title: Subject 100339, P+57D

description: Column name in processed data file: 40


title: Fibroblasts_3d Dex_Rep4

description:
Fibro_4d4
Bulk Mars-Seq (3' end-RNA-seq)

value: Dexamethasone


title: Subject 100320, B+3H

description: Column name in processed data file: 38

value: MVA-BN-Filo

value: Boost


title: low miR-1825 expression-colorectal cancer tissue 1

first: Jingbo

last: Sun

state: Guangdong Province

address: No. 1023-1063, Shatai South Road, Baiyun District

institute: School of Basic Medical Sciences, Southern Medical University

data_processing:
Pre-processing of sequencing reads / Quality Control Raw reads were treated with Trimmomatictools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using theFastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to humanreference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively.
If a circRNA can be detected by both methods, it will be consided as an identified circRNA.
Assembly: GRCh37/ hg19
Supplementary files format and content: txt file includes RPM for each sample

source_name: colorectal cancer tissue

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
Briefly, rRNAs were removed from Total RNA using RiboCoprRNA Depletion Trial kit(LEXOGEN， Australia) , thenRNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. Subsequently, thepurified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptorligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kitfor Illumina (NEB, USA). The library products were evaluated using the Agilent 2200 TapeStation andQubit(Thermo Fisher Scientific, USA) and then sequenced on Illumina (Illumina, USA) withpaired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
circRNA-seq

value: colorectal cancer tissue

value: low miR-1825 expression


title: low miR-1825 expression-colorectal cancer tissue 3


title: high miR-1825 expression-colorectal cancer tissue 1

value: high miR-1825 expression


title: high miR-1825 expression-colorectal cancer tissue 2


title: high miR-1825 expression-colorectal cancer tissue 3


title: low miR-1825 expression-colorectal cancer tissue 2


title: Fibroblasts_Untreated_Rep4

description:
Fibro_ut5
Bulk Mars-Seq (3' end-RNA-seq)


title: 33hpi_CHX-treated_rep3

value: ICR

value: embryo

value: wild type


title: irCLIP, SH-SY5Y, WT, rep2

city: Berkeley

first: Yeon

last: Lee

state: CA

address: 1 Barker Hall

institute: UC Berkeley

description:
irCLIP-seq
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 WT rep 2

data_processing:
Pre-mRNA splicing analysis using JUM.2.0.2 software to detect pre-mRNA splicing patterns was performed as described before (Lee et al. 2018). AP-value of 0.05 was used as the statistical cutoff for differentially spliced AS events. Expressed genes for GO-terminology enrichment analysis was generated using cufflinks.v2.1.1(Trapnell et al. 2009) using the following parameters: --library-type fr-firststrand -m 100 -s 10, then filtered for FPKM > 1.
For Differential expression analysis, uniquely mapped reads were mapped to hg38 using STAR_2.5.3a_modified version using --outFilterMultimapNmax 1. Read counts were calculated using HTSeq script htseq-count with the following specifications: -s yes -r pos -f. Differential gene expression analysis was performed using DESeq2 (Love et al. 2014) using CPM cutoff. The expression cutoff (CPM) value was determined according to the library size and normalization factors, roughly equal to 10/LwhereLis the minimum library size in millions (Chen et al. 2016).
The Quick irCLIP-seq reads were preprocessed prior to mapping using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Reads were quality-filtered based on quality score (fastq_quality_filter -q 25 -p 80), and PCR duplicates were collapsed (fastx_collapser). Only uniquely mapped reads were used for further analysis. The reads were mapped tohg38using STAR using the following parameters: --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped fastx --outSAMtype BAM SortedByCoordinate. Uniquely mapped reads were filtered and then used for cluster identification using pycrac/1.2.3.0 (Webb et al. 2014). irCLIP clusters were generated using at least ten overlapping unique cDNA reads generated after removal of PCR duplicates (pyClusterReads.py --cic=10). pyCalculateFDRs were used to filter out statistically significant clusters over the regions with a read coverage of at least 5 (--min=10) and FDRp< 0.05. De novo binding motifs for hnRNPA1 wild type and mutant protein were determined using STREME (Bailey 2021) using the following parameter: streme --verbosity 1 --oc --rna --minw 8 --maxw 15 --pvt 0.05.
Assembly: hg38
Supplementary files format and content: counts.txt files, significant_clusters.bed files

source_name: neuroblasts

growth_protocol: Human SH-SY5Y cells (American Type Culture Collection) were maintained at 37°C in DMEM/F-12 (Gibco™, 11320082) medium supplemented with 10% FBS, 1% Pen-Strep. Human FLP-In™ T-REx™ 293 (Invitrogen™, R78007) cells were maintained in D-MEM™ (high glucose), 10% FBS, 2mM L-glutamine, and 1% Pen-Strep.

extract_protocol: RNA isolation was performed using the RNeasy Minikit (Qiagen, 74104), followed by 30 min. of DNase treatment (Ambion, AM2238) at 37°C, poly(A)+ RNA transcripts were isolated [NEBNext poly(A) mRNA magnetic isolation module; New England Biolabs, E7490] from 1 µg of total RNA for RNA library preparation and sequencing using NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (New England Biolabs, E7420S) according to the manufacturer’s instruction.

treatment_protocol: Tetracycline (Tet)-inducible 293 FLP-In hnRNPA1 wild type and hnRNPA1 mutant (D262V) cells were induced with 1 µg/mL Tetracycline (Tet) for 72 hr prior to harvest. SH-SY5Y cells were differentiated accordingly to a published a protocol (Shipley et al. 2016) with the following modification. F12/DMEM media with 10% FBS was used in place of EMEM media with 15% FBS as basic growth media. 2.5% FBS F12/DMEM with 1X Pen/Strep, 2 mM Glutamine, 10 uM RA was used as Differentiation Media 1. 1% FBS F12/DMEB with 1X Pen/Strep, 2 mM Glutamine, 10 µM RA was used as Differentiation Media 2. F12/DMEM with 1X B-27, 20 mM KCl, 1X Pen/Strep, 2 mM GlutamaxI, 50 ng/mL BDNF, 2 mM dibutyryl cyclic AMP (db-cAMP), 10 uM RA was used as Differentiation Media 3. SH-SY5Y cells were differentiated as described previously (Shipley et al. 2016), and harvested on day 18 for imaging experiments and RNA-seq library preparation.

value: neuroblasts

value: neuroblastoma cells

value: wildtype


title: Subject 100320, B+1D

description: Column name in processed data file: 37


title: irCLIP, SH-SY5Y, WT, rep3

description:
irCLIP-seq
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 WT rep 3


title: 31hpi_CHX-treated_rep3

source_name: 31hpi_mid 2 cells

value: 31hpi_mid 2 cells


title: Subject 100320, D0

description: Column name in processed data file: 36

value: Blood

value: Control


title: Fibroblasts_3d Dex_Rep3

description:
Fibro_4d3
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus

value: WT


title: Fibroblasts_3d Dex_Rep2

description:
Fibro_4d2
Bulk Mars-Seq (3' end-RNA-seq)

value: Male

value: Dexamethasone


title: 31hpi_CHX-treated_rep2


title: irCLIP, SH-SY5Y, WT, rep1

description:
irCLIP-seq
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 WT rep 1


title: Subject 100320, P+3H

description: Column name in processed data file: 35

value: Prime


title: 33hpi_CHX-treated_rep1

value: 33hpi_late 2 cells


title: 33hpi_control_rep1


title: irCLIP, SH-SY5Y, mut, rep3

description:
irCLIP-seq
Sh-SY_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 D262V mut rep 3

value: mutant


title: Fibroblasts_3d Dex_Rep1

description:
Fibro_4d1
Bulk Mars-Seq (3' end-RNA-seq)


title: 31hpi_CHX-treated_rep1


title: Subject 100320, P+85D

description: Column name in processed data file: 34


title: Subject 100320, B+7D

description: Column name in processed data file: 33

value: MVA-BN-Filo

value: Boost


title: Fibroblasts_18h Dex_Rep3

description:
Fibro_18h3
Bulk Mars-Seq (3' end-RNA-seq)


title: irCLIP, SH-SY5Y, mut, rep1

description:
irCLIP-seq
Sh-SY_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 D262V mut rep 1


title: irCLIP, SH-SY5Y, mut, rep2

description:
irCLIP-seq
Sh-SY_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP SH-SY5Y hnRNPA1 D262V mut rep 2


title: 31hpi_control_rep3

value: ICR

value: embryo


title: Fibroblasts_18h Dex_Rep2

description:
Fibro_18h2
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100320, P+7D

description: Column name in processed data file: 32


title: irCLIP, 293 Flp-In, WT, rep3

description:
irCLIP-seq
Flp_In_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 WT rep 3

source_name: embryonickidney

value: embryonickidney

value: Flp-In™ T-REx™ 293

value: immortalized human embryonic kidney cells

value: induced with 1 µg/mL Tetracycline (Tet) for 72 hr prior to harvest


title: 31hpi_control_rep1

value: 31hpi_mid 2 cells

value: wild type


title: Fibroblasts_18h Dex_Rep1

description:
Fibro_18h1
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus


title: 31hpi_control_rep2


title: 25hpi_CHX-treated_rep3

source_name: 25hpi_early 2 cells

value: 25hpi_early 2 cells


title: irCLIP, 293 Flp-In, WT, rep1

description:
irCLIP-seq
Flp_In_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 WT rep 1

value: wildtype


title: Subject 100364, D0

description: Column name in processed data file: 30

value: Blood

value: Control


title: Fibroblasts_untreated_Rep4

description:
fibro_ut4
Bulk Mars-Seq (3' end-RNA-seq)

treatment_protocol: Mice were either untreated, or treated for 1 or 3 days with sublethal irradiation (425rad).

value: WT

value: Male

value: Untreated


title: Subject 100364, P+85D

description: Column name in processed data file: 31

value: Prime


title: Subject 100364, P+3H

description: Column name in processed data file: 29


title: Fibroblasts_untreated_Rep5

description:
fibro_ut5
Bulk Mars-Seq (3' end-RNA-seq)


title: irCLIP, 293 Flp-In, WT, rep2

description:
irCLIP-seq
Flp_In_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 WT rep 2


title: 25hpi_CHX-treated_rep2

value: ICR


title: Subject 100364, B+7D

description: Column name in processed data file: 28

value: MVA-BN-Filo

value: Boost


title: irCLIP, 293 Flp-In, mut, rep2

description:
irCLIP-seq
Flp_In_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 D262V mut rep 2

value: embryonickidney

value: Flp-In™ T-REx™ 293

value: mutant


title: 25hpi_CHX-treated_rep1

value: embryo


title: irCLIP, 293 Flp-In, mut, rep3

description:
irCLIP-seq
Flp_In_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 D262V mut rep 3

value: immortalized human embryonic kidney cells

value: induced with 1 µg/mL Tetracycline (Tet) for 72 hr prior to harvest


title: Fibroblasts_untreated_Rep2

description:
fibro_ut2
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus


title: Subject 100364, B+3H

description: Column name in processed data file: 27


title: 25hpi_control_rep2

value: 25hpi_early 2 cells

value: wild type


title: Subject 100364, B+1D

description: Column name in processed data file: 26

value: Blood


title: Fibroblasts_untreated_Rep1

description:
fibro_ut1
Bulk Mars-Seq (3' end-RNA-seq)

value: WT


title: irCLIP, 293 Flp-In, mut, rep1

description:
irCLIP-seq
Flp_In_mut_merged_count_output_reads.cic10.gtf.significant_clusters.bed
irCLIP Flp-In Tet-induced hnRNPA1 D262V mut rep 1


title: 25hpi_control_rep1


title: Fibroblasts_3d irradiation_Rep4

description:
fibro_3d4
Bulk Mars-Seq (3' end-RNA-seq)

value: Male

value: Sublethal irradiation


title: Fibroblasts_untreated_Rep3

description:
fibro_ut3
Bulk Mars-Seq (3' end-RNA-seq)

value: Untreated


title: 17hpi_CHX-treated_rep2

value: ICR


title: Fibroblasts_3d irradiation_Rep3

description:
fibro_3d3
Bulk Mars-Seq (3' end-RNA-seq)


title: Fibroblasts_3d irradiation_Rep2

description:
fibro_3d2
Bulk Mars-Seq (3' end-RNA-seq)


title: 17hpi_CHX-treated_rep1


title: Fibroblasts_3d irradiation_Rep1

description:
fibro_3d1
Bulk Mars-Seq (3' end-RNA-seq)


title: Fibroblasts_1d irradiation_Rep5

description:
fibro_1d5
Bulk Mars-Seq (3' end-RNA-seq)


title: 25hpi_control_rep3


title: Differentiated, heterozygous mut, rep1

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V heterozygous mut rep 1

value: neuroblasts

value: neuroblastoma cells

value: Differentiated for 18d


title: Differentiated, WT, rep2

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 WT rep 2

value: wildtype


title: Differentiated, WT, rep1

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 WT rep 1


title: Differentiated, heterozygous mut, rep2

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V heterozygous mut rep 2

value: mutant


title: 17hpi_control_rep2

value: embryo


title: 17hpi_control_rep1


title: Differentiated, WT, rep3

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 WT rep 3


title: Fibroblasts_3d irradiation_Rep5

description:
fibro_3d5
Bulk Mars-Seq (3' end-RNA-seq)


title: Differentiated, homozygous mut, rep3

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V homozygous mut rep 3


title: 17hpi_CHX-treated_rep3


title: Fibroblasts_1d irradiation_Rep4

description:
fibro_1d4
Bulk Mars-Seq (3' end-RNA-seq)


title: Differentiated, heterozygous mut, rep3

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V heterozygous mut rep 3


title: Differentiated, homozygous mut, rep2

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V homozygous mut rep 2


title: 13hpi_CHX-treated_rep3


title: Fibroblasts_1d irradiation_Rep3

description:
fibro_1d3
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100295, D0

description: Column name in processed data file: 23

value: Control


title: Subject 100295, P+7D

description: Column name in processed data file: 19

value: Prime


title: Subject 100295, B+3H

description: Column name in processed data file: 20

value: MVA-BN-Filo

value: Boost


title: Subject 100295, B+1D

description: Column name in processed data file: 21


title: Subject 100295, P+3H

description: Column name in processed data file: 18


title: Subject 100364, P+7D

description: Column name in processed data file: 24


title: Subject 100295, B+7D

description: Column name in processed data file: 22


title: Fibroblasts_1d irradiation_Rep2

description:
fibro_1d2
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus


title: Differentiated, homozygous mut, rep1

description:
RNA-seq
Differentiated.SH_SY5Y.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y differentiated hnRNPA1 D262V homozygous mut rep 1


title: Subject 100364, P+1D

description: Column name in processed data file: 25

value: Blood


title: 17hpi_control_rep3

value: wild type


title: 13hpi_CHX-treated_rep2


title: undifferentiated, WT, rep3

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 WT rep 3


title: Fibroblasts_1d irradiation_Rep1

description:
fibro_1d1
Bulk Mars-Seq (3' end-RNA-seq)

value: WT

value: Male


title: ILC2_control_Rep3

description:
ILC2_UT3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx

data_processing:
Data was processed using UTAP transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Excel files include raw counts, normalized abundance measurements and DESeq2 analysis.

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TM and DNase. ILC2 were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were injected I.P. with dexamethasone (200ug/10gr body weight) or vehicle (8% EtOH in PBS) 3 days or 18 hours before sacrificed.

value: Vehicle


title: 13hpi_CHX-treated_rep1

value: ICR


title: Subject 100277, B+7D

description: Column name in processed data file: 16


title: 13hpi_control_rep3


title: ILC2_control_Rep2

description:
ILC2_UT2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: 13hpi_control_rep2


title: undifferentiated, homozygous mut, rep3

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 D262V homozygous mut rep 3

value: neuroblasts


title: ILC2_control_Rep1

description:
ILC2_UT1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: Subject 100277, B+3H

description: Column name in processed data file: 14


title: MII_control_rep3

source_name: MII oocytes

value: MII oocytes

value: oocyte


title: ILC2_3d Dex_Rep3

description:
ILC2_3d3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx

value: Dexamethasone


title: 13hpi_control_rep1


title: Subject 100277, P+1D

description: Column name in processed data file: 11


title: Subject 100277, D0

description: Column name in processed data file: 10


title: Subject 100277, P+7D

description: Column name in processed data file: 13


title: Subject 100295, P+1D

description: Column name in processed data file: 17


title: ILC2_3d Dex_Rep2

description:
ILC2_3d2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: MII_control_rep1


title: MII_control_rep2


title: ILC2_3d Dex_Rep1

description:
ILC2_3d1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: Subject 100277, B+1D

description: Column name in processed data file: 15


title: undifferentiated, WT, rep2

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 WT rep 2

value: neuroblastoma cells

value: wildtype


title: Spleen, AS treated, replicate 1

city: Edinburgh

first: Jianxuan

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

country: United Kingdom

institute: Roslin Institute

description: 10X Chromium, 3’ v3.1 chemistry

data_processing:
Mapping of reads to the genome, assignment of reads to cellular barcodes, and collapsing of unique molecular identifiers (UMIs) was performed with StarSolo v2.7.8a. The genome index was generated with standard settings and “sjdbOverhang” set to 149. The reads were then mapped with the “STAR” command and following settings: "soloCBstart" = 1, "soloCBlen" = 16, "soloUMIstart" = 17, "soloUMIlen" = 12, "soloBarcodeReadLength" = 0, "soloUMIfiltering" = MultiGeneUMI_CR, "soloCellFilter" = EmptyDrops_CR, "outFilterMatchNmin" = 66, "outFilterScoreMin" = 30, "outFilterMatchNminOverLread" = 0.4, "outFilterScoreMinOverLread" = 0.4, "soloMultiMappers" = EM, "limitOutSJcollapsed" = 2000000, "soloCellReadStats" = Standard.
Assembly: Salmo Salar Ensembl 106 genome
Supplementary files format and content: Tab separated value (tsv) and matrix (mtx) format. Contains STARsolo raw and filtered gene names (features.tsv), cell barcodes (barcodes.tsv), UMI count (matrix.mtx) and the sum of STARsolo unique+multi-gene UMI count (UniqueAndMult-EM.mtx)

molecule: nuclear RNA

organism: Salmo salar

source_name: Spleen

extract_protocol:
Approximately 45mg of each frozen spleen sample was placed in a 6-well tissue culture plate (Stem Cell Technologies) with 1 ml TST (2 mL of 2X ST buffer + 120 µL of 1% Tween-20 + 20 µL of 2% BSA brought up to 4 ml with nuclease-free water). The tissue was minced using Noyes Spring Scissors for 10 min on ice. The resulting homogenate was filtered through a 40 µm Falcon cell strainer, and a further 1 mL of TST was added to wash the well and filter. The volume was brought up to 5 mL using 3 mL of 1X ST buffer (diluted from 2xST buffer [292 µl of 146 mM NaCl, 100 µl of 10 mM Tris-HCl pH 7.5, 10 µl of 1 mM CaCl2, 210 µl of 21 mM MgCl2, brought up to 10ml with nuclease-free water]). The sample was centrifuged at 4°C for 5 min at 500g before the resulting pellet was re-suspended in 1 ml 1X ST buffer and the recovered nuclei were filtered through a 40 µm and a 20 µm Falcon cell strainer, Hoechst stained, visually inspected under a fluorescent microscope, and counted using a Bio-Rad TC20.
Spleen nuclei were processed through the 10X Chromium Single Cell Platform using the ChromiumTM Single Cell 30 Library and Gel Bead Kit v3.1 and ChromiumTM Single Cell A Chip Kit (both 10X Genomics) as per the manufacturer’s protocol. For each sample, the nuclei were loaded into a channel of a Chromium 3’ Chip and partitioned into droplets using the Chromium controller before the captured RNA for each nucleus was barcoded and reverse transcribed. The resulting cDNA was PCR amplified for 14 cycles, fragmented, and size selected before Illumina sequencing adaptor and sample indexes were attached.

treatment_protocol: Twenty fish were anaesthetized using 2-phenoxyethanol (2.5ml in 10L water/ 0.0025% v/v) and given an intraperitoneal injection of either PBS (0.5 mL) (n=10), or the pathogenic Hooke strain of A. salmonicida (2 × 105 colony-forming units / mL in PBS; 0.5 mL/fish) (n=10). Sampling was performed 24 h post-injection. The fish were killed using a Schedule 1 method following overdose anaesthetization using 2-phenoxyethanol (0.1% v/v) and destruction of the brain. Fish were immediately sampled, with spleen samples (approx. 100mg) flash frozen on dry ice before storage at -80°C prior to snRNA-Seq library construction

value: Spleen

value: AS treatment


title: ILC2_18h Dex_Rep2

description:
ILC2_18h2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: ILC2_18h Dex_Rep3

description:
ILC2_18h3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx


title: Spleen, AS treated, replicate 2

description: 10X Chromium, 3’ v3.1 chemistry


title: undifferentiated, WT, rep1

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 WT rep 1


title: Subject 100251, B+1D

description: Column name in processed data file: 8

value: MVA-BN-Filo


title: Spleen, PBS treated, replicate 2

description: 10X Chromium, 3’ v3.1 chemistry

value: PBS treatment


title: Subject 100251, P+3H

description: Column name in processed data file: 7

value: Prime


title: Il33Het_ILC2_3d Dex_Rep5

description:
IL33_KO_73
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Thymus

value: Il33 Het


title: Subject 100251, B+7D

description: Column name in processed data file: 6

value: Blood

value: Boost


title: Il33Het_ILC2_3d Dex_Rep4

description:
IL33_KO_72
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Male


title: Spleen, PBS treated, replicate 1

description: 10X Chromium, 3’ v3.1 chemistry


title: Subject 100277, P+3H

description: Column name in processed data file: 9


title: Il33KO_ILC2_3d Dex_Rep5

description:
IL33_KO_71
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Il33 KO


title: Subject 100251, B+3H

description: Column name in processed data file: 4


title: Il33KO_ILC2_3d Dex_Rep4

description:
IL33_KO_70
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx


title: Subject 100251, P+7D

description: Column name in processed data file: 3


title: Subject 100251, P+85D

description: Column name in processed data file: 5


title: Spinal_snRNA-seq_9

city: Chengdu

first: Donghang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

data_processing:
Basecalls performed using  bcl2fastq.gz tools
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the fastq.gz reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices

source_name: Spinal cord

extract_protocol:
Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.

value: Spinal cord

value: 38 years old


title: undifferentiated, homozygous mut, rep1

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 D262V homozygous mut rep 1

value: neuroblasts

value: mutant


title: undifferentiated, homozygous mut, rep2

description:
RNA-seq
Undifferentiated.SH_SY5Y.D262V.merged.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
SH-SY5Y undifferentiated hnRNPA1 D262V homozygous mut rep 2

value: neuroblastoma cells


title: Spinal_snRNA-seq_8

value: 35 years old


title: Il33Het_ILC2_3d Dex_Rep3

description:
IL33_KO_68
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Dexamethasone


title: Subject 100277, P+85D

description: Column name in processed data file: 12


title: Subject 100251, P+1D

description: Column name in processed data file: 2


title: Spinal_snRNA-seq_7

value: 51 years old


title: Mouse neutrophil subset,OTT SPL,IMM, replicate 2

city: Singapore

first: Melissa

last: Ng

address: 8A Biomedical Grove, #03-06 Immunos Building, Singapore

country: Singapore

institute: Singapore Immunology Network

library_source: genomic

data_processing:
Paired-end sequencing reads of length 2 x 150 bp were trimmed with cutadapt (ver. 2.5) and quality checked using FASTQC before aligning to the mm10 (GRCm38) mouse reference genome using bwa (ver. 0.7.17). Low quality alignments (MAPQ < 30), secondary alignments, unmapped reads and reads with unmapped mate were discarded using samtools. For reads with multiple alignments only five best alignments were retained. PCR duplicates were removed using Picard MarkDuplicates.
The remaining clean alignments were analyzed for fragment length distribution using the ATACseqQC (ver. 1.10.4) . Read alignments to the positive strand were shifted 4 bp downstream and alignments to the negative strand were shifted 5bp upstream to centre the reads on the transposon binding events. Subsequently, peaks were called using macs2 (ver. 2.1.1.20160309) callpeak command with the parameters “-p 0.01 --shift -150 --extsize 300 --nomodel -B --SPMR --keep-dup all --call-summits”. Fold enrichment and p-value tracks normalized to input were produced using macs2 bdgcmp command (options -m FE and -m ppois respectively). Peaks with a q-value < 0.01 were shortlisted. Peaks in the blacklisted regions specified by ENCODE project were removed.
For each of the conditions (cell phenotype and tissue of origin) pooled samples were generated by pooling together reads from all individual replicates of the same condition. These pooled samples were also analyzed in the same manner as above. Peaks called in the pooled samples were compared against peaks called in the individual samples of the same condition using irreproducible discovery rate (IDR) framework (ver 2.0.4.2). High quality reproducible peaks were shortlisted based on IDR < 0.05. Subsequently, the IDR peaks from all conditions were merged using “bedtools merge” to generate a final set of peaks. Counts of reads aligned at each peak interval in each sample was determined using summarizeOverlaps function of the GenomicAlignments R package (ver. 1.22.1)
The counts were loaded into edgeR (75) for differential accessibility analysis where a negative binomial generalized linear model (GLM) extended with quasi-likelihood methods was fitted to the counts data, dispersions were estimated and differential peak intensity across sample groups was determined by the quasi-likelihood F-test method using FDR (false discovery rate) < 0.05, and log2 fold change > 1. DeepTools (3.1.0) was used to generate normalized bigWigs from pooled biological replicates, with scaling factors calculated from the reciprocal of normalization factors derived from edgeR calcNormFactors() multipled by library size (per million). Normalized bigwig files were visualized with Integrative Genomics Viewer (IGV 2.7.2).
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing IDR peaks and associated counts per peak for each sample

molecule: genomic DNA

growth_protocol: The luciferase-stable pancreatic ductal adenocarcinoma FC1242L cell line was generated as described in Leong et al., and was derived from the FC1242 cell line (kind gift from Dr Dannielle Engle, Tuveson lab, Cold Spring Harbour Laboratory) derived from Pdx1Cre; KrasG12D/+; Trp53R172H/+ (KPC) mice. FC1242L was culturecultured in complete media (cDMEM) comprising Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal calf serum (FCS), 1% Penicillin-Streptomycin (Gibco) and seeded at a density of 2 X 10^5 cells/mL in T75 cell culture flask. Cells were grown at 37°C in 5% CO2 incubator until they reached 80% confluency. Upon reaching confluency, cells were trypsinized with pre-warmed 0.25% Trypsin with Ethylenediaminetetraacetic acid (EDTA), phenol red (Gibco) for 5 minutes at 37°C in 5% CO2 incubator, washed with pre-warmed cDMEM and counted, before seeding at a density of 2 X 10^5 cells/mL for the next passage.

extract_protocol:
Tumor: At 6 weeks post injection, tumors were excised from tumor-bearing mice and weighed before mincing into smaller pieces using surgical scissors. Digestion mix (RPMI, 10% FCS, 500U/mL DNase I, 385U/mL collagenase D) was added to the minced tumor and incubated at 37°C for 30 minutes. Digestion enzymes were quenched with FACS buffer, and minced tumors were transferred into the gentleMACS™ C tubes (Miltenyi Biotec) for mechanical homogenization by the Xiril Dispomix using 2 rounds of Program 5 (20 seconds). Homogenized cells were filtered through 70-µm nylon mesh filter and washed with 20mL FACS buffer. Samples were then spun down at 400g for 5 minutes before RBC lysis with 1 X RBC lysis buffer for 3 minutes. Cells were washed filtered through a 70-µm nylon mesh filter. Blood: Murine blood was collected via cardiac puncture or incision in the submandibular region using a 5mm single-use lancet. 200 µL was transferred into an Eppendorf tube containing 20 µL of 0.5M EDTA. Blood samples were then lysed in 1 X red blood cell (RBC) lysis buffer (eBioscience) for 4 min. Samples were quenched with fluorescence-activated cell sorting (FACS) Buffer (1 X PBS, 4mM EDTA, 3% FCS) and spun down at 400g for 5 minutes. RBC lysis was repeated for a second time for another 2 minutes. Spleen: Spleens were excised from mice and single-cell suspensions were obtained by homogenizing spleen samples through a 70-µm nylon mesh filter with FACS buffer. Samples were then spun down at 400g for 5 minutes and lysed with 1 X RBC lysis buffer for 3 minutes. Cells were quenched with FACS buffer and filtered through a 70-µm nylon mesh filter. Bone marrow: A 23-gauge needle through the marrow cavity of the femur and the bone marrow was flushed out with 2 ml of FACS buffer using a 1ml syringe. For sorting purposes that required large cell numbers, both femur and tibia bones were used. Cells were then filtered and washed with FACS buffer, cells were spun down at 400g for 5 minutes. Sorting and hashtag labelling: Total neutrophils were sorted from the bone marrow, spleen, blood, and tumors from pancreatic tumor mice and identified as Lin-CD45+CD115-Ly6ClowSiglec-F-Gr1+CD11b+Ly6G+. Mature neutrophils were further identified as CD101+ while immature neutrophils were CD101-.
ATAC-seq was performed based on the Omni-ATAC protocol. 50,000 cells per condition were sorted, washed in FACS buffer, and pelleted before lysis for 3 minutes in Lysis Buffer containing 0.1% v/v NP-40, 0.1% v/v Tween-20 and 0.01% v/v Digitonin. Nuclei were then pelleted and transposed with Tn5 (Illumina) at 37oC, for 30 minutes on a thermomixer at 1000 rpm, before DNA purification, indexing and library preparation was carried out. Samples were checked for nucleosomal patterning via Bioanalyzer before pooling at an equimolar ratio for sequencing on a HiSeqX (Illumina) with paired-end 150 reads.

treatment_protocol: Mice were administered intrapancreatic injections of FC1242L tumor cells. The mice were anaesthetized, the pancreas was exposed by surgical excision, and 10,000 FC1242L cels were re-suspended in 1X phosphate buffered saline (PBS) and mixed with Matrigel (BD) in a 1:1 ratio, and were injected as a volume of 50 µL into the body of the pancreas to form a visible bolus.

value: Spleen

tag: phenotype

value: Orthotopic tumor

value: MAT


title: Subject 100251, D0

description: Column name in processed data file: 1

value: Control


title: Il33Het_ILC2_3d Dex_Rep2

description:
IL33_KO_64
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Thymus

value: Il33 Het


title: Il33KO_ILC2_3d Dex_Rep3

description:
IL33_KO_67
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx


title: Mouse neutrophil subset,OTT SPL,IMM, replicate 3

value: IMM


title: Mouse neutrophil subset,OTT SPL,MAT,, replicate 3


title: Mouse neutrophil subset,OTT SPL,MAT, replicate 2


title: Mouse neutrophil subset,OTT SPL,MAT, replicate 1


title: Spinal_snRNA-seq_5

value: 49 years old


title: Il33KO_ILC2_3d Dex_Rep2

description:
IL33_KO_63
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Il33 KO

value: Male


title: Spinal_snRNA-seq_10

value: Spinal cord

value: 46 years old


title: ILC2_18h Dex_Rep1

description:
ILC2_18h1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_dex.xlsx

value: WT


title: Spinal_snRNA-seq_4

value: 59 years old


title: Il33Het_ILC2_3d Dex_Rep1

description:
IL33_KO_62
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx


title: pRPS5A-DOF2.1-GR, control1h, repeat2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

data_processing:
Illumina CASAVA software used for basecalling.
Single-end reads were trimmed for adaptor sequences and aligned to the TAIR10 genome using GSNAP
The HTSeq python tool was used to summarize read counts
R package edgeR was used for statistical analysis
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files generated from HTSeq quantification, contain number of reads

organism: Arabidopsis thaliana

source_name: root meristem

growth_protocol: Seeds were bleach sterilized and stratified for 24h at 4°C. Seeds were sown on ½ MS plates and grown for 5 days in a growth room at 22°C.

extract_protocol:
300 individual root tips were sampled per sample and three biological repeats per time point were used. Root tips were harvested directly into liquid nitrogen, RNA was extracted using the RNeasy kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit.

treatment_protocol: Dexamethasone (DEX) treatment was performed by transferring plants from ½ MS to 10µM DEX supplemented medium and continuing growth for the indicated time.

value: root meristem

value: control


title: Mouse neutrophil subset,OTT SPL,IMM, replicate 1


title: pRPS5A-DOF2.1-GR, control1h, repeat1


title: Mouse neutrophil subset,WT BM,MAT, replicate 3

source_name: Bone marrow

value: Bone marrow

value: Wild type


title: Spinal_snRNA-seq_3

value: 50 years old


title: Spinal_snRNA-seq_2


title: Il33KO_ILC2_3d Dex_Rep1

description:
IL33_KO_61
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_IL33KO_dex.xlsx

value: Dexamethasone


title: Spinal_snRNA-seq_6

value: 47 years old


title: Il25WT_ILC2_3d Dex_Rep3

description:
il25_3d_94_wt
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Thymus

value: Il25 WT


title: pRPS5A-DOF2.1-GR, control1h, repeat3


title: Spinal 7_spatial

data_processing:
Basecalls performed using  bcl2fastq tools
Visum spatial gene expression was processed using Visum spatial gene expression slide and Reagent Kit (10x Genomics, PN-1000184).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices
Library strategy: spatial transcriptomics

extract_protocol:
Samples were immediately cleaned from the blood and connective tissue and frozen on dry ice. Spinal cord tissues were cut transversely, parts were embedded in optimal cutting temperature (OCT) compound for spatial transcriptomics. Cryosections were cut at 10-μm thickness and mounted onto the GEX arrays. Sections were placed on a Thermocycler Adaptor with the active surface facing up and were incubated at 37°C for 1 min. Then, sections were fixed with methyl alcohol at -20°C for 30 min, followed by staining with hematoxylin and eosin (H&E) (Eosin, Dako CS701, Hematoxylin Dako S3309, bluing buffer CS702).
Visum spatial libraries were constructed using Visum spatial Library construction kit (10x Genomics, PN-1000184) according to the manufacture’s introduction.

value: 51 years old


title: pRPS5A-DOF2.1-GR, DEX4h, repeat3

value: DEX 4h


title: Spinal 6_spatial


title: Il25WT_ILC2_3d Dex_Rep1

description:
il25_3d_92_wt
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: pRPS5A-DOF2.1-GR, DEX2h, repeat3

value: DEX 2h


title: Il25WT_ILC2_3d Dex_Rep2

description:
il25_3d_93_wt
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Male


title: pRPS5A-DOF2.1-GR, DEX4h, repeat2


title: Mouse neutrophil subset,WT BM,MAT, replicate 2

value: MAT


title: pRPS5A-DOF2.1-GR, DEX4h, repeat1


title: Mouse neutrophil subset,WT BM,IMM, replicate 3

value: IMM


title: Spinal 5_spatial

value: Spinal cord

value: 49 years old


title: Il25KO_ILC2_3d Dex_Rep3

description:
il25_3d_86_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Il25 KO


title: pRPS5A-DOF2.1-GR, DEX2h, repeat2

value: root meristem


title: Spinal 4_spatial

value: 59 years old


title: Il25KO_ILC2_3d Dex_Rep2

description:
il25_3d_85_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: Spinal 3_spatial


title: pRPS5A-DOF2.1-GR, DEX2h, repeat1


title: Il25KO_ILC2_3d Dex_Rep1

description:
il25_3d_84_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: pRPS5A-DOF2.1-GR, DEX1h, repeat3

value: DEX 1h


title: Spinal 2_spatial


title: pRPS5A-DOF2.1-GR, DEX1h, repeat2


title: Il25WT_ILC2_18h Dex_Rep4

description:
il25_18h_wt4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: DRG 7_single-end

description: This sample includes a single R1 fastq file.

source_name: DRG

extract_protocol:
Samples were immediately cleaned from the blood and connective tissue and frozen on dry ice.The whole ganglia were embedded in OCT for spatial transcriptomics.Cryosections were cut at 10-μm thickness and mounted onto the GEX arrays. Sections were placed on a Thermocycler Adaptor with the active surface facing up and were incubated at 37°C for 1 min. Then, sections were fixed with methyl alcohol at -20°C for 30 min, followed by staining with hematoxylin and eosin (H&E) (Eosin, Dako CS701, Hematoxylin Dako S3309, bluing buffer CS702).
Visum spatial libraries were constructed using Visum spatial Library construction kit (10x Genomics, PN-1000184) according to the manufacture’s introduction.

value: DRG


title: Il25WT_ILC2_18h Dex_Rep3

description:
il25_18h_wt3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Dexamethasone


title: Mouse neutrophil subset,WT BM,IMM, replicate 1

value: Bone marrow

value: Wild type


title: Mouse neutrophil subset,OTT BLD,MAT, replicate 2

source_name: Blood

value: Blood

value: Orthotopic tumor


title: Mouse neutrophil subset,OTT BLD,IMM, replicate 3


title: Mouse neutrophil subset,WT BM,MAT, replicate 1


title: Mouse neutrophil subset,WT BM,IMM,replicate 2


title: Mouse neutrophil subset,OTT BLD,MAT, replicate 1


title: Il25WT_ILC2_18h Dex_Rep2

description:
il25_18h_wt2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Thymus

value: Il25 WT


title: pRPS5A-DOF2.1-GR, DEX1h, repeat1


title: DRG 7

value: 51 years old


title: DRG 6

value: 47 years old


title: Il25KO_ILC2_18h Dex_Rep4

description:
il25_18h_109_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Male


title: Il25WT_ILC2_18h Dex_Rep1

description:
il25_18h_wt1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: Mouse neutrophil subset,OTT BM,MAT, replicate 2

value: MAT


title: Il25KO_ILC2_18h Dex_Rep3

description:
il25_18h_108_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: Mouse neutrophil subset,OTT BM,IMM, replicate 3

value: IMM


title: DRG 4


title: Mouse neutrophil subset,OTT BM,MAT, replicate 3


title: Mouse neutrophil subset,OTT BLD,IMM, replicate 2


title: Mouse neutrophil subset,OTT BLD,IMM, replicate 1


title: DRG 5

value: 49 years old


title: DRG 3

value: 50 years old


title: Il25KO_ILC2_18h Dex_Rep2

description:
il25_18h_107_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx

value: Il25 KO


title: Mouse neutrophil subset,OTT BM,IMM, replicate 2


title: DRG 2

value: 59 years old


title: Il25KO_ILC2_18h Dex_Rep1

description:
il25_18h_106_ko
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO_dex_males_umi_counts_20210805_175015.xlsx


title: IL25KO_ILC2_irradiated_Rep4

description:
il25ko_3d_irr_ko311
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx

treatment_protocol: Mice were either untreated, or treated for 3 days with sublethal irradiation (425rad), intra-thymic injection with 0.3ug rIL-25, or both.

value: IL25 KO

value: Sublethal irradiation


title: IL25KO_ILC2_irradiated_Rep3

description:
il25ko_3d_irr_ko310
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx


title: IL25KO_ILC2_irradiated_Rep1

description:
il25ko_3d_irr_ko308
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx


title: IL25WT_ILC2_irradiated_Rep4

description:
il25ko_3d_irr_wt5
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx

value: IL25 WT


title: ALI day 17 - donor 16

city: Utrecht

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
10x Genomics
LX244

data_processing:
Illumina output  (bcl files) converted to fastq files using mkfastq (CellRanger v7.0.1)
Alignment, filtering, barcode and UMI counting done using cellranger count (CellRanger v7.0.1)
For tissue samples, SNP-based demultiplexing using souporcell
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: Per sample filtered_feature_bc_matrix output from CellRanger (v7.0.1); includes gene-barcode matrices, genes, barcodes (demultiplexed for LX255_LX256)
Supplementary files format and content: For tissue sample, Souporcell output for k= 4 clusters

source_name: human conjunctiva organoids donor 16

extract_protocol:
Tissue samples were obtained one month before the processing. At time of sampling, these were immediately minced in the operating room and placed in 1 mL of CellBanker 1 (Amsbio, 11888) on dry ice. The samples were stored at -80 °C until further processing. On the day of the sort, the 4 biopsies were thawed, pooled and washed with 10 mL of AdDMEM+++.  To dissociate the samples, cells were resuspended in 1 mL of 0.25% Trypsin/EDTA (Gibco) and 10 U/mL DNase I (Sigma Aldrich, DN25) and incubated in a 37 °C water bath, while checking the advancement of dissociation regularly under the microscope. Using a pre-wet narrowed Pasteur pipette, the cell suspensions were mechanically dissociated by pipetting up and down. The cell suspensions were washed twice with AdDMEM+++.  The cell suspensions from 17 day-old ALI cultures were resuspended in 1 mL FACS buffer (PBS-MQ + 10% Fetal bovine serum - Sigma-Aldrich, F7524). The tissue cell suspension was treated for 5 minutes at RT with red blood cell lysis buffer (Sigma Aldrich, 11814389001), before being washed once with AdDMEM+++. Finally, the cell suspension was resuspended in 1 mL FACS buffer. The cell suspensions that were multiplexed (i.e. conditions 1, 2, 3, 4 and 6) were incubated in labelling oligos CMO303, CMO304, CMO305, CMO306 and CMO307, respectively, for 15 minutes at RT. Then, cells were washed with 6 mL FACS buffer and resuspended in 1 mL of FACS buffer.  Immediately before the sort, DAPI (ThermoFisher Scientific, D1306) and DRAQ5 (Biostatus, 62251) were added to the cell suspensions. Living cells (that is DAPI- and DRAQ5+) were sorted on a BD Jazz sorter (BD Bioscience) into FACS buffer. 30,000 cells were used for library preparation.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.1

value: human conjunctiva organoids donor 16

value: ALI day 17


title: Conjunctiva tissue

description:
10x Genomics
LX237

source_name: 4 pooled healthy bulbar conjunctiva biopsies


title: ALI day 17 - donor 4

description:
10x Genomics
LX243

source_name: human conjunctiva organoids donor 4

value: human conjunctiva organoids donor 4


title: IL25KO_ILC2_irradiated_Rep2

description:
il25ko_3d_irr_ko309
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx

source_name: Thymus

value: Thymus


title: Organoids EM, DM, and ALI day 0, day 3 and ALI + IL4/13

description:
10x Genomics
LX255_LX256

source_name: Human conjunctiva organoids - CMO303/TX294: donor 16, p5; CMO304/TX295: donor 16, p4; CMO305/TX296: donor 16, p6; CMO306/TX297: donor 16, p5; CMO307/TX298: donor 4, p4

value: Human conjunctiva organoids - CMO303/TX294:donor 16, p5; CMO304/TX295:donor 16, p4; CMO305/TX296:donor 16, p6; CMO306/TX297:donor 16, p5; CMO307/TX298:donor 4, p4


title: IL25WT_ILC2_irradiated_Rep2

description:
il25ko_3d_irr_wt2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx


title: SampleTag10 Normal

city: Hainan

first: Dandan

last: Su

address: No.3 Xueyuan Road, Longhua District

institute: Hainan Medical College

description:
TM-697
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: control group

extract_protocol:
Follicular fluid was extracted from three patients in the infertile group with polycystic ovary syndrome and three patients in the normal group, and single-cell whole-transcriptome sequencing libraries were constructed using the BD Platform R hapsody Reverse Transcription Kit and the BD R hapsody Whole Transcriptome Amplification Kit.
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol

value: granulosa cells

value: control group


title: IL25WT_ILC2_irradiated_Rep3

description:
il25ko_3d_irr_wt3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx

value: Male


title: SampleTag12 Normal

description:
TM-699
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided


title: SampleTag11 Normal

description:
TM-698
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided


title: Mouse neutrophil subset,OTT BM,MAT, replicate 1

value: Bone marrow

value: Orthotopic tumor

value: MAT


title: SampleTag10 Infertility

description:
TM-693
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided

source_name: polycystic ovary syndrome (PCOS) infertile group


title: SampleTag11 Infertility

description:
TM-694
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided

value: polycystic ovary syndrome (PCOS) infertile group


title: IL25WT_ILC2_irradiated_Rep1

description:
il25ko_3d_irr_wt1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL25KO3dirr_new_umi_counts_20230314_183611.xlsx


title: ILC2_irradiated_and_injected_rep3

description:
both_ILC_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: WT

value: Female

value: Irradiation and rIL-25 injection


title: ILC2_irradiated_and_injected_rep2

description:
both_ILC_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: Mouse neutrophil subset,OTT BM,IMM, replicate 1

value: IMM


title: Mouse neutrophil subset,OTT TUM,IMM, replicate 3

source_name: Tumor

value: Tumor


title: Mouse neutrophil subset,OTT TUM,MAT, replicate 1


title: Mouse neutrophil subset,OTT TUM,IMM, replicate 1


title: Mouse neutrophil subset,OTT TUM,IMM, replicate 2


title: Mouse neutrophil subset,OTT TUM,MAT, replicate 2


title: Mouse neutrophil subset,OTT TUM,MAT, replicate 3


title: ILC2_injected_rep3

description:
inj_ILC_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: Intra-thymic rIL-25 injection


title: MDAMB231_1307_1

city: Heidelberg

first: Birgitta

middle: E.

last: Michels

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

institute: DKFZ

description: S1 cell, 50 bp sequencing

data_processing:
Poly-A trimming, Artifact removal: custom, in-house pipeline
Mapping to human genome: Bowtie, version 0.12.9, ref.: Langmead B et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, 10:R25, 2009.
Create index file: Samtools, version 1.14, ref.: Danecek P et al., Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) giab008, Bonfield JK et al., HTSlib: C library for reading/writing high-throughput sequencing data, GigaScience (2021) 10(2) giab007
Intersection of mapped reads with isomiR sequences: bedtools multicov, version 2.27.1, ref.: Quinlan AR. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics. 2014 Sep 8;47:11.12.1-34. doi: 10.1002/0471250953.bi1112s47. PMID: 25199790; PMCID: PMC4213956; Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824 using a gff file containing -3 to +3 5' and 3' isomiR sequences for human micro RNAs, ref.: Ibing et al., On the impact of batch effect correction in TCGA isomiR expression data, NAR Cancer, 2021.
Differential expression analysis: DESeq2, version 1.38.0, ref.: Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology,  15(12):550 (2014) using apeglm (version 1.20.0) for effect size shrinkage, ref.: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. 10.1093/bioinformatics/bty895
genome build/assembly: human genome 38
processed data files format and content: Excel file containing raw read counts, rpms and results from differential expression analysis.

source_name: breast, adenocarcinoma

growth_protocol: Cells were cultured in RPMI-1640 (Gibco, #21875034) supplemented with 10% FBS and 1% Pen/Strep at 37°C and 5%CO2 in a humidified incubator.

extract_protocol:
Cells were lysed in Qiazol and total RNA was extracted using the Qiagen miRNAeasy kit (Cat.No.: 217084) according to the manufacturer's protocol.
The library was prepared using the NEBNext Small RNA Library Prep Set for Illumina (Cat.No. E7330S) and the NEBNext Multiplex Oligos for Illumina (Index Primers Set 2, Cat.No. E7500S) following the manufacturers instructions. For sample clean-up after PCR amplification, the Monarch PCR & DNA Cleanup Kit (NEB, Cat.No.: #T1030) was used. As described in the library preparation kit, Agencourt AMPure XP Beads (Beckman Coulter, Inc. #A63881) were used for size selection.

treatment_protocol: In short, MDA-MB-231 cells were retrovirally transduced with contructs encoding pre-miR-1307 or C.elegans control pre-miRNAs and selected based on the puromycin resistance conferred by the vector using 2µg/ml puromycin. Prior to RNA extraction, expression of the transgene was induced by doxycycline for 72h.

value: breast, adenocarcinoma

value: cell line

value: pre-miR 1307 overexpression


title: MDAMB231_1307_3

description: S1 cell, 50 bp sequencing


title: MDAMB231_1307_2

description: S1 cell, 50 bp sequencing


title: MDAMB231_cnt2_3

description: S1 cell, 50 bp sequencing

value: ctrl2 (cel-miR-239b) overexpression


title: ILC2_injected_rep2

description:
inj_ILC_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: Thymus


title: D18(D15)_TV_1

type: RNA

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

institute: INSERM UMRS-1139

description: Syntax of the sample names:  DayPregnancy_TissueType_ReplicateNumber. Where the DayPregnancy is either D8, D12, D18 for embryos and D12(D8), D15(D12), D18(D12), D18(D15) for TV. Where the TissueType is either, ICM, TE, ED, EET, TV.

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 5 days.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics - Raw data set : Feature extraction with Imagene 5.5 software from BioDiscovery (Proteigene)

data_processing: Intensity = Signal Mean - Normalization = Signal mean were normalized by the mean of all the intensities on the array.

organism: Bos taurus

label_protocol: aRNA was retro-transcribed and directly labelled with [alpha-33P]dATP as described (Degrelle et al., 2008). 500ng of aRNA was mixed with 500ng of random hexamers in a volume of 25µl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5µl 10X PCR buffer, 5µl 25mM MgCl2, 5 µl 0,1 mM DTT, 2,5µl 10mM mix dGTP, dCTP and dTTP, 2,5µl water, 50 µCi [alpha-33P]dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1µl RNAse H- and incubation at 37°C for 20 min. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: IVT amplified RNA from each sample was synthesized with the MessageAmpTM aRNA Kit (Ambion) according to Degrelle et al., 2008 (IVT during 10h). aRNA was purified on Mini Quick Spin RNA columns (Roche Diagnostic).

treatment_protocol: Tissues were collected and immediately snap-frozen. Total RNA from bovine embryos and TV were extracted with RNeasy Mini kit (Qiagen). RNA quality was first verified by A260/280 absorbance ratios.

tag: daypregnancy

tag: tissuetype

value: TV

tag: replicatenumber


title: ILC2_injected_rep1

description:
inj_ILC_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: D18(D12)_TV_2


title: MDAMB231_cnt2_2

description: S1 cell, 50 bp sequencing


title: ILC2_irradiated_rep2

description:
irr_ILC_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: Sublethal irradiation


title: ILC2_irradiated_rep3

description:
irr_ILC_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: SampleTag09 Infertility

description:
TM-692
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided

value: granulosa cells


title: ILC2_irradiated_rep1

description:
irr_ILC_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: ILC2_untreated_rep3

description:
UT_ILC_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: Untreated


title: ILC2_irradiated_and_injected_rep1

description:
both_ILC_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: ILC2_untreated_rep2

description:
UT_ILC_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx


title: MDAMB231_cnt1_1

description: S1 cell, 50 bp sequencing

value: ctrl1 (cel-miR-67) overexpression


title: MDAMB231_cnt1_3

description: S1 cell, 50 bp sequencing


title: MDAMB231_cnt2_1

description: S1 cell, 50 bp sequencing


title: shATG7-IAV2

city: Fuzhou

first: JiLong

last: Chen

address: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University

data_processing:
Data preprocessing and genomic alignment. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
LncRNAs prediction, Expression analysis and Interaction research. In order to generate SAM file, we used BWA software to align the sequencing reads of each sample with reference genome. Then CIRI software was used to scan for PCC signals (paired chiastic clipping signals), and LncRNA sequences were predicted based on junction reads and GT-AG cleavage signals.
Using the RPM algorithm to quantify the LncRNAs, and normalizing the number of junction reads counts and foldchange by DESeq. Enrichment of differentially expressed LncRNAs was analysised through the annotation information of LncRNAs source transcripts.
Read count extraction and normalization were performed using CLC genomic benchwork
Gene structure optimization and New transcript prediction. Comparing the merged transcripts with the gene annotation information of the reference sequence through Cuffcompare, assembled transcripts would be lengthened during 5’ or 3’region. It could be considered as optimization of the gene structure. Comparing the new annotation information and known annotation information to obtain new transcript information. With the above comparison results, new transcript predictions could be performed at the same time. Assembly results must satisfy the following conditions to be considered as new transcripts: 200 bp or more apart from the existing annotation gene; and not less than 180 bp in length.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: ATG7 knockdown cells and control cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.
TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: ATG7 knockdown cells and control cells were infected with PR8 influenza virus(MOI=0.5) for 16 hours

value: alveolar epithelial cells

value: ATG7 knockdown

value: PR8 infection for 16 hours


title: shATG7-IAV3

department: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences

institute: Fujian Agriculture and Forestry University


title: mCj org KO 2

data_processing:
Sequencing was performed at Single Cell Discoveries, a sequencing service provider located in the Netherlands using an adapted version of the CEL-seq protocol. In brief:
Total RNA was extracted using Qiagen RNA extraction kit following the manufacturer's instrustion and used for library preparation and sequencing. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq [Hashimshony et al. 2012; PMID: 22939981 and Simini et al, 2014; PMID: 25500896]. In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the reference transcriptome using BWA MEM [Li and Durbin, 2009; PMID 20080505]. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file including read counts for all samples

source_name: mouse conjunctiva organoids

growth_protocol: WT and KO organoids were grown in expansion medium (EM) for 7 days.

extract_protocol:
After a week, organoids were retrieved from BME and resuspended in 350 µL of RLT buffer (Qiagen). RNA was extracted using the RNeasy extraction kit (Qiagen).
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (Hashimshony et al., 2016; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.

value: mouse conjunctiva organoids

value: Pax6 KO

value: mouse expansion medium for 7 days

tag: barcode

value: bc


title: IAV-3

value: WT


title: MDAMB231_cnt1_2

description: S1 cell, 50 bp sequencing

tag: tissue

value: breast, adenocarcinoma

value: cell line


title: mCj org KO 3

tag: treatment


title: mCj org KO 1


title: mCj org WT 2

value: Pax6 WT


title: IAV-2


title: D18(D12)_TV_1


title: D15(D12)_TV_1


title: ILC2_untreated_rep1

description:
UT_ILC_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_irr.xlsx

value: Thymus

value: Female


title: mCj org WT 1


title: IAV-1


title: shATG7-IAV1


title: YAP5SA Drop-Seq 3

description:
Drop-Seq on dissociated cardiac tissue.
processed data file: YAP5SA_DropSeq.meta.data.csv
processed data file: YAP5SA_DropSeq.scale.data.csv
processed data file: YAP5SA_DropSeq.raw.data.csv

data_processing:
The raw FastQ files were converted to BAMs with Picard tools (MergeSamFiles) and then used as input for STAR alignment, cell barcode correction, and digital gene expression (DGE) matrix generation via the Droplet-based RNA-seq tools software package (available at http://mccarrolllab.com/dropseq/). The minimum gene per cell threshold was set to 500 for inclusion into the final digital expression matrix. Subsequently, DGEs from each experiment were merged and then we imported the comprehensive DGE into Seurat (version 2.3.4) where normalization was performed according to package default settings. Batch effects were corrected for with harmony (Korsunsky, et al., 2019).
Genome_build: not provided
Supplementary_files_format_and_content: YAP5SA_DropSeq.meta.data.csv: metadata
Supplementary_files_format_and_content: YAP5SA_DropSeq.scale.data.csv: dge
Supplementary_files_format_and_content: YAP5SA_DropSeq.raw.data.csv: dge

source_name: Dissociated cardiac tissue

extract_protocol:
Adult hearts from indicated genotypes were dissected, cannulated, and then dissociated into a single-cell suspension via collagenase digestion (Collagenase A, Roche) on a custom built Langendorff apparatus as described previously (Monroe et al., 2019) with minor modifications. In short, we performed cardiomyocyte enrichment whereby cardiomyocytes were allowed to settle by gravity for 5 minutes at room temperature after washes in a calcium free Tyrode’s buffer and the supernatant, containing non-CMs was put into new tube and spun down at 700 x g and the pellet containing CMs was washed and spun down at 300 x RPM. Finally, cells were combined in the final step and counted prior to dilution and input into Drop-seq rig. We also performed CM-enrichment batches whereby only the CM enriched fractions were used for Drop-seq. Dissociated cells were diluted to a concentration of 200 cells per µL in PBS with 0.01% BSA. Drop-seq was then performed according to (Macosko et al., 2015). Here cells were co-encapsulated into nano-liter sized droplets containing barcoded microparticles (ChemGenes, catalog number Macosko201110) and lysis buffer using a custom microfluidics device (FlowJEM, Toronto, Canada). After droplet breakage, reverse transcription (Thermo), and exonuclease treatment (NEB) all cDNA was PCR amplified (KAPA), pooled, purified with Ampure XP beads (Beckman Coulter), and ran on a Fragment analyzer (Advanced Analytical Technologies, Inc.) for quality control, quantification, and size determination.
Library preparation was performed with the Illumina Nextera XT kit, and libraries were triple purified with Ampure XP beads (Beckman Coulter). All libraries were sequenced on an Illumina NextSeq500 instrument.

value: Yap5SA+/tg; Myh6-MCM

value: Dissociated cardiac tissue

value: Adult

tag: manipulation

value: Tamoxifen


title: shATG7-3

tag: cell type

value: alveolar epithelial cells

value: without PR8 infection


title: D15_EET_1

value: EET


title: YAP5SA Drop-Seq 2

tag: age


title: D15(D12)_TV_2

value: TV


title: shATG7-2

value: ATG7 knockdown


title: shATG7-1


title: D18(D15)_TV_2


title: D12_EET_2


title: YAP5SA Drop-Seq CM-enriched

description:
Drop-Seq on enriched cardiomyocytes.
processed data file: YAP5SA_DropSeq.meta.data.csv
processed data file: YAP5SA_DropSeq.scale.data.csv
processed data file: YAP5SA_DropSeq.raw.data.csv

source_name: Cardiomyocytes

value: Enriched cardiomyocytes


title: con-3


title: Control Drop-Seq 3


title: con-2


title: Control Drop-Seq 2


title: D15_ED_2

value: ED


title: D12_EET_1


title: D15_ED_1


title: D15_EET_2


title: con-1

value: WT


title: Control Drop-Seq CM-enriched


title: Zebrafish, EC, 24hpf, Aktmutant

status: Public on Jan 10 2024

city: New Haven

first: Joey

middle: J.

last: Ghersi

state: CT

address: 300 George street

department: School of Medicine

institute: Yale University

description: Raw fastq files

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software Version 5.0.0
Downstream analysis were performed on R studio using Seurat
Supplementary files format and content: Tab-separated values files and matrix files
Assembly: Assembly: Lawson Annotation V4.3.2
Supplementary files format and content: 3 files of barcodes, features and matrix

organism: Danio rerio

source_name: FAC sorted cells

growth_protocol: Normal zebrafish growth condition

extract_protocol:
Wild-type, aktmutant, Tg(kdrl:mCherry) tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells, which had 85% cell viability, were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10,000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 (CG000204) was used to generate libraires according to manufacturer intructions
10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 (CG000204) was used to generate libraires according to manufacturer intructions
Transcriptomic single cell, 10x genomics

treatment_protocol: No treatments

value: FAC sorted cells

value: Endothelial Cells

value: Aktmutant


title: Zebrafish, EC, 24hpf, WT

description: Raw fastq files


title: D12_ED_2


title: D18_ED_1


title: D18_ED_2


title: WT6-KP2

city: pittsburgh

first: Janet

state: PA

address: 3459 fifth ave, MUH NW632

institute: University of pittsburgh

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software 6.0.0.
Assembly: mm10
Supplementary files format and content: Tab-sepearated values files and matrix files.

source_name: Lung

extract_protocol:
12-week-old age- and sex-matched Stat1-/- and wild type mice were intratracheally inoculated with 5x103 CFU K. pneumoniae clinical isolate W42 grown to mid-log phase. After 24 hours the mice were euthanized by an overdose of isoflurane. Uninfected age and sex matched naïve mice served as untreated controls. Whole mouse lungs were digested with collagenase A and DNAse I then filtered through 70mm sterile cell strainer to generate single cells suspensions. Neutrophils were depleted using Anti-Ly-6G MicroBeads (mouse) from Miltenyi Biotec. Cell viability was checked by Cellometer Auto 2000 Automatic Cell Viability Counter system (Nexcelom).
library was performed according to the manufactere's instructions (single cell 5'V2 protocol, 10x Genomics).

value: Lung


title: WT2-KP1

description: 10x Genomics


title: KO-KP2

description: 10x Genomics


title: KO-KP1

description: 10x Genomics


title: WT-Contrl1

description: 10x Genomics


title: D18_EET_2


title: WT14_W42_24h

city: Pittsburgh

first: Zeyu

last: Xiong

state: Pennsylvania

address: 3459 5th Ave, MUH W631

department: Medicine

institute: University of Pittsburgh

data_processing:
RNA-Seq data were mapped against mouse genomic sequence, gene sequence, and mRNA sequence.
Differential expression analysis was performed using DESeq software package
Assembly: GRCm38
Supplementary files format and content: Stat1_KO_24vsWT_24_deg.txt
Supplementary files format and content: Stat1_KO_24vsWT_24_deg_all.txt

extract_protocol:
Lungs were harvested from WT and Stat1-/- mice at 0h or 24h after intratracheal infection with 103 CFU of KP. RNA was purified from lung tissue using an RNeasy Plus Universal Mini kit (catalog 73407) according to the manufacturer’s instructions (Qiagen), purified RNA was sequenced by Novogene.
Libraries using the Illumina platform and paired-end reads were generated.

value: klebsiella pneumoniae


title: WT15_W42_24h


title: D12_ED_1


title: WT13_W42_24h


title: STAT4115_24h

value: Stat1 Knockout


title: STAT4114_24h


title: KO-Contrl2

description: 10x Genomics


title: STAT4110_24h


title: STAT4112_24h


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 5 [Z5_Cab_1inv]

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

data_processing:
Salmon calculated TPM values
Assembly: GRCm38
Supplementary files format and content: Excel format (XLSX), TPM values

source_name: Mammary Gland

extract_protocol:
RNA was extracted from the organoids using the Qiagen miRNeasy Mini Kit (Catalog #217004). Manufacturer's protocols were followed for the procedure
rRNA was removed using the Epicentre Ribo-Zero Kit (#20040526, Illumina). Isolated total RNA was then fragmented, reverse transcribed to cDNA, and prepped for sequencing with NEBNext Ultra RNA Library Prep (#E7770, Illumina)

value: Mammary Gland

value: Organoids

value: Cabergoline (0.2 mg/Kg)

tag: time point

value: 1-Day Post-Lactation Involution Period


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 4 [Z4_Cab_1inv]

tag: genotype


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 3 [Z3_Cab_1inv]


title: D12(D8)_TV_2


title: WT-5

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
The image data measured by the high- throughput sequencer are converted into sequence data ( reads) by CASAVA base recognition.
Raw data ( raw reads) of fastq format were firstly processed through in- house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
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).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/ groups ( two biological replicates per condition) was performed using the DESeq2 R 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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: proximal jejunum

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: proximal jejunum


title: cKO-4

value: HuR cKO


title: cKO-2


title: WT-3


title: cKO-1


title: cKO-3


title: WT-6


title: WT-1


title: WT-4


title: cKO-5


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 2 [Z2_Cab_1inv]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 5 [X5_Mult_1inv]

value: untreated


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 1 [Z1_Cab_1inv]


title: WT16_W42_24h


title: D18_EET_1

value: EET


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 2 [X2_Mult_1inv]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 4 [X4_Mult_1inv]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 3 [X3_Mult_1inv]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (1 Day) 1 [X1_Mult_1inv]


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 4 [F4_Mult_AD]

value: 60-Day Post-Lactation Involution Period


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 5 [F5_Mult_AD]


title: D12(D8)_TV_1

value: TV


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 2 [F2_Mult_AD]


title: D8_TE_1

value: TE


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 3  [F3_Mult_AD]


title: Cabergoline-Treated Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 1 [F1_Mult_AD]


title: D8_ICM_2

value: ICM


title: D8_ICM_1


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 5 [D5_Mult_lact]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 4 [D4_Mult_lact]


title: Brca1/P53-Deficient Mammary Gland Organoids from Age-Matched Nulliparous Mice 3 [A3_Nulip]

value: Age-Matched with 60 Days Post-Lactational Involution


title: D8_TE_2


title: Brca1/P53-Deficient Mammary Gland Organoids from Age-Matched Nulliparous Mice 4 [A4_Nulip]


title: Brca1/P53-Deficient Mammary Gland Organoids from Age-Matched Nulliparous Mice 2 [A2_Nulip  ]


title: Brca1/P53-Deficient Mammary Gland Organoids from Age-Matched Nulliparous Mice 1 [A1_Nulip  ]