title: TE11 cells, vehicle control rep 2

city: Philadelphia

first: Kelly

middle: A

last: Whelan

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

data_processing:
Rsubread 2.10
DESeq 2 1.36
Assembly: GRCm38

growth_protocol: TE11 ESCC 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 and purified using RNAeasy kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc.) following manufacturer's protocols.

treatment_protocol: The cells were treated with 0.07% DMSO (vehicle), 200 µM of Diclofenac for 48 hours

value: Esophageal squamous cell carcinoma cells


title: TE11 cells, Diclofenac rep 1

status: Public on Mar 17 2023

type: SRA

state: PA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

value: 200 µM of Diclofenac


title: MM_9

city: Pamplona

first: Jose A.

last: Martinez-Climent

state: Navarra

address: Avda. Pio XII, 55

department: Division of Hemato-Oncology

country: Spain

institute: Center for Applied Medical Research CIMA and School of Medicine, University of Navarra

data_processing:
Basecalls performed bcl2fastq version v2.20
Reads were trimmed using trimmomatic version 0.38
Reads were aligned to the mm10 and hg38 genome assembly using STAR version 2.6.1c
Assembly: mm10 and hg38
Supplementary files format and content: raw data fastq and normalized count tables for mouse and raw count table to human

source_name: MM Plasma cell

extract_protocol:
RNA from lised cells was extracted using the Dynabeads mRNA DIRECT purification kit.
Libraries were sequenced in an Illumina NextSeq 500 at a sequence depth of 10 million reads per sample.

tag: tissue

value: Bone Marrow (BM)

value: MM Plasma cell

tag: disease state

value: Multiple Myeloma (MM)


title: MM_69


title: MM_8


title: MM_62


title: TE11 cells, Diclofenac rep 2


title: TE11 cells, Diclofenac rep 4


title: MM_77


title: MM_79


title: MM_55


title: MM_57


title: MM_63


title: MM_54


title: TE11 cells, vehicle control rep 3


title: TE11 cells, Diclofenac rep 3


title: MM_47


title: TE11 cells, vehicle control rep 1


title: MM_46


title: MM_71


title: MM_45


title: MM_4


title: MM_38


title: MM_39


title: MM_6


title: MM_36


title: MM_50


title: MM_7


title: MM_34


title: MM_32


title: MM_3


title: MM_27


title: MM_26


title: MM_25


title: MM_30


title: MM_31


title: MM_2


title: MM_29


title: MM_33


title: MM_23


title: MM_13


title: MM_35


title: MM_37


title: MM_11


title: MGUS_9

source_name: MGUS Plasma cell

value: MGUS Plasma cell

value: Monoclonal Gammopathy of Undetermined Significance (MGUS)


title: MM_1


title: MM_12


title: MGUS_3


title: MM_10


title: MGUS_8


title: MGUS_5


title: MGUS_4


title: MGUS_2


title: MGUS_11


title: MM_22


title: MM_21


title: BMPC_9_0

source_name: Control Plasma cell

value: Control Plasma cell

value: Healthy Control


title: MM_16


title: MGUS_1


title: BMPC_8_0


title: BMPC_7_3


title: BMPC_7_1


title: BMPC_7_2


title: BMPC_7_0


title: BMPC_6_0


title: MGUS_7


title: Naive-2

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
COUNTING - cuffdiff --library-type fr-firststrand --FDR 0.05 -u -b REF.fa -p 24 -o cuffResults_PROJECT_pool REF.gtf
Assembly: GRCm38.p4 + Gencode-M6 Annotation
Supplementary files format and content: frm_genes.count_tracking.txt - Externally weighted counts for each sample at the gene level
Supplementary files format and content: frm_genes.fpkm_tracking.txt - Normalized expression values for each sample at the gene level

organism: Mus musculus

source_name: in vitro

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the Illumina HiSeq 2500 (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample.

value: primary CD8 T cell

tag: genotype

value: WT


title: Activated_CD8-2_R


title: Activated_OTI-3


title: CD8 T cells, WT, ID 2-2

city: San Francisco

first: Karl

middle: Mark

last: Ansel

state: CA

address: 500 Parnassus Ave

department: Microbiology

institute: University of California, San Francisco

description: WT

data_processing:
The 11 nucleotide 3’ adapter (GTGTCTTTACACAGCTACGGCGTCG) was trimmed from demultiplexed reads using cutadapt (https://github.com/marcelm/cutadapt).
Reads from biological and technical replicates were concatenated into single files for each genotype.
Reads were aligned to the mm10 genome using bowtie2. For the the Malat1-scr/scr samples reads were aligned to a custom mm10 genome which contained a 5 nucleotide scramble in the Malat1:miR-15/16 binding region so as to match the genome of the Malat1^scr/scr cells. This was done to ensure lack of binding to the region was not due to alignment issues with the mutant genome.
To assess Ago2 binding, aligned HITS-CLIP reads were integrated across the follow genomic annotations: lncRNA genes from mouse Noncode v6 (http://www.noncode.org/download.php); miRNA target binding sites from TargetScan V7.2 (https://www.targetscan.org/cgi-bin/targetscan/data_download.mmu80.cgi); mm10 introns, exons, 3’UTRs, and coding genes from UCSC genome table browser (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10). To assess differences in target binding at specific 3’ UTR sites between WT and Malat1scr/scr cells, reads within each 3’ UTR were normalized to the total reads contained in the given 3’ UTR for each genotype. To identify regions of significant Ago2 binding above background, so-called “peaks”, we used the Piranha algorithm (https://github.com/smithlabcode/piranha) on our HITS-CLIP data which had miRNA expression sites removed.
Assembly: mm10
Supplementary files format and content: TargetScan_sums_Ansel_Wheeler.csv contains summary level read depth integrations at and +/- 15 nt around TargetScan predicted microRNA binding sites. Normalized data indicate read depths at a binding region normalized to all binding events in the 3’ UTR of the identified target gene.

source_name: Spleen

growth_protocol: CD8+ T cells were isolated from spleens using negative selection from the EasySep Mouse CD8+ T Cell Isolation Kit (cat# 19853). Cells were counted using trypan blue staining and the nexelcom cellometer spectrum. Cultures were started via stimulation with plate bound αCD3 (1 μg/mL, clone 2C11) and αCD28 (1 μg/mL, clone 37.51); plates coated overnight in PBS with Ca++ & Mg++ at 4°C. Cells were plated in Kool AID complete media (DMEM high glucose media supplemented with 10% FCS, pyruvate, nonessential amino acids, MEM vitamins, L-arginine, L-asparagine, L-glutamine, folic acid, beta mercaptoethanol, penicillin, and streptomycin) and spun at 450 r.c.f. for 5 minutes at 25°C to begin stimulation.Cells were stimulated for 3 days with αCD3 and αCD28 antibodies and grown with kool aid complete media. Subsequently the cells were rested and expanded in kool aid complete media for 2 days supplemented with 100 U/mL recombinant Human IL-2 (R&D Systems Cat# 202-IL-010/CF).

extract_protocol:
1*10^6 cells were used to UV crosslink RNA and protein followed by Ago2 immuno-precipitation as described in Gagnon et al 2018 and Loeb et al 2012.
Precipitated Ago2-RNA complexes were subject to Rnase treatment, 3’ linker ligation, SDS-PAGE isolation, proteinase treatment, and 5’ linker ligation as described in Gagnon et al 2018 and Loeb et al 2012

value: Spleen

tag: clip antibody

value: Wako 2D9

value: CD8+ T cells

tag: strain


title: CD8 T cells, WT, ID 2-1

description: WT


title: Pre-IP input [Pre_507]

city: Atlanta

first: David

last: Weinshenker

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description: Filtered_normalized_logTransformed_counts_for_GEO.xlsx

data_processing:
Fastq files were alligned to mm10 with STAR in Galaxy
FeatureCounts were obtained using R Bioconductor
Read count filtering and normalization was completed with R Bioconductor
Assembly: mm10
Supplementary files format and content: Filtered normalized counts grouped in an Excel spreadsheet

source_name: Pre-IP input

extract_protocol: RNA libraries for RNA-seq were prepared by Novogene using a Library Prep Kit following manufacturer's protocols

value: total hindbrain

value: EYFP


title: IP enriched [IP_508]

source_name: IP enriched

value: noradrenergic

value: hTyr


title: Pre-IP input [Pre_505]


title: Pre-IP input [Pre_511]


title: IP enriched [IP_506]


title: IP enriched [IP_501]


title: Pre-IP input [Pre_508]


title: Pre-IP input [Pre_512]


title: Pre-IP input [Pre_506]


title: Pre-IP input [Pre_504]


title: IP enriched [IP_509]


title: IP enriched [IP_502]


title: IP enriched [IP_510]


title: Pre-IP input [Pre_510]


title: IP enriched [IP_511]


title: IP enriched [IP_504]


title: IP enriched [IP_507]


title: IP enriched [IP_505]


title: Pre-IP input [Pre_509]


title: IP enriched [IP_512]


title: Pre-IP input [Pre_502]


title: Pre-IP input [Pre_501]


title: Naive-1


title: Activated_CD8-1


title: Naive-3


title: LI_5.2

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

description: bulk RNA seq of presorted populations

data_processing:
TrimGalore (version 0.4.0)
FastQC (version 0.11.2)
Pseudo-alignment with Kallisto (version 0.42.5)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tsv files including TPM

source_name: PDGFRahi FB (ESAM-1-PDPN+CD34- cells)

extract_protocol:
small and large intestines from three individual mice were made into single cell suspensions and sorted based on exclusion of dead, Lineage, CD31+, BP3+, EpCAM+, NCAMhi cells before positive gating of individual mesenchymal stromal cell subsets (as defined here) was subjected to bulk RNA-seq.
Libraries were constructed with the Ovation Ultralow system V2 kit, following the manufacturer’s instructions.

treatment_protocol: Adult mice were untreated and 8-10 week old

tag: sorting

value: Intestinal sorted stromal cells

value: Colonic lamina propria

value: Fibroblast

tag: replicate


title: LI_5.3

description: bulk RNA seq of presorted populations


title: SI_1.3

description: bulk RNA seq of presorted populations

source_name: Pericytes (PDGFRa-ESAM-1+PDPN- cells)

value: Small intestinal lamina propria

value: pericytes


title: SI_2.1

description: bulk RNA seq of presorted populations

source_name: SMCs (PDGFRa-ESAM-1+PDPN+ cells)

value: SMC


title: SI_1.1

description: bulk RNA seq of presorted populations


title: SI_2.2

description: bulk RNA seq of presorted populations


title: SI_1.2

description: bulk RNA seq of presorted populations


title: SI_3.2

description: bulk RNA seq of presorted populations

source_name: Igfbp5+ FB and CD81+ FB (ESAM-1-PDGFRaintCD34+ cells)


title: SI_2.3

description: bulk RNA seq of presorted populations


title: SI_3.1

description: bulk RNA seq of presorted populations


title: CD8 T cells, Malat1-scr, ID 2-2

description: SCR

value: Wako 2D7


title: CD8 T cells, WT, ID 1-1

description: WT

value: Wako 2D8


title: CD8 T cells, WT, ID 1-2

description: WT


title: SI_3.3

description: bulk RNA seq of presorted populations


title: SI_4.2

description: bulk RNA seq of presorted populations

source_name: PDGFRahi FB (ESAM-1-PDGFRahiCD34- cells)


title: SI_4.3

description: bulk RNA seq of presorted populations


title: SI_5.1

description: bulk RNA seq of presorted populations

source_name: Fgfr2+ FB (ESAM-1-PDGFRaintCD34- cells)


title: SI_4.1

description: bulk RNA seq of presorted populations


title: CD8 T cells, Malat1-scr, ID 1-2

description: SCR

value: Wako 2D6


title: SI_5.3

description: bulk RNA seq of presorted populations


title: LI_5.1

description: bulk RNA seq of presorted populations


title: LI_4b.3

description: bulk RNA seq of presorted populations

source_name: Fgfr2+ FB (ESAM-1-PDPNhiCD34+CD90- cells)


title: CD8 T cells, Malat1-scr, ID 1-1

description: SCR


title: LI_4b.2

description: bulk RNA seq of presorted populations


title: CD8 T cells, Malat1-scr, ID 2-1

description: SCR


title: CD8 T cells, miR-15/16 KO, ID 1-1

description: dKO

value: Wako 2D4


title: CD8 T cells, miR-15/16 KO, ID 2-2

description: dKO

value: Spleen

value: Wako 2D5


title: CD8 T cells, miR-15/16 KO, ID 2-1

description: dKO

value: CD8+ T cells


title: CD8 T cells, miR-15/16 KO, ID 1-2

description: dKO


title: SI_5.2

description: bulk RNA seq of presorted populations


title: LI_4a.2

description: bulk RNA seq of presorted populations

source_name: CD90+ FB (ESAM-1-CD34+PDPNhiCD90+ cells)


title: LI_4b.1

description: bulk RNA seq of presorted populations


title: LI_4a.1

description: bulk RNA seq of presorted populations


title: LI_4a.3

description: bulk RNA seq of presorted populations


title: LI_3.1

description: bulk RNA seq of presorted populations

source_name: CD81+ FB (ESAM-1-PDPNintCD34+CD90- cells)


title: LI_3.3

description: bulk RNA seq of presorted populations


title: LI_1.2

description: bulk RNA seq of presorted populations


title: LI_1.3

description: bulk RNA seq of presorted populations


title: LI_3.2

description: bulk RNA seq of presorted populations


title: 72h_3

description: Column 72h_3 within deSeq2_counts.txt

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.6.4, featurecounts, -s 0 -t exon -g gene_name
Assembly: GRCm38.p4 + Gencode-M22 Annotation
Supplementary files format and content: Raw gene counts

source_name: Lung

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NextSeq550 sequencer (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample.

value: Lung

value: Primary

value: T cell

tag: time point

value: WT

value: CAR expression


title: pre_2

description: Column pre_2 within deSeq2_counts.txt


title: Sp_LN_b_1

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - cutadapt v1.18 "--no-indels -g ACCG -a GTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTCG -m 20 -M 20 --trimmed-only"
MAPPING - bowtie v1.2.2 "-n 2 -l 20"
READ COUNTING - subread v1.6.1, featurecounts, "-s 0 -t CDS -g gene_id/gene_name"
Assembly: Custom CRISPR panel, included as pMSCVURP.tar.gz within the delivery
Supplementary files format and content: counts.txt - Raw counts per barcode within the panel
Supplementary files format and content: countsPerGene.txt - Cumulative raw counts for a given gene captured by the panel

source_name: Splenn/LN

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
Amplification and barcoding of sgRNAs was performed following the manufacturer’s specifications for constructing CRISPR pooled lentiviral sgRNA libraries (Cellecta, Mountain View, CA). Briefly, an initial round of 25 cycles of PCR was performed using 100ng genomic DNA to amplify sgRNA sequences.  Amplicons from the first PCR were used in a second PCR of 9 cycles to add index, P5, and P7 sequences for Illumina sequencing. The final sequencing libraries were quantified using the Qubit dsDNA assay (ThermoFisher) and assessed for size using the Tapestation D1000 assay (Agilent). The pooled sequencing libraries were then size-selected for the size range of 340-425bp using the PippinHT (Sage Science). Libraries were sequenced on a NextSeq550 High-output flowcell (Illumina) to obtain single-end 50-nt reads.

value: Splenn/LN

value: OT-I


title: 72h_1

description: Column 72h_1 within deSeq2_counts.txt


title: Sp_LN_b_2


title: L_L_2

source_name: Lung/Liver

value: Lung/Liver


title: Before_3

value: in vitro


title: LI_1.1

description: bulk RNA seq of presorted populations

value: Intestinal sorted stromal cells

value: Colonic lamina propria

value: pericytes


title: pre_3

description: Column pre_3 within deSeq2_counts.txt


title: Sp_LN_b_4


title: L_L_4


title: pre_1

description: Column pre_1 within deSeq2_counts.txt


title: 72h_2

description: Column 72h_2 within deSeq2_counts.txt


title: L_L_5


title: dmsod8_2

city: New York

first: Alice

last: Tang

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medicine

description: murine iGATA6 cells (Turbendian et al., 2013)

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized read counts

source_name: ESC-derived cardiac progenitor cells cultured for two days in DMSO

growth_protocol: Cardiac progenitor cells were derived from an inducible Gata6 mESC line (Turbendian et al, 2013), grown in a serum free differentiation media composed of Isocove's modified Dulbecco's medium, Ham's F-12, B-27, N-2, penicillin/streptomycin, 0.05% BSA, ascorbic acid, L-glutamine, and 1-thioglycerol. Cardiac progenitor cells were then cultured in RPMI 1640 media supplemented with ascorbic acid, L-glutamine, B-27 minus Vitamin A, N-2, penicillin/streptomycin, non-essential amino acids, and 1-thioglycerol.

extract_protocol:
Cells were lysed and harvested on Day 10 using Qiagen RNeasy Mini kit (cat# 74106). Illumina TruSeq Prep was used with 1ug of total RNA for constructing sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either 10 μM final concentartion of Cucubitacin or equivalent volume of DMSO on Day 6 of culture

value: ES-derived cardiac progenitor cells


title: Before_2

source_name: in vitro


title: cucurd8_2

source_name: ESC-derived cardiac progenitor cells cultured for two days in 10 μM Cucurbitacin I Hydrate


title: cucurd8_1


title: Before_1


title: dmsod8_1


title: Ant1A114P,A123D/+_4

city: Syracuse

first: Liam

last: Coyne

address: 750 E Adams St

institute: SUNY Upstate Medical University

data_processing:
All data processed in Partek Flow
Adaptors trimmed with minimum read length of 19.
Bases were trimmed for end minimum quality level (phred) of 25
Trimmed reads aligned to the genome with STAR - 2.7.3a
Aligned reads Quantifed to annotation model (Partek E/M)
Gene counts normalized with median ratio
DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized quantification values for each Sample

molecule: polyA RNA

source_name: Skeletal Muscle_Quadriceps

extract_protocol:
Skeletal muscle was disputed in QIAzol lysis reagent, using the Qiagen TissueRuptor. RNA was then extracted using the Qiagen miRNeasy Mini Kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep kit, using 1ug Total RNA as input.

value: Skeletal Muscle_Quadriceps

tag: Sex

value: M

tag: age

value: 9 months

tag: biological replicate

value: biol rep 4


title: Ant1A114P,A123D/+_3

value: biol rep 3


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet, rep6

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
RNA-Seq reads were trimmed using Trim Galore (version 0.4.4; https://github.com/FelixKrueger/TrimGalore) to remove adapters and bases with quality score below 20.
Reads were aligned to the mm9 mouse genome with STAR (version 2.5.4; PMID 23104886).
HOMER (version 4.9; PMID 20513432) was used to generate a gene count matrix from uniquely mapped reads.
Assembly: mm9
Supplementary files format and content: raw count matirx (tab-delimited matrix of raw gene counts by sample)

source_name: aorta

extract_protocol:
The mice were sacrificed and perfused by cardiac puncture with 10 ml of ice-cold PBS supplemented with 20 U/ml heparin and placed on ice for dissection. The entire thoracic aorta (i.e., the ascending aorta, the aortic arch and the descending aorta up to the diaphragm) was extracted and used in bulk RNA-Seq library preparation. The adventitia was mechanically removed under a dissection microscope and discarded. The tissue samples were flash-frozen and cryogenically pulverized using the Cellcrusher cryo-press cooled with liquid nitrogen. Total RNA was isolated and treated with DNase I using the Absolutely RNA Nanoprep Kit (Agilent). RNA was quantified using the Bioanalyzer RNA 6000 pico assay (Agilent).
Bulk RNA-Seq libraries were prepared using the SMARTer v2 Stranded Total RNA-Seq Pico Kit (Takara Bio).

value: aorta

tag: diet

value: 3 months high-fat diet

value: female


title: Ant1A114P,A123D/+_2

value: biol rep 2


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet, rep5

value: male


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet, rep4


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet, rep1


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet, rep2


title: WT-3

value: WT


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep5

value: 1 month high-fat diet


title: WT-4


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep6


title: WT-1

value: biol rep 1


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep3


title: aorta, LDLR-/- ApoB100/100, chow diet, rep6

value: chow


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep2


title: WT-2


title: aorta, LDLR-/- ApoB100/100, chow diet, rep4


title: aorta, LDLR-/- ApoB100/100, chow diet, rep5


title: Ant1A114P,A123D/+_1


title: iTreg cells 3

city: Vienna

first: Winfried

middle: F

last: Pickl

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

data_processing:
fastq generation incl. demultiplexing and adapter trimming, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
count normalization and transformation, DESeq2 v1.22.2
Assembly: GRCm38
Supplementary files format and content: plain text, raw counts per gene, one file per sample

source_name: T cells

growth_protocol: Cells were cultured at 37°C , 5 % CO2, and stimulated with 2*105 BMDCs together with rArt v 1 [1 µg/mL].

extract_protocol:
1*10^6 FACS sorted T cells at time-point 0 and after 120 h were lysed and processed using the Qiagen RNeasy mini-kit according to manufacturers recommendations.
NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Cells were untreated and processed after FACS sort for naive T cells (time-point zero) or treated with DMSO, BX-795 or an iTreg differentiation mix (TGF-b, anti-IL-4, anti-IFN-g)

value: stimulated/differentiated T cells

value: TGF-b [20 ng/mL], anti IL-4 [5 ug/mL], anti-IFN-g [5 ug/mL] plus BMDCs plus rArt v 1 [1 ug/mL]

tag: cell subtype

value: iTreg


title: naive T cells 3

value: naive T cells

value: untreated time point 0

value: naive T cell


title: T effector cells 4

value: DMSO plus BMDCs plus rArt v 1 [1 ug/mL]

value: T effector cell


title: Th-IL-2 cells 3

value: BX-795 [0.24 uM] plus BMDCs plus rArt v 1 [1 ug/mL]


title: aorta, LDLR-/- ApoB100/100, chow diet, rep3

value: aorta


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep1


title: iTreg cells 4


title: T effector cells 3


title: Th-IL-2 cells 4


title: Th-IL-2 cells 2


title: iTreg cells 2


title: aorta, LDLR-/- ApoB100/100, chow diet, rep2


title: aorta, LDLR-/- ApoB100/100, chow diet, rep1


title: T effector cells 2


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, rep4


title: naive T cells 4


title: aorta, wild type, chow diet, rep5

value: wild type


title: aorta, wild type, chow diet, rep6

value: female


title: aorta, wild type, chow diet, rep4

value: male


title: iTreg cells 1


title: Th-IL-2 cells 1


title: aorta, wild type, chow diet, rep3


title: T effector cells 1


title: aorta, wild type, chow diet, rep2


title: STING-N153S expressing MC38, 2

city: München

first: Jürgen

last: Ruland

address: Einsteinstraße 25

country: Germany

institute: Technical University of Munich

data_processing:
Data were processed using the published Drop-seq pipeline (v1.0) to generate sample- and genewise UMI tables (Macosko et al., 2015).
Assembly: The reference genome (GRCm38) was used for alignment. Transcript and gene definitions were used according to the GENCODE Version M25.
Supplementary files format and content: matrix with counts per sample
Supplementary files format and content: table with genotype of each sample

growth_protocol: MC38 tumor cells were cultivated in standard DMEM growth medium

extract_protocol:
RNA was harvested using the RNeasy micro plus kit (Qiagen)
Library preparation for bulk sequencing of poly(A)-RNA was performed as described previously (Parekh et al., 2016). Briefly, the barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs), and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO), and full-length cDNA was amplified with primers binding to the TSO site and the adaptor. An NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated, and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve better cluster recognition.

value: Colon adenocarcinoma


title: STING-N153S expressing MC38, 3


title: naive T cells 1


title: STING-N153S expressing MC38, 1


title: parental MC38, 2

value: WT


title: YFP51_YFP_Cg1_GC_B_cell_S23

source_name: Germinal B cell

value: Bone Marrow (BM)

value: Germinal B cell

tag: model

value: Control


title: O3_96_RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina sequencing reads (~32 million paired-end reads per sample) were de-multiplexed using bcl2fastq/2.20.0
Reads were trimmed to remove adapter sequences using trimmomatic/0.39. The quality of the resulting FASTQs was assessed using FASTQC/0.11.9 and reads were aligned to the mouse reference genome (assembly GRCm38/mm10, concatenated with the ERCC transcripts) using STAR/2.7.5b.
BAM files were sorted and indexed using samtools/1.10, and duplicates were removed using picard/2.20.8. The BAM files were then filtered to retain alignments with a minimum mapping quality of 10 using samtools/1.10.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. H3 and input reads were subtracted from H3K27me3 and IgG respectively with bigwigCompare.
The featureCounts function of the Rsubread R package/2.6.4 was used to estimate counts for all genes and ERCC transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location
Supplementary_files_format_and_content: count file was generated with featureCounts function of the Rsubread R package/2.6.4.

source_name: mouse liver

extract_protocol:
RNA was isolated from frozen tissue by homogenization in Trizol followed by isopropanol precipitation. The RNA was further purified using RNeasy columns (Qiagen). An on-column DNase I digestion was performed during the purification step to remove genomic DNA. The RNA amount and integrity were confirmed using the Qubit RNA HS Assay Kit and RNA IQ Assay (Thermo Fisher) respectively.
~Total RNA (~1 µg) was used to make RNA-seq libraries following the Zymo-Seq Ribo-free Total RNA Library Kit (Zymo Research) instructions with dual indexing. Prior to ribo-depletion, total RNA from young livers were spiked with 2 µl of a 1:100 dilution of ERCC Ex-fold mix 1 while that from old livers were spiked with 2 µl of 1:100 dilution of ERCC Ex-fold mix 2 (Thermo Fisher). Library quality and quantity was confirmed on a BioAnalyzer (Agilent) DNA HS chip. Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (New England Biolabs).

treatment_protocol: Old as treated group

value: liver

tag: group

value: old


title: O2_120_RNA


title: O3_120_RNA


title: O1_240_RNA


title: parental MC38, 3

tag: cell line

tag: cell type


title: O1_120_RNA

tag: tissue


title: YFP50_YFP_Cg1_GC_B_cell_S23

tag: disease state


title: parental MC38, 1

tag: genotype


title: YFP72_YFP_Cg1_GC_B_cell_S24


title: 8329_pB2IC_MM_S22

source_name: MM Plasma cell

value: MM Plasma cell

value: Multiple Myeloma (MM)


title: O2_72_RNA


title: O1_96_RNA


title: O3_48_RNA


title: 8332_pB2IC_MM_S15


title: naive T cells 2

value: naive T cells

tag: treatment

value: untreated time point 0

value: naive T cell


title: 6174_pB2IC_MM_S13


title: O3_72_RNA

tag: strain


title: 249_pB2IC_MM_S4


title: aorta, wild type, chow diet, rep1

value: chow


title: O1_48_RNA


title: O3_240_RNA


title: 8323_pB2IC_MM_S26


title: 8327_pB2IC_MM_S25


title: O2_240_RNA


title: 1485_pB2IC_MM_S15


title: 8850_pB2IC_MM_S15


title: O2_48_RNA


title: O1-bef_RNA

value: before


title: O2_96_RNA


title: O1_72_RNA


title: Y2_240_RNA

value: young


title: O3-bef_RNA


title: 1496_pB2IC_MGUS_S6

source_name: MGUS Plasma cell

value: MGUS Plasma cell

value: Monoclonal Gammopathy of Undetermined Significance (MGUS)


title: 1508_pB2IC_MGUS_S7


title: O2-bef_RNA


title: 1487_pB2IC_MGUS_S6


title: Y3_240_RNA


title: 1492_pB2IC_MGUS_S7


title: Y1_240_RNA


title: 3869_MMSetB2IC_MM_S20


title: 3086_MMSetB2IC_MM_S21


title: Y1_120_RNA


title: 3874_MMSetB2IC_MM_S20


title: Y2_120_RNA


title: 2582_MMSetB2IC_MGUS_S12


title: Y3_120_RNA


title: 3868_MMSetB2IC_MGUS_S11


title: 3180_MMSetB2IC_MM_S21


title: 3873_MMSetB2IC_MGUS_S12


title: 3191_CD1B2IC_MM_S18


title: 3173_CD1B2IC_MM_S19


title: Y2_96_RNA


title: Y1_96_RNA


title: 3197_CD1B2IC_MM_S19


title: Y2_72_RNA


title: 9496_CD1B2IC_MM_S18


title: 3470_CD1B2IC_MGUS_S10


title: 8074_cMafB2IC_MM_S17


title: Y3_48_RNA


title: 8192_cMafB2IC_MM_S17


title: Y2_48_RNA


title: Y3_bef_RNA


title: Y1_bef_RNA


title: 3048_cMafB2IC_MM_S16


title: Y3_96_RNA


title: Y3_72_RNA


title: 3502_cMafB2IC_MGUS_S9


title: 3042_cMafB2IC_MM_S16


title: MEP, Tmprss6-/-, rep 2

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description:
RNA-seq from Tmprss6-/-  MEP cells
MEP_KO_2

data_processing:
After quality control (FastQC version 0.11.5), reads generated from each sample were aligned to the mouse genome (GRCm38.p3) with STAR (version 2.5.3a,–quantMode GeneCounts), using the Gencode M15 transcript annotation as a transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR Bioconductor package, using a double threshold on the log2 fold change (absolute value >0.5) and corresponding statistical significance (P < 0.05).
Assembly: GRCh38.p3
Supplementary files format and content: MEP_counts.txt: tab-delimited text file including gene annotations (columns 1-8) and sample-specific counts of aligned reads.

source_name: murine megekaryocytic-erythroid progenitor (MEP)

extract_protocol:
lineage depletion with EasySep (Stem Cell Tecnologies), Incubate cells in (PBS, 1%BSA, 1mMEDTA) with the following antibodies: Lineage cocktail-PECy7, cKit-APC, Sca-BV421, FcgRI/III-APCR700, CD150-PE, CD105-PerCPCy5.5, CD41-BV511.
QIAGEN RNeasy microkit protocol
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing
Nextera XT DNA Sample Preparation kit


title: MEP, Tmprss6-/-, rep 3

description:
RNA-seq from Tmprss6-/-  MEP cells
MEP_KO_3


title: MEP, Tmprss6-/-, rep 1

description:
RNA-seq from Tmprss6-/-  MEP cells
MEP_KO_1


title: 3498_cMafB2IC_MGUS_S8


title: MEP, WT, rep 3

description:
RNA-seq from WT MEP cells
MEP_WT_3


title: Y1_72_RNA


title: 3313_cMafB2IC_MGUS_S8


title: MEP, WT, rep 2

description:
RNA-seq from WT MEP cells
MEP_WT_2


title: Y1_48_RNA


title: 3469_CD1B2IC_MGUS_S10


title: 6434_B2IKC_MM_S14


title: 4294_B2IKC_MM_S23


title: MEP, WT, rep 1

description:
RNA-seq from WT MEP cells
MEP_WT_1


title: 6430_B2IKC_MM_S16


title: 2358_B2IKC_MM_S34


title: Y2_bef_RNA


title: 3253_B2IKC_MM_S1


title: 3903_B2IKC_MGUS_S5


title: 3940_B2IKC_MGUS_S5


title: Responder-1

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

email: jhw51@pitt.edu, wangj28@upmc.edu

address: 5117 Centre Avenue, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

description: Adaptive Biotechnologies’ ImmunoSEQ platform

library_source: genomic

data_processing:
Processed data file from Immunoseq data analyzer for each sample is submitted
Supplementary files format and content: Processed data files from Immunoseq data analyzer
Library strategy: TCR-seq

molecule: genomic DNA

source_name: Tumor

growth_protocol: A223 tumors were injected into C57BL/6J mice. When tumor size reached ~250-350mm3, tumor-bearing mice were randomized into two groups: control vs. anti-PD-L1, treated with PBS or anti-PD-L1 monoclonal antibody (mAb), respectively.  Tumors  were collected from responding and non-responding mice for CD8 T cell isolation followed by TCRβ DNA sequencing

extract_protocol: Tumors were removed from 3 responder mice (1R, 2R, 3R) and 4 non-responder mice (4NR, 5NR, 6NR, 7NR); tumors were digested, and CD8 T cells were isolated followed by genomic DNA (gDNA) extraction. gDNA was subjected to ImmunoSeq TCR beta chain sequencing.

value: Tumor

value: CD8 T cells

value: 6-8 weeks old

tag: tumor state

value: Responder


title: Non-Responder-2

value: Non-responder


title: Responder-3


title: 29_GFP

first: Jeremy

middle: Michael

last: Shea

address: 513 Parnassus Avenue

department: Anatomy

data_processing:
library strategy: hMeDIP-Seq
FASTQ reads were aligned to the mouse genome (mm10) using Bowtie2 with default parameters.
MACS2 callpeak was used to find peaks between the conditions using the BAM output.
Bedgraph files were outputted from MACS2 for each condition.
Assembly: mm10
Supplementary files format and content: Bedgraph files of combined samples from each condition

source_name: Hippocampal neurons

growth_protocol: 3 month old mice were stereotactically injected with lentivirus with either GFP or Tet2 expression cassettes under the control of the synapsin promoter

extract_protocol:
Nuclei were isolated from hippocampi followed by FACS isolation of neuronal nuclei. DNA was extracted from neuronal nuclei.
Equal amounts of DNA were sonicated to 300-500bp followed by end cleanup and NEB-Next adapter ligation. DNA was treated with USER enzyme followed by DNA cleanup. DNA was denatured, and subjected to immunoprecipitation with a 5-hydroxymethylcytosine antibody (ActiveMotif) followed by extensive washing. Captured DNA was amplified by PCR and purified.

treatment_protocol: Mice were maintained for 60 days after injection and then euthanized for neuronal isolation

value: Neurons

value: GFP


title: Responder-2


title: Non-Responder-4


title: Non-Responder-1


title: SC20_B2IC_MM_S6

value: Bone Marrow (BM)

value: MM Plasma cell


title: 5263_B2IC_MM_S18

value: Multiple Myeloma (MM)


title: 3910_B2IKC_MGUS_S4


title: 6538_B2IC_MM_S13


title: Non-Responder-3


title: 28_Tet2OE

value: Tet2 OE


title: 3911_B2IC_MGUS_S3


title: 26Tet2OE


title: 5937_B2IC_MM_S14


title: 27_GFP


title: 25_Tet2OE


title: 9_GFP


title: 1121_B2IC_MGUS_S4


title: 1148_B2IC_MGUS_S2


title: 1108_B2IC_MGUS_S3


title: 6_Tet2OE


title: 4_Tet2OE


title: 3_GFP


title: SC30_MIC_MM_S21

value: MIC


title: 2Tet2OE


title: SC40_MIC_MM_S33


title: 1_GFP


title: 8582_MIC_MM_S17


title: 3178_MIC_MM_S22


title: SC80_MIC_MGUS_S7


title: 3608_MIC_MM_S22


title: ChIP-D8-rep1-input

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamCoverage (bin size = 1)

source_name: ES R1

growth_protocol: Serum+Lif

extract_protocol:
10min formaldehyde fixation followed by sonication . Immunoprecipitation was performed using ChIP-IT kit (#53040, Active Motif) following manufacturer's protocol. Experiments were done in duplicates.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from <1 ng to 10ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: We used ML-792, a highly selective inhibitor of the SUMO E1 enzyme, to decrease the global level of SUMOylation in mouse ES cells between D1 and D3. ChIP-seq were performed at D1 and D8 after SUMO recovery.

tag: chip antibody


title: ChIP-D1-rep1-input


title: 8991_MIC_MM_S24

data_processing:
Basecalls performed bcl2fastq version v2.20
Reads were trimmed using trimmomatic version 0.38
Reads were aligned to the mm10 and hg38 genome assembly using STAR version 2.6.1c
Assembly: mm10 and hg38
Supplementary files format and content: raw data fastq and normalized count tables for mouse and raw count table to human

extract_protocol:
RNA from lised cells was extracted using the Dynabeads mRNA DIRECT purification kit.
Libraries were sequenced in an Illumina NextSeq 500 at a sequence depth of 10 million reads per sample.


title: 8985_MIC_MGUS_S28


title: ChIP-D8-rep1-Zfp57

value: Zfp57 ( Abcam #ab45341)


title: ChIP-D8-rep2-Zfp57


title: 8982_MIC_MGUS_S5


title: ChIP-D1-rep2-Zfp57


title: ChIP-D8-rep2-Kap1

value: Kap1 ( Abcam #ab10483)


title: 8936_MIC_MGUS_S3


title: MIC18_MIC_MGUS_S13


title: 8995_MIC_MGUS_S2


title: ChIP-D1-rep1-Kap1


title: SC60_Maf_MIC_MM_S11


title: ChIP-D1-rep1-Zfp57


title: 9399_Maf_MIC_MM_S30


title: 8994_MIC_MM_S9


title: 9312_Maf_MIC_MM_S8


title: ChIP-D1-rep2-SUMO-2_3

value: SUMO-2_3 ( Abcam #ab3742)


title: ChIP-D8-rep2-SUMO-2_3


title: ChIP-D8-rep2-input


title: ChIP-D1-rep2-input


title: 8476_MIC_MM_S31


title: Pool9_YFP_Control_S35

source_name: Control Plasma cell

value: Control Plasma cell

value: Control


title: ChIP-D8-rep2-inputSUMO-1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Libraries were aligned with bowtie2 with default parameter on mouse and fly genomes together. We filtered all alignment on MAPQ (mapping quality value) 30 with samtools . We deduplicated libraries with picard tool4. We used the number of reads mapped on fly genome as spike-in value and we downsampled libraries according to manufacturer instruction.
Genome_build: mm10
Supplementary_files_format_and_content: we merged the replicates by using mean values and generated bigwig coverage track

treatment_protocol: We used ML-792, a highly selective inhibitor of the SUMO E1 enzyme, to decrease the global level of SUMOylation in mouse ESCs, with two rounds of 48 h treatments (2.5mM) between D1 and D3, D8 and D10

value: ES cells

tag: growth protocol

value: Serum+Lif

value: control

tag: time


title: YFP72_Cg1_Control_Cp_S2


title: Pool7_YFP_Control_S32


title: Pool6_YFP_Control_S27


title: ChIP-D1-rep2-inputSUMO-1


title: YFP61_Cg1_Control_Cp_S1


title: ChIP-D1-rep2-Kap1


title: ChIP-D8-rep1-Kap1


title: ChIP-D8-rep1-inputSUMO-1


title: ChIP-D1-rep2-SUMO-1

value: SUMO-1 (Abcam #ab32058)


title: ChIP-D8-rep2-SUMO-1


title: E12.5 Stromal cells SI replicate 02

description: single cell RNA sequencing analysis of intestinal adult stroma cells at homeostasis

data_processing:
Demultipexing and alignment of reads with CellRanger  v3.1.0 for replicates 02.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Genome_build: mm10-2.1.0
Supplementary_files_format_and_content: tsv.gz & mtx.gz

source_name: E12.5 Stromal cells SI

extract_protocol:
Two independent experiments with three-five embryos/experiment. Small and large intestine (including cecum) were dissected out prior to single cell suspensions and sorting (Live, CD45-, Ter119-, CD31-, EpCAM-, Itgb1+, YFP+) of mesenchymal stromal cells for scRNA-seq.
Single cell RNA-seq libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3' Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) or 5' kit Chromium Single Cell 5′ Library & Gel Bead Kit (10x Genomics, PN-1000006), and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223).

treatment_protocol: Untreated E12.5 embryos

value: EYFP (C57BL/6)

value: Small intestinal lamina propria

value: Mesenchymal stromal cells


title: ChIP-D1-rep1-inputSUMO-1


title: E12.5 Stromal cells SI replicate 01


title: E12.5 Stromal cells LI replicate 02

source_name: E12.5 Stromal cells LI

value: Colonic lamina propria


title: E12.5 Stromal cells LI replicate 01


title: RNA-Seq_HCT116_si-circRERE-1

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

country: China

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: hg38

growth_protocol: RKO cells were cultured in DMEM medium supplemented with 10% FBS. And HCT116 cells were cultured in 1640 medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: Normal condition

value: human colorectal cancer cell

value: cicRERE knock down

value: si-circRERE


title: PAR-CLIP Matrin3_rep3

city: Bethesda

first: Ashish

last: Lal

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

data_processing:
Illumina software used for basecalling.
The analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Assembly: hg19
Supplementary files format and content: csv files including binding sites positions

extract_protocol:
Matrin-3 PAR-CLIP method was performed in three biological replicates as described previously (Benhalevy et al., 2017; Hafner et al., 2010). We used anti-Matrin3 antibody (Bethyl Laboratories, Catalog No. A300-591A) for the immunoprecipitation of RNPs.
Small RNA cDNA library preparation protocol was performed as described in Benhalevy et al., (2017).

value: Colorectal cancer cell line

value: anti-Matrin3 antibody


title: ChIP-D10-rep2-inputHistone


title: ChIP-D8-rep1-SUMO-2_3


title: Grafted Stromal cells LI

source_name: Graft sorted LI stromal cells

extract_protocol:
Enlarged grafts were dissected out and made into single cell suspensions and sorted (Live, CD45-, Ter119-, BP3-, CD31-, EpCAM-, L1CAM-, Itgb1+, YFP+) MSCs sorted for scRNA-seq.
Single cell RNA-seqg libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3' Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) or 5' kit Chromium Single Cell 5′ Library & Gel Bead Kit (10x Genomics, PN-1000006), and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223).

treatment_protocol: Embryonic EYFP+ SI and LI were grafted under adult WT kidney capsules and left for 4 weeks.

value: Grafted colonic lamina propria


title: RNA-Seq_RKO_siCTL

source_name: RKO

value: RKO

value: WT

value: siCTL


title: ChIP-D1-rep1-SUMO-2_3

value: SUMO-2_3 ( Abcam #ab3742)


title: Grafted Stromal cells SI

source_name: Graft sorted SI stromal cells

value: Grafted small intestinal lamina propria


title: RNA-Seq_RKO_si-circRERE-1


title: YFP71_TFP_Cg1_Control_Cp_S1

first: Jose A.

last: Martinez-Climent

address: Avda. Pio XII, 55

value: Bone Marrow (BM)

value: Control Plasma cell

value: Control


title: PAR-CLIP Matrin3_rep2


title: ChIP-D8-rep2-inputHistone

value: ES cells

value: Serum+Lif

value: control


title: PAR-CLIP Matrin3_rep1


title: siMatrin3  rep3

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using TopHat.
Gene expression was quantified using RSEM
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with TRIzol™ Reagent
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep

value: 48 hours siMatrin3


title: Stromal cells LI replicate 01

data_processing:
Demultipexing and alignment of reads with CellRanger v3.0.2 for replicates 01 and v3.1.0 for replicates 02.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Genome_build: mm10 (replicates 01) and mm10-2.1.0 (replicates 02)
Supplementary_files_format_and_content: tsv.gz & mtx.gz

source_name: Intestinal sorted stromal cells

extract_protocol:
Two independent experiments with three female mice/experiment. Muscularis externa was removed from small and large intestine prior to single cell suspensions and sorting (Live, CD45-, Ter119-, CD31-, BP3-, EpCAM-, L1CAM-, Itgb1+) of mesenchymal stromal cells for scRNA-seq.
Single cell RNA-seqg libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3' Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) or 5' kit Chromium Single Cell 5′ Library & Gel Bead Kit (10x Genomics, PN-1000006), and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223).

value: Colonic lamina propria

value: Mesenchymal stromal cells


title: siMatrin3  rep2

value: Colorectal cancer cell line


title: siMatrin3  rep1


title: ChIP-D8-rep1-SUMO-1

value: SUMO-1 (Abcam #ab32058)


title: RNA-Seq_HCT116_siCTL

value: human colorectal cancer cell


title: Stromal cells  SI replicate 01

value: Small intestinal lamina propria


title: siCTRL  rep3

value: 48 hours siCTRL


title: siCTRL  rep2


title: siCTRL rep1


title: ChIP-D1-rep2-inputHistone


title: ChIP-D10-rep2-H3K9me3

value: H3K9me3 (Abcam #ab8898)


title: ChIP-D3-rep2-inputHistone


title: xrn1-H41A SPAAC seq 3

city: Piscataway

first: Megerditch

last: Kiledjian

address: 604 Allison Road

institute: Rutgers University

data_processing:
reads were processed for quality control and adapter removal with fastp 0.23.2
transcript quantification was performed with kallisto 0.48.0
Assembly: GCF_00146045.2_R64
Supplementary files format and content: reads counts for all samples as a csv

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD and harversted at exponential phase

extract_protocol:
Total RNA from yeast strains was isolated with the acidic hot phenol method (Kohrer and Domdey, 1991) and treated with DNase (Promega) according to the manufacturer’s protocol. Total RNA from human cells was isolated using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol and treated with DNase as explained above to eliminate DNA. To enrich for poly-adenylated RNA, total RNA purified as above was used as the input for the Poly(A) Purist MAG Kit (Thermo Fisher Scientific) following the manufacturer’s protocol
SMART-Seq HT (Takara) and Illumina Nextera XT
RNA Seq (SPAAC (Copper-free Strain-promoted azide-alkyne cycloaddition (SPAAC) ) and DSPAAC Seq (decapping of m7G RNA samples with Dcs1 followed by SPAAC)). Thes two methods allow labeling of NAD capped RNA moleculules with biotin, which is then used as a bait for affinity purification.

value: SPAAC


title: ChIP-D1-rep1-SUMO-1


title: xrn1-H41A SPAAC seq 2


title: ChIP-D8-rep2-H3K9me3


title: run8_ELS_M7_iX22

description:
counts_run8.csv.gz
meta_run8.csv

data_processing:
We used the MARS-seq2.0 pipeline, the reads structure is as follow : R1 : 5I.4P.66M (ignore 5 first bases, followed by 4 nt of plate barcode and finally the 66 nt of the insert), R2 : 7W.8R.1I (7 nt of well barcodes, 8nt of UMIs and 1 nt ignore)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts tables and metadata files (including FACS output)

growth_protocol: Serum+Lif (D1,D3,D8,D10). N2B27 + Lif (D18, ESC_N2B27Lif, Gastruloid_AgW, ESC_AgW, Gastruloid_F2, Gastruloid_F5, ELS_M7)

extract_protocol:
Cells were sorted into 384-well cell capture plates using a BD FACSAria III Cell Sorter (BD Biosciences) to collect live cells and sort only singlets. Plates were snap frozen on dry ice and stored at -80°C until further processing. All single cell libraries were prepared with the same conditions and reagents using the MARS-seq protocol as previously described (Jaitin et al, Science, 2014).
All single cell libraries were prepared with the same conditions and reagents using the MARS-seq protocol as previously described (Jaitin et al, Science, 2014). Briefly, a Bravo Automated Liquid Handling Platform (Agilent) was used to reverse transcribe (Invitrogen #18080085) mRNA into cDNA with an oligonucleotide containing both the unique molecule identifiers (UMIs) and cell barcodes. Unused oligonucleotides were removed by Exonuclease I (New England Biolabs #M0293S) treatment. cDNAs were pooled (each pool containing half of a 384-well plate) for second strand synthesis (New England Biolabs #E6111S) and in vitro transcription amplification (New England Biolabs #E2040S). DNA template was removed (Invitrogen #AM2238) before fragmenting (Invitrogen #AM8740) and ligating (New England Biolabs #M0204S) resulting RNA to an oligo containing the pool barcode and Illumina sequences. Finally, RNA was reverse transcribed (Agilent Technologies #600107) and libraries were amplified (Roche #7958935001). Libraries were quantified with a Qubit 2.0 (Invitrogen) and their size distribution was determined by a 4200 TapeStation System (Agilent Technologies). Finally, libraries were pooled at equimolar concentration and sequenced on an Illumina NextSeq500, in 8 sequencing runs, using high-output 75 cycles v2.5 kits (Illumina #20024906).
ScRNA-seq (MARS-seq)

value: ES cell


title: run8_ELS_M7_iX23

description:
counts_run8.csv.gz
meta_run8.csv


title: ChIP-D3-rep2-H3K9me3


title: xrn1-H41A SPAAC seq 1


title: xrn1-H41A DSPAAC Seq 3

value: DSPAAC


title: run8_ELS_M7_iX21

description:
counts_run8.csv.gz
meta_run8.csv


title: xrn1-H41A DSPAAC Seq 2


title: xrn1-H41A DSPAAC Seq 1


title: ChIP-D1-rep2-H3K9me3


title: xrn1-H41A Regular RNA Seq 3


title: ChIP-D10-rep2-H3K27me3

value: H3K27me3 (Millipore #07-449)


title: xrn1-H41A Regular RNA Seq 2


title: run8_ELS_M7_iX19

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX24

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX20

description:
counts_run8.csv.gz
meta_run8.csv


title: xrn1-H41A Regular RNA Seq 1


title: WT-SPAAC Seq 3

value: WT


title: ChIP-D3-rep2-H3K27me3

value: ES cells


title: ChIP-D8-rep2-H3K27me3

value: Serum+Lif


title: run8_ELS_M7_iX18

description:
counts_run8.csv.gz
meta_run8.csv

value: control


title: Negative Ctrl-DSPAAC Seq for WT


title: ChIP-D1-rep2-H3K27me3


title: WT-SPAAC Seq 2


title: WT-SPAAC Seq 1


title: WT-DSPAAC Seq 2


title: ChIP-D10-rep2-H3K4me3

value: H3K4me3 (Active Motif #39159)


title: run8_ELS_M7_iX08

description:
counts_run8.csv.gz
meta_run8.csv


title: Negative Ctrl-DSPAAC Seq for xrn1-H41A


title: WT-DSPAAC Seq 1


title: ChIP-D8-rep2-H3K4me3


title: WT Regular RNA Seq 2


title: WT Regular RNA Seq 1


title: ChIP-D3-rep2-H3K4me3


title: WT Regular RNA Seq 3


title: run8_ELS_M7_iX05

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX04

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX17

description:
counts_run8.csv.gz
meta_run8.csv


title: WT-DSPAAC Seq 3


title: ChIP-D1-rep2-H3K4me3


title: run8_ELS_M7_iX06

description:
counts_run8.csv.gz
meta_run8.csv


title: ChIP-D3-rep1-inputHistone


title: run8_ELS_M7_iX02

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX07

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX01

description:
counts_run8.csv.gz
meta_run8.csv


title: run8_ELS_M7_iX03

description:
counts_run8.csv.gz
meta_run8.csv


title: ChIP-D8-rep1-inputHistone


title: ChIP-D1-rep1-inputHistone


title: ChIP-D10-rep1-H3K9me3


title: run7_Gastruloid_F5_iX32

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_Gastruloid_F5_iX31

description:
counts_run7.csv.gz
meta_run7.csv


title: Sperm from cauda Dex sample, biological rep 6

type: RNA

city: Toronto

first: Christopher

last: Casciaro

state: ON

address: 1 King's College Circle

department: Department of Physiology

country: Canada

institute: University of Toronto

description: miRNA levels in sperm

hyb_protocol: 16 hours at 48C

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with the Affymetrix Transcriptome Analysis Console 4.0.1(TAC) software using RMA+DMG and removing batch effects. Differential analysis was conducted between control and Dex groups for both caput and cauda microarrays and calculated using one-way ANOVA with Benjamini-Hochberg Step-UP FDR correction

label: Biotin

organism: Cavia porcellus

source_name: Cauda sperm

label_protocol: 800ng of total RNA was used. Samples were labelled with FlashTag Biotin according to the manufacturer’s instructions

growth_protocol: 12-week-old adult male Dunkin-Hartley guinea pigs were singly housed on a 12-hour light-dark cycle. Food and water were available ad libitum.

extract_protocol: Total RNA was extracted from caput and cauda sperm using Trizol, according to the manufacturer’s recommendations, with some modifications.  RNA was extracted from a total of 24 sperm samples. (Caput control n=6, Caput Dex n=6, Cauda control n=6, Cauda Dex n=6)

treatment_protocol: Control guinea pigs (n=6) were given untreated water. Guinea pigs in the Dex group (n=6) were given the sGC Dexamethasone 21-phospate disodium salt in their drinking water every other day for 48 days. Weight and water measurements were taken so that Dex-treated animals would receive  ~3mg/kg Dex in the drinking water. Sperm was isolated from the caput and cauda section of the epididymis following euthanasia.

value: Cauda sperm

tag: Sex

value: male

value: Dex water


title: Sperm from cauda Dex sample, biological rep 4

description: miRNA levels in sperm


title: ChIP-D8-rep1-H3K9me3


title: Sperm from cauda Dex sample, biological rep 5

description: miRNA levels in sperm


title: Sperm from cauda Dex sample, biological rep 2

description: miRNA levels in sperm


title: run7_Gastruloid_F5_iX30

description:
counts_run7.csv.gz
meta_run7.csv


title: ChIP-D3-rep1-H3K9me3


title: Sperm from cauda Dex sample, biological rep 1

description: miRNA levels in sperm


title: ChIP-D1-rep1-H3K9me3


title: ChIP-D10-rep1-inputHistone


title: Sperm from cauda control sample, biological rep 5

description: miRNA levels in sperm

value: control water


title: run7_Gastruloid_F5_iX29

description:
counts_run7.csv.gz
meta_run7.csv


title: ChIP-D10-rep1-H3K27me3


title: Sperm from cauda control sample, biological rep 3

description: miRNA levels in sperm


title: Sperm from cauda Dex sample, biological rep 3

description: miRNA levels in sperm


title: Sperm from cauda control sample, biological rep 6

description: miRNA levels in sperm


title: run7_Gastruloid_F5_iX27

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_Gastruloid_F5_iX28

description:
counts_run7.csv.gz
meta_run7.csv


title: ChIP-D8-rep1-H3K27me3


title: ChIP-D3-rep1-H3K27me3


title: run7_Gastruloid_F5_iX26

description:
counts_run7.csv.gz
meta_run7.csv


title: Sperm from cauda control sample, biological rep 4

description: miRNA levels in sperm


title: Sperm from cauda control sample, biological rep 2

description: miRNA levels in sperm


title: run7_Gastruloid_F5_iX25

description:
counts_run7.csv.gz
meta_run7.csv


title: Sperm from caput Dex sample, biological rep 2

description: miRNA levels in sperm

source_name: Caput sperm

value: Caput sperm


title: Sperm from caput Dex sample, biological rep 6

description: miRNA levels in sperm


title: Sperm from caput Dex sample, biological rep 3

description: miRNA levels in sperm


title: ChIP-D1-rep1-H3K27me3


title: Sperm from cauda control sample, biological rep 1

description: miRNA levels in sperm


title: ChIP-D10-rep1-H3K4me3


title: Sperm from caput Dex sample, biological rep 1

description: miRNA levels in sperm


title: Sperm from caput control sample, biological rep 6

description: miRNA levels in sperm


title: Sperm from caput control sample, biological rep 1

description: miRNA levels in sperm


title: Sperm from caput Dex sample, biological rep 5

description: miRNA levels in sperm


title: Sperm from caput control sample, biological rep 3

description: miRNA levels in sperm


title: Sperm from caput Dex sample, biological rep 4

description: miRNA levels in sperm


title: Sperm from caput control sample, biological rep 5

description: miRNA levels in sperm


title: ChIP-D8-rep1-H3K4me3


title: run7_Gastruloid_F5_iX22

description:
counts_run7.csv.gz
meta_run7.csv


title: Sperm from caput control sample, biological rep 4

description: miRNA levels in sperm


title: run7_Gastruloid_F5_iX20

description:
counts_run7.csv.gz
meta_run7.csv


title: ChIP-D3-rep1-H3K4me3


title: run7_Gastruloid_F5_iX19

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_Gastruloid_F5_iX24

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6high_Stim_D9_A3272

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: cRNA samples were hybridized to an Illumina HumanWG-6_V3_0_R3_11282955  BeadChip array for 14-20 hour at 580C in an Illumina Hybridization Oven (Illumina Inc.).

scan_protocol: Arrays were washed and scanned following the protocols in the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (Illumina).

data_processing: Signal data were extracted from the image files with the Gene Expression module of the GenomeStudio software (Illumina, Inc.)

organism: unidentified

source_name: Healthy Donor PBMC

label_protocol: 500 ng of total RNA was used to make cDNA and label cRNA using the Ambion Illumina TotalPrep RNA Amplification kit (Invitrogen).

growth_protocol: FACS-sorted naïve, CCR6neg, CCR6low, CCR6int and CCR6high subsets of CD4+ T cells were used for isolating RNA

extract_protocol: using RNeasy Mini Kit (Qiagen)

treatment_protocol: without and with prior activation with 20 ng/ml PMA and 1 mM ionomycin for 3 h at 37oC under 5% CO2

value: Healthy

value: PBMC

tag: biosample

tag: donor

tag: pma treatment

value: Stim

tag: t-cell subset


title: ChIP-D1-rep1-H3K4me3


title: run7_Gastruloid_F5_iX18

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_Gastruloid_F5_iX17

description:
counts_run7.csv.gz
meta_run7.csv


title: D10-rep2 (RNA-Seq)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
For RNA-seq paired-end reads were mapped applying the 2-pass mapping mode of STAR v2.5.0a; best unique matches of concordant pairs were kept.
Mapped pairs were deduplicated with the Picar toolkit v1.94 and reads summarized over annotations with the featureCounts function of the Rsubread R package v1.26.0.
Genome_build: mm10
Supplementary_files_format_and_content: tabular file of raw counts for each libraries

extract_protocol:
RNA was harvested using Trizol reagent.
Total RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.


title: D8-rep2 (RNA-Seq)


title: run7_Gastruloid_F5_iX16

description:
counts_run7.csv.gz
meta_run7.csv


title: D3-rep2 (RNA-Seq)


title: CCR6neg_Stim_D9_A3268


title: CCR6low_Stim_D8_A3263


title: naive_Stim_D9_A3266

value: naive


title: run7_Gastruloid_F5_iX15

description:
counts_run7.csv.gz
meta_run7.csv

value: ES cell


title: ROpos_Stim_D9_A3267

description: not used in final analysis

value: ROpos


title: CCR6plus_Stim_D8_A3262


title: ROpos_NoStim_D9_A3232

description: not used in final analysis

value: NoStim


title: naive_NoStim_D9_A3231


title: CCR6int_Stim_D8_A3264


title: D1-rep2 (RNA-Seq)


title: CCR6plus_Stim_D9_A3269


title: run7_Gastruloid_F2_iX14

description:
counts_run7.csv.gz
meta_run7.csv


title: D10-rep1 (RNA-Seq)


title: CCR6low_Stim_D9_A3270


title: run7_Gastruloid_F2_iX13

description:
counts_run7.csv.gz
meta_run7.csv


title: D8-rep1 (RNA-Seq)


title: CCR6high_NoStim_D9_A3237


title: run7_Gastruloid_F2_iX12

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_Gastruloid_F2_iX11

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6int_NoStim_D9_A3236


title: CCR6high_NoStim_D10_A3230


title: CCR6plus_NoStim_D9_A3234


title: CCR6neg_NoStim_D9_A3233


title: CCR6plus_NoStim_D10_A3227


title: CCR6low_NoStim_D9_A3235


title: D1-rep1 (RNA-Seq)


title: CCR6low_NoStim_D10_A3228


title: CCR6int_NoStim_D10_A3229


title: run7_Gastruloid_F2_iX10

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6neg_NoStim_D10_A3226


title: mC-D10-rep3

data_processing:
Bisulfite libraries were processed with the Bismark pipeline1 using bowtie2 aligner2 with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tabular file (chrom, start, strand, reads methyl, reads unmethyl)

extract_protocol:
DNA was purified using the Quick-DNA Midiprep plus kit from Zymo Research (#D4075)
The library construction was performed using the NEBNext Enzymatic Methyl-seq kit from New England Biolabs (#E7120S).


title: run7_Gastruloid_F2_iX09

description:
counts_run7.csv.gz
meta_run7.csv


title: ROpos_NoStim_D10_A3225

description: not used in final analysis


title: naive_NoStim_D10_A3224


title: D3-rep1 (RNA-Seq)


title: CCR6low_NoStim_D6_A3221


title: CCR6high_NoStim_D6_A3223


title: mC-D8-rep3


title: mC-2i-rep3


title: CCR6plus_NoStim_D6_A3220


title: mC-D1-rep3


title: naive_NoStim_D6_A3217


title: mC-D3-rep3


title: CCR6int_NoStim_D6_A3222


title: run7_empty_iX21

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_empty_iX23

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_D18_iX08

description:
counts_run7.csv.gz
meta_run7.csv


title: run7_empty_iX06

description:
counts_run7.csv.gz
meta_run7.csv


title: mC-2i-rep2


title: run7_D18_iX07

description:
counts_run7.csv.gz
meta_run7.csv


title: mC-D10-rep2


title: CCR6neg_Stim_D8_A3261


title: ROpos_NoStim_D6_A3218

description: not used in final analysis


title: CCR6neg_NoStim_D6_A3219


title: run7_D18_iX05

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6high_NoStim_D3_A3216


title: naive_Stim_D8_A3259


title: mC-D8-rep2


title: mC-D3-rep2


title: CCR6int_Stim_D6_A3257


title: run7_D18_iX03

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6high_Stim_D6_A3258


title: mC-D1-rep2


title: CCR6high_Stim_D5_A3251


title: mC-2i-rep1


title: CCR6neg_Stim_D6_A3254


title: mC-D10-rep1


title: CCR6plus_Stim_D6_A3255


title: run7_D18_iX02

description:
counts_run7.csv.gz
meta_run7.csv


title: naive_Stim_D6_A3252


title: ROpos_Stim_D6_A3253

description: not used in final analysis


title: run7_D18_iX01

description:
counts_run7.csv.gz
meta_run7.csv


title: CCR6plus_Stim_D5_A3248


title: mC-D8-rep1


title: mC-D3-rep1


title: ROpos_Stim_D8_A3260

description: not used in final analysis


title: CCR6int_Stim_D5_A3250


title: run6_Gastruloids_iX31

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6low_Stim_D5_A3249


title: Sperm from caput control sample, biological rep 2

description: miRNA levels in sperm


title: CCR6low_Stim_D6_A3256


title: run6_Gastruloids_iX32

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6high_Stim_D4_A3244


title: run6_Gastruloids_iX30

description:
counts_run6.csv.gz
meta_run6.csv


title: ROpos_Stim_D5_A3246

description: not used in final analysis


title: mC-D1-rep1


title: CCR6neg_Stim_D5_A3247


title: CCR6plus_Stim_D4_A3241


title: run6_Gastruloids_iX29

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6int_Stim_D4_A3243


title: naive_Stim_D5_A3245


title: CCR6neg_Stim_D4_A3240


title: Sample 8_AU1038_STRSS4

city: León

first: Vanesa

last: Robles

state: León

address: Facultad de Ciencias Biológicas y Ambientales. Campus de Vegazana. Área de Biología Celular

department: Molecular Biology

institute: Universidad de León

data_processing:
Mapped with STAR/2.7.8a
Quantified with RSEM/1.3.0 using release 104 of ensembl.
Assembly: GRCz11
Supplementary files format and content: TSV
Supplementary files format and content: Raw counts

organism: Danio rerio

source_name: Larva

extract_protocol:
RNA was harvested using with Qiazol; a miRNeasy tissue kit (Qiagen). Only samples meeting the requirements (3 µg of RNA; RNA integrity number (RIN) > 8) were used in RNA-seq analysis.
KAPA RNA Hyperprep with RiboErase for FFPE samples

value: Larva

value: WT

value: Paternal Chronic Stressed (21 days)


title: CCR6low_Stim_D4_A3242


title: run6_Gastruloids_iX28

description:
counts_run6.csv.gz
meta_run6.csv

value: control


title: run6_Gastruloids_iX27

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 6_AU1036_STRSS2


title: run6_Gastruloids_iX26

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 5_AU1035_STRSS1


title: Sample 7_AU1037_STRSS3


title: run6_Gastruloids_iX25

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 4_AU1028_CTRL4

value: Control


title: naive_Stim_D4_A3238


title: ROpos_Stim_D4_A3239

description: not used in final analysis


title: CCR6neg_Stim_D7_A3115


title: CCR6plus_Stim_D7_A3116


title: naive_Stim_D7_A3113


title: Sample 3_AU1027_CTRL3


title: CCR6int_Stim_D7_A3118


title: CCR6low_Stim_D7_A3117


title: CCR6high_Stim_D3_A3112


title: run6_Gastruloid_F5_iX23

description:
counts_run6.csv.gz
meta_run6.csv


title: ROpos_Stim_D7_A3114

description: not used in final analysis


title: Sample 1_AU1024_CTRL1


title: CCR6int_Stim_D3_A3111


title: CCR6low_NoStim_D3_A3214


title: run6_Gastruloid_F5_iX22

description:
counts_run6.csv.gz
meta_run6.csv


title: run6_Gastruloid_F5_iX21

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 2_AU1026_CTRL2


title: run6_Gastruloid_F5_iX24

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6plus_NoStim_D3_A3213


title: CCR6int_NoStim_D3_A3215


title: CCR6neg_NoStim_D3_A3212


title: run6_Gastruloid_F5_iX20

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6low_Stim_D3_A3110


title: CCR6neg_Stim_D3_A3108


title: ROpos_NoStim_D3_A3211

description: not used in final analysis


title: CCR6plus_Stim_D3_A3109


title: Sample 5_AU1011_STRSS1

data_processing:
Alignment using STAR 2.7.8a using ENCODE parameters
Quantification using RSEM 1.3.0
Quantification with annotation Ensembl release 104
Assembly: GRCz11
Supplementary files format and content: TSV file with raw counts

source_name: Testicle

extract_protocol: RNA was harvested using with Qiazol; a miRNeasy tissue kit (Qiagen). Only samples meeting the requirements (3 µg of RNA; RNA integrity number (RIN) > 8) were used in RNA-seq analysis.

value: Testicle

value: Chronically Stressed (21 days)


title: run6_Gastruloid_F5_iX19

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 7_AU1015_STRSS3


title: Sample 6_AU1012_STRSS2


title: run6_Gastruloid_F5_iX17

description:
counts_run6.csv.gz
meta_run6.csv


title: Sample 4_AU1009_CTRL4


title: Sample 3_AU1008_CTRL3


title: Sample 2_AU1007_CTRL2


title: CCR6high_DC_A6452

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450_15017482_v.1.2 using standard Illumina protocol

scan_protocol: Illumina HiSeq using standard protoocol

data_processing:
Genome Studio 2011.1
Average Beta (normalized using Genome Studio 2011.1)

label: biotin

label_protocol: Bisulfite conversion of genomic DNA (500 ng) was performed using the Zymo Research EZ DNA Methylation kit (Zymo Research) according to the manufacturer’s recommendations for the Illumina Infinium assay. The bisulfite conversion incubation was processed using alternative thermocycler settings as outlined in the “Alternative Incubation Conditions When Using the Illumina Infinium® Methylation” section of the Zymo instruction manual appendix.

growth_protocol: CD4+ T cells were isolated from elutriated lymphocytes by negative selection using RosetteSep CD4+ T cell enrichment cocktail (StemCell Technologies) followed by Ficoll/Hypaque (Amersham Biosciences) density centrifugation according to the protocol from StemCell Technologies. If necessary, red blood cells were removed using Pharm Lyse (BD Biosciences) according to the manufacturer’s protocol. For staining cells were suspended in 250 μl of Hanks Balanced Salt Solution (HBSS, Mediatech) containing 4% fetal bovine serum (FBS, GeminiBio) and incubated with following antibodies: anti-CD4, anti-CD45RO, and anti-CCR6 for 30 min at room temperature. In some experiments, in addition to these antibodies, cells were incubated with anti-CD25 and anti-CD62L, anti-CXCR5, anti-CXCR3 and anti-CCR4 antibodies. All antibodies were against human antigens. Cells were washed and resuspended in HBSS plus 4% FBS. CD4+ T cells were sorted into CD45RO- (naïve), and CD45RO+ subsets, and the CD45RO+ subset was further separated into CCR6neg, CCR6pos, and, within the CCR6pos cells, into CCR6low, CCR6int and CCR6high subsets. For in vitro polarization experiments, cells were sorted into naïve (CD4+CD45RO-CD25-CXCR5-CCR4-CXCR3-), CCR6neg (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6- or CD4+CD45RO+CD25-CXCR5- CCR4-CCR6- or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6-), CCR6low (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6low or CD4+CD45RO+CD25-CXCR5-CCR4-CCR6low or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6low), and CCR6high (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6high or CD4+CD45RO+CD25-CXCR5-CCR4-CCR6high or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6high). All cell sorting was done using a FACSAria Cell Sorter (BD Biosciences).  By post-sort analysis, the purity of populations was 95-99%. Cells were used for experiments immediately after sorting.

extract_protocol: DNeasy kit (Qiagen).

treatment_protocol: DNA isolated immediately after sorting

tag: cell culture


title: run6_Gastruloid_F2_iX16

description:
counts_run6.csv.gz
meta_run6.csv

tag: cell line


title: ROpos_Stim_D3_A3107

description: not used in final analysis

tag: cell type


title: CCR6high_Stim_D2_A2880


title: run6_Gastruloid_F5_iX18

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6int_DD_A6457


title: run6_Gastruloid_F2_iX15

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6int_DC_A6451


title: CCR6plus_Stim_D2_A2877


title: CCR6low_Stim_D2_A2878


title: ROpos_Stim_D2_A2875

description: not used in final analysis


title: CCR6neg_Stim_D2_A2876


title: CCR6int_Stim_D2_A2879


title: naive_Stim_D2_A2874


title: naive_Stim_D3_A3106


title: CCR6low_DD_A6456


title: CCR6neg_DC_A6449


title: CCR6neg_DD_A6455


title: Sample 1_AU1006_CTRL1

tag: tissue


title: CCR6high_DD_A6458

tag: disease state


title: run6_Gastruloid_F2_iX14

description:
counts_run6.csv.gz
meta_run6.csv


title: run7_D18_iX04

description:
counts_run7.csv.gz
meta_run7.csv


title: ROpos_DC_A6448

description: not used in final analysis


title: dyrk1a_WT2

city: New Haven

first: Hellen

last: Weinschutz Mendes

state: Connecticut

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

data_processing:
DESeq2 (v 1.22.1)
Low quality reads were trimmed and adaptor contamination was removed using Trim Galore (v0.5.0, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed reads were mapped to the Danio rerio reference genome (GRCz11) using HISAT2 (v2.1.0) (Kim et al., 2019)
Gene expression levels were quantified using StringTie (v1.3.3b) (Pertea et al., 2015) with gene models (release 103) from the Ensembl
Differentially expressed genes (adjusted p value < 0.05, fold change cutoff = 2) were identified using DESeq2 (v 1.22.1) (Love et al., 2014)
Assembly: GRCz11
Supplementary files format and content: tab-delimited CSV files include read values for each Sample

source_name: Whole-Brain

extract_protocol:
Total RNA was extracted from isolated larval heads with the eyes removed (1 head per sample) using the RNeasy Micro Kit (Qiagen) or the Invitrogen RecoverAll  RNA Isolation Kit (Invitrogen). To control for background variation, RNA was extracted from sibling- or cousin-matched larvae from heterozygous incrosses of scn1labΔ44/+, chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish
RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit (Cat# E6420L)
Sequencing was done at 25 million reads/sample using NovaSeq 6000 (Illumina) (Yale Center for Genome Analysis)

value: Whole-Brain

value: whole-brain cells

tag: genotype

value: Wild-type


title: ROpos_DD_A6454

description: not used in final analysis

value: Healthy


title: dyrk1a_WT4


title: Naive_DD_A6453

value: PBMC

value: Naive


title: run6_Gastruloid_F2_iX12

description:
counts_run6.csv.gz
meta_run6.csv

tag: treatment


title: Naive_DC_A6447


title: run6_Gastruloid_F2_iX13

description:
counts_run6.csv.gz
meta_run6.csv


title: run6_Gastruloid_F2_iX11

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6high_DB_A6394


title: dyrk1a_WT1


title: CCR6int_DB_A6393


title: CCR6high_DA_A6388


title: dyrk1a_HET4

value: Heterozygous


title: run6_Gastruloid_F2_iX10

description:
counts_run6.csv.gz
meta_run6.csv

value: ES cell


title: CCR6int_DA_A6387


title: run6_empty_iX09

description:
counts_run6.csv.gz
meta_run6.csv


title: dyrk1a_HET3


title: CCR6low_DB_A6392


title: dyrk1a_HET2


title: CCR6low_DA_A6386


title: run6_empty_iX07

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6neg_DA_A6385


title: ROpos_DB_A6390

description: not used in final analysis

value: ROpos


title: CCR6neg_DB_A6391


title: run6_empty_iX05

description:
counts_run6.csv.gz
meta_run6.csv


title: dyrk1a_HOM5

value: Homozygous


title: Naive_DB_A6389


title: Naive_DA_A6383


title: ROpos_DA_A6384

description: not used in final analysis


title: run6_D18_iX08

description:
counts_run6.csv.gz
meta_run6.csv


title: dyrk1a_HOM2


title: run6_D18_iX06

description:
counts_run6.csv.gz
meta_run6.csv


title: CCR6low_DC_A6450


title: run6_D18_iX04

description:
counts_run6.csv.gz
meta_run6.csv


title: run6_D18_iX03

description:
counts_run6.csv.gz
meta_run6.csv


title: scn1lab_WT2


title: WT, rep3

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

state: WA

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

country: Australia

institute: The Kids Research Institute

description:
WT_3
small RNA

data_processing:
TrimGalore v0.6.544 using cutadapt v1.1845 was used in paired in mode to remove Illumina adapter sequences.
Trimmed reads were pre-aligned to the mouse reference non-coding transcripts obtained from GENCODE (gencode.vM29.ncRNA_transcripts.fa) with bowtie2 v2.4.5 using default parameters to remove non-coding transcripts.
The remaining transcripts were mapped to the mouse reference genome obtained from Ensembl (Mus_musculus.GRCm39.dna_sm.primary_assembly.fa, Mus_musculus.GRCm39.106.gff3) using STAR v2.7.8a46 (--alignEndsType Extend5pOfRead1 –outFilterMatchNminOverLread 0.9 –outFilterMunltimapNmax 3 –alignIntronMax 2500).
Aligned reads were analysed for ribosome footprints using fivepseq v1.0.059 with the same mouse reference gff3 file used for alignment and using cumulative scores for control vs. knockout comparisons that generated KO and WT codon pauses files.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include codon pauses.
Library strategy: Ribo-Seq

source_name: mouse brain

extract_protocol:
RNA was isolated from mouse brain homogenates.
Sequencing was performed using the Illumina NovaSeq platform, according to the Illumina small RNA-Seq protocol.

value: brain


title: KO, rep3

description:
KO_3
small RNA


title: E15_Heart_MATR3_CharmeKO_IgG

city: Rome

first: Monica

last: Ballarino

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description: Matr3 CLIP-seq in condition of CharmeKO

data_processing:
Reads were trimmed for adaptor sequence/low-quality sequence using a combination of Trimmatic and Cutadapt software (see methods for further details).
Trimmed reads were mapped to mm10 using STAR aligner (2.7.7a)
PCR duplicates were removed using MarkDuplicates tool included in the Picard suite version 2.24.1
Peaks were called using Piranha version 1.2.1 with parameters –x -s –u 0. See Methods for a complete description of peaks processing steps.
bigWig files were generated using the bamCoverage function from deepTools. Score represents the normalized reads coverage at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: Heart

extract_protocol: CLIP-seq libraries were prepared accordiing to Trio RNA-Seq protocol (Tecan Genomics, Redwood City, CA)

treatment_protocol: Embryonic hearts were pestled 2 min in PBST. The homogenate was then filtered in 70 μm strainer to purify the cardiac cells. Cells were UV-crosslinked at 4,000 mJ

tag: strain

value: Heart

tag: clip antibody

value: Rabbit IgG (Immunoreagents Inc. Rb-003-N)


title: WT, rep2

description:
WT_2
small RNA


title: KO, rep1

description:
KO_1
small RNA


title: dyrk1a_HOM3


title: run6_D18_iX02

description:
counts_run6.csv.gz
meta_run6.csv

value: control


title: scn1lab_WT1


title: E15_Heart_MATR3_CharmeKO2

description: Matr3 CLIP-seq in condition of CharmeKO

value: MATR3 (Bethyl cat#A300-591A)


title: scn1lab_WT3


title: dyrk1a_HOM1


title: KO, rep2

description:
KO_2
small RNA


title: run5_Gastruloid_AgW_iX24

description:
counts_run5.csv.gz
meta_run5.csv


title: E15_Heart_CharmeKO_INP

description: Matr3 CLIP-seq in condition of CharmeKO


title: run5_Gastruloid_AgW_iX23

description:
counts_run5.csv.gz
meta_run5.csv


title: CCR6high_Stim_D7_A3119

value: Stim


title: scn1lab_HET1


title: TM7 CYP male

city: Ljubljana

first: Dominika

last: Peskar

address: Vrazov trg 2

department: Institute for Cell Biology

country: Slovenia

institute: Faculty of Medicine

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including Hisat2, FeatureCounts and Novogene's wrapped scripts.
High quality reads were aligned to mouse (Ensembl GRCm39) reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. The fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of five groups (CYP animals vs Ctrl animals, Ctrl males vs Ctrl females, CYP males vs CYP females, CYP males vs Ctrl females, CYP females vs Ctrl females; three animals per group) was performed using DESeq2 R package (1.20.0). P value was calculated using the negative binomial distribution and the resulting p values were adjusted using the Benjamini-Hochberg’s approach for controlling the false discovery rate.
The clusterProfiler (v. 3.8.1) software was used for enrichment analysis of differentially expressed genes, including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome database
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample, comparing CYP vs Ctrl mice (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample, comparing CYP vs Ctrl males (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample, comparing CYP vs Ctrl females (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample, comparing Ctrl males vs Ctrl females (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample, comparing CYP males vs CYP females (gene_count.txt)

source_name: urinary bladder

extract_protocol:
RNA was extracted using QIAzol Lysis Reagent and RNeasy Plus Universal Mini Kit (both Qiagen, Hilden, Germany) according to the manufacturer’s protocols. Library preparation was performed by Novogene Co., Ltd, using at least 0.5 ug high-quality total RNA input per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: Mice were treated with 80 mg/kg CYP dissolved in sterile NaCl intraperitoneally, every other day for 8 days (day 0, 2, 4, 6). Control animals were treated with corresponding volumes of sterile NaCl.

value: urinary bladder

value: male

value: CYP (80 mg/kg), 4 applications


title: run6_D18_iX01

description:
counts_run6.csv.gz
meta_run6.csv


title: E15_Heart_MATR3_CharmeKO1

description: Matr3 CLIP-seq in condition of CharmeKO


title: TF6 CYP female

value: female


title: run5_Gastruloid_AgW_iX20

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX18

description:
counts_run5.csv.gz
meta_run5.csv


title: scn1lab_HET2

value: Whole-Brain

value: whole-brain cells


title: run5_Gastruloid_AgW_iX19

description:
counts_run5.csv.gz
meta_run5.csv


title: WT, rep1

description:
WT_1
small RNA


title: TM11 CYP male


title: TF9 CYP female


title: TF15 CYP female


title: run5_Gastruloid_AgW_iX17

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX21

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX22

description:
counts_run5.csv.gz
meta_run5.csv


title: scn1lab_HET3


title: TM5 CYP male


title: scn1lab_HOM1


title: LPS Day 6 resident IM replicate 1

city: Denver

first: William

last: Janssen

state: CO

address: 1400 Jackson St

institute: National Jewish Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped, tab-separated values files and matrix files

source_name: lung

extract_protocol:
Mice were euthanized and anti-CD45 antibody was instilled into the trachea. After 4 minutes, anti-CD45 solution was aspirated and bronchoalveolar lavage (BAL) was performed. Lungs were perfused by injecting 10 mL of PBS through the right ventricle during which lungs visibly blanched. Lung tissue was finely chopped with a razor blade and then incubated at 37C in 1 mL of 0.4 mg/mL Liberase TM for 25 min. Following incubation, tissue was pipetted rapidly up and down to further disaggregate, then filtered through 100 μm filters. Lung cells were pelleted and resuspended in then filter through 70 μm filters then resuspended HBSS containing 0.3% BSA and 0.3 mM EDTA. Cells were sorted using FACS into 3 bins: 1) CD45+ cells (live, CD45+), 2) resident IMs (live, CD45+, CD64+, CD88+, IT CD45-, tdT+), or 3) recruited IM (live, CD45+, CD64+, CD88+, IT CD45-, tdT-). Cells were manually counted using a hemocytometer and resuspended at 1x 10^6 cells/ml in 0.06% BSA in PBS solution.
Library was contructed according to manufacturer's instructions. Single cells were captured using a Chromium Box (10x Genomics, Pleasanton, CA, USA). Libraries were sequenced using the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA).  Sequencing was targeted to 5,000 cells in the CD45+ library, 3,000 cells in each of the IM sorts with sequencing depth of 100,000 reads per cell.

treatment_protocol:
Intraperitoneal Tampoxifen (0.25 mg/g) every 3 days for 1 week at age 10-12 weeks, 4 weeks prior to:
Intratracheal E. coli O111:B4 LPS (20 μg)

value: CX3CR1-ERT2 x R26-stopfl/fl-TdTomato (C57BL6/J background)

value: lung

tag: flow sorting

value: IMres

tag: days after_lps


title: LPS Day 6 resident IM replicate 3

description: 10x Genomics


title: CM4 Ctrl male


title: CM12 Ctrl male


title: CF3 Ctrl female


title: scn1lab_HOM3


title: LPS Day 6 resident IM replicate 2

description: 10x Genomics


title: CM8 Ctrl male


title: CF1 Ctrl female


title: polyA siMatrin3 rep2

data_processing:
RTA 1.18.64 software used for basecalling.
Sequenced reads were trimmed for low-quality bases using Cutadapt, then mapped to hg19 genome using STAR 2.5.1
Gene expression was quantified using RSEM
Assembly: hg19
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep

value: Colorectal cancer cell line

value: 72 hours + 48 hours siMatrin3


title: polyA siMatrin3 rep3


title: polyA siMatrin3 rep1


title: LPS Day 6 recruited IM replicate 3

description: 10x Genomics

value: IMrec


title: scn1lab_HOM2

value: Homozygous


title: CF10 Ctrl female


title: polyA siCTRL rep3

value: 72 hours + 48 hours siCTRL


title: LPS Day 6 recruited IM replicate 1

description: 10x Genomics


title: polyA siCTRL rep2


title: LPS Day 6 recruited IM replicate 2

description: 10x Genomics


title: LPS Day 6 CD45+ replicate 3

description: 10x Genomics


title: run5_Gastruloid_AgW_iX14

description:
counts_run5.csv.gz
meta_run5.csv

value: control

value: ES cell


title: LPS Day 6 CD45+ replicate 2

description: 10x Genomics


title: LPS Day 6 CD45+ replicate 1

description: 10x Genomics


title: LPS Day 3 resident IM replicate 3

description: 10x Genomics


title: LPS Day 3 resident IM replicate 2

description: 10x Genomics


title: run5_Gastruloid_AgW_iX10

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX11

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX12

description:
counts_run5.csv.gz
meta_run5.csv


title: LPS Day 3 recruited IM replicate 4

description: 10x Genomics


title: TBT43

city: Guangzhou

first: Lu

last: Xiao

address: Guangzhou North Avnue

institute: Nanfang Hospital, Southern Medical University

description: processed data file: Processed_data_count.txt

data_processing:
Solexa pipeline version 1.8 was used for base-calling.
Raw sequencing data was pre-processed by cutadapt 1.14, and aligned to hg19 by hisat2 2.0.5.
Reads were aligned to several transcriptome banks using String Tie 1.3.1c. Expression was measured by FPKM (Fragments Per Kilobase of gene/transcript model per Million mapped fragments). Ballgown 2.8.4 was used for differential expression analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed_data_count.txt: Tab-delimited text file contains gene name and FPKM of three samples.

source_name: TEAD4 knockout human embryonic stem cells after trophoblast differentiation

growth_protocol: Wild type hESCs H1 and two clones of TEAD4 knockout hESCs were induced towards trophoblast-like cells under BAP treatment. Cells were seeded with as 1.5×10e4 /cm2 on Matrigel coated plates and collected for analysis on Day9.

extract_protocol:
Total RNA was extracted by using TRIZOL Reagent (Life Technologies) following the manufacturer's instructions.
1~2 μg total RNA were used for establishing sequencing libraries with KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

value: hESCs derived trophoblast-like cells

tag: gene editing

value: TEAD4 knockout clone 1


title: LPS Day 3 recruited IM replicate 3

description: 10x Genomics

tag: Sex

value: male


title: TBH1

source_name: human embryonic stem cells after trophoblast differentiation

value: wild type


title: LPS Day 3 resident IM replicate 1

description: 10x Genomics


title: LPS Day 3 resident IM replicate 4

description: 10x Genomics


title: run5_Gastruloid_AgW_iX09

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_Gastruloid_AgW_iX15

description:
counts_run5.csv.gz
meta_run5.csv


title: polyA siCTRL rep1


title: LPS Day 3 recruited IM replicate 2

description: 10x Genomics


title: LPS Day 3 recruited IM replicate 1

description: 10x Genomics


title: Oogonia_2_MS330_142

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.).
Read counts per genes were calculated using HTseq v0.11.0.
For allelic expression analysis, read data were re-mapped using masked MacFas5.0 reference, as described above.
Mapped BAM files were processed with SNPsplit and masked MacFas5.0 reference to split into paternal and maternal allele
Read counts per genes were calculated using HTseq for both BAM, separately.
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Macaca fascicularis

source_name: Embryonic fibroblasts

extract_protocol:
Total RNA extraction from 5000-20000 cells were carried out using Nucleospin RNA XS extraction kit (Takara, 740902).
cDNA synthesis was performed as described previously (Nakamura et al, 2015). Briefly, 0.2ng/µL of V1(dT)24 sequence was annealed to the 3’ end of the 1ng of total RNA by incubation at 70ºC for 90 seconds. Reverse transcription was performed by adding 133U/µL of SuperScript III (Invitrogen, 1089075) and serial incubation at 50ºC for 5 min and at 70ºC for 10 min. The residual primers were excised by treating with 0.5U/µL of Exonuclease I (Takara, 2650A) at 37ºC for 30 min followed by 80ºC for 25 min. Poly-A was added to the 3’ end of the cDNA by incubating at 37ºC 15 min and 70ºC for 10 min in the presence of 3mM dATPs (GE Healthcare, 28-4065-01) and 0.75U/µL terminal nucleotidyl transferase (TdT, Invitrogen, 10533-065). For cDNA amplification, the cDNA was applied to thermal cycling in the presence of 0.62 µM of V3(dT)24 and V1(dT)24, 0.05U/µL Ex Taq HS (Takara, RR006).

value: Embryonic fibroblasts

value: wildtype


title: TBT45

value: TEAD4 knockout clone 2


title: LPS Day 3 CD45+ replicate 3

description: 10x Genomics

value: CX3CR1-ERT2 x R26-stopfl/fl-TdTomato (C57BL6/J background)


title: run5_ESC_AgW_iX32

description:
counts_run5.csv.gz
meta_run5.csv


title: LPS Day 3 CD45+ replicate 2

description: 10x Genomics

value: lung


title: run5_Gastruloid_AgW_iX13

description:
counts_run5.csv.gz
meta_run5.csv


title: Oogonia_1_MS277_001


title: LPS Day 3 CD45+ replicate 1

description: 10x Genomics


title: run5_ESC_AgW_iX31

description:
counts_run5.csv.gz
meta_run5.csv


title: run5_ESC_AgW_iX30

description:
counts_run5.csv.gz
meta_run5.csv


title: Homeostasis resident IM replicate 2

description: 10x Genomics

value: IMres


title: Homeostasis resident IM replicate 1

description: 10x Genomics


title: run5_ESC_AgW_iX28

description:
counts_run5.csv.gz
meta_run5.csv


title: Homeostasis recruited IM replicate 3

description: 10x Genomics


title: Homeostasis resident IM replicate 3

description: 10x Genomics


title: run5_ESC_AgW_iX27

description:
counts_run5.csv.gz
meta_run5.csv


title: Homeostasis CD45+ replicate 3

description: 10x Genomics


title: Homeostasis CD45+ replicate 1

description: 10x Genomics