title: bulk_RNA_MMRF_2259

description: Raw data obtained from dbGaP Accession: phs000748

data_processing:
Gene expression was estimated from FASTQ using Kallisto v0.43.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Patient BMMC, aspirate, CD138+ sorted,  bulk RNAseq, MMRF cohort

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) for WU cohort 1 samples.
Libraries for WU cohort 1 were uniquely dual-indexed with 10bp fragments and sequenced to a depth of 80 million.

value: Multiple myeloma (MM)

value: BMMC

value: Bone Marrow


title: bulk_RNA_MMRF_2251

status: Public on Jan 17 2023

type: SRA

city: St. Louis

first: Ravi

last: Vij

state: MO

address: 660 S Euclid Ave

department: Oncology

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: diagnosis

tag: cell type

tag: tissue


title: bulk_RNA_MMRF_2168


title: AB6368

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: paired-end (read2 used to read cell and molecule barcodes only)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
M_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Left limb- autopod

growth_protocol: Experiments were performed in the Weizmann Institute of Science

extract_protocol:
Forelimb tissues were disassociated using enzymatic digestion. E10.5-E11.5 forelimbs were digested with pre-heated 0.25% trypsin in DMEM medium (ThermoFisher) and incubated for 10 min at 37°C, gently pipetting every 3 min. E12.5-E14.5 forelimbs were digested with 1.5 mg/ml  collagenase type V (Sigma-Aldrich) in DMEM at 37°C for 10-15 min, gently pipetting every 5 min until the tissue completely dissolved. The digestion reaction was stopped by addition of DMEM supplemented with 10% FBS and 1% Pen-Strep. Cell suspensions were filtered through a 40-µm nylon mesh and collected by centrifugation at 1000 rpm for 7 min at 4°C. Supernatant was removed and cells were resuspended in 500 µl ice-cold MACS buffer (with 0.5% BSA and 2 mM EDTA in PBS) and used immediately for fluorescence-activated cell sorting (FACS).
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Induction of Cre recombinase was performeds by administration of 5 mg/ml tamoxifen in corn oil X5 body weight by oral gavage. For harvesting of embryos, timed-pregnant females were euthanized by cervical dislocation.

tag: strain

tag: organ

value: limb

tag: selection marker

value: tomato-

tag: treatment

tag: mouse id

tag: timepoint

tag: replicate


title: bulk_RNA_MMRF_2038


title: bulk_RNA_MMRF_1967


title: bulk_RNA_MMRF_1941


title: HCT116.DKO12.pLenti.FasL.zero.rep2

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples

source_name: Korean Collection for Type Cultures (KCTC) and edited by Synthego

extract_protocol:
Cell lysates were subjected to pull down with a GW182 FLAG-GST-T6B peptide isolated using anti-FLAG M2 Magnetic beads. RNA was extracted using Trizol followed by an ethanol precipitation.
Small RNA-Seq libraries were generated using illumina TruSeq small RNA adapters. RNA 19-35 nucleotides were size selected by Urea-PAGE gel extraction after each round of adapter ligation. The final library ~156 bp was size selected on an agarose-TBE gel. Final cDNA quality was assessed by Agilent Bioanalyzer and DNA concetration was determined by Qubit.

treatment_protocol: HCT116 cells were spin-infected with pLenti-CD95L wild-type, NP, Zero, SIL, or pLenti empty vector in the presence of 8 ug/ml polybrene. Infected cells were selected with 2 mg/ml puromycin. Cells were flash frozen 100 hours after infection.

tag: cell line

value: HCT116 Drosha CD95 d.k.o. clone #12

tag: treatment/infection

value: Cells were transduced with pLenti -CD95L zero


title: HCT116.DKO12.pLenti.FasL.zero.rep1

description: Single Read


title: AB6367

value: tomato+


title: bulk_RNA_MMRF_1424


title: AB6366

source_name: Left limb-proximal


title: bulk_RNA_MMRF_1413


title: bulk_RNA_MMRF_1325


title: AB6370


title: bulk_RNA_MMRF_1695


title: HCT116.DKO12.pLenti.FasL.NP.rep1

description: Single Read

value: Cells were transduced with pLenti -CD95L NP


title: HCT116.DKO12.pLenti.FasL.NP.rep2

description: Single Read


title: bulk_RNA_MMRF_1686


title: AB6191


title: HCT116.DKO12.pLenti.FasL.WT.rep2

description: Single Read

value: Cells were transduced with pLenti -CD95L wild-type


title: HCT116.DKO12.pLenti.FasL.WT.rep1

description: Single Read


title: bulk_RNA_MMRF_1720


title: AB6369


title: bulk_RNA_MMRF_1641


title: AB6190


title: bulk_RNA_MMRF_1777


title: bulk_RNA_MMRF_1537


title: bulk_RNA_MMRF_1640


title: HCT116.DKO12.pLenti.rep2

description: Single Read

value: Cells were transduced with pLenti empty vector


title: AB6189


title: AB6188


title: bulk_RNA_83942

description: RNA extracted using Qiagen Rneasy Mini Kit

source_name: Patient BMMC, aspirate, unsorted, bulk RNAseq, WU cohort 1


title: HCT116.DicerKO.pLenti.FasL.rep2

description: Single Read

source_name: Korean Collection for Type Cultures

treatment_protocol: HCT116 wt, Drosha k.o., and Dicer k.o. cells were spin-infected with pLenti-CD95L NP or pLenti empty vector in the presence of 8 ug/ml polybrene. Infected cells were selected with 2 mg/ml puromycin. Cells were flash frozen 100 hours after infection.

value: HCT116 Dicer k.o. clone #43


title: AB6365


title: bulk_RNA_MMRF_1505


title: HCT116.DKO12.pLenti.rep1

description: Single Read


title: HCT116.DicerKO.pLenti.FasL.rep1

description: Single Read


title: bulk_RNA_60359_2


title: bulk_RNA_98433


title: AB6186

source_name: embryonic forelimb

value: GFP-tomato+

value: Tamoxifen


title: bulk_RNA_MMRF_1267


title: bulk_RNA_59114_2


title: bulk_RNA_60359_1


title: AB6185

value: GFP+tomato-


title: bulk_RNA_59114_1


title: HCT116.DroshaKO.pLenti.FasL.NP.rep2

description: Single Read

value: HCT116 Drosha k.o. clone #40


title: HCT116.DroshaKO.pLenti.FasL.NP.rep1

description: Single Read


title: bulk_RNA_56203_2


title: AB6184

value: GFP-tomato-


title: AB6183


title: bulk_RNA_47499

value: Multiple myeloma (MM)


title: AB6182


title: bulk_RNA_27522_2

value: BMMC


title: HCT116.Parental.pLenti.FasL.NP.rep2

description: Single Read

value: HCT116 wild-type


title: AB6181

value: limb


title: bulk_RNA_25183

value: Bone Marrow


title: HCT116.Parental.pLenti.FasL.NP.rep1

description: Single Read


title: AB6187

value: GFP+tomato+


title: bulk_RNA_27522_1


title: AB6180

source_name: Right limb-autopod

value: tomato-


title: MCF10A_RNA_seq, time point 6h, TGF-beta1 treated, replication 2

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

data_processing: none provided by the submitter

growth_protocol: MCF10A cells were cultivated in GibcoTM Advanced DMEM/F12 with 5 % (v/v) horse serum, 1 % (v/v) penicillin/streptomycin, 20 ng/ml human EGF, 0.5 μg/ml hydrocortisone, 0.1 μg/ml cholera toxin, and 10 μg/ml insulin at 37 °C and 5 % CO2

extract_protocol:
Total RNA was isolated using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany)
Sequencing libraries were prepared using the TruSeq Stranded RNA Sample Prep Kit (Illumina) and paired-end sequenced (2x100 bp) on an HiSeq 4000 sequencing device (Illumina) at 50 million reads per sample.

treatment_protocol: Cells received recombinant human TGFβ1 (#100-21, PeproTech, Rocky Hill, NJ, USA) at a final concentration of 5 ng/ml, or a corresponding volume of solvent solution containing 0.1 % BSA in PBS. TGFβ1 and solvent were refreshed every 48 h in experiments with extended treatment times.

value: immortalized human mammary epithelial cell line

tag: genotype

value: WT

tag: time

value: 6 hours


title: bulk_RNA_77570


title: AB6179

value: tomato+


title: StemScale_Ly_IWR1_3

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using CLC Genomics Workbench (Qiagen) software.
Supplementary files format and content: csv files include Name, Chromosome, Region, Expression value, TPM, RPKM,,, for each Sample

growth_protocol: Human iPS cells were cultured in adherent or suspension culture conditions

extract_protocol:
RNA was extracted using FastGene RNA Premium Kit (Nippon Genetics) with on-column Dnase I treatment
RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs)
Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina).
RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs)

treatment_protocol: These human iPS cells were treated with LY or IWR1 or not

value: Human induced pluripotent stem cells

value: Suspension in Stemscale+IWR1,LY333531


title: StemScale_Ly_IWR1_2


title: StemScale_Ly_IWR1_1


title: StemScale_3

value: Suspension in Stemscale


title: MCF10A_RNA_seq, time point 24h, TGF-beta1 treated, replication 2

value: 24 hours


title: MCF10A_RNA_seq, time point 12h, TGF-beta1 treated, replication 2

value: 12 hours


title: AB5786

value: GFP+tomato-

value: Tamoxifen


title: IL17B-3

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

country: China

institute: West China Hospital, Sichuan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the mouse genome GRCm38 using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/)  enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Gene expression in each sample

source_name: BMDM

growth_protocol: Bone marrow was extracted from the femur of mice, washed, cells were counted and seeded at the concentration of 1x107 per 10 cm dish in 10 mL of DMEM supplemented with 25 ng/mL murine macrophage colony-stimulating factor (R&D Systems), 10% FBS (Gibco), and 1% penicillin and streptomycin (Gibco). After 3 days, fresh differentiation culture media were added and cells were collected on day 7 for further experiments.

extract_protocol:
Total RNAs were extracted from BMDM samples using Trizol (Invitrogen, Carlsbad, CA, USA) ) according to manual instruction.Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on MIGSEQ2000 (BGI-Shenzhen, China).

treatment_protocol: BMDM were stimulated with IL17B (200ng/ml) for 6 hours and mRNA in BMDM were extracted for RNAseq.

value: wild type

value: BMDM


title: IL17B-1


title: StemScale_2


title: IL17B-2


title: bulk_RNA_27522_4

value: Multiple myeloma (MM)

value: BMMC


title: AB6178

source_name: Right limb-proximal

value: limb


title: StemScale_1


title: MCF10A_RNA_seq, time point 48h, TGF-beta1 treated, replication 2

value: 48 hours


title: control-3


title: Floating_Ly_IWR1_3


title: MCF10A_RNA_seq, time point 72h, TGF-beta1 treated, replication 2

value: immortalized human mammary epithelial cell line

value: 72 hours


title: AB5784

value: GFP+tomato+


title: AB5785

value: GFP-tomato-


title: control-2


title: MCF10A_RNA_seq, time point 3h, TGF-beta1 treated, replication 2

value: WT

value: 3 hours


title: MCF10A_RNA_seq, time point 0, solvent treated, replication 2

value: Solvent

value: 0 hour


title: Floating_Ly_IWR1_2

value: Human induced pluripotent stem cells


title: AB5783

value: GFP-tomato+


title: AB5762

value: Tamoxifen


title: MCF10A_RNA_seq, time point 24, TGF-beta1 treated, replication 3

value: 24 hours


title: Floating_Ly_IWR1_1


title: Floating_Ly_3


title: MCF10A_RNA_seq, time point 0, solvent treated, replication 3

value: 0 hours


title: MCF10A_RNA_seq, time point 3h, TGF-beta1 treated, replication 1


title: MM+DMSP-3

first: Noa

last: Barak-Gavish

address: POB 26

department: Plant and Environmental Sciences

data_processing:
Raw reads were quality trimmed using Cutadapt (84) (-q 20 -m 20) in addition to removal of adapters. Reads were mapped to Sulfitobacter D7 genome assembly (GCA_003611275.1) using Bowtie2 in end-to-end mode, and reads were counted on genes using HTseq, in the strict mode.
Gene expression was quantified using DESeq2
Genome_build: Sulfitobacter D7 genome assembly (GCA_003611275.1)
Supplementary_files_format_and_content: Tab delimited file includes raw counts, normalized and DESeq2 analysis

organism: Sulfitobacter sp. D7

source_name: Bacterial cells grown in liquid media

growth_protocol: Bacteria were grown for 24 h in 28°C, 160 rpm

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). For disruption of cell pellets we used the OmniLyse lysis kit (Claremontbio). The rest of the RNA extraction protocol was according to manufacturer’s instruction.
Library preparation was carried out according to the RNA-seq protocol developed by Avraham et al., 2016. DNA was removed using TURBO DNase (Ambion), RNA was fragmented and phosphorylated (at the 3’prime) using FastAP thermosensitive alkaline phosphatase (Thermo Scientific). RNA from each sample was ligated with unique RNA barcoded adaptors at the 3’, ensuring the strandedness of each transcript, using T4 RNA ligase 1 (NEB). RNA samples were pooled and treated with RiboZero (Gram-Negative Bacteria) kit (Illumina, San Diego, CA, USA) following manufacturer’s instructions in order to remove ribosomal RNA. Samples were reversed transcribed using AffinityScript RT Enzyme (Agilent) to form cDNA, and amplified by PCR.

treatment_protocol: Bacterial cell pellets were obtained from 200 mL (MM treatments) or 160 mL (CM treatments) cultures by 2-step centrifugation: 10,000g, 10 min followed by 14,000g, 10 min, all at 4°C. Pellets were flash frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: condition

value: Minimal media +DMSP

tag: culture method

value: grown in liquid media


title: AB5761

value: limb


title: AB5760

value: GFP+tomato-


title: MM+DMSP-2


title: MM-3

value: Minimal media


title: AB5759


title: MM+DMSP-1


title: MCF10A_RNA_seq, time point 6h, TGF-beta1 treated, replication 1

value: immortalized human mammary epithelial cell line

value: 6 hours


title: Floating_Ly_2


title: AB5758

value: GFP+tomato+


title: Floating_Ly_1


title: Floating_IWR1_2


title: Floating_IWR1_3


title: MM-2


title: MM-1


title: AB5757


title: Floating_IWR1_1


title: MCF10A_RNA_seq, time point 24h, TGF-beta1 treated, replication 1

value: WT


title: control-1

value: wild type

value: BMDM


title: MCF10A_RNA_seq, time point 48h, TGF-beta1 treated, replication 1

value: 48 hours


title: AB5756


title: MCF10A_RNA_seq, time point 72h, TGF-beta1 treated, replication 1

value: 72 hours


title: AB5755

value: GFP-tomato-


title: Floating_3

value: Human induced pluripotent stem cells

value: Suspension


title: MCF10A_RNA_seq, time point 0, solvent treated, replication 1

value: Solvent

value: 0 hour


title: MCF10A_RNA_seq, time point 12h, TGF-beta1 treated, replication 1

value: 12 hours


title: Floating_1


title: AB5754

value: limb

value: GFP-


title: StatCM-1

value: Stationary conditioned media

value: grown in liquid media


title: AB5753

value: GFP+


title: ExpCM+DMSP-3

value: Exponential conditioned media +DMSP


title: iPSC-derived induced neurons (day 51, replicate 1)

city: Boston

first: Kasper

last: Lage

state: MA

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
We ran Trim Galore (v0.6.7) to trim adapters and low-quality reads using “--stringency 7” and other default settings for Illumina paired-end reads.
Sequence alignment was performed using HISAT2 (v2.2.1) with the “--rna-strandness FR” setting; index files for the GRCh38 reference genome with transcripts were downloaded from the HISAT2 website (https://daehwankimlab.github.io/hisat2/download/).
The htseq-count script in Htseq (v0.13.5) was used to generate gene counts from aligned reads with “--stranded yes --minaqual 1” and other default settings; GRCh38 GTF gene annotation file was obtained from Ensembl (release 84).
The EdgeR package (v3.34.0) was used to remove low-count genes (min.count=5 in filterByExpr function) before calculating normalized gene counts (method=“TMM” in calcNormFactors function).
Assembly: GRCh38
Supplementary files format and content: Raw gene counts matrix (generated by htseq-count)

source_name: induced neurons

growth_protocol: Glutamatergic patterned induced neurons (iNs) were differentiated from an induced PSC line (iPS hDFn 83/22 iNgn2#9 [iPS3]) as described in Pintacuda et al. (PMID: 33972534), and cells were harvested at days 0, 21, and 51 for RNA-seq.

extract_protocol:
Cell culture medium was rapidly removed from cells cultured on 150mm Petri dishes and 5 mL of Trizol reagent (Life Technologies) was added. After total RNA extraction, samples were treated with DNase using the Ambion DNA-free DNase Treatment kit (Life Technologies) according to the manufacturer’s instructions, and resuspended in water. Samples were subsequently centrifuged at 13,000 rpm for 20 min at 4°C.
Libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit (Illumina), with the incorporation of dUTP in the second strand synthesis.

value: iPS hDFn 83/22 iNgn2#9 [iPS3]

value: induced neurons

tag: differentiation time

value: day 51


title: iPSC-derived induced neurons (day 51, replicate 3)


title: Adherent_3

value: Adherent


title: AB5728

value: GFP+tomato+

value: Tamoxifen


title: ExpCM+DMSP-2


title: ExpCM+DMSP-1


title: AB5727

value: GFP-tomato+


title: StatCM-3


title: iPSC-derived induced neurons (day 21, replicate 2)

value: day 21


title: iPSC-derived induced neurons (day 21, replicate 3)


title: AB5726

value: GFP+tomato-


title: ExpCM-3

value: Exponential conditioned media


title: RNA-Seq C10

city: Wuhan

first: Can

last: Chen

state: Hubei

address: Donghu Road

department: Department of Epidemiology and Biostatistics, School of Public Health

institute: Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: colorectal cancer

extract_protocol:
10 CRC tissues removed tumors or biopsy specimens, flash freozen by dry ice, and RNA was harvested using TRIzol (Invitrogen, USA)
RNA libraries were prepared for sequencing using stranded library preparation with Ribo-off rRNA Depletion Kit (Ribobio, China) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Seqhealth, China)

value: colorectal cancer


title: Adherent_1

value: Human induced pluripotent stem cells


title: iPSC-derived induced neurons (day 0, replicate 1)

source_name: iPSCs

value: iPSCs

value: day 0


title: StatCM-2

value: Stationary conditioned media

value: grown in liquid media


title: Adherent_2


title: ExpCM-2


title: AB5725

value: limb

value: GFP-tomato-


title: Floating_2

value: Suspension


title: RNA-Seq C9


title: AB5418


title: ExpCM-1


title: ADRENAL_5932_MOET

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

library_source: genomic

data_processing:
The WGBS clean reads were aligned to the bovine reference genome (bosTau 9) using the Bismark Bisulfite Read Marker (v 0.22.3)
The percent of methylated cytosines was calculated as the number of methylated cytosines/total number of cytosines x 100.
Cytosines were annotated with the nearest (no specific cut-off) transcription start site (TSS) and with gene structures (promoter, exon, intron, CpG islands or shores) through Genomation (Bioconductor/R). Promoters and CpG shore were defined as ± 1000 bp and ± 2000 bp of the TSS and CpG islands, respectively.
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file listing the genomic positions, and the corresponding annotation, the number of methylated cytosines, the total number of cytosines, and the percentage of methylated cytosines at each position.

molecule: genomic DNA

organism: Bos taurus

source_name: Adrenal

extract_protocol:
Tissues samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the gDNA extraction, quality control, library preparation, and sequencing. All samples met the requirements for library preparation (GC content between 35%-65% for extracted gDNA).
The gDNA samples were subjected to Whole Genome Bisulfite Sequencing (WGBS), through bisulfite library preparation and PE100 sequencing with 45Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by the BGI Company.

value: Adrenal

tag: embryo origin

value: MOET

tag: age (days)

tag: weight at_birth_(kg)

tag: weight at_sample_collection_(kg)


title: RNA-Seq C8

tag: tissue


title: AB5417

tag: strain

tag: organ

tag: selection marker


title: ADRENAL_5841_IVP

value: IVP


title: RNA-Seq C7


title: AB5416

tag: treatment

value: Tamoxifen

tag: mouse id

tag: timepoint


title: E. faecalis OG1RF grown in FMC medium lacking FeSO4.  Replicate 3

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

data_processing:
Read mapping was performed on a Galaxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the E. faecalis OG1RF genome (CP002621.1)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Assembly: CP002621.1
Supplementary files format and content: The processed .csv data files indicate the number of reads obtained for each open reading frame (OG1RF_xxxxx) for each sample after each of four original raw data files (.fastq) were compiled and mapped against the E. faecalis OG1RF genome (CP002621.1) using Galaxy as described above.

organism: Enterococcus faecalis OG1RF

growth_protocol: E. faecalis OG1RF was grown to mid-log phase in the chemically defined FMC medium prepared with or without 80uM FeSO4

extract_protocol:
Total RNA was isolated from homogenized E. faecalis cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcodes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing (RNA-seq) at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.

treatment_protocol: Cultures were harvested by centrifugation, washed in RNA Protect bacterial reagent (Qiagen) and subjected to another round of cenrtrifugation.  The pellets were then stored at -80C until RNA extraction.

value: Iron-free medium


title: ADRENAL_5833_IVP


title: RNA-Seq C6


title: E. faecalis OG1RF grown in FMC medium lacking FeSO4.  Replicate 2


title: AB5415

tag: replicate


title: iPSC-derived induced neurons (day 0, replicate 2)

tag: cell line

value: iPS hDFn 83/22 iNgn2#9 [iPS3]

tag: cell type


title: ADRENAL_3218_MOET


title: RNA-Seq C5


title: E. faecalis OG1RF grown in FMC medium supplemented with 80uM FeSO4.  Replicate 3

value: Complete medium


title: AB5414

value: GFP+tomato+


title: E. faecalis OG1RF grown in FMC medium lacking FeSO4.  Replicate 1


title: RNA-Seq C4

value: colorectal cancer


title: AB5413

value: GFP-tomato+


title: RNA-Seq C3


title: E. faecalis OG1RF grown in FMC medium supplemented with 80uM FeSO4.  Replicate 2


title: E. faecalis OG1RF grown in FMC medium supplemented with 80uM FeSO4.  Replicate 1


title: ADRENAL_3209_IVP


title: ADRENAL_3213_MOET


title: AB5411


title: RNA-Seq C2


title: AB5402


title: RNA-Seq C1


title: Tcrm_Control_5dpi_FB

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
feature barcode
hastags and antibody tags

library_source: other

data_processing:
The sequencing data was processed using CellRanger software (version 7.0.0).
genome build/assembly: mm10
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; raw gene count, clonotypes and contigs

molecule: other

source_name: Heart and MedLN

extract_protocol:
Heart and medistinal lymph nodes were collected from control adult mice at 5 days post myocardial infarction surgery. All tissues were kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL for 30 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining.Before hashtag staining, samples were labeled with Myhca614-629 tetramer construct as described in the methods section. Afterwards, each condition (e.g Heart, 5d, MI) was stained with a different Hashtag TotalSeq C antibody to enable multiplexing plus the TotalseqC anti-APC antibody to detect tetramer positive cells. T-helper cells were defined as live, lineage (CD11b,CD8a,CB220) negative and CD4+  events and were FACS sorted cells pooled heart and MedLN samples. After sorting, cells were combined at different ratios for single cell RNA sequencing application.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 30,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v2 Chemistry according to manufacturer ´s instructions.

value: Heart and MedLN

value: Lymphocyte

value: CD4+ T-cells

value: Balb/C

tag: time point

value: sham and MI operation


title: TESTICLE_5932_MOET

source_name: Testicle

value: Testicle


title: C10,H3K27ac,Input

data_processing:
Raw data quality control were performed using FastQC version v0.11.5
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of hg38 reference genome(ftp://ftp.ensembl.org/pub/grch38/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.*.fa.gz) using STAR software (version 2.5.3a) with default parameters.
The RSeQC(version 2.6)was used for reads distribution analysis.
Assembly: bigWig files were generated using bowtie2 version 2.2.6, deeptools and samtools with default parameters.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

extract_protocol:
CRC tissue was fixed in 1% formaldehyde for 10min at room temperature, after which 0.125M glycine was added and the mixture was sat for 5min to terminate the crosslinking reaction. The tissue was then treated with cell lysis buffer and nucleus was collected by centrifuging at 800g for 5min at 4 °C. Next, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA. Antibodies against H3K27ac (Abcam, USA) and a nonspecific rabbit IgG (Santa Cruz, USA) were incubated overnight with the crosslinked protein and DNA for immunoprecipitation reactions with protein A/G magnetic beads. DNA fragments were purified and collected by a Dr.GenTLE Precipitation Carrier kit (Takara, Japan).
Libraries were prepared for sequencing using stranded Illumina protocols


title: Tcrm_Control_5dpi_VDJ

description:
VDJ
single cell VDJ

data_processing:
The sequencing data was processed using CellRanger software (version 7.0.0).
genome build/assembly: GRCm38
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; raw gene count, clonotypes and contigs


title: TESTICLE_5841_IVP


title: Tcrm_Control_5dpi_GEX

description: single cell GEX

library_source: transcriptomic single cell


title: C9,H3K27ac,Input


title: AB5401

value: limb


title: A2_FB

data_processing:
The sequencing data was processed using CellRanger software (version 6.0.1).
Genome_build: mm10-2020-A for GEX and GRCm38 5.0.0 for V(D)J
Supplementary_files_format_and_content: tsv; gene barcode matrices and feature barcode matrix
Supplementary_files_format_and_content: csv;High-level descriptions of each clonotype and annotations of each high-confidence, cellular contig.

source_name: T lymphocytes from heart

extract_protocol:
Heart and medistinal lymph nodes were collected from TCR-M transferred adult mice at 5 and 7 days post myocardial infarction surgery. All tissue was kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL for 30 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining. Each condition (e.g Heart, 5d, MI) was stained with Hashtag TotalSeq C antibody to enable multiplexing. T-helper cells defined ad live, lineage (CD11b,CD8a,CB220) negative and CD4+ and TCR-M cells defined as live, lineage negative, CD4+ Thy1.1+ were FACS sorted from pooled heart and MedLN samples. After sorting, cells were combined in different ratios for single cell RNA sequencing application.
The same multiplexed sample were processed in parallel in 2 sets of libraries (set 1: A7, A9, A1 and set 2: A8, A10, A2). Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v2 Chemistry according to manufacturer ´s instructions.

tag: library type

value: feature barcoding (antibody tags)

value: T lymphocytes from heart


title: TESTICLE_5833_IVP

value: IVP


title: AB5399

value: GFP-tomato-

value: Tamoxifen


title: AB5400

value: GFP+tomato-


title: A10_VDJ

value: VDJ recombination


title: AB5412


title: C7,H3K27ac,Input


title: AB5398

value: GFP+


title: ADRENAL_3217_MOET

value: Adrenal

value: MOET


title: A8_GEX

value: gene expression


title: C6,H3K27ac,Input

value: colorectal cancer


title: TESTICLE_3217_MOET


title: AB5397

value: GFP-


title: A1_FB

value: Balb/C


title: TESTICLE_3213_MOET


title: C5,H3K27ac,Input


title: AB5396


title: A9_VDJ


title: C4,H3K27ac,Input


title: C8,H3K27ac,Input


title: AB5395


title: A7_GEX


title: TESTICLE_3209_IVP


title: TESTICLE_3208_IVP


title: PITUITARY_5932_MOET

source_name: Pituitary

value: Pituitary


title: CC-14

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

data_processing:
Base calling with Bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCm38.p5 based on accession NCBI:GCA_000001635.7 with ensembl annotation
Supplementary_files_format_and_content: .csv file with expression estimation with RSEM.

source_name: corpus callosum

extract_protocol:
Trizol extraction followed by Turbo DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded RNA w/ rRNA Reduction
RNA-Seq, mouse, 2x150bp, 70M reads, 1 lane of S4 flowcell

tag: genotype

tag: background strain

value: FVB/N Taconic

tag: Sex

value: male

value: corpus callosum


title: PITUITARY_5841_IVP

tag: embryo origin

tag: age (days)

tag: weight at_birth_(kg)


title: CC-11

tag: tissue


title: AB5393

tag: strain

tag: organ

value: limb

value: GFP-tomato+


title: PITUITARY_5833_IVP

value: IVP

tag: weight at_sample_collection_(kg)


title: C10,H3K27ac,CST


title: CC-4


title: CC-16

value: WT


title: AB5390

tag: selection marker

value: GFP+tomato+

tag: treatment

value: Tamoxifen

tag: mouse id


title: AB5392

value: GFP+tomato-

tag: timepoint

tag: replicate


title: C9,H3K27ac,CST


title: AB5391

value: GFP-tomato-


title: PITUITARY_3217_MOET

value: MOET


title: PITUITARY_3218_MOET


title: AB5389


title: AB5394


title: C8,H3K27ac,CST


title: PITUITARY_3213_MOET


title: CC-15


title: AB5324


title: CC-12


title: C3,H3K27ac,Input


title: C2,H3K27ac,Input


title: TESTICLE_3218_MOET

value: Testicle


title: AB5323


title: PITUITARY_3209_IVP


title: CC-3


title: C1,H3K27ac,Input

value: colorectal cancer


title: PITUITARY_3208_IVP


title: Hip-14

source_name: hippocampus

value: hippocampus


title: C5,H3K27ac,CST


title: HYPOTHALAMUS_5932_MOET

source_name: Hypothalamus

value: Hypothalamus


title: AB5321


title: C4,H3K27ac,CST


title: AB5322


title: Hip-11


title: Hip-4


title: AB5320


title: C7,H3K27ac,CST


title: C3,H3K27ac,CST


title: ADRENAL_3208_IVP

value: Adrenal


title: C6,H3K27ac,CST


title: CC-5

value: FVB/N Taconic


title: AB5319


title: Hip-3

value: male


title: C2,H3K27ac,CST


title: HYPOTHALAMUS_3218_MOET


title: C1,H3K27ac,CST


title: AB5177


title: HYPOTHALAMUS_3217_MOET


title: HYPOTHALAMUS_3213_MOET


title: Hip-16


title: Hip-15


title: C10

data_processing:
Raw data quality control were performed using FastQC version v0.11.5
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Clean Reads were further treated with FastUniq(version 1.1)to eliminate duplication.
Deduplicated reads were mapped to the reference genome of  hg38 reference genome using bowtie2 software (version 2.2.6) with default parameters.
The RSeQC(version 2.6)was used for reads distribution analysis.The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2).
bigWig files were generated using bowtie2 version 2.2.6, deeptools and samtools with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
CRC tissue was treated with cell lysis buffer and nucleus was collected by centrifuging for 10min at 500g at 4 °C.
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit (Vazyme, China)


title: C9


title: AB5155


title: HYPOTHALAMUS_5841_IVP


title: Hip-12


title: AB5154


title: Hip-5


title: C8


title: HYPOTHALAMUS_3208_IVP


title: HYPOTHALAMUS_3209_IVP


title: C7


title: HYPOTHALAMUS_5833_IVP


title: PA-treated PTEC3

city: Suita

first: Jun

last: Nakamura

state: Osaka

address: Box D11, 2-2 Yamada-oka

department: Nephrology

institute: the University of Osaka Graduate School of Medicine

data_processing:
Illumina package bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat (v2.1.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: Immortalized cultured wild-type PTECs

extract_protocol:
PTECs were treated with either BSA or PA-bound BSA for six hours, and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: proximal tubular epithelial cells

value: PA

tag: treatment time

value: 6 hours


title: PA-treated PTEC2


title: AB5152

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
M_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: embryonic forelimb

value: limb

value: GFP-tomato+


title: AB5156


title: C6


title: AB5153

value: GFP+tomato+


title: C5


title: AB5151

value: Tamoxifen


title: MUSCLE_5841_IVP

source_name: Muscle

value: Muscle

value: IVP


title: C4


title: AB5150

value: GFP-tomato-


title: MUSCLE_5932_MOET

value: MOET


title: BSA-treaeted PTEC3

value: BSA


title: PA-treated PTEC1


title: MUSCLE_5833_IVP


title: MUSCLE_3218_MOET


title: C3

value: colorectal cancer


title: BSA-treaeted PTEC2


title: MUSCLE_3217_MOET


title: AB4592

description: read2 used to read cell and molecule barcodes concatenated to R1 header


title: AB4591


title: BSA-treaeted PTEC1


title: C2


title: C1


title: MUSCLE_3209_IVP


title: CD45+ immune cells W-7

city: Jinan

first: Yibing

last: Wang

address: Jingshi road

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
fastp quality control were using fastp version: 0.20.1 (https://github.com/OpenGene/fastp)
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads. [Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. bioRxiv, 2018: 274100.]
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD52+ immune cells

extract_protocol:
The digestion solution was composed of collagenase II (3.5 mg/mL, Solarbio, China), DNase I (0.02 mg/mL, Solarbio, China), hyaluronidase (30 U/mL, Solarbio, China), 5% FBS-1640 (Gibco, USA), and DPBS (Gibco, USA). Samples were washed, the digestion solution was added to the tissue, and the tissue was cut and incubated at 37°C for 1 h. The digestion solution was passed through a 40-µm cell strainer and then centrifuged at 500 x g for 5 min. The reaction was terminated by adding erythrocyte lysate for 5 min and centrifuging twice at 300 x g for 5 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Streptozotocin (120 mg/kg, Sigma-Aldrich, USA, S0130) was administered to 4-week-old C57BL6J mice after 12 h of fasting. Blood glucose was measured after 7 days of stabilization, and mice with glucose levels ≥16.5 mmol/L (300 mg/dL) were considered diabetic and were used for the operation.

value: skin

value: control wound


title: AB4589

extract_protocol:
Forelimb tissues were disassociated using enzymatic digestion. E10.5-E11.5 forelimbs were digested with pre-heated 0.25% trypsin in DMEM medium (ThermoFisher) and incubated for 10 min at 37°C, gently pipetting every 3 min. E12.5-E14.5 forelimbs were digested with 1.5 mg/ml  collagenase type V (Sigma-Aldrich) in DMEM at 37°C for 10-15 min, gently pipetting every 5 min until the tissue completely dissolved. The digestion reaction was stopped by addition of DMEM supplemented with 10% FBS and 1% Pen-Strep. Cell suspensions were filtered through a 40-µm nylon mesh and collected by centrifugation at 1000 rpm for 7 min at 4°C. Supernatant was removed and cells were resuspended in 500 µl ice-cold MACS buffer (with 0.5% BSA and 2 mM EDTA in PBS) and used immediately for fluorescence-activated cell sorting (FACS).
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)


title: CD45+ immune cells W-5

source_name: CD51+ immune cells


title: CD45+ immune cells W-3

source_name: CD50+ immune cells


title: AB4588


title: LIVER_5932_MOET

source_name: Liver

value: Liver


title: MUSCLE_3208_IVP


title: AB4586

value: GFP+tomato-


title: CD45+ immune cells D-7

source_name: CD48+ immune cells

value: STZ-induced diabetic wound


title: AB4587


title: CD45+ immune cells W-1

source_name: CD49+ immune cells


title: LIVER_5833_IVP


title: Ha_Foxp3_2

city: Guadalajara

first: Natalia

last: García

state: Jalisco

address: Sierra Mojada 800

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

data_processing:
The sequencing quality of the returned data (FASTQ archives) was analyzed with FASTQC (Version 0.11.9)
Alignment to the Homo sapiens genome (Version 42) (GRCh38.p13) was performed with Subjunc aligner (Version 2.0.0) from the Rsubread package (Version 3.14)
BAM files were processed with featureCounts (Version 2.0.1) for generation or counts tables
Normalization of reads counts as FPKM (Fragments per Kilobase of exon per Million Mapped Fragments) was achieved using DESeq2 tool (Version 1.36.0) from Galaxy web-platform
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text files include FPKM values, log2(fold-change), statistical parameters; gene identification is showed as ENSEMBL code and gene name

source_name: HaCaT

growth_protocol: Transduced HaCaT cells were maintained in DMEM supplemented with 4.5 g/L glucose, 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with Quick-RNA miniprep plus kit (Cat. No. R1058, Zymo Research, Irvine, CA) according to the manufacturers’ instructions. independent sample duplicates of total RNA from HaCaT-T pLVX and HaCaT- FOXP3Δ2Δ7 were sent to Novogen Bioinformatics Technology Co., Ltd (Beijing, China) preserved in RNAstable (Cat. No. 93221-001, Biomatrica, San Diego, CA) for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HaCaT cells were infected with at least 5 IFU per cell of lentiviral particles containing the FOXP3Δ2Δ7 ORF and after 72 h of infection, 0.5 μg/mL of puromycin (Cat. No. A1113803, Gibco, Waltham, MA) was added to the cell culture.

tag: source

value: Skin

tag: cell line

value: HaCaT

value: Non-tumorigenic keratinocytes


title: Ha_Foxp3_1


title: Ha_Plvx_2

value: Empty pLVX


title: LIVER_5841_IVP


title: AB4585

value: limb


title: Lung,13.5,rep3

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

description: 10X Genomics

data_processing:
Sequenced ST libraries were processed using Space Ranger 1.0.0 Pipeline (10X Genomics).
Reads were aligned to the human reference genome to obtain an expression matrix.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
One of the two lungs (preferentially the left), from each donor, was snap frozen in cryomatrix and further used for histological analyses. We cut 10-12μm-thick tissue sections with a cryostat (Leica CM3050S or analogue) and collected them onto poly-lysine coated slides (VWR Cat No. 631-0107)
Spatial Gene Expression libraries (n=9) (6-13 pcw) were generated with the Visium Spatial Gene Expression Slide & Reagent kit (PN-1000184; 10X Genomics Inc.), according to manufacturer's protocol

value: Lung

tag: age

tag: donor


title: CD45+ immune cells D-3

source_name: CD46+ immune cells


title: LIVER_3218_MOET

tag: embryo origin

tag: age (days)


title: Lung,13.5,rep4

description: 10X Genomics

tag: tissue


title: Ha_Plvx_1


title: Lung,13.5,rep2

description: 10X Genomics


title: AB4590

tag: strain

value: Tamoxifen


title: CD45+ immune cells D-5

source_name: CD47+ immune cells


title: MUSCLE_3213_MOET

value: Muscle

tag: weight at_birth_(kg)


title: LIVER_3217_MOET

tag: weight at_sample_collection_(kg)


title: CD45+ immune cells D-1

source_name: CD45+ immune cells


title: AB4086

tag: organ

tag: selection marker

value: GFP-tomato+


title: LIVER_3213_MOET

value: MOET


title: Lung,13.5,rep1

description: 10X Genomics


title: LIVER_3209_IVP

value: IVP


title: Young MuSC, FAP, MΦ scRNA-Seq 3

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Alevin (a tool integrated with the Salmon software) was used to create per-cell level gene-count matrix.
Genome_build: mm10
Supplementary_files_format_and_content: *quants_mat.gz: compressed count matrices; *quants_mat_cols.txt: column Header (Gene-ids) of the matrix; *quants_mat_rows.txt: Row Index (CB-ids) of the matrix; *quants_tier_mat.gz : Tier categorization of the matrix.
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/

source_name: Young MuSC, FAP, MΦ scRNA-Seq

extract_protocol:
Satellite cells (ITGA7+, CD31-, CD11b-, CD45-, Sca1-), fibro-adipogenic progneitor cells (Sca1+, ITGA7-, CD31-, CD11b-, CD45-), and macrophages (F4/80+, CD11b+, CD45+, CD31-) were isolated by Fluorescence-Activated Cell Sorting (FACS) to receive an estimated total of 2500 cells.
Libraries were created using Chromium Single Cell 3' Reagent Kits (v3 Chemistry).

value: 5 weeks

value: skeletal muscle

value: satellite cells, macrophages, fibro-adipofenic progenitor cells


title: AB4084

first: Ido

last: Amit

address: 234 Herzl st.

value: GFP+tomato+

tag: treatment

tag: mouse id


title: Young MuSC, FAP, MΦ scRNA-Seq 2


title: LIVER_3208_IVP

value: Liver


title: AB4083

tag: timepoint

tag: replicate


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 72h, TGF-beta1 treated, replication 2

data_processing: none provided by the submitter

extract_protocol:
Total RNA was isolated using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany)
Sequencing libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina) and subjected to 2x150 bp paired-end sequencing on a NovaSeq 6000 sequencing device (Illumina) at 50 million reads per library.

tag: cell type

value: immortalized human mammary epithelial cell line

tag: genotype

value: JUNB  knock-out

tag: time

value: 72 hours


title: SC30_Dox_Combo_3_(7_days) [NSP_SEN_COMBO_3]

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

organism: Mus

source_name: in vitro senescent NSP (trametinib/palbociclib) cells

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppress p53 expression. In order to restore p53 expression and therefore induce senescence, doxycycline-containing media was replaced with doxycycline-free media for 6 days and senescent cells were seeded and collected on day 8 after doxycycline withdrawal. For perturbing BRD4-dependent transcriptional programs, cells were treated with 500 nM of JQ1 (S7110, Selleck Chem) for 48 h prior to harvest, starting JQ1 at day 6 after restoring p53 (off-dox), when NSP cells are fully senescent. For drug-induced senescence experiments, p53-suppressed (on-dox) NSP cells were treated with trametinib + palbociclib, or cisplatin for 7 days. The concentration of DMSO corresponded to the drug treatment and does not exceed 1:1,000 dilution of total media volume, which shows no discernable toxicity to cultured cells. For IFN-γ of proliferating or senescent populations, the indicated doses of mouse recombinant IFN-γ was administrated to proliferating and senescent (p53-restored) NSP cells after 24 h of cell seeding and cells were harvested after 24 h of IFN-γ treatment.

extract_protocol:
Total RNA was extracted using using TRIzol (Thermo Fisher Scientific) following the manufacturer’s instructions.
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

tag: sample type

value: Cell line

value: Doxycycline Off


title: AB4098

city: Rehovot

institute: Weizmann Institute of Science

value: limb

value: GFP-tomato-


title: AB4010

value: GFP+tomato-

value: Tamoxifen


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 72h, TGF-beta1 treated, replication 1

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

tag: cell line


title: Aged MuSC, FAP, MΦ scRNA-Seq 3

source_name: Aged MuSC, FAP, MΦ scRNA-Seq

tag: age

value: 23 months


title: Young MuSC, FAP, MΦ scRNA-Seq 1


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 72h, TGF-beta1 treated, replication 2


title: AB4009


title: SC27_Dox_DMSO_3_(7_days) [NSP_PRO_DMSO_3]

source_name: in vitro proliferating (DMSO) NSP cells


title: AB4082

source_name: embryonic forelimb


title: SC28_Dox_Combo_1_(7_days) [NSP_SEN_COMBO_1]


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 72h, TGF-beta1 treated, replication 1


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 24h, TGF-beta1 treated, replication 2

value: 24 hours


title: SC29_Dox_Combo_2_(7_days) [NSP_SEN_COMBO_2]


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 24h, TGF-beta1 treated, replication 2


title: AB4007


title: AB4008

value: GFP-tomato+


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 24h, TGF-beta1 treated, replication 1


title: AB4085


title: Aged myoblast WGBS 3

data_processing:
Illumina BaseSpace software was used for basecalling.
Reads were adaptor trimmed using trim-galore (Default setting, Phred score: 20).
Reads were aligned to the mm10 genome using bismark (internal bowtie2 aligner’s default settings and allowing one mismatch) followed by deduplication. Bismark methylation extraction --paired-end --ignore_r2 2. Bismark CpG report files were generated with coverage2cytosine.
The differential methylation regions were identified with DMRcaller’s (R/Bioconductor) function computeDMRsReplicates (context = "CG", method = "bins", binSize = 100, test = "betareg", minCytosinesCount = 4, minProportionDifference = 0.4, pValueThreshold = 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: DMR_old_vs_young_Replicates_bins.csv, file contains the differentially methylated region coordinates, Gain/Loss state, and adjusted p-value
Supplementary_files_format_and_content: Bismark CpG report: genome-wide cytosine methylation report for CpG sites, described in: https://github.com/FelixKrueger/Bismark/tree/master/Docs#optional-genome-wide-cytosine-report-output

source_name: Aged myoblast WGBS

growth_protocol: Primary Myoblasts were cultured on collagen-coated plates in growth media (HAM's F10 supplemented with 20% FBS, 1% penicillin/streptomycin and 2.5 ng/ml basic Fibroblast Growth Factor, bFGF), and passaged after reaching 60-70% confluency.

extract_protocol:
Genomic DNA was extracted using phenol/chloroform/isoamyl alcohol solution (Invitrogen  #15593-031). Primary myoblasts were pelleted at 0.6xg for 10 minutes and snap frozen in liquid  nitrogen before use. When all samples were collected, cell pellets were thawed on ice and lysed  in 400ul lysis buffer (40nM Tris-HCl pH8.0; 1% (vol/vol) Triton X-100; 0.1% (vol/vol) SDS; 4  mM EDTA (pH 8.0) and 300 mM NaCl). Cell lysates were incubated at 37°C for 45 minutes  with 10ul RNase A (Invitrogen, cat#12091-021), followed by a 1h15min incubation at 45°C with  10ul of Proteinase K (10mg/ml Millipore, cat#70663). 1 volume of phenol/chloroform were then  added to each lysate, and samples were vortexed vigorously and centrifuged at maximum speed  for 3 minutes. The aqueous layer was retained and mixed with 2 volumes of 100% EtOH.  Samples were snap frozen in liquid nitrogen for 3 minutes, thawed on ice, and centrifuged for 20  minutes at maximum speed. The supernatant was discarded, and the DNA pellet was washed 3x  with 750ul of 75% EtOH, spinning each time at maximum speed for 12 minutes. The DNA was  then air-dried and resuspended in TE buffer.
Genomic DNA was sheared using COVARIS, and libraries were constructed using the NxSeq AmpFREE low DNA Library Kit by Lucigen. Bisulfite conversion was done using the EZ-96 DNA Methylation-GoldTM MagPrep kit by Zymo Research.

treatment_protocol: Bisulfite treatment

value: 21 months

value: primary myoblasts


title: Aged MuSC, FAP, MΦ scRNA-Seq 4

value: skeletal muscle

value: satellite cells, macrophages, fibro-adipofenic progenitor cells


title: SC25_Dox_DMSO_1_(7_days) [NSP_PRO_DMSO_1]


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 24h, TGF-beta1 treated, replication 1


title: Aged myoblast WGBS 2


title: NSP_SEN_IFNg_IFNg_50pg_2 [NSP_SEN_IFNG_2]

source_name: in vitro senescent (p53-restored) NSP cells + IFNg


title: AB4006


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 6h, TGF-beta1 treated, replication 2

value: 6 hours


title: Aged myoblast WGBS 1


title: NSP_SEN_IFNg_IFNg_50pg_1 [NSP_SEN_IFNG_1]


title: AB4005


title: NSP_SEN_IFNg_0pg_2 [NSP_SEN_UT_2]

source_name: in vitro senescent (p53-restored) NSP cells untreated


title: Aged MuSC, FAP, MΦ scRNA-Seq 1


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 6h, TGF-beta1 treated, replication 2

value: immortalized human mammary epithelial cell line


title: Young myoblast WGBS 1

source_name: Young myoblast WGBS

value: 5 weeks


title: Young myoblast WGBS 3


title: Young myoblast WGBS 2


title: SC26_Dox_DMSO_2_(7_days) [NSP_PRO_DMSO_2]


title: Aged MuSC, FAP, MΦ scRNA-Seq 2


title: NSP_PRO_IFNg_50pg_2 [NSP_PRO_IFNG_2]

source_name: in vitro proliferating NSP cells + IFNg

value: Doxycycline On


title: WT36_BD

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

data_processing:
Illumina Casava software used for basecalling.
The FastQC (FastQC v0.11.3) and cut-adapt (v1.1) were used to filter sequencing reads of low quality.
Then reads were mapped to mouse genome build mm10 using TopHat (TopHat v2.0.11) with default parameters. The HTseq (v0.9.1) was used for raw read counts. The DESeq2 (DESeq2 v3.1) was used for selecting differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

source_name: oxyntic area of mouse stomach

growth_protocol: Four- to 80-week-old sstr2 knockout and wild type mice were used for RNA sequencing

extract_protocol:
Total RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to the manufacture instruction
The RNA sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina)
RNA sequencing was performed using the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads

value: wild type


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 6h, TGF-beta1 treated, replication 1

city: Freiburg

institute: Albert-Ludwigs-Universität Freiburg

value: JUNB  knock-out


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 0, solvent treated, replication 2

value: Solvent

value: 0 hour


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 6h, TGF-beta1 treated, replication 1


title: WT35_BD


title: WT31_BD


title: NSP_PRO_IFNg_50pg_1 [NSP_PRO_IFNG_1]

value: Cell line


title: NSP_PRO_IFNg_0pg_2 [NSP_PRO_UT_2]

source_name: in vitro proliferating NSP cells untreated


title: pGMR_bon; yki-RNAi_rep3

first: Alexey

last: Veraksa

address: 100 William T. Morrissey Blvd.

department: Biology Department

institute: University of Massachusetts Boston

data_processing:
Adaptor removal and size filtering by Cutadapt (v2.9)
tRNAs, rRNA, snRNA and snoRNA removal by Bowtie 2 (v2.3.5.1)
Genome mapping by STAR (v2.7.0e)
Gene counting by featureCounts (Subread v1.6.2)
Differential gene expression analysis by DEseq2 (v1.30.1) through DEBrowser (v1.16.3)
Genome_build: BDGP6
Supplementary_files_format_and_content: Text files with raw gene counts
Supplementary_files_format_and_content: Comma-separated values files with differentially expressed genes and values

organism: Drosophila melanogaster

source_name: Bon overexpression with knockdown of Yki

growth_protocol: D. melanogaster crosses were carried out at 25 °C on standard medium.

extract_protocol:
Dissected pupal eyes were immediately transferred to 100 μl of TRIzol (Thermo Fisher Scientific, Cat# 15596026) and kept at RT for 5 min to lyse. Samples in TRIzol were stored at -80°C until 60 pupal eyes for each genotype were collected. All TRIzol samples for each genotype were then thawed and combined, and the volume was brought up to 500 μl per sample. Total RNA was extracted twice by adding 100 μl of chloroform, vigorously shaking for 15 secs, incubating at RT for 3 min, centrifuging at 11,000 rcf at 4°C for 15 min, and collecting the aqueous phase. The total RNA was then precipitated by adding 1 volume of 70% ethanol (v/v in RNase-free water), and purified with RNeasy Mini Kit (QIAGEN, Cat# 74104, 79254).
The RNA-seq libraries were prepared from 100 ng of total RNA per genotype with NEBNext Ultra II RNA Library Prep Kit mRNA Isolation Module (NEB, Cat# E7775S, E7490S, E7500S). Quality control and sequencing of the RNA-seq libraries were performed by GENEWIZ, Inc. using Agilent TapeStation and Illumina HiSeq 4000 with a 2x150 paired-end configuration.

treatment_protocol: White pupae were staged for 40 hrs at 25 °C, and pupal eyes were dissected within 1 hr at RT in ice cold RNase-free 1x PBS.

value: Pupal retina

value: UAS-bon-mCherry/+; pGMR-GAL4/UAS-yki-RNAi (BDSC #34067)

tag: developmental stage

value: 40-41 hrs after puparium formation


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 0, solvent treated, replication 2


title: WT28_BD


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 65, time point 0, solvent treated, replication 1


title: WT40_BD


title: NSP_PRO_IFNg_0pg_1 [NSP_PRO_UT_1]


title: WT25-2_BD


title: pGMR_bon; yki-RNAi_rep1

tag: tissue


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 72h, TGF-beta1 treated, replication 2

value: JUNB WT

value: 72 hours


title: WT24_BD

tag: strain


title: NSP_SEN_IFNg_0pg_1 [NSP_SEN_UT_1]

value: Doxycycline Off


title: In vitro_SEN_JQ1_500nM_2_(2days) [NSP_SEN_JQ1_2]

source_name: in vitro senescent (p53-restored) NSP cells + JQ1


title: pGMR_bon_rep3

source_name: Bon overexpression

value: UAS-bon-mCherry/+; pGMR-GAL4/+


title: WT23_BD


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 72h, TGF-beta1 treated, replication 1


title: In vitro_SEN_JQ1_500nM_3_(2days) [NSP_SEN_JQ1_3]


title: JUNB_WT_Mut_RNA_seq, JUNB KO, cell clone 1, time point 0, solvent treated, replication 1


title: In vitro_SEN_JQ1_500nM_1_(2days) [NSP_SEN_JQ1_1]


title: In vitro_SEN_DMSO_3_(2days) [NSP_SEN_3]

source_name: in vitro senescent (p53-restored) NSP cells


title: pGMR_bon_rep2


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 72h, TGF-beta1 treated, replication 1


title: Il17b-/- and WT mice+ DSS-1 mixed sample (non-demultiplexed)

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

data_processing:
The sequenced data (.fastq files) were processed via the BD Rhapsody analysis cloud pipeline on Seven Bridges (https://www.sevenbridges.com). For the bioinformatics pipeline, we used BD WTA Multiplex Rhapsody Analysis Pipeline Version 1.8, which is used as an APP with simple setting. First, we upload all files for reads, Reference Genome, and Transcriptome Annotation to the server. Then, we setup the APP with the Input section. The raw reads of WTA and SMK sequencing were selected for Reads section. For WTA reference Genome, we selected GRCm38-PhiX-gencodevM19-20181206.tar as reference to annotate the genes. File of 'gencodevM19-20181206.gtf' was selected under Transcriptome Annotation'. Then, we setup the APP setting with the Multiplexing-settings. Sample tags version was selected with 'single-cell Multiplex Kit-mouse', which contains the reference sequences for sample tags. After setup, we run the pipeline. The pipeline automatically identified cell labels with barcode and molecular indices, and gene was determined by mapping to mouse genome GRCm38 reference. Four samples were demultiplexed by alignment with the sample tag reference sequences and resulting in processed data of '_RSEC_MolsPerCell.cs' for each four samples, which were used for downstream bioinformatic analysis.
The prcessed data for 4 samples were analyzed with SeqGeq software from BD. The 4 samples were first concatenated to one sample to do downstream analysis. First QC and normalization were down with SeqGeq software. The cells passed QC were analyzed with plugins of Seurat with default parameters to do the dimensionality reduction with UMAP, clustering, and differential expressed gene analysis between clusters. For comparing the difference between samples, we grouped 2 WT mice sample as WT group and 2 Il17b-/- mice sample as Il17b-/- group by gating the sample ID. Then the same clustering was applied to the groups. The same UMAP and clustering were applied to each sample to compare the difference. The pseudo-time analysis was performed using the plugin of Monocle. The heatmap was also created in SeqGeq. Gene enrichment analysis was performed using Metascape webtool (www.metascape.org)
Genome_build: GRCm38-PhiX-gencodevM19-20181206.tar
Supplementary_files_format_and_content: Processed data files are  molecules per gene per cell, based on RSEC, CSV format.

source_name: colon lamina propria CD45+ immune cells

extract_protocol:
The pooled cells were loaded on a BD Rhapsody™ Cartridge for capturing the single cells by pairing one cell with one barcoded beads. Then the cells were lysed to release mRNA, which were captured by barcoded oligo on bead, which has the cell label information and unique molecular identifiers information. Then the beads were retrieved from Cartridge into one tube and performed reverse transcription. The cDNA of captured mRNA was first synthesized on BD Rhapsody™ Cell Capture Beads as described in the instrument user guides. At the same time, the barcode information from BD Rhapsody Cell Capture Beads is also added to Sample Tags during reverse transcription.
To generate the Sample Tag sequencing libraries, the extended Sample Tags are first denatured from the BD Rhapsody Cell Capture Beads, which are later amplified through a series of PCR steps. Meanwhile, the whole transcriptome amplification library is generated directly from the BD Rhapsody Cell Capture Beads using a random priming approach, followed by an index PCR step according to BD Rhapsody protocol. Both the whole transcriptome mRNA and Sample Tag library were both sequenced on Illumina nova6000.

treatment_protocol: Colons were dissected, carefully cleaned with ice-cold PBS and cut into large fragments (0.5–1 cm) and intestinal epithelial cells were removed by incubation in digestion solution of Ca2+ and Mg2+ free PBS with 5mM EDTA  and 1mM dithiothreitol  . Remaining tissue was digested using PBS with Ca2+ and Mg2+ supplemented with 0.3mg/ml collagenase VIII (Sigma-Aldrich) and 0.3mg/ml DNase I (Dingguo Changsheng) and 5% FBS (Gbico). The cell suspension was passed through a 70 μm and a 40 μm cell strainer sequencially.The  single cell suspensions of each colon LP sample were stained with the anti-mouse CD45-biotin (30-F11, BD ebioscience) and a separate sample tag (sample tag 1 to 4) using the mouse immune Single-Cell Multiplexing Kit (BD bioscience), which can provide us sequence 4 samples for a single cell library preparation. The sample tag is also anti-CD45 antibody labeled with unique sample barcode oligo tag and a poly A tail, which also can be  captured with barcoded beads.Then CD45+ immune cells were sorted using Streptavadin microbeads Kit (Miltenyi) using MACS (Miltenyi Biotech). Viability of the final cell suspension was calculated using a hemocytometer and Trypan blue (Corning) exclusion and was routinely > 85%. Four samples were labelled with sample tags and pooled together for downstream single cell capture and sequence.

tag: strain background

tag: genotype/variation

value: Il17b-/- and wild type; mixed sample (non-demultiplexed)

value: 2.5% (w/v) dextran sulfate sodium (DSS) for  6 days

value: colon

value: colon lamina propria CD45+ immune cells

tag: sample tag

value: SampleTag01; Sample 1 (KO25)

value: SampleTag02; Sample 2( KO27)

value: SampleTag03; Sample 3 (WT97)

value: SampleTag04; Sample 4 (WT111)


title: WT19_BD

value: wild type


title: WT20_BD


title: pGMR_bon; yki-RNAi_rep2


title: WT30_BD


title: In vitro_SEN_DMSO_2_(2days) [NSP_SEN_2]

value: Cell line


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 72h, TGF-beta1 treated, replication 2

value: immortalized human mammary epithelial cell line


title: WT16_BD


title: pGMR_mCherry_rep2

source_name: Wild type control for Bon overexpression

value: Pupal retina

value: UAS-mCherry (BDSC #35787)/pGMR-GAL4


title: pGMR_bon_rep1

value: 40-41 hrs after puparium formation


title: In vitro_SEN_DMSO_1_(2days) [NSP_SEN_1]


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 24h, TGF-beta1 treated, replication 2

value: JUNB WT

value: 24 hours


title: WT15_BD


title: pGMR_mCherry_rep1


title: In vitro_PRO_JQ1_500nM_3_(2_days) [NSP_PRO_JQ1_3]

source_name: in vitro proliferating NSP cells + JQ1

value: Doxycycline On


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 24h, TGF-beta1 treated, replication 1


title: In vitro_PRO_JQ1_500nM_2_(2_days) [NSP_PRO_JQ1_2]


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 24h, TGF-beta1 treated, replication 1


title: WT11_BD


title: In vitro_PRO_JQ1_500nM_1_(2_days) [NSP_PRO_JQ1_1]


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 6h, TGF-beta1 treated, replication 2

value: 6 hours


title: WT08_BD


title: In vitro_PRO_DMSO_3_(2_days) [NSP_PRO_3]

source_name: in vitro proliferating NSP cells


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 6h, TGF-beta1 treated, replication 2


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 6h, TGF-beta1 treated, replication 1


title: In vitro_PRO_DMSO_2_(2_days) [NSP_PRO_2]


title: KO80_BD

value: SSTR2 knockout


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 6h, TGF-beta1 treated, replication 1


title: In vitro_PRO_DMSO_1_(2_days) [NSP_PRO_1]


title: KO79_BD


title: KO67_BD


title: In vivo NSP_51 [NSP_51]

source_name: in vivo bulk tumor (p53-restored)

growth_protocol: C57BL/6N female mice aged 8-9 weeks old were injected via hydrodynamic tail vein injection (HTVI) with a sterile 2 ml (or 1/10 of mouse body weight) 0.9% NaCl solution containing 5 μg of pT3-EF1a-NrasG12D-IRES-rtTA (Tet-On system) and 20 ug of pT3-TRE-tRFP-shp53 transposon vectors along with 5ug CMV-SB13 transposase (5:1 ratio) through the lateral tail vein. Doxycycline was administered to mice via 625 mg/kg doxycycline-containing food pellets (Harlan Teklad) at least 4 days before injection. The tumor was harvested at 5-7 weeks after injection for cell line isolation.

extract_protocol:
To extract tissue RNA, freshly isolated tumor chunk was first stored in RNA-later solution (AM7024, Thermo Scientific) to preserve RNA integrity until extraction and RNeasy kit (74106, Quiagen) was used to purified tissue RNA following the manufacturer instructions
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

value: Whole tissue

value: Doxycycline Off


title: In vivo NSP_49 [NSP_49]


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 0, solvent treated, replication 2

value: Solvent

value: 0 hour


title: KO59_BD


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 0, solvent treated, replication 2


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 24h, TGF-beta1 treated, replication 2


title: In vivo NSP_47 [NSP_47]


title: WT12_BD


title: In vivo NSP_44 [NSP_44]


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 2, time point 0, solvent treated, replication 1


title: KO57_BD


title: In vivo NSP_42 [NSP_42]


title: Donor 3, ROCKi-6D⁺6D⁻

city: London

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

country: United Kingdom

institute: University College London

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation was carried out using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0 (Ensembl 93) - https://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

growth_protocol: Keratinocytes were plated out at a density of 4 × 104/cm2 in culture flasks containing lethally irradiated 3T3-J2 cells (i3T3) and cultivated in a humidified atmosphere at 37°C with 10% CO2. Subconfluent cells were passaged and re-seeded at a density of 1.5 × 104/cm2 with i3T3 in Green’s medium. Fresh isolated cells (P0) or cells with passage 1 (P1) were used in this study.

extract_protocol:
Skin samples were obtained from healthy children (10- to 16-year-olds) undergoing plastic surgery for ear reconstruction, following informed consent.  Briefly, subcutaneous and adipose tissue were carefully removed from skin samples and the rest of the tissue was cut into small pieces (2 x 2 mm) and incubated with 0.02 U/mL neutral protease in PBS for 3 hours at 37 °C to detach epidermis from the dermis. The epidermis was then transferred to 0.25% trypsin in 0.01% EDTA solution for 5 minutes to dissociate the epidermis into single cells.
Approximately 3,000 live cells from each group were loaded into one channel of the Chromium Chip G using the Single Cell reagent kit v3.1 (10X Genomics, CA, US) for capturing single cell Gel-Bead Emulsion using the Chromium controller. Following single cell capture, cells were lysed, and cDNA of individual cells were synthesized within the Gel-Bead Emulsion and was used for library preparation. cDNA was amplified and size-selected using SPRISelect (Beckman Coulter, Germany, #B23317) following the manufacturer’s protocol. 25ng of the size-selected cDNA of each sample were used to construct Illumina sequencing libraries. Libraries were pooled at equal concentration and sequenced on the NextSeq2000 Illumina sequencing platform at 50,000 reads per cell.

treatment_protocol: Keratinocytes were treated with 10µM of Y-27632 for indicated period of time in the article.

value: Keratinocytes

value: 10-16 years old


title: WT07_BD

value: wild type


title: KO50_BD


title: In vivo NSP_50 [NSP_50]

source_name: in vivo bulk tumor (p53-suppressed)


title: KO48_BD


title: Donor 3, ROCKi-6D⁺

description: 10x Genomics


title: KO51_BD


title: In vivo NSP_52 [NSP_52]


title: In vivo NSP_40 [NSP_40]


title: Donor 3, Control-6D⁻

description: 10x Genomics


title: KO46_BD


title: In vivo NSP_43 [NSP_43]


title: Donor 2, ROCKi-6D⁺6D⁻

description: 10x Genomics


title: Donor 2, Control-6D⁻6D⁻

description: 10x Genomics


title: In vivo NSP_45 [NSP_45]


title: Donor 3, Control-6D⁻6D⁻

description: 10x Genomics


title: KO47_BD


title: KO58_BD


title: Donor 2, ROCKi-6D⁺

description: 10x Genomics


title: JUNB_WT_Mut_RNA_seq, WT, cell clone 27, time point 0, solvent treated, replication 1


title: In vivo NSP_41 [NSP_41]


title: KO35_BD


title: Donor 2, Control-6D⁻

description: 10x Genomics


title: KO23_BD


title: Donor 1, ROCKi-6D⁺6D⁻

description: 10x Genomics


title: KO22_BD


title: 101_KO14_BD


title: Donor 1, Control-6D⁻

description: 10x Genomics


title: KO33_BD


title: KO09_BD


title: Donor 1, ROCKi-6D⁺

description: 10x Genomics


title: Ctrl_2

status: Public on Jan 16 2023

city: Uppsala

first: Taija

last: Mäkinen

address: Dag Hammarskjölds v 20

department: Immunology, Genetics and Pathology, IGP

institute: Uppsala University, Rudbeck Laboratory

description:
LEC.WT.skin.RData
LEC.Pik3ca.WT

data_processing:
Illumina Casava1.8 software was used for basecalling
Alignement to the mouse reference genome GRCm38 and Gallus gallus PIK3CA sequence (NCBI nucleotide sequence id: NM_001004410) using tophat (version 2.1.1)
Filtering duplicated reads using samtools software (version 0.1.18)
Summarizing gene counts using Subread package (featureCounts function, version 1.4.6-p5)
Raw expression data were processed further in R (version 3.5.1 and version 4.0.3); QC: removing cells <  3 cells, < 200 genes or 50,000 reads counts, > 10% reads derived from the mitochondrial genome. Further processing using Seurat package (version: 3.1.1 and 4.0.1): normalization using LogNormalize function, , graph-based clustering analysis  (Louvain method) and non-linear dimensional reduction (UMAP). Three processed datasets are provided containing raw counts and metadata corresponding to the Figures 5B,6A and 6D of the manuscript.Datasets were generated in two steps in which a LEC population was extracted from the control and mutant datasets individually after removal of contaminating cells identified as epithelial cells/keratinocytes, fibroblasts, mural cells and immune cells based on DEG analysis (Supplemental Data Set 9 of the manuscropt). In the second step, LECs from the control and mutant mice were integrated, and additional small clusters with neuronal, immune cell and fibroblast identities were removed (Supplemental Data Set 9 of the manuscript).  Batch correction using Seurat's canonical correlation analysis (CCA) was performed to generate clusters from control ear skin Ctrl1-3 (Figure 5B) . Batch correcting using Harmony package (version: 1.0) was performed to obtain clusters from mutant samples Pik3ca1-5 (Figure 6A) as well as for integration with the control dataset (Figure 6D).
Assembly: GRCm38; NM_001004410
Supplementary files format and content: .Rdata file including two objects "counts" and "meta.data"
Supplementary files format and content: Matrix table with raw gene counts for every sample/ cell (express_matrix) + gene length and gene title files organized in folders corresponding to the individual plates/samples

source_name: Ear Skin

extract_protocol:
Ear skin was first digested in 5 mg/ml Collagenase II in PBS supplemented with 0.2 mg/ml DNaseI and 0.2% FBS, followed by filtering through 50 µm filters (CellTricks). Fc-receptors were blocked with rat anti-mouse CD16/32 antibody (eBioscience), followed by staining using Podoplanin-APC and CD31-Pe-Cy7 antibodies. Dump channel included erythrocytes and immune cells (labeled using CD45-eF450, CD11b-eF450 and Ter119-eF450) and dead cells (SYTOX Blue dead stain (Life Technology)). The sorting into 384-well plates was performed with a 100 µm nozzle on BD FACS AriaIII CellSorter (BD BioScience Flow Cytometry System equipped with four lasers: 405, 488, 561, 633 nm).
Smart-Seq2 library preparation according to Picelli S et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 2014;9(1):171–181.

treatment_protocol: 4-OHT dissolved in acetone (10 mg/ml) was administered topically to the dorsal side of each ear of 3-week-old mice.

value: Cre-

tag: disease state

value: helathy

value: 5 weeks

value: skin

value: FACs sorted LECs

tag: facs sorting

value: Podoplanin and CD31

tag: plate id


title: Ctrl_3

description:
LEC.WT.skin.RData
LEC.Pik3ca.WT

tag: treatment

value: healthy


title: Ctrl_1

description:
LEC.WT.skin.RData
LEC.Pik3ca.WT


title: Pik3ca_5_plate2

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT

value: Cre+

value: disease:Lymphatic malformations


title: Pik3ca_2

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT


title: Pik3ca_3_plate1

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT


title: Pik3ca_1

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT


title: Pik3ca_3_plate2

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT


title: Pik3ca_4

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT


title: whole blood, PT184-postART

type: genomic

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

country: Spain

institute: CNIC

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
preprocessSheet.tsv:  snoob normalized beta values
signalSheet.tsv:  Unmethylated and methylated signal intensities

label: bisulfite converted

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Whole Blood samples using the MagPurix Blood DNA Extraction Kit 200  according to standard instructions

tag: individual

tag: gender

value: female

value: YES

tag: week

value: whole blood

value: sample post ART


title: KO34_BD

tag: genotype

value: SSTR2 knockout


title: whole blood, CTL43

value: male

value: NO

tag: time

value: control sample


title: Pik3ca_5_plate1

description:
LEC.Pik3ca.Rdata
LEC.Pik3ca.WT

tag: cell type


title: whole blood, PT185-postART

tag: age


title: whole blood, PT182-postART


title: whole blood, PT183-postART


title: whole blood, PT184-preART

value: sample pre ART


title: Donor 1, Control-6D⁻6D⁻

description: 10x Genomics

value: Keratinocytes

value: 10-16 years old


title: whole blood, PT183-preART


title: whole blood, PT180-preART


title: whole blood, PT180-postART


title: whole blood, CTL41


title: whole blood, PT179-postART


title: whole blood, PT182-preART


title: whole blood, PT185-preART


title: whole blood, PT181-postART


title: whole blood, PT181-preART


title: whole blood, PT177-postART


title: whole blood, PT178-preART


title: whole blood, CTL44


title: whole blood, CTL39


title: whole blood, PT179-preART


title: whole blood, PT178-postART


title: whole blood, PT177-preART


title: whole blood, CTL40


title: whole blood, CTL38


title: whole blood, PT176-postART


title: whole blood, CTL37


title: whole blood, PT175-postART


title: whole blood, PT173-preART


title: whole blood, CTL35


title: whole blood, CTL34


title: whole blood, CTL36


title: whole blood, CTL42


title: whole blood, PT174-postART


title: whole blood, CTL33


title: whole blood, CTL32


title: whole blood, PT172-postART


title: whole blood, PT173-postART


title: whole blood, CTL30


title: whole blood, PT174-preART


title: whole blood, CTL27


title: whole blood, CTL26


title: whole blood, PT172-preART


title: whole blood, PT171-preART


title: whole blood, PT176-preART


title: whole blood, PT171-postART


title: whole blood, CTL28


title: whole blood, PT169-postART


title: whole blood, CTL24


title: whole blood, CTL29


title: whole blood, PT175-preART


title: whole blood, PT169-preART


title: whole blood, CTL23


title: whole blood, PT170-preART


title: whole blood, PT165-postART


title: whole blood, PT164-preART


title: whole blood, PT166-postART


title: whole blood, CTL31


title: whole blood, PT163-postART


title: whole blood, PT163-preART


title: whole blood, CTL22


title: whole blood, CTL21


title: whole blood, PT167-preART


title: whole blood, CTL25


title: whole blood, CTL19


title: whole blood, PT167-postART


title: whole blood, PT170-postART


title: whole blood, CTL17


title: whole blood, CTL18


title: whole blood, PT162-preART


title: whole blood, CTL16


title: whole blood, CTL15


title: whole blood, CTL14


title: whole blood, PT162-postART


title: whole blood, CTL13


title: whole blood, PT166-preART


title: whole blood, PT165-preART


title: whole blood, PT168-preART


title: whole blood, PT161-preART


title: whole blood, CTL10


title: whole blood, PT164-postART


title: whole blood, PT160-postART


title: whole blood, CTL11


title: whole blood, CTL 20

source_name: CTL 20

value: CTL 20


title: whole blood, PT160-preART


title: whole blood, PT159-postART


title: whole blood, PT168-postART


title: whole blood, CTL8


title: whole blood, CTL9


title: whole blood, CTL7


title: whole blood, CTL6


title: whole blood, PT158-postART


title: whole blood, PT159-preART


title: whole blood, CTL5


title: whole blood, CTL4


title: whole blood, PT157-preART


title: whole blood, CTL3


title: whole blood, PT156-preART


title: whole blood, PT157-postART


title: whole blood, PT158-preART


title: whole blood, CTL12


title: whole blood, CTL1


title: whole blood, PT152-postART


title: whole blood, PT156-postART


title: whole blood, PT161-postART


title: whole blood, CTL2


title: whole blood, PT154-preART


title: whole blood, PT153-postART


title: whole blood, PT153-preART


title: whole blood, PT155-preART


title: whole blood, PT155-postART


title: whole blood, PT152-preART


title: whole blood, PT154-postART


title: whole blood, PT151-preART


title: whole blood, PT150-preART


title: whole blood, PT149-preART


title: whole blood, PT148-preART


title: whole blood, PT150-postART


title: whole blood, PT151-postART


title: whole blood, PT144-postART


title: whole blood, PT148-postART


title: whole blood, PT149-postART


title: whole blood, PT147-preART


title: whole blood, PT146-preART


title: whole blood, PT147-postART


title: whole blood, PT146-postART


title: whole blood, PT143-postART


title: whole blood, PT145-preART


title: whole blood, PT145-postART


title: whole blood, PT142-preART


title: whole blood, PT143-preART


title: whole blood, PT141-postART


title: whole blood, PT140-postART


title: whole blood, PT142-postART


title: whole blood, PT141-preART


title: whole blood, PT140-preART


title: whole blood, PT136-preART


title: whole blood, PT139-postART


title: whole blood, PT137-postART


title: whole blood, PT138-postART


title: whole blood, PT138-preART


title: whole blood, PT139-preART


title: whole blood, PT136-postART


title: whole blood, PT135-preART


title: whole blood, PT137-preART


title: whole blood, PT132-postART


title: whole blood, PT134-preART


title: whole blood, PT134-postART


title: whole blood, PT133-postART


title: whole blood, PT133-preART


title: whole blood, PT144-preART


title: whole blood, PT132-preART


title: whole blood, PT131-preART


title: whole blood, PT130-postART


title: whole blood, PT129-postART


title: whole blood, PT130-preART


title: whole blood, PT127-postART


title: whole blood, PT126-postART


title: whole blood, PT131-postART


title: whole blood, PT125-preART


title: whole blood, PT128-preART


title: whole blood, PT127-preART


title: whole blood, PT125-postART


title: whole blood, PT126-preART


title: whole blood, PT123-postART


title: whole blood, PT124-preART


title: whole blood, PT124-postART


title: whole blood, PT128-postART


title: whole blood, PT122-postART


title: whole blood, PT135-postART


title: whole blood, PT121-postART


title: whole blood, PT120-postART


title: whole blood, PT118-preART


title: whole blood, PT122-preART


title: whole blood, PT117-postART


title: whole blood, PT129-preART


title: whole blood, PT120-preART


title: whole blood, PT118-postART


title: whole blood, PT119-preART


title: whole blood, PT113-preART


title: whole blood, PT117-preART


title: whole blood, PT116-postART


title: whole blood, PT114-postART


title: whole blood, PT115-postART


title: whole blood, PT115-preART


title: whole blood, PT116-preART


title: whole blood, PT114-preART


title: whole blood, PT109-preART


title: whole blood, PT112-preART


title: whole blood, PT111-preART


title: whole blood, PT110-postART


title: whole blood, PT111-postART


title: whole blood, PT110-preART


title: whole blood, PT109-postART


title: whole blood, PT108-postART


title: whole blood, PT108-preART


title: whole blood, PT106-postART


title: whole blood, PT107-preART


title: whole blood, PT105-postART


title: whole blood, PT107-postART


title: whole blood, PT106-preART


title: whole blood, PT105-preART


title: whole blood, PT123-preART


title: whole blood, PT103-postART


title: whole blood, PT102-postART


title: whole blood, PT104-preART


title: whole blood, PT101-postART


title: whole blood, PT121-preART


title: whole blood, PT113-postART


title: whole blood, PT102-preART


title: whole blood, PT119-postART


title: whole blood, PT100-preART


title: whole blood, PT100-postART


title: whole blood, PT98-postART


title: whole blood, PT112-postART


title: whole blood, PT99-preART


title: whole blood, PT98-preART


title: whole blood, PT99-postART


title: whole blood, PT97-preART


title: whole blood, PT97-postART


title: whole blood, PT94-preART


title: whole blood, PT96-preART


title: whole blood, PT93-preART


title: whole blood, PT95-preART


title: whole blood, PT95-postART


title: whole blood, PT104-postART


title: whole blood, PT94-postART


title: whole blood, PT101-preART


title: whole blood, PT103-preART


title: whole blood, PT93-postART


title: whole blood, PT96-postART


title: whole blood, PT92-postART


title: whole blood, PT89-postART


title: whole blood, PT91-postART


title: whole blood, PT91-preART


title: whole blood, PT90-preART


title: whole blood, PT92-preART


title: whole blood, PT90-postART


title: whole blood, PT85-postART


title: whole blood, PT89-preART


title: whole blood, PT88-postART


title: whole blood, PT86-postART


title: whole blood, PT88-preART


title: whole blood, PT86-preART


title: whole blood, PT85-preART


title: whole blood, PT84-postART


title: whole blood, PT83-preART


title: whole blood, PT82-postART


title: whole blood, PT81-preART


title: whole blood, PT83-postART


title: whole blood, PT84-preART


title: whole blood, PT80-preART


title: whole blood, PT82-preART


title: whole blood, PT81-postART


title: whole blood, PT78-postART


title: whole blood, PT79-preART


title: whole blood, PT77-postART


title: whole blood, PT80-postART


title: whole blood, PT79-postART


title: whole blood, PT87-preART


title: whole blood, PT75-preART


title: whole blood, PT73-preART


title: whole blood, PT87-postART


title: whole blood, PT78-preART


title: whole blood, PT76-postART


title: whole blood, PT76-preART


title: whole blood, PT74-postART


title: whole blood, PT74-preART


title: whole blood, PT75-postART


title: whole blood, PT72-postART


title: whole blood, PT71-postART


title: whole blood, PT70-preART


title: whole blood, PT69-preART


title: whole blood, PT72-preART


title: whole blood, PT71-preART


title: whole blood, PT67-postART


title: pGMR_mCherry_rep3

city: Boston

value: Pupal retina

value: UAS-mCherry (BDSC #35787)/pGMR-GAL4

tag: developmental stage

value: 40-41 hrs after puparium formation


title: whole blood, PT77-preART

tag: tissue


title: whole blood, PT68-postART


title: whole blood, PT66-preART


title: whole blood, PT69-postART


title: whole blood, PT65-preART


title: whole blood, PT70-postART


title: whole blood, PT64-postART


title: whole blood, PT68-preART


title: whole blood, PT67-preART


title: whole blood, PT65-postART


title: whole blood, PT63-preART


title: whole blood, PT64-preART


title: whole blood, PT63-postART


title: whole blood, PT57-preART


title: whole blood, PT60-preART


title: whole blood, PT73-postART


title: whole blood, PT62-preART


title: whole blood, PT62-postART


title: whole blood, PT61-preART


title: whole blood, PT66-postART


title: whole blood, PT59-preART


title: whole blood, PT57-postART


title: whole blood, PT59-postART


title: whole blood, PT58-preART


title: whole blood, PT58-postART


title: whole blood, PT49-preART


title: whole blood, PT61-postART


title: whole blood, PT44-postART


title: whole blood, PT16-postART


title: whole blood, PT44-preART


title: whole blood, PT18-postART


title: whole blood, PT48-preART


title: whole blood, PT49-postART


title: whole blood, PT56-preART


title: whole blood, PT48-postART


title: whole blood, PT33-postART


title: whole blood, PT33-preART


title: whole blood, PT16-preART


title: whole blood, PT60-postART


title: whole blood, PT27-preART


title: whole blood, PT20-postART


title: whole blood, PT35-preART


title: whole blood, PT40-preART


title: whole blood, PT40-postART


title: whole blood, PT35-postART


title: whole blood, PT20-preART


title: whole blood, PT47-preART


title: whole blood, PT27-postART


title: whole blood, PT47-postART


title: whole blood, PT15-postART


title: whole blood, PT15-preART


title: whole blood, PT29-preART


title: whole blood, PT43-postART


title: whole blood, PT56-postART


title: whole blood, PT31-preART


title: whole blood, PT18-preART


title: whole blood, PT52-preART


title: whole blood, PT31-postART


title: whole blood, PT38-postART


title: whole blood, PT29-postART


title: whole blood, PT28-postART


title: whole blood, PT22-preART


title: whole blood, PT43-preART


title: whole blood, PT38-preART


title: whole blood, PT37-postART


title: whole blood, PT37-preART


title: whole blood, PT28-preART


title: whole blood, PT55-postART


title: whole blood, PT36-preART


title: whole blood, PT50-preART


title: whole blood, PT42-postART


title: whole blood, PT22-postART


title: whole blood, PT46-preART


title: whole blood, PT32-postART


title: whole blood, PT24-preART


title: whole blood, PT42-preART


title: whole blood, PT50-postART


title: whole blood, PT32-preART


title: whole blood, PT36-postART


title: whole blood, PT19-postART


title: whole blood, PT52-postART


title: whole blood, PT14-postART


title: whole blood, PT14-preART


title: whole blood, PT19-preART


title: whole blood, PT39-postART


title: whole blood, PT17-preART


title: whole blood, PT55-preART


title: whole blood, PT17-postART


title: whole blood, PT41-postART


title: whole blood, PT34-preART


title: whole blood, PT30-postART


title: whole blood, PT41-preART


title: whole blood, PT24-postART


title: whole blood, PT30-preART


title: whole blood, PT34-postART


title: whole blood, PT12-postART


title: whole blood, PT54-preART


title: whole blood, PT21-postART


title: whole blood, PT12-preART


title: whole blood, PT13-preART


title: whole blood, PT54-postART


title: whole blood, PT11-postART


title: whole blood, PT46-postART


title: whole blood, PT53-postART


title: whole blood, PT39-preART


title: whole blood, PT11-preART


title: whole blood, PT23-postART


title: whole blood, PT53-preART


title: whole blood, PT51-preART


title: whole blood, PT45-postART


title: whole blood, PT26-preART


title: whole blood, PT9-preART


title: whole blood, PT9-postART


title: whole blood, PT21-preART


title: whole blood, PT23-preART


title: whole blood, PT26-postART


title: whole blood, PT10-postART


title: whole blood, PT5-postART


title: whole blood, PT10-preART


title: whole blood, PT7-preART


title: whole blood, PT8-preART


title: whole blood, PT6-preART


title: whole blood, PT25-preART


title: whole blood, PT51-postART


title: whole blood, PT4-postART


title: whole blood, PT6-postART


title: whole blood, PT1-postART


title: whole blood, PT3-postART


title: whole blood, PT2-postART


title: whole blood, PT2-preART


title: whole blood, PT4-preART


title: whole blood, PT3-preART


title: whole blood, PT1-preART


title: whole blood, PT45-preART