title: 11885X15_Adult Control

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description: 11885X15_151016_D00550_0296_BC7HLRANXX_4_1

data_processing:
Paired-end FASTQ reads were preprocessed using Trimmomatic for adaptor removal and with the quality filtering/clipping MAXINFO parameter set to 50:0.2 (Bolger, Lohse, & Usadel, 2014; DOI: 10.1093/bioinformatics/btu170) .
The effective read length of the libraries was extended using the FLASH tool that merged overlapping paired-end reads (Magoč & Salzberg, 2011; DOI: 10.1093/bioinformatics/btr507).
All reads (extended and non-overlapping paired-end) were mapped by the STAR RNA-seq aligner (version 2.5.0c; Dobin et al., 2013; DOI: 10.1093/bioinformatics/bts635) to the GRCh37/hg19 reference genome with splice junction annotations built using the 2-pass mapping strategy with known junctions from the GENCODE comprehensive gene annotation GTF file (Release 19, https://www.gencodegenes.org) and novel junctions detected in the first pass mapping.  Sorted bam alignments files were filtered for secondary alignments and retained only uniquely mapped reads.
The MAJIQ/Voila v1.0.5 (Modeling Alternative Junction Inclusion Quantification) software was used to detect and quantify splice variation from the filtered bam alignment files (Vaquero-Garcia et al., 2016; DOI: 10.7554/eLife.11752).  MAJIQ Builder used Ensembl transcriptome annotations downloaded from http://majiq.biociphers.org/download/DB/ensembl.hg19.gff3 and the 42 RNA-seq samples configured as individual experiments to construct splice graphs and detect known/novel local splicing variations.  Relative inclusion values (“percent selected index” or PSI) of splice junctions within LSVs were calculated using the MAJIQ psi command with parameters minreads = 2 and minpos = 1.  The Voila psi command generated tab-delimited output with sample level PSI values and genomic coordinates for exons and splice junctions.
The featureCounts program (version 1.5.1) was used to summarize the gene level expression values as integer number (Liao et al., 2014; DOI: 10.1093/bioinformatics/btt656).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: counts, bigwig

source_name: Adult Control

extract_protocol:
Frozen muscle biopsies (~ 4 milligrams) were cut on a cryostat (20 microns) and homogenized with a 26-gauge needle in 400 microliters of 20 mM Tris*Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, and 1% Triton X-100.  RNA was extracted using TRIzol® and precipitated with isopropanol according to the manufacturer’s instruction (Life Technologies).
Total RNA (~1 microgram) was depleted of human cytoplasmic and mitochondrial rRNA using tiling oligodeoxynucleotides and the RNase H digestion method (Adiconis et al., 2013; DOI: 10.1038/nmeth.2483).  Illumina TruSeq Stranded Total RNA library kits were used to prepare indexed libraries.

tag: age at biopsy

value: 27 yrs

tag: sample type

value: skeletal muscle biopsy sample

tag: sample group

value: adult control


title: 11885X14_Adult Control

status: Public on Feb 03 2023

type: SRA

country: USA

description: 11885X14_151016_D00550_0296_BC7HLRANXX_4_1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: 28 yrs


title: 11885X11_Adult Control

description: 11885X11_151016_D00550_0296_BC7HLRANXX_4_1

value: 25 yrs


title: 11885X16_Adult Control

description: 11885X16_151016_D00550_0296_BC7HLRANXX_4_1

value: 26 yrs


title: 11885X12_Adult Control

description: 11885X12_151016_D00550_0296_BC7HLRANXX_4_1


title: 11885X13_Adult Control

description: 11885X13_151016_D00550_0296_BC7HLRANXX_4_1

value: 19 yrs


title: Normal_retina,rep1

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

country: China

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with default settings
Trimmed sequence reads were mapped to hg38 using STAR with default settings
Read count extraction were performed using featurecounts with default settings
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

extract_protocol:
Total RNA samples were isolated using TRIzol reagent (Life Technologies, NY, USA).
The PA-seq libraries were constructed by following the protocol published before by Ni et al. (BMC Genomics,2013).The concentration of the RNA-seq libraries was measured by Qubit fluorometry (Life Technologies, NY, USA) before loading onto the Illumina HiSeq2000 platform.

tag: tissue

tag: genotype

value: WT

tag: treatment

value: cell differentiation


title: HeLa_WT_biol rep2

city: Hangzhou

first: Ge

last: Bai

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang university

data_processing:
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads
Genomic alignment (version from Ensembl genome browser) was using STAR(version:  2.7.10a) to get uniquely mapping reads
The reads count value of each gene was calculated by FeatureCounts (version:2.0.1)
Assembly: hg38
Supplementary files format and content: Tab-separated reads count value file

source_name: HeLa

extract_protocol:
CLIP was performed as previously described with slight modifications (Liu et al., 2016). HeLa cells were seeded in 10 cm dish and then transfected with plasmids expressing V5-tagged GlyRSWT, GlyRSP234KY or GlyRSP234KY-L42A. After 24 hours, cells were treated with 250 μM AS for 1 hour, then the medium was aspirated and the cells were washed twice with 5 mL ice-cold PBS. Subsequently, 4 ml of ice-cold PBS was added to the culture dish and the cells were irradiated once with 400 mJ/cm2 at 254 nm in UV-linker (UVP-CL-1000) on ice. After irradiation, the cells were scraped, collected, and lysed on ice with 1 mL lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 1×Protease Inhibitor Cocktail and 2.5 U/μL RNase inhibitor). After 30 min of incubation, the cell lysates were centrifuged at 12, 000 rpm, at 4℃ for 15 min, and then the supernatant was carefully collected and added 6 μg G3BP1 antibody (Santa cruz), then the mixture was incubated at 4˚C with gentle rotation overnight. The next day, the mixture was subsequently added 80 μL of protein A/G beads (Invitrogen), and continued to incubate at 4˚C with gentle rotation. After 4 hours, the supernatant was discarded and the beads were washed 3 times with 1 mL of high-salt buffer (5 × PBS supplemented with 0.1% SDS and 1% Nonidet P-40) and another 3 times with 1 mL of wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2 and 0.2% Tween-20). Subsequently, the beads were treated with 2 mg/mL proteinase K at 50˚C for 1 h, then magnetically separated, discarded, and the supernatant was added 1 mL Trizol reagent. Finally, protein-bind RNA were extracted using Trizol reagent and were precipitated by ethanol.
The CLIP RNA was assessed by Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit(Thermo Fisher Scientifc,USA). Briefly, CLIP RNA were fragmented to approximately 200bp. Then, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®(Life Technologies, USA) and then sequenced on Illumina （Illumina,USA）platformat with pair-end 150bp at Ribobio Co. Ltd (Ribobio, China).

tag: cell line

value: HeLa

tag: cell type

value: epithelial


title: 09_dNAB6_0min

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: RNAseq

data_processing:
Alignment. Command: STAR --readFilesIn file1.fastq file2.fastq --genomeDir index_file
samtools view -bS file.sam
samtools sort file.bam
samtools index -b file.bam
Coverage map (+strand). Command: bamCoverage -b file.bam --binSize 1 --filterRNAstrand forward --normalizeUsing CPM
Coverage map (-strand). Command: bamCoverage -b file.bam --binSize 1 --filterRNAstrand reverse --normalizeUsing CPM
Read counting. Command: featureCounts file.bam -a annotation.gtf --largestOverlap --extraAttributes gene_name -s 2 -T 50 -p -B
Assembly: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping. The genome and associated annotation file are included as part of this submission.
Supplementary files format and content: The .txt files (generated using featureCounts) contain information on the number of reads mapping to each transcript. The bigwig files provide coverage maps across the yeast genome.
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 14 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.65 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -d genome.novoindex
Further collapsing of reads aligning to the same location and with identical random barcodes.
Coverage maps. Command: pyGTF2bedGraph.py --gtf annotation_file.gtf -c chromosome_lengths.txt -t reads
Read counting. Command: pyReadCounters.py -f file.bam --file_type=novo --sense --gtf=annotation_file.gtf
Assembly: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary files format and content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedGraph files provide coverage maps across the yeast genome.

organism: Saccharomyces cerevisiae

source_name: haploid cells

growth_protocol: For RNAseq experiments (1-50), cells were cultured to 0.125 OD600 and either harvested directly or treated with Congo Red and harvested 1, 2, or 4 hours later.  Approximately 5 OD600 units were collected by centrifugation and frozen at -80°C.  For CRAC experiments (51-54), cells were cultured to 0.4 OD600 in 700 mL SD -TRP medium containing 2% glucose. Cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C.

extract_protocol:
For RNAseq experiments (1-50), cells were lysed with zirconia beads and vortexing, and RNA was extracted using hot phenol-chloroform. The CRAC (samples 51-54) protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson et al., 2020.
RNAseq libraries were prepared from 500ng of each total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the manufacturer's protocol. The CRAC (samples 51-54) protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson et al., 2020.

tag: strain

tag: congo red

tag: timepoint

value: 0 hr


title: HeLa_WT_biol rep1


title: 08_dMRN1_2CR_240min

description: RNAseq

value: 2 ug/uL

value: 4 hr


title: 12167X8_DM1

description: 12167X8_160219_D00294_0222_BC8HKKANXX_6_1

value: 55 yrs

value: adult myotonic dystrophy


title: 12167X7_DM1

description: 12167X7_160219_D00294_0222_BC8HKKANXX_6_1

value: 41 yrs


title: 07_dMRN1_2CR_120min

description: RNAseq

value: 2 hr


title: FB-sufficient airway epithelial cells, infected, 4 h, rep 3

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

description:
Sample-6 ,ID 82218
WT-3

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

growth_protocol: CFB-/- airway epithelial cells and their parent clones (CFB+/+) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (1% penicillin and streptomycin) at 5% CO2 in 37C

extract_protocol:
After 4h of Infection, cells were washed with PBS and harvested by adding Trypsin. RNA was isolated using Rneasy mini plus kit (Qiagen). 1 microgram of total RNA was used for the construction of sequencing libraries.
oligo-dT

treatment_protocol: Cells were plated on 35 mm plate  one day before infection  with a confluency of 80-90% at the time of infection and then infected with Pa57-15 for 4h in DMEM without antibiotics

value: Airway Epithelial cell

value: CFB+/+

value: Infected with PA57-15 for 4h


title: FB-sufficient airway epithelial cells, infected, 4 h, rep 2

description:
Sample-5 ,ID 82217
WT-2


title: 12167X5_DM1

description: 12167X5_160219_D00294_0222_BC8HKKANXX_6_1

value: skeletal muscle biopsy sample


title: 12167X4_DM1

description: 12167X4_160219_D00294_0222_BC8HKKANXX_6_1

value: 44 yrs


title: FB-sufficient airway epithelial cells, infected, 4 h, rep 1

description:
Sample-4 ,ID 82216
WT-1


title: FB-deficient airway epithelial cells, infected, 4 h, rep 3

description:
Sample-3 ,ID 82215
FBKO-3

value: CFB-/-


title: 06_dMRN1_2CR_60min

description: RNAseq

value: 1 hr


title: 12167X11_DM1

description: 12167X11_160219_D00294_0222_BC8HKKANXX_6_1

value: 57 yrs


title: 12167X10_DM1

description: 12167X10_160219_D00294_0222_BC8HKKANXX_6_1

value: 49 yrs


title: 05_dMRN1_0min

description: RNAseq


title: FB-deficient airway epithelial cells, infected, 4 h, rep 2

description:
Sample-2, ID 82214
FBKO-2


title: 04_wt_2CR_240min

description: RNAseq

value: wild type


title: 03_wt_2CR_120min

description: RNAseq


title: 02_wt_2CR_60min

description: RNAseq


title: 11885X2_DM1

description: 11885X2_151016_D00550_0296_BC7HLRANXX_3_1

value: 38 yrs


title: 11885X4_DM1

description: 11885X4_151016_D00550_0296_BC7HLRANXX_3_1

value: 29 yrs


title: STB48h, H3K27ac, CHIP-seq, rep1

city: Yangzhou

first: Cui

last: Du

state: Jiangsu

address: NO.88 University South Road

institute: Yangzhou University

library_source: genomic

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4.
Raw reads were aligned to the reference genome (GRCh38) using Bowtie v2.3.5 (Langmead and Salzberg 2012) with default settings.
Reads aligned to multiple genomic loci were discarded using samtools v1.13 (Li, et al. 2009) with the parameter -q 2.
PCR duplicates were removed using the rmdup function of samtools v1.13 (Li, et al. 2009).After confirming the data reproducibility, reads from biological replicates were pooled together for further analysis.
Peak calling was performed with MACS v2.2.6 (Zhang, et al. 2008) with default settings, with H3K9me3 and H3K27me3 called as broad peaks while others as narrow peaks. The called peaks were further cleaned by removing those overlap ENCODE Blacklist V2 regions (Amemiya, et al. 2019).
Assembly: GRCh38
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: genomic DNA

source_name: syncytiotrophoblast

extract_protocol:
Cell samples were fixed (hTSC, STB24h and STB48h) by 1% formaldehyde solution and ultrasonic using a BioRuptor sonicator (Diagenode). After ultrasonic, fragmented chromatin was centrifuged to remove debris, and 5% of the volume was used as an input control. The rest was incubated with anti-H3K27ac (abcam, ab4729) and anti-H3K4me3 (abcam, ab8580) bound to 20 μl protein A magnetic beads (Invitrogen) on a rotator at 4℃ overnight.
DNA was purified and Illumina libraries were constructed using the KAPA DNA Hyper Prep Kit (KK8502) following the manufacturer’s instruction and sequenced on an Illumina Novaseq 6000.

value: syncytiotrophoblast

tag: antibody

value: H3K27ac (abcam, ab4731)

tag: time


title: STB24h, Input, CHIP-seq, rep1


title: CTRLC57AllOther1_S3_L002

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
3'-end
ONC-retina.mtx, ONC-retina_gene.tsv, ONC-retina_cell.tsv, ONC-retina_celltype.tsv

data_processing:
For 10x 3' v2 data, the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
For 10x 3' v3 data, the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Assembly: GRCm38
Supplementary files format and content: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary files format and content: celltype.tsv, a tab-delimited file with annotated cell type information for each cell
Supplementary files format and content: gene.tsv, gene names (row names of the sparse count matrix)

organism: Mus musculus

source_name: Mouse retina

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Eyecups were dissected in HBSS+HEPES and digested in trypsin/EDTA, after which RPE sheets were released by manual shaking into 20% FBS in HBSS+HEPES, and dissociated into single cell suspensions using manual trituration. Single cell suspensions were incubated with anti-CD90, CD45, CD140a and GLAST antibodies (conjugated to various fluorophores) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded. Collected cells were loaded into 10X Chromium Single Cell Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ V2 or V3 platforms (10X Genomics, Pleasanton, CA) following the manufacturer’s protocols. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina NextSeq 500 or HiSeq X.

treatment_protocol: C57BL/6J and Vglut2:cre;Stp15 mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. Eyecups were trypsinized and gently shaken to release RPE cells.

tag: Sex

value: Male

tag: age

value: 6-8 weeks

tag: time point

value: Ctrl

tag: version


title: CtC57GLAST_S5_L003


title: STB48h, Input, CHIP-seq, rep1


title: 01_wt_0min

description: RNAseq

value: 0 hr


title: 11832X3_DM1

description: 11832X3_150911_D00550_0290_AC7JV1ANXX_8_1

tag: age at biopsy

value: adult myotonic dystrophy


title: hTSC, Input, CHIP-seq, rep1

source_name: human trophoblast stem cell

value: human trophoblast stem cell


title: Midbrain_NGLY1_KO_3

city: Rockville

first: Wei

last: Zheng

state: MD

address: 9800 Medical Center Dr

department: National Center for Translational Sciences

institute: National Institutes of Health

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each

extract_protocol:
Total RNA was isolated using the Rneasy Midi kit and quality determined using a Bioanalyzer 6100.
Directional RNA-seq was performed with 100 ng of total RNA using the TruSeq Stranded mRNA library preparation kit.

value: midbrain organoid

value: Midbrain differentiation from iPSC

value: Day 90


title: Midbrain_NGLY1_KO_1


title: CrC571dCd45Cd140aR1_S2_L002


title: STB24h, H3K27ac, CHIP-seq, rep1

value: H3K27ac (abcam, ab4730)


title: hTSC, H3K27ac, CHIP-seq, rep1

value: H3K27ac (abcam, ab4729)


title: FB-deficient airway epithelial cells, infected, 4 h, rep 1

description:
Sample-1, ID 82213
FBKO-1

value: Airway Epithelial cell

value: CFB-/-

value: Infected with PA57-15 for 4h


title: Midbrain_NGLY1_594_2


title: Cr2wC57GLAST_S4_L003


title: 11885X3_DM1

description: 11885X3_151016_D00550_0296_BC7HLRANXX_3_1

value: 44 yrs

tag: sample type

value: skeletal muscle biopsy sample


title: Midbrain_NGLY1_594_3


title: STB48h, H3K4me3, CHIP-seq, rep1

value: syncytiotrophoblast

value: H3K4me3 (abcam, ab8582)


title: Midbrain_NGLY1_KO_2


title: 11832X1_DM1

description: 11832X1_150911_D00550_0290_AC7JV1ANXX_8_1

value: 35 yrs

tag: sample group


title: C57d14cd45cd140a2_S10_L007

value: Male

value: 6-8 weeks


title: 11832X4_DM1

description: 11832X4_150911_D00550_0290_AC7JV1ANXX_8_1

value: 39 yrs

value: adult myotonic dystrophy


title: Midbrain_NGLY1_594_1

value: midbrain organoid


title: Midbrain_NGLY1_519_3

value: Midbrain differentiation from iPSC


title: 11885X1_DM1

description: 11885X1_151016_D00550_0296_BC7HLRANXX_3_1


title: C57d14cd45cd140a2_S10_L005


title: C57d14cd45cd140a2_S10_L006


title: 11545X3_DM1

description: 11545X3_150515_D00550_0254_AC6GGPANXX_4_1

value: 30 yrs


title: hTSC, H3K4me3, CHIP-seq, rep1

value: human trophoblast stem cell

value: H3K4me3 (abcam, ab8580)


title: STB24h, H3K4me3, CHIP-seq, rep1

value: H3K4me3 (abcam, ab8581)


title: C57d14cd45cd140a2_S10_L004


title: 11832X2_DM1

description: 11832X2_150911_D00550_0290_AC7JV1ANXX_8_1

value: 34 yrs


title: 11885X9_Pediatric Control

description: 11885X9_151016_D00550_0296_BC7HLRANXX_3_1

source_name: Pediatric Control

value: 2 yrs

value: pediatric control


title: Midbrain_WT_PCS_3

source_name: MB-PCS

value: MB-PCS

value: WT

value: Day 90


title: C57d14cd45cd140a2_S10_L003


title: 11885X8_Pediatric Control

description: 11885X8_151016_D00550_0296_BC7HLRANXX_3_1

value: 8 yrs

value: skeletal muscle biopsy sample


title: C57d14cd45cd140a2_S10_L002

value: Male

value: 6-8 weeks


title: mouse feces_16S_barcode

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Purified products were sequenced using the Illumina MiSeq platform . FASTQ data was processed and analyzed using Quantitative Insights into Microbial Ecology 2 (QIIME2) version 2019.4 32. Single-end sequences were demultiplexed, and reads were denoised and clustered using Divisive Amplicon Denoising Algorithm (DADA2) 31. Primers were trimmed off and single end reads were truncated to ≥150 base pairs. A phylogenetic tree was constructed and features were assigned taxonomy using Greengenes reference database with 99% confidence 31.
Analysis was performed on a rarefied feature table of 7340 reads per sample after filtration of mitochondria and chloroplast sequences.
Supplementary files format and content: Xlsx file includes OTUs, taxonomy and reads per sample.
Library strategy: 16S DNA-seq

organism: synthetic construct

growth_protocol: Mouse grown under SPF conditions

extract_protocol:
DNA was extracted from fecal samples using the Invitrogen Purelink™ Microbiome DNA Purification Kit according to the manufacturer’s instructions, following two minutes of bead beating (Bio Spec). Following DNA extraction, the V4 variable region of the bacterial 16S rRNA gene was amplified by polymerase chain reaction (PCR) using the 515F and 806R primers, and each sample received a unique 515F barcoded primer. Primer sequences used were: 515F- (barcode) 5′-AATGATACGGCGACCACCGAGATCTACACGCTAGCCTTCGTCGCTATGGTAATTGTG TGYCAGCMGCCGCGGTAA-3′ and 806 R 5′- CAAGCAGAAGACGGCATACGAGATAGTCAGTCAGCCGGACTACHVGGGTWTCTAAT -3′ 31.
PCR reactions were carried out with the Primestar taq polymerase (Takara) for 30 cycles of denaturation (95 °C), annealing (55 °C) and extension (72 °C), and a final elongation at 72 °C. Amplicons were purified using AMPure magnetic beads (Beckman Coulter), and subsequently quantified using Picogreen dsDNA quantitation kit (Invitrogen). Samples were pooled at equal concentrations (50 ng/µl), loaded on 2% E-Gel (Thermo Fisher), and purified using NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).

treatment_protocol: No treatment

tag: tissue

value: multiplexed sample:F121A and WT


title: 11885X6_Pediatric Control

description: 11885X6_151016_D00550_0296_BC7HLRANXX_3_1

value: 9 yrs


title: C57d14cd45cd140a1_S9_L007


title: Midbrain_WT_PCS_2

value: midbrain organoid

tag: genotype

value: Midbrain differentiation from iPSC


title: 11545X4_DM1

description: 11545X4_150515_D00550_0254_AC6GGPANXX_4_1

value: 32 yrs

value: adult myotonic dystrophy


title: C57d14cd45cd140a1_S9_L006


title: 11885X5_Pediatric Control

description: 11885X5_151016_D00550_0296_BC7HLRANXX_3_1

value: 13 yrs


title: C57d14cd45cd140a1_S9_L005


title: Midbrain_NGLY1_519_2

tag: treatment


title: Midbrain_WT_JB_3

source_name: MB-JB

tag: cell line

value: MB-JB


title: Midbrain_WT_PCS_1

tag: cell type


title: C57d14cd45cd140a1_S9_L004

tag: strain


title: 11885X17_Pediatric Control

description: 11885X17_151016_D00550_0296_BC7HLRANXX_4_1

value: 2 yrs


title: Midbrain_WT_JB_2


title: Midbrain_WT_JB_1


title: STB96h, RNA-seq, rep3

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4
Raw reads were aligned to the reference genome (GRCh38) using STAR v2.7.3 (Dobin, et al. 2013).
Obtaining gene-level read counts using the featureCount function from subread v2.0.0 (Liao, et al. 2013)
calculated TPM value for each gene using RSEM(Li and Dewey 2011)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

extract_protocol:
For the extraction of RNA, total RNA was isolated from three biological repeats with the TRI reagent (Thermo Fisher Scientific).
Ribosome RNA was removed before the chain-specific library was constructed. Each sample was sequencing as 100 bp paired-end reads with MGISEQ-2000.

value: syncytiotrophoblast

value: Wild-type


title: 11885X18_Pediatric Control

description: 11885X18_151016_D00550_0296_BC7HLRANXX_4_1

value: 5 yrs

value: pediatric control


title: 11885X10_Pediatric Control

description: 11885X10_151016_D00550_0296_BC7HLRANXX_3_1

value: 4 yrs


title: Midbrain_NGLY1_519_1

value: Day 90


title: C57d14cd45cd140a1_S9_L003

value: Male


title: Midbrain_WT_5659_3

value: WT


title: C57d14cd45cd140a1_S9_L002

value: 6-8 weeks


title: STB96h, RNA-seq, rep2


title: 11832X5_Pediatric Control

description: 11832X5_150911_D00550_0290_AC7JV1ANXX_8_1

value: 0.1 yrs

value: skeletal muscle biopsy sample


title: C5748hGLAST_S1_L007

description:
3'-end
ONC-retina.mtx, ONC-retina_gene.tsv, ONC-retina_cell.tsv, ONC-retina_celltype.tsv


title: 14404X5_CDM

description: 14404X5_170629_D00550_0441_BCB8HLANXX_5_1

source_name: CDM

value: 8 yrs

value: congenital myotonic dystrophy (CDM)


title: Midbrain_WT_5659_2

value: midbrain organoid

value: Midbrain differentiation from iPSC


title: 11885X7_Pediatric Control

description: 11885X7_151016_D00550_0296_BC7HLRANXX_3_1

value: 12 yrs


title: Midbrain_WT_5659_1


title: STB96h, RNA-seq, rep1


title: STB72h, RNA-seq, rep3


title: C5748hGLAST_S1_L005


title: C5748hGLAST_S1_L004


title: 14404X3_CDM

description: 14404X3_170629_D00550_0441_BCB8HLANXX_5_1

value: 11 yrs


title: C5748hGLAST_S1_L003


title: STB72h, RNA-seq, rep1

value: syncytiotrophoblast


title: STB48h, RNA-seq, rep3

value: Wild-type


title: STB72h, RNA-seq, rep2


title: C5748hGLAST_S1_L002


title: 11832X6_CDM

description: 11832X6_150911_D00550_0290_AC7JV1ANXX_8_1

value: 0.2 yrs


title: 11545X8_CDM

description: 11545X8_150515_D00550_0254_AC6GGPANXX_4_1

value: 16 yrs


title: 14404X1_CDM

description: 14404X1_170629_D00550_0441_BCB8HLANXX_5_1


title: STB48h, RNA-seq, rep2


title: 13707X1_CDM

description: 13707X1_160923_D00550_0378_AC9T73ANXX_8_1

value: 10 yrs


title: STB48h, RNA-seq, rep1


title: C5748hGLAST_S1_L006


title: 11545X7_CDM

description: 11545X7_150515_D00550_0254_AC6GGPANXX_4_1

value: 1 yrs


title: STB24h, RNA-seq, rep2


title: C5724hGLAST_S4_L004

value: Male


title: STB24h, RNA-seq, rep3


title: 14404X4_CDM

description: 14404X4_170629_D00550_0441_BCB8HLANXX_5_1

value: 14 yrs


title: 11545X6_CDM

description: 11545X6_150515_D00550_0254_AC6GGPANXX_4_1


title: STB24h, RNA-seq, rep1


title: 11545X5_CDM

description: 11545X5_150515_D00550_0254_AC6GGPANXX_4_1

value: 7 yrs


title: C5724hGLAST_S4_L003

value: 6-8 weeks


title: C5724hGLAST_S4_L002


title: 14404X2_CDM

description: 14404X2_170629_D00550_0441_BCB8HLANXX_5_1

value: 6 yrs

value: skeletal muscle biopsy sample


title: C5724hGLAST_S4_L006


title: P3 HiChIP_H3K27ac_rep3

city: Nanjing

first: Zhang

last: Jing

address: Nanjing University

institute: Nanjing University

data_processing:
RNA-seq: The adaptors-trimmed and quality-filtered reads were mapped to mm10 or rn6 using HISAT2 version 2.1.0 with default parameters. Transcript assembly was performed using StringTie version 1.3.5. Expression levels measured as fragments per kilobase of exon model per million mapped fragments (FPKM).
ATAC-seq: Raw reads were trimmed for adaptor with cutadapt and aligned to mm10 using Bowtie2. The duplications in aligned reads were excluded by Picard Mark Duplicates. The unduplicated reads were used to call peaks with MACS2. ENCODE blacklist regions were removed. For visualization, bigwig files were generated using bedGraphToBigWig.
HiChIP: Raw reads were trimmed for adaptor with cutadapt. The reads passed quality control were aligned to mm10  using the HiC-Pro pipeline.  Default settings were used to  assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices.
Genome_build: RNA-seq: mm10 (mouse) and rn6 (rat), ATAC-seq: mm10, HiChIP: mm10.

source_name: Cardiomyocyte

extract_protocol:
Genomic DNA was extracted with DNA Clean & Concentrator kit(ZYMO).
Libraries were constructed according to the Illumina instruction.

treatment_protocol: Cardiomyocytes from embryonic day 18.5 and postnatal days 1/3/7 of mouse and postnatal days 1 of rats were isolated from left ventricles. Rat cardiomyocytes were treated with the 100 nM TSA one day after plating  and DMSO was used as negative control. 1 million cells were harvested in TRIzol RNA Isolation Reagents (Thermo, 15596018) for  RNAseq. 50000 cells were harvested and transposed with Tn5 transposase for ATAC-seq. 3 million cells were were harvested and fixed with 1% formaldehyde for HiChIP. MboI restriction enzyme was used to digest chromatin in HiChIP.

tag: restriction enzyme

value: MboI


title: C5724hGLAST_S4_L007


title: SC HBV 3 HTA 2.0

type: RNA

city: Chengdu

first: Chengxia

last: Xie

address: Wangjiang Campus, Sichuan University, Wuhou District

institute: Sichuan University

description: PBMCs at 3, SC HBV group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The raw data for the microarray was uploaded to Gminix-Cloud Biotechnology Information (GCBI; http://www.gcbi.com.cn/gclib/html/index) for further study, and then analyzed the data using Robust Multichip Analysis algorithm.

label: biotin

source_name: PBMCs from the SC HBV patient

label_protocol: Affymetrix Human Transcriptome Array 2.0 was used for differentially expressed lncRNAs and mRNAs detection, while Affymetrix miRNA 4.0 was used for miRNAs detection.

growth_protocol: The peripheral blood mononuclear cells (PBMCs) were obtained from three patients with SC HBV and three patients with CHB.

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: The peripheral blood mononuclear cells (PBMCs) were separated from patients blood, and collected for further total RNA extraction.

value: PBMCs

tag: disease state

value: SC HBV


title: hTSC, RNA-seq, rep2

value: human trophoblast stem cell


title: hTSC, RNA-seq, rep3


title: SC HBV 2 HTA 2.0

description: PBMCs at 2, SC HBV group


title: P3 HiChIP_H3K27ac_rep2


title: hTSC, RNA-seq, rep1


title: CHB 2 HTA 2.0

description: PBMCs at 2, CHB group

source_name: PBMCs from the CHB patient

value: CHB


title: E18.5 HiChIP_H3K27ac_rep3


title: SP-25c-T1

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

data_processing:
Raw reads were treated with Trimmomatic tool (v0.36) to remove adapter sequences and low-sequencing-quality bases using the following options: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36. Filtered reads from each library were aligned to genome assemblys of T. pubescens FBCC735 and P. centrifuga FBCC195 available at JGI Mycocosm, https://mycocosm.jgi.doe.gov/mycocosm,  using STAR (v2.7.10a). The raw gene counts were used to calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKMs) based on total exon length derived from gff3 annotations available at JGI Mycocosm .
Assembly: T. pubescens FBCC735 and P. centrifuga FBCC195 available at JGI Mycocosm, https://mycocosm.jgi.doe.gov/mycocosm
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
The geneIDs in the counts files are the IDs listed in the proteome sequences derived from the Genome assembly on JGI Mycocosm database, https://mycocosm.jgi.doe.gov/Phlcen1/Phlcen1.home.html and https://mycocosm.jgi.doe.gov/Trapub1/Trapub1.home.html.

organism: Trametes pubescens

source_name: Mycelium sample

growth_protocol: Briefly, T. pubescens FBCC735 and P. centrifuga FBCC195 were maintained on 2% malt agar plates, from which four plugs (diameter, 7 mm) were used to inoculate 100-ml 2% malt extract liquid cultures. Stationary cultures were incubated at 25°C and 15°C for 21 days, respectively, for T. pubescens and P. centrifuga. The fungus was cultivated on solid-state cultures containing 2 g (dry weight) of Norway spruce (Picea abies) wood sticks (approximately 2.5 by 0.3 by 0.2 cm) or wheat (Triticum aestivum) straw pieces (2 cm in length) on top of 1% water agar at 25°C for 21 days.

extract_protocol:
The moisture content of the cultures was adjusted to 60% with sterile H2O. The stationary cultures were inoculated with 4 ml of homogenized fungal mycelium from low-nitrogen asparagine medium (pH 4.5), supplemented with 1% glycerol and incubated at 25°C for 21 days. RNA was extracted using CsCl ultracentrifugation and checked using a fragment analyzer (Advanced Analytical Technologies).
Purification of mRNA, synthesis of cDNA library and sequencing on the Illumina HiSeq 2500 platform were performed at the GenomeScan in the Netherlands, https://www.genomescan.nl/.

value: growth on spruce at 25°C

value: Mycelium


title: SP-25c-T2


title: C5724hGLAST_S4_L005


title: SC HBV 1 HTA 2.0

description: PBMCs at 1, SC HBV group


title: WS-25c-T1

value: growth on wheat straw at 25°C


title: WS-25c-T2


title: CHB 1 HTA 2.0

description: PBMCs at 1, CHB group


title: P3 HiChIP_H3K27ac_rep1


title: SP-15c-T2

value: growth on spruce at 15°C


title: HEK-293 plus pCMV-TDP-43-ADAR rep1

city: Waltham

first: Katharine

last: Abruzzi

address: 415 South St.

department: Biology

institute: HHMI; Brandeis University

data_processing:
Trim reads:cutadapt -q 20 --trim-n --minimum-length=10 -o $file1 -p $file2 $infile1 $infile2
Align via STAR : STAR  --runThreadN 8 --outFilterMismatchNoverLmax 0.06 --outFileNamePrefix $prefix"_" --outFilterMatchNmin 15 --outFilterMultimapNmax 1  --genomeDir $star_indices --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignMatesGapMax 25000 --readFilesIn $file1 $file2
remove PCR duplicates:java -Xmx4g -jar $PICARD_JAR MarkDuplicates --INPUT $input_for_picard --OUTPUT $dupremove_bam --METRICS_FILE dup.txt --VALIDATION_STRINGENCY LENIENT --REMOVE_DUPLICATES true --TMP_DIR tmp --ASSUME_SORTED true
generate raw read counts:python -m HTSeq.scripts.count -q -r pos -f bam $sort_out --stranded=no --minaqual=10 $gtf_file > $prefix"_unique_raw.txt"
generate transcript counts:stringtie -A $prefix"_gene_abundance.txt" -o $assembled_transcript -p 6 -e -G $gtf_file $sort_out
Assembly: GRChg38.p13
Supplementary files format and content: Bedgraph file listing all potential editing sites

molecule: polyA RNA

extract_protocol:
400 GFP-positive cells were isolated by FACS sorting and lysed in 100µl of Lysis buffer
Libaries were constructed using Smart-seq2 protocol


title: E18.5 HiChIP_H3K27ac_rep2


title: E18.5 HiChIP_H3K27ac_rep1


title: SP-15c-T1


title: P7 RNA-seq rep2


title: HEK-293 plus pCMV-APOBEC rep1

value: pCMV-APOBEC


title: HEK-293 plus pCMV-ADAR rep1

value: pCMV-ADAR


title: WS-15c-T2

value: growth on wheat straw at 15°C


title: WS-15c-T1


title: P3 RNA-seq rep2


title: CHB 3 HTA 2.0

description: PBMCs at 3, CHB group


title: P3 RNA-seq rep1


title: Porphyromonas gingivalis W83 NO stress [WT83_00_NO_B]

city: Huntsville

first: Marie-Claire

last: Boutrin

address: 7000 Adventist Blvd NW

institute: Oakwood University

data_processing:
The mapped reads were then processed using Cufflinks (http://cufflinks.cbcb.umd.edu/) for transcript assembly. Read counts for each annotated gene in the P. gingivalis W83 genome assembly version ASM758v1 were calculated, normalized as reads per million mapped reads (RPM), and then transformed into log2 scale. To avoid infinite values, 1 count was added to each gene before log2 transformation.
The quality of reads was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads were filtered by Trimmomatic-0.22 (http://www.usadellab.org/cms/index.php?page=trimmomatic), including removing: 1) reads with sequencing adapters; 2) the 5’-end 5 bases of each read; 3) reads with more than 20 bases of ‘N’ nucleotides; 4) reads with low quality; and 5) reads with length less than 36 bases after trimmed. Trimmed reads were mapped to P. gingivalis W83 genome (NCBI accession ID: NC_002950) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). The mapped reads were then processed using Cufflinks (http://cufflinks.cbcb.umd.edu/) for transcript assembly. Read counts for each annotated gene in the P. gingivalis W83 genome assembly version ASM758v1 were calculated, normalized as reads per million mapped reads (RPM), and then transformed into log2 scale. To avoid infinite values, 1 count was added to each gene before log2 transformation. Differentially expressed genes (DEGs) were determined with a non-stringent p-value cutoff of ≤ 0.05 and a fold change (FC) ≥ 1.5 (both up regulated and down regulated) compared with wild type W83. The Gene Ontology (GO) functional clustering and pathway analyses were done using NCBI DAVID Bioinformatics Tool (http://david.abcc.ncifcrf.gov/home.jsp) and KEGG GENES Database (https://www.kegg.jp/kegg/genes.html).
Supplementary files format and content: The processed data file is an excel file "RNAseq data_CdhR involvement in Pg in NO stress.xlsx" that includes data on fold change in gene expression for controls and NO-stressed samples. Genes IDs, p values of test, log2 of fold change, fold change and description of the sample are listed in columns entitled "Gene symbol, p value, Log2 (Fold change), Fold change, and GroupA_B(A/B)".
Assembly: P. gingivalis W83 genome assembly version ASM758v1

organism: Porphyromonas gingivalis

source_name: Porphyromonas gingivalis W83 NO stress

growth_protocol: Fresh cultures of P. gingivalis strains (mutants and wild type) were grown from overnight cell cultures under anaerobic conditions at 37ºC in BHI broth. P. gingivalis strains were grown to early exponential phase (OD600:~0.3) in BHI broth under anaerobic conditions at 37ºC.

extract_protocol:
Total RNA was extracted from the NO-stressed samples and controls using a total RNA isolation kit (Promega, WI). Additional DNase treatment was carried out using DNase kit (Ambion, Austin, TX).
The library was generated using RiboMinus Transcriptome Isolation Kit (Life Technologies, CA) and NEXTflex RNA-Seq Kit (Bioo Scientific, TX) following the vendors’ protocols. Briefly, 2 μg total RNA (20 μl) was hybridized with 4 μl of RiboMinus probe in 100 μl hybridization buffer at 37 ºC for 5 min, which was then cooled on ice for at least 30 seconds. The sample was transferred into an Eppendorf tube containing RiboMinus Beads resuspended in 100 μl hybridization buffer, which was incubated at 37 ºC for 15 min to allow beads to bind with probes. The tube was placed on a magnetic separator for 1 min to pellet the rRNA-probe complex. The supernatant containing RiboMinus RNA was transferred into a new tube. The RiboMinus RNA was concentrated by ethanol precipitation and was resuspended in 14 μl nuclease free water. Five μl of NEXTflex RNA Fragmentation buffer (Bioo Scientific, TX) was mixed with the 14 μl RiboMinus RNA. The mixture was incubated at 95 ºC for 10 min and then chilled on ice immediately. The first and second strand cDNAs were synthesized following the Bioo Scientific protocol and the NEXTflex RNA-Seq barcode was ligated to double strand cDNA after the end repair and adenylation for multiplexing. The library was amplified by PCR.
RNA seq. The quality of each RNA-Seq library was checked using Agilent Bioanaylzer and DNA 1000 Nano chip and the library was quantified using Qubit (Life Technology, CA). The libraries (20 samples) were loaded into a single lane of Illumina V3 flow cell for cluster generation and the sequencing was done on Illumina HiScanSQ with 100 x 100 BP of paired-end reads.

treatment_protocol: At OD600~0.3 time point, the bacteria cultures were stressed with Diethylamine (DEA) NONOate (15µl, 24mM stock concentration) for the NO stress studies. Untreated wild type and mutant strains cell cultures grown under the same conditions were used as controls. Samples were taken after 15 mins of NO stress treatment and controls were taken from untreated cultures at the same time.

tag: growth stage

value: Fresh culture, OD600~0.3

value: bacteria

value: wild type

value: DEA-treated, 15 mins


title: HEK-293 plus pCMV-TDP-43-APOBEC rep1


title: HEK-293 plus pCMV-EGFP_only rep1

description:
CR_SEQ_6
control sample to use as a baseline for identifying RNA editing


title: HEK-293 plus pCMV-ADAR rep2


title: Porphyromonas gingivalis W83 control [WT83_00_YY_A]

source_name: Porphyromonas gingivalis W83 control

value: untreated, 15 mins


title: Porphyromonas gingivalis W83 control [WT83_00_YY_B]


title: Porphyromonas gingivalis W83 NO stress [WT83_00_NO_A]


title: HEK-293 plus pCMV-TDP-43-ADAR rep2


title: HEK-293 plus pCMV-APOBEC rep2


title: P1 RNA-seq rep2


title: P7 ATAC-seq rep2


title: Porphyromonas gingivalis PG1236-37-deficient mutant NO stress [X1236-37_00_NO_B]


title: E18.5 RNA-seq rep1


title: SP-25c-P2

organism: Hermanssonia centrifuga


title: E18.5 RNA-seq rep2


title: HEK-293 plus pCMV-TDP-43-APOBEC rep2


title: Porhyromonas gingivalis PG1236-37-deficient mutant NO stress [X1236-37_00_NO_A]


title: P1 RNA-seq rep1


title: Porphyromonas gingivalis PG1236-37-deficient mutant control [X1236-37_00_YY_B]


title: Mic60 KO cells, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information.
DESeq2 was used for differential expression analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Mic60_RNAseq.txt: Processed data file contains the raw counts for each gene.

source_name: PC3 cell line

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions. RNA was treated with Turbo DNA-free kit (life technologies) and quality checked with TapeStation (Agilent).
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions.

value: Mic60 KO

tag: replicate


title: P7 ATAC-seq rep1


title: WS-25c-P2


title: HEK-293 plus pCMV-EGFP_only rep2

description:
CR_SEQ_1
control sample to use as a baseline for identifying RNA editing


title: Porphyromonas gingivalis PG1236-37-deficient mutant control [X1236-37_00_YY_A]


title: WS-25c-P1


title: Mic60 KO cells, replicate 2


title: Porphyromonas gingivalis PG1236-deficient mutant NO stress [X1236_00_NO_B]


title: Mic60 KO cells, replicate 1


title: SP-15c-P2


title: P3 ATAC-seq rep1


title: P7 RNA-seq rep1


title: Porphyromonas gingivalis PG1236-deficient mutant NO stress [X1236_00_NO_A]


title: Mic60 WT cells, replicate 3

value: Mic60 WT


title: P1 ATAC-seq rep1


title: Mic60 WT cells, replicate 2


title: WS-15c-P2


title: Mic60 WT cells, replicate 1


title: Pophyromonas gingivalis PG1236-deficient mutant control [X1236_00_YY_B]


title: WS-15c-P1


title: E18.5 ATAC-seq rep2


title: E18.5 ATAC-seq rep1


title: SP-15c-P1


title: Pophyromonas gingivalis PG1236-deficient mutant control [X1236_00_YY_A]


title: SP-25c-P1


title: ATAC_8wpw1_Ctrl_Rep1

status: Public on Feb 02 2023

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description:
Cultured cells from Ctrl (non-memory) region
ATAC_8wpw1_CTRL-idr.conservative_peak.narrowPeak.gz

data_processing:
Bowtie278  was used to align reads to the mouse reference genome UCSC mm10.
Peak calling was performed with MAC2.

source_name: Lrig1 GL Sca1+ epidermal cells

extract_protocol:
Lrig1 GL Sca1+ cells  were FACS sorted and collected into lysis buffer for DNA extraction and transpose with TN5 transposase
NexteraXT indexing

value: Lrig1 GL Sca1+ epidermal cells

tag: protocol


title: ATAC_8wpw1_Distal_Rep2

description:
Cultured cells from Distal memory region
ATAC_8wpw1_MEM-idr.conservative_peak.narrowPeak.gz


title: ATAC_8wpw1_Distal_Rep1

value: Cultured cells from Distal memory region


title: 0w_PRT4165_Rep1

description:
PRT4165 treated epidermis
ATAC_0w_PRT-idr.conservative_peak.narrowPeak.gz

value: PRT4165 treated epidermis


title: 0w_Vehicle_Rep2

description:
Vehicle treated epidermis
ATAC_0w_AC-idr.conservative_peak.narrowPeak.gz

value: Vehicle treated epidermis


title: 0w_Vehicle_Rep1


title: P3 ATAC-seq rep2


title: 8w_pw1_Rep2

description:
8 weeks after first wound induction
ATAC_8wpw1-idr.conservative_peak.narrowPeak.gz

value: 8 weeks after first wound induction


title: 1w_pw2_Rep2

description:
1 week after seconf wound induction
ATAC_1wpw2-idr.conservative_peak.narrowPeak.gz

value: 1 week after seconf wound induction


title: 8w_pw1_Rep1


title: 1w_pw2_Rep1


title: 1w_pw1_Rep2

description:
1 week after first wound induction
ATAC_1wpw1-idr.conservative_peak.narrowPeak.gz

value: 1 week after first wound induction


title: P1 ATAC-seq rep2


title: 1w_pw1_Rep1


title: 0w_Rep2

description:
Homeostasis
ATAC_0w-idr.conservative_peak.narrowPeak.gz

value: Homeostasis


title: 0w_Rep1


title: UV_W_Rep2

description:
Wounded and UVB treated epidermis
ATAC_UV_W-idr.conservative_peak.narrowPeak.gz

value: Wounded and UVB treated epidermis


title: UV_W_Rep1


title: UV_Rep1

description:
UVB treated epidermis
ATAC_UV-idr.conservative_peak.narrowPeak.gz

value: UVB treated epidermis


title: UV_Rep2


title: 8wpw1_Distal_Rep5

data_processing:
Reads were next aligned to the mouse reference genome (UCSC mm10/GRCm38) using HiSat2 v2.2.01
Gene expression levels were quantified with featureCounts v1.6.12 (options: -t exon -g gene_name) using the GENCODE (https://www.gencodegenes.org) release M20 annotation
Gene expression counts of each cell population were next analysed using the edgeR3 R/Bioconductor package
Assembly: mm10
Supplementary files format and content: rawcounts

growth_protocol: Lrig1 GL Sca1+ cells  were FACS sorted and cultured in keratinocytes complete media for 1 weeks

extract_protocol:
Smart-Seq2 protocol
For extracted RNA, indexed cDNA libraries were obtained following the NexteraXT Illumina protocol
minibulk RNA-seq

tag: time

value: 8w pw1

tag: region

value: Distal memory region


title: 0w_PRT4165_Rep2


title: ATAC_8wpw1_Ctrl_Rep2

value: Cultured cells from Ctrl (non-memory) region


title: 8wpw1_Distal_Rep6


title: 8wpw1_Distal_Rep3


title: 8wpw1_Ctrl1_rep3

value: Ctrl (non-memory) region


title: 8wpw1_Distal_Rep1


title: 8wpw1_Ctrl1_rep4


title: 8wpw1_Ctrl1_rep7


title: 8wpw1_Ctrl1_rep5


title: 8wpw1_Ctrl1_rep2


title: 8wpw1_Ctrl1_rep1


title: OE_MI4_T3

city: Atlanta

first: Avraham

last: Shakked

state: GA

address: 1760 Haygood Dr NE

institute: Emory University

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release, using htseq-count
Normalization was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel files includes the normalized counts, pvalues and log ratios

source_name: Heart

extract_protocol:
RNA was extracted and purified from PBS-perfused, liquid N2-frozen, powdered whole heart tissue using an miRNeasy kit (Qiagen, 217004) according to manufacturer' instructions
Inhouse poly A based RNA seq

value: Heart

value: OE

value: MI - Rediff


title: OE_MI3_T3


title: OE_Sham3_T3

value: Sham - Rediff


title: OE_MI1_T3


title: OE_Sham1_T3


title: WT_MI3_T3

value: WT


title: OE_MI2_T3


title: Differentiated Patient-Derived Human Trophoblast Organoids

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

country: Canada

institute: The University of British Columbia

library_source: transcriptomic single cell

data_processing:
For all samples the 10X Genomics Cell Ranger version 3.0 software was used for read alignment by STAR and counting against the hg19 reference transcriptome, using default parameters.
Assembly: hg19
Supplementary files format and content: For each sample, three processed data files were generated as .tsv files. These include one barcode file with cell barcode sequences that correspond to column indices, one feature file with gene counts that correspond to row indices, and one matrix file for the count matrix.

source_name: Fetal Placenta

growth_protocol: Trophoblast organoid cultures were maintained in 100% growth-factor reduced matrigel submersed in trophoblast organoid media, as described in Shannon et al. 2021.

extract_protocol:
RNA from all samples was prepared using TriZol reagent followed by Rneasy Mini Kit purification, following manufacturer protocol. RNA purity was confirmed by NanoDrop Spectrophotometry and integrity confirmed by Agilent BioAnalyzer. Only RNA with a RIN > 8.0 was used for sequencing.
Libraries were constructed using the 10X Genomics chromium single cell 3’ reagent v2 chemistry kit for all placental tissue samples and using the chromium single cell 3’ reagent v3 chemistry kit for all trophoblast organoid samples at a read depth of 50,000 reads/cell for undifferentiated and a read depth of 150,000 reads/cell for EVT-differentiated PD-TOrg samples.

treatment_protocol: Trophoblast organoid differentiation into EVT was achevied by removing trophoblast organoid media, and replacing it with EVT differentiation media lacking CHIR99021 and R-spondin in the basal media

value: Trophoblast Organoids

value: Fetal Placenta

tag: state

value: EVT-differentiated

tag: days culture_in_wnt-_media

tag: pooled

value: Yes (n=3 placentas)

tag: gestational age

tag: fetal sex

value: Mixed Male and Female

tag: maternal age

tag: maternal bmi

tag: maternal smoking_status

value: No

tag: maternal diabetes

tag: anti-hypertensive drug_exposure

tag: anti-inflammatory drug_exposure


title: Undifferentiated Patient-Derived Human Trophoblast Organoids

tag: cell type

tag: tissue

value: Regenerative


title: 8wpw1_Distal_Rep4

value: Lrig1 GL Sca1+ epidermal cells

tag: genotype

tag: treatment


title: WT_MI2_T3


title: OE_Sham2_T3


title: 8wpw1_Distal_Rep2

tag: time

value: 8w pw1


title: WT_MI1_T3


title: WT_MI4_T3


title: WT_Sham3_T3


title: OE_MI4_T2

value: MI - Intermediate


title: 8wpw1_Ctrl1_rep8

tag: region


title: WT_Sham1_T3


title: 8wpw1_Ctrl1_rep6


title: WT_Sham4_T3


title: WT_Sham2_T3


title: OE_MI3_T2


title: OE_MI1_T2


title: OE_Sham4_T2

value: Sham - Intermediate


title: OE_Sham2_T2


title: OE_Sham3_T2


title: OE_Sham1_T2


title: WT_MI3_T2


title: WT_MI2_T2


title: WT_Sham4_T2


title: WT_Sham3_T2


title: WT_Sham1_T2


title: OE_MI1_T1

value: MI - Dediff


title: OE_sham4_T1

value: Heart

value: Sham - Dediff


title: OE_MI2_T1

value: OE


title: OE_MI3_T1


title: OE_MI4_T1


title: OE_sham2_T1


title: WT_MI4_T1


title: OE_sham1_T1


title: OE_sham3_T1


title: WT_sham3_T1


title: WT_MI2_T1


title: WT_sham4_T1


title: WT_MI4_T2


title: WT_sham2_T1


title: Jun-cKO.replicate

city: Beijing

first: Siling

last: Fu

address: No. 7, Science Park Road

institute: National Institute of Biological Sciences, Beijing.

data_processing:
The Single-end RNA-seq raw reads were aligned to mm10 reference genome using STAR (V2.7.2a).
The number of reads was assigned to protein-coding genes using featureCounts (V1.6.4). Signiﬁcantly differentially expressed genes were identiﬁed with P value < 0.01 and log2(fold change) > 0.5 by edgeR (V3.28.1).
Assembly: mm10

source_name: lung

extract_protocol:
The lymphatic endothelial cells (CD45–CD31+GFP+) were sorted from Prox1-CreER;Junf/+;Rosa26-mTmG (Control) and Prox1-CreER;Junf/f;Rosa26-mTmG (Jun cKO) mouse lungs at P0 (3 to 5 mice were pooled for each experiment group).
RNA was isolated from 1 X 104 murine lung LECs using an Arcturus PicoPure RNA isolation kit (KIT0204, Applied Biosystems) following the instructions. The RNA was then ampliﬁed using an Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (KIT0525, Applied Biosystems) following the instructions. cDNA libraries were generated using the NEB Next Ultra II DNA library prep kits (E7645L, New England Biolabs) and adapters in VAHTS DNA Adapters set1/2 for Illumina (N801-01/ N802-01, Vazyme). cDNA libraries were subsequently sequenced by Illumina Hiseq 2500 with 79 read lengths.

value: lung

value: lymphatic endothelial cells

tag: age

value: post natal day 0


title: Jun-Ctrl.replicate


title: WT_sham1_T1

value: WT


title: LECs, Jun-Ctrl

extract_protocol:
The  lymphatic endothelial cells (CD45–CD31+GFP+) were sorted from Prox1-CreER;Junf/+;Rosa26-mTmG (Control) and Prox1-CreER;Junf/f;Rosa26-mTmG (Jun cKO) mouse lungs at P0 (3 to 5 mice were pooled for each experiment group).
RNA was isolated from 1 X 104 murine lung LECs using an Arcturus PicoPure RNA isolation kit (KIT0204, Applied Biosystems) following the instructions. The RNA was then ampliﬁed using an Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (KIT0525, Applied Biosystems) following the instructions. cDNA libraries were generated using the NEB Next Ultra II DNA library prep kits (E7645L, New England Biolabs) and adapters in VAHTS DNA Adapters set1/2 for Illumina (N801-01/ N802-01, Vazyme). cDNA libraries were subsequently sequenced by Illumina Hiseq 2500 with 79 read lengths.


title: LECs, P0

data_processing:
Droplet-based sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.1.0, 10x Genomics Inc) using the Mus musculus genome (mm10).
The expression datasets were further processed using R “Seurat” package (V2.3.4). The distribution of nGenes, nUMI, and mitochondrial reads ratio were plotted. The cells used in the study were extracted using cutoff for nGene<5000, nUMI<25000, percent.mito<0.1.to remove potential empty droplets and doublets.
The UMI count is normalized to 10,000 in each cell and log transformed.
Assembly: mm10
Supplementary files format and content: cloupe, h5

extract_protocol:
The  lymphatic endothelial cells (CD45–CD31+GFP+) were sorted from mouse lungs at E14.5, E16.5, E18.5, and P0 (3 to 5 mice were pooled for each experiment group). The lymphatic endothelial cell suspensions were co‐encapsulated in droplets with barcoded beads by using the Chromium Controller (10X Genomics).
Single cell cDNA synthesis, amplification and sequencing libraries were generated using the Single Cell 3' Reagent Kit as the 10x Genomics protocol. The libraries were sequenced by Illumina HiSeq 2500.


title: LECs, E18

value: embryonic day 18.5


title: WT_Sham2_T2


title: LECs, Jun-cKO


title: LECs, E14

value: embryonic day 14.5


title: LECs, E16

value: embryonic day 16.5


title: miRNA Wild-type Male mouse brain at E15.5 M1

city: Dunedin

first: Susanna

last: Szakats

address: 270 Great King St

country: New Zealand

institute: University of Otago

data_processing:
miRDeep2 workflow
Cutadapt (v. 1.15) to remove adaptor sequence
Bowtie (v. 1.2.1) to map sequences to predefined pre-miRNA precursors, mature miRNA sequences, and the mm9 reference geome, allowing up to 2 mismatches.
Assembly: mm9
Supplementary files format and content: comma separated files with raw counts for known miRNAs (from miRBase v. 21)

source_name: whole brain

extract_protocol:
RNA was extracted using the Purelink RNA miniprep kit (Ambion), following the manufacturer’s instructions. 1-2 μg RNA was used for library construction.
Illumina TruSeq Library Prep was performed following manufacturer's instructions with 1 μg RNA input.

value: whole brain

tag: developmental stage

tag: Sex

value: male

value: wild-type


title: WT_MI3_T1


title: miRNA Wild-type Male mouse brain at E15.5 M3


title: WT_MI1_T1


title: miRNA Wild-type female mouse brain at E15.5 F3

value: female


title: miRNA Wild-type Male mouse brain at E15.5 M2


title: miRNA Wild-type female mouse brain at E15.5 F2


title: RNA Wild-type Male mouse brain at E15.5 M1

data_processing:
Galaxy Australia (v. 18.05)
Trimmomatic (v. 0.32, default settings) removed sequencing adapters and sequences below a quality threshold of phred < 30
Tophat (v. 2.1.1) aligned trimmed sequences to the reference genome mm9
Cufflinks (v. 2.2.1) assembled aligned reads into transcripts, then Cuffmerge (v. 2.2.1.0) merged all Cufflinks assemblies to create a master transcriptome
featureCounts (v. 1.5.1) quantified transcripts in each cufflinks assembly against the master transcriptome
Assembly: mm9
Supplementary files format and content: comma separated values of raw counts of transcripts


title: RNA Wild-type female mouse brain at E15.5 F3


title: RNA Wild-type female mouse brain at E15.5 F2


title: RNA Wild-type female mouse brain at E15.5 F1


title: miRNA Wild-type female mouse brain at E15.5 F1


title: RNA Wild-type Male mouse brain at E15.5 M3


title: Chlamydomonas - SS1 antibody m6A-IP-seq

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

description: m6A-IP seq

data_processing:
Reads were aligned to their corresponding genome using bwa (0.7.12).
Peaks were called using MACS2 (q-value 0.01) with either input and/or IgG IP-seq control as background
Genome_build: dm6 for S2-DSRC and Drosophila embryo samples; TAR19 for Arabidopsis samples; Creinhardtii_281_v5_0_nonnuclear for C.reinhardtii
Supplementary_files_format_and_content: narrowPeak files, called peaks of signal enrichment

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii cells

growth_protocol: Grown in TAP media until log phase under continuous illumination at 100uM photons/m2/sec.

extract_protocol: Cells were pelleted and combined with 1.2 mL of Buffer A supplemented with 1% sodium dodecyl sulfate (Sigma L3771), 0.5% polyvinylpyrrolidone (Sigma PVP40) and fresh 1% 2-Mercaptoethanol (Sigma M3148) in a Dounce homogenizer. Tissue was ground using a “B” pestle until homogenous. The lysate was transferred in 200 μl aliquots to 1.5 mL microfuge tubes and all samples were mixed with 3 μl Proteinase K and incubated for 1 hour at 50°C. The DNA was purified by adding 200 μl (1:1) of phenol:chloroform:isoamyl alcohol 25:24:1 (saturated with 10mM Tris, pH 8.0, 1mM EDTA) then mixed by vigorous tube inversions and incubated for 10 min at RT.

tag: m6a-mtase treatment

value: Untreated

tag: anti-dna-m6a antibody

value: SS1 - Synaptic System Ab. 202 003

tag: replicate


title: Chlamydomonas - MP1 antibody m6A-IP-seq

description: m6A-IP seq

value: MP1 - Millipore Sigma ABE572


title: Chlamydomonas - Input Control

description: IP-seq

value: Input Control


title: V73_A6_Batch1

description: Cells collected from wound bed region

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Assembly: mm10-GRCm38
Supplementary files format and content: Tab-delimited text file of raw read counts matrix per gene/cell.

source_name: Murine Epidermal cells

extract_protocol: Lrig1 GL cells were  isolated  from tail epidermis at 8w pw1  time point. Sca1+ cells were sorted to enrich for upper-HF cells into lysis buffer and processed for scRNA-seq, using the Smart-Seq2 protocol

value: Lrig1 GL Sca1+ epidermal cells

tag: batch

tag: plate

tag: well

tag: population

value: L1 Sca-1+


title: V73_A5_Batch1

description: Cells collected from wound bed region


title: V68_G8_Batch2

description: Cells collected from Ctrl (non-memory) region


title: V68_G4_Batch2


title: V68_G2_Batch2


title: V73_A12_Batch1

description: Cells collected from wound bed region


title: V68_G7_Batch2


title: V68_G1_Batch2


title: V68_G5_Batch2


title: V68_G9_Batch2


title: V68_G10_Batch2


title: V73_A11_Batch1

description: Cells collected from wound bed region


title: V68_F9_Batch2


title: V68_F8_Batch2


title: V68_F7_Batch2


title: V68_G11_Batch2


title: V68_F6_Batch2


title: RNA Wild-type Male mouse brain at E15.5 M2


title: V68_F11_Batch2


title: V68_E9_Batch2


title: V68_F4_Batch2


title: V68_F5_Batch2


title: V68_E8_Batch2


title: V68_E7_Batch2


title: V68_E5_Batch2


title: V68_F10_Batch2


title: V68_E4_Batch2


title: V68_E2_Batch2


title: V68_G6_Batch2


title: V68_E1_Batch2


title: V68_E11_Batch2


title: V68_D9_Batch2


title: V68_D7_Batch2


title: V68_C9_Batch2


title: V68_D3_Batch2


title: V68_D4_Batch2


title: V68_C7_Batch2


title: V68_E10_Batch2


title: V68_D11_Batch2


title: V68_D6_Batch2


title: V68_D1_Batch2


title: V68_C6_Batch2


title: V68_C2_Batch2


title: V68_D12_Batch2


title: V68_C10_Batch2


title: V68_C8_Batch2


title: V68_C3_Batch2


title: V68_B6_Batch2


title: V68_B8_Batch2


title: V68_B5_Batch2


title: V68_B3_Batch2


title: V68_B11_Batch2


title: V68_B2_Batch2


title: V68_A7_Batch2


title: V68_A5_Batch2


title: V68_A11_Batch2


title: V68_A12_Batch2


title: V67_H9_Batch1


title: V67_H6_Batch1


title: V67_G5_Batch1


title: V67_F7_Batch1


title: V67_F12_Batch1


title: V67_F11_Batch1


title: V68_B9_Batch2


title: V67_E9_Batch1


title: V67_G11_Batch1


title: V67_E8_Batch1


title: V68_A9_Batch2


title: V67_D5_Batch1


title: V67_E5_Batch1


title: V67_D9_Batch1


title: V67_C3_Batch1


title: V67_E10_Batch1


title: V67_D11_Batch1


title: V68_A6_Batch2


title: V67_B7_Batch1


title: V67_E11_Batch1


title: V67_B10_Batch1


title: V67_A9_Batch1


title: V67_A8_Batch1


title: V67_B11_Batch1


title: V67_G12_Batch1


title: V67_A5_Batch1


title: V67_F9_Batch1


title: V67_A3_Batch1


title: V67_A12_Batch1


title: V67_E4_Batch1


title: V67_A10_Batch1


title: C178_H9_L5_1W_RepU_93

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of raw read counts matrix per gene/cell.

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: Lgr5-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior to wounding.

tag: strain

value: CBA C57BL/6 mixed

value: Keratinocytes

value: RepU


title: C178_H10_L5_1W_RepU_94

tag: cell type


title: C178_H8_L5_1W_RepU_92


title: C178_H1_L5_1W_RepU_85


title: C178_H7_L5_1W_RepU_91


title: C178_G9_L5_1W_RepU_81


title: C178_G10_L5_1W_RepU_82


title: C178_G7_L5_1W_RepU_79


title: C178_G8_L5_1W_RepU_80


title: C178_G5_L5_1W_RepU_77


title: C178_G6_L5_1W_RepU_78


title: C178_G4_L5_1W_RepU_76


title: C178_G2_L5_1W_RepU_74


title: C178_F10_L5_1W_RepU_70


title: C178_F11_L5_1W_RepU_71


title: C178_F8_L5_1W_RepU_68


title: C178_F7_L5_1W_RepU_67


title: C178_F9_L5_1W_RepU_69


title: C178_F12_L5_1W_RepU_72


title: C178_F6_L5_1W_RepU_66


title: C178_F5_L5_1W_RepU_65


title: C178_F4_L5_1W_RepU_64


title: C178_F2_L5_1W_RepU_62


title: C178_F3_L5_1W_RepU_63


title: C178_F1_L5_1W_RepU_61


title: C178_G11_L5_1W_RepU_83


title: C178_E10_L5_1W_RepU_58


title: C178_G3_L5_1W_RepU_75


title: C178_G12_L5_1W_RepU_84


title: C178_E9_L5_1W_RepU_57


title: C178_E8_L5_1W_RepU_56


title: C178_E6_L5_1W_RepU_54


title: C178_E7_L5_1W_RepU_55


title: C178_E5_L5_1W_RepU_53


title: C178_E4_L5_1W_RepU_52


title: C178_E2_L5_1W_RepU_50


title: C178_D10_L5_1W_RepU_46


title: C178_D9_L5_1W_RepU_45


title: C178_D12_L5_1W_RepU_48


title: C178_D8_L5_1W_RepU_44


title: C178_D5_L5_1W_RepU_41


title: C178_D11_L5_1W_RepU_47


title: C178_D4_L5_1W_RepU_40


title: C178_C11_L5_1W_RepU_35


title: C178_D2_L5_1W_RepU_38


title: C178_D1_L5_1W_RepU_37


title: C178_E11_L5_1W_RepU_59


title: C178_C10_L5_1W_RepU_34


title: C178_C9_L5_1W_RepU_33


title: C178_D3_L5_1W_RepU_39


title: C178_C8_L5_1W_RepU_32


title: C178_C7_L5_1W_RepU_31


title: C178_C6_L5_1W_RepU_30


title: C178_E3_L5_1W_RepU_51


title: C178_E1_L5_1W_RepU_49


title: C178_C3_L5_1W_RepU_27


title: C178_C2_L5_1W_RepU_26


title: C178_C4_L5_1W_RepU_28


title: C178_B11_L5_1W_RepU_23


title: C178_B10_L5_1W_RepU_22


title: C178_B9_L5_1W_RepU_21


title: C178_B6_L5_1W_RepU_18


title: C178_B8_L5_1W_RepU_20


title: C178_B3_L5_1W_RepU_15


title: C178_B2_L5_1W_RepU_14


title: C178_A11_L5_1W_RepU_11


title: C178_A10_L5_1W_RepU_10


title: C172_H10_L5_9W_RepS_94

value: RepS


title: C178_B4_L5_1W_RepU_16


title: C172_H9_L5_9W_RepS_93


title: C172_H8_L5_9W_RepS_92


title: C172_H5_L5_9W_RepS_89


title: C172_H7_L5_9W_RepS_91


title: C172_H4_L5_9W_RepS_88


title: C172_H3_L5_9W_RepS_87


title: C172_H6_L5_9W_RepS_90


title: C172_G12_L5_9W_RepS_84


title: C172_H2_L5_9W_RepS_86


title: C172_G11_L5_9W_RepS_83


title: C172_G10_L5_9W_RepS_82


title: C178_C5_L5_1W_RepU_29


title: C172_G9_L5_9W_RepS_81


title: C172_G8_L5_9W_RepS_80


title: C172_G7_L5_9W_RepS_79


title: C172_G4_L5_9W_RepS_76


title: C172_G6_L5_9W_RepS_78


title: C178_B5_L5_1W_RepU_17


title: C172_G3_L5_9W_RepS_75


title: C172_G2_L5_9W_RepS_74


title: C172_F11_L5_9W_RepS_71


title: C172_F12_L5_9W_RepS_72


title: C172_F10_L5_9W_RepS_70


title: C172_G5_L5_9W_RepS_77


title: C172_F7_L5_9W_RepS_67


title: C172_F9_L5_9W_RepS_69


title: C172_F4_L5_9W_RepS_64


title: C172_F3_L5_9W_RepS_63


title: C172_F5_L5_9W_RepS_65


title: C172_F6_L5_9W_RepS_66


title: C172_F1_L5_9W_RepS_61


title: C172_E4_L5_9W_RepS_52


title: C172_E12_L5_9W_RepS_60


title: C172_E3_L5_9W_RepS_51


title: C172_E5_L5_9W_RepS_53


title: C172_E2_L5_9W_RepS_50


title: C172_E10_L5_9W_RepS_58


title: C172_F2_L5_9W_RepS_62


title: C172_E1_L5_9W_RepS_49


title: C172_E11_L5_9W_RepS_59


title: C172_D12_L5_9W_RepS_48


title: C172_D11_L5_9W_RepS_47


title: C172_D10_L5_9W_RepS_46


title: C172_D9_L5_9W_RepS_45


title: C172_D5_L5_9W_RepS_41


title: C172_D7_L5_9W_RepS_43


title: C172_D6_L5_9W_RepS_42


title: C172_D3_L5_9W_RepS_39


title: C172_D4_L5_9W_RepS_40


title: V68_E3_Batch2


title: C172_D2_L5_9W_RepS_38


title: C172_D1_L5_9W_RepS_37


title: C172_C12_L5_9W_RepS_36


title: C172_C11_L5_9W_RepS_35


title: C172_C9_L5_9W_RepS_33


title: C172_B12_L5_9W_RepS_24


title: C172_C1_L5_9W_RepS_25


title: C172_C2_L5_9W_RepS_26


title: C172_C4_L5_9W_RepS_28


title: C172_B7_L5_9W_RepS_19


title: C172_B10_L5_9W_RepS_22


title: C172_B9_L5_9W_RepS_21


title: C172_C3_L5_9W_RepS_27


title: C172_B6_L5_9W_RepS_18


title: C172_B3_L5_9W_RepS_15


title: C172_B5_L5_9W_RepS_17


title: C172_B1_L5_9W_RepS_13


title: C172_A7_L5_9W_RepS_7


title: C172_D8_L5_9W_RepS_44


title: C172_B2_L5_9W_RepS_14


title: C172_A10_L5_9W_RepS_10


title: C172_A6_L5_9W_RepS_6


title: C137_H11_L5_0W_RepQ_95

value: RepQ


title: C172_C10_L5_9W_RepS_34


title: C137_H9_L5_0W_RepQ_93


title: C137_G12_L5_0W_RepQ_84


title: C172_C6_L5_9W_RepS_30


title: C137_G10_L5_0W_RepQ_82


title: C137_H10_L5_0W_RepQ_94


title: C172_B11_L5_9W_RepS_23


title: C137_G9_L5_0W_RepQ_81


title: C137_G8_L5_0W_RepQ_80


title: C137_G3_L5_0W_RepQ_75


title: C137_G1_L5_0W_RepQ_73


title: C137_G5_L5_0W_RepQ_77


title: C137_G4_L5_0W_RepQ_76


title: C137_F12_L5_0W_RepQ_72


title: C137_G2_L5_0W_RepQ_74


title: C172_A3_L5_9W_RepS_3


title: C137_F11_L5_0W_RepQ_71


title: C137_F10_L5_0W_RepQ_70


title: C137_F9_L5_0W_RepQ_69


title: C137_F7_L5_0W_RepQ_67


title: C137_H8_L5_0W_RepQ_92


title: C137_G11_L5_0W_RepQ_83


title: C137_F8_L5_0W_RepQ_68


title: C137_F2_L5_0W_RepQ_62


title: C137_F6_L5_0W_RepQ_66


title: C137_F5_L5_0W_RepQ_65


title: C137_E12_L5_0W_RepQ_60


title: C137_E10_L5_0W_RepQ_58


title: C137_F4_L5_0W_RepQ_64


title: C137_E11_L5_0W_RepQ_59


title: C137_E7_L5_0W_RepQ_55


title: C137_E5_L5_0W_RepQ_53


title: C137_E8_L5_0W_RepQ_56


title: C137_F1_L5_0W_RepQ_61


title: C137_E4_L5_0W_RepQ_52


title: C137_G7_L5_0W_RepQ_79


title: C137_G6_L5_0W_RepQ_78


title: C137_E6_L5_0W_RepQ_54


title: C137_E2_L5_0W_RepQ_50


title: C137_D10_L5_0W_RepQ_46


title: C137_E1_L5_0W_RepQ_49


title: C137_D12_L5_0W_RepQ_48


title: C137_D9_L5_0W_RepQ_45


title: C137_D11_L5_0W_RepQ_47


title: C137_F3_L5_0W_RepQ_63


title: C137_D6_L5_0W_RepQ_42


title: C137_D7_L5_0W_RepQ_43


title: C137_D5_L5_0W_RepQ_41


title: C137_D4_L5_0W_RepQ_40


title: C137_D3_L5_0W_RepQ_39


title: C137_D2_L5_0W_RepQ_38


title: C137_D1_L5_0W_RepQ_37


title: C137_C12_L5_0W_RepQ_36


title: C137_C11_L5_0W_RepQ_35


title: C137_C9_L5_0W_RepQ_33


title: C137_C10_L5_0W_RepQ_34


title: C137_C8_L5_0W_RepQ_32


title: C137_C6_L5_0W_RepQ_30


title: C137_C5_L5_0W_RepQ_29


title: C137_C4_L5_0W_RepQ_28


title: C137_E3_L5_0W_RepQ_51


title: C137_C2_L5_0W_RepQ_26


title: C137_B10_L5_0W_RepQ_22


title: C137_D8_L5_0W_RepQ_44


title: C137_B12_L5_0W_RepQ_24


title: C137_C1_L5_0W_RepQ_25


title: C137_B11_L5_0W_RepQ_23


title: C137_B3_L5_0W_RepQ_15


title: C137_B4_L5_0W_RepQ_16


title: C134_H4_L5_8W_RepO_88

value: RepO


title: C134_G12_L5_8W_RepO_84


title: C137_B2_L5_0W_RepQ_14


title: C134_H6_L5_8W_RepO_90


title: C134_G10_L5_8W_RepO_82


title: C134_G9_L5_8W_RepO_81


title: C134_G8_L5_8W_RepO_80


title: C134_G6_L5_8W_RepO_78


title: C134_G11_L5_8W_RepO_83


title: C134_G5_L5_8W_RepO_77


title: C134_G4_L5_8W_RepO_76


title: C137_C7_L5_0W_RepQ_31


title: C134_G2_L5_8W_RepO_74


title: C134_G3_L5_8W_RepO_75


title: C134_F12_L5_8W_RepO_72


title: C134_F11_L5_8W_RepO_71


title: C134_F10_L5_8W_RepO_70


title: C134_F7_L5_8W_RepO_67


title: C134_F9_L5_8W_RepO_69


title: C134_F5_L5_8W_RepO_65


title: C134_F4_L5_8W_RepO_64


title: C134_H10_L5_8W_RepO_94


title: C134_F3_L5_8W_RepO_63


title: C134_F2_L5_8W_RepO_62


title: C134_F1_L5_8W_RepO_61


title: C134_E11_L5_8W_RepO_59


title: C134_E12_L5_8W_RepO_60


title: C134_E10_L5_8W_RepO_58


title: C134_E7_L5_8W_RepO_55


title: C134_E5_L5_8W_RepO_53


title: C134_E3_L5_8W_RepO_51


title: C134_E2_L5_8W_RepO_50


title: C134_D11_L5_8W_RepO_47


title: C134_E4_L5_8W_RepO_52


title: C134_E6_L5_8W_RepO_54


title: C134_D10_L5_8W_RepO_46


title: C134_E1_L5_8W_RepO_49


title: C134_D9_L5_8W_RepO_45


title: C134_F8_L5_8W_RepO_68


title: C134_D8_L5_8W_RepO_44


title: C134_D7_L5_8W_RepO_43


title: C134_D12_L5_8W_RepO_48


title: C134_D5_L5_8W_RepO_41


title: C134_D2_L5_8W_RepO_38


title: C134_C11_L5_8W_RepO_35


title: C134_D6_L5_8W_RepO_42


title: C134_D1_L5_8W_RepO_37


title: C134_C10_L5_8W_RepO_34


title: C134_C9_L5_8W_RepO_33


title: C134_C8_L5_8W_RepO_32


title: C134_C7_L5_8W_RepO_31


title: C134_C6_L5_8W_RepO_30


title: C134_E8_L5_8W_RepO_56


title: C134_E9_L5_8W_RepO_57


title: C134_C4_L5_8W_RepO_28


title: C134_C3_L5_8W_RepO_27


title: C134_C2_L5_8W_RepO_26


title: C134_C1_L5_8W_RepO_25


title: C134_B10_L5_8W_RepO_22


title: C134_B11_L5_8W_RepO_23


title: C134_B9_L5_8W_RepO_21


title: C134_B6_L5_8W_RepO_18


title: C134_B8_L5_8W_RepO_20


title: C134_B7_L5_8W_RepO_19


title: C134_A10_L5_8W_RepO_10


title: C134_A3_L5_8W_RepO_3


title: C134_B4_L5_8W_RepO_16


title: C134_B1_L5_8W_RepO_13


title: C134_A6_L5_8W_RepO_6


title: C134_A9_L5_8W_RepO_9


title: C134_B2_L5_8W_RepO_14


title: C181_H7_L5_1w_RepV_91

value: RepV


title: C134_A7_L5_8W_RepO_7


title: C181_H8_L5_1w_RepV_92


title: C134_A8_L5_8W_RepO_8


title: C181_H6_L5_1w_RepV_90


title: C181_H4_L5_1w_RepV_88


title: C181_H5_L5_1w_RepV_89


title: C181_H11_L5_1w_RepV_95


title: C181_H1_L5_1w_RepV_85


title: C181_G9_L5_1w_RepV_81


title: C181_H3_L5_1w_RepV_87


title: C181_H2_L5_1w_RepV_86


title: C181_H10_L5_1w_RepV_94


title: C181_G12_L5_1w_RepV_84


title: C181_G2_L5_1w_RepV_74


title: C181_G6_L5_1w_RepV_78


title: C181_G4_L5_1w_RepV_76


title: C134_A4_L5_8W_RepO_4


title: C181_G5_L5_1w_RepV_77


title: C181_H9_L5_1w_RepV_93


title: C181_G11_L5_1w_RepV_83


title: C181_F7_L5_1w_RepV_67


title: C181_F8_L5_1w_RepV_68


title: C181_F9_L5_1w_RepV_69


title: C181_F6_L5_1w_RepV_66


title: C181_F5_L5_1w_RepV_65


title: C181_F4_L5_1w_RepV_64


title: C181_G10_L5_1w_RepV_82


title: C181_F12_L5_1w_RepV_72


title: C181_F11_L5_1w_RepV_71


title: C181_F1_L5_1w_RepV_61


title: C181_G1_L5_1w_RepV_73


title: C181_F3_L5_1w_RepV_63


title: C181_F10_L5_1w_RepV_70


title: C181_E9_L5_1w_RepV_57


title: C181_F2_L5_1w_RepV_62


title: C181_E8_L5_1w_RepV_56


title: C181_E7_L5_1w_RepV_55


title: C181_E6_L5_1w_RepV_54


title: C181_G8_L5_1w_RepV_80


title: C181_G7_L5_1w_RepV_79


title: C181_G3_L5_1w_RepV_75


title: C181_E3_L5_1w_RepV_51


title: C181_E1_L5_1w_RepV_49


title: C181_E10_L5_1w_RepV_58


title: C181_E2_L5_1w_RepV_50


title: C181_D7_L5_1w_RepV_43


title: C181_D9_L5_1w_RepV_45


title: C181_D4_L5_1w_RepV_40


title: C181_D8_L5_1w_RepV_44


title: C181_E12_L5_1w_RepV_60


title: C181_D10_L5_1w_RepV_46


title: C181_D1_L5_1w_RepV_37


title: C181_D2_L5_1w_RepV_38


title: C181_D11_L5_1w_RepV_47


title: C181_E4_L5_1w_RepV_52


title: C181_C2_L5_1w_RepV_26


title: C181_C4_L5_1w_RepV_28


title: C181_C8_L5_1w_RepV_32


title: C181_C6_L5_1w_RepV_30


title: C181_C7_L5_1w_RepV_31


title: C181_C5_L5_1w_RepV_29


title: C181_D5_L5_1w_RepV_41


title: C181_D12_L5_1w_RepV_48


title: C181_C9_L5_1w_RepV_33


title: C181_C12_L5_1w_RepV_36


title: C181_C3_L5_1w_RepV_27


title: C181_C11_L5_1w_RepV_35


title: C181_C10_L5_1w_RepV_34


title: C181_E11_L5_1w_RepV_59


title: C181_B9_L5_1w_RepV_21


title: C181_B8_L5_1w_RepV_20


title: C181_D6_L5_1w_RepV_42


title: C181_D3_L5_1w_RepV_39


title: C181_B7_L5_1w_RepV_19


title: C180_H7_L5_1w_RepU_91


title: C180_H9_L5_1w_RepU_93


title: C181_A4_L5_1w_RepV_4


title: C181_B2_L5_1w_RepV_14


title: C181_A5_L5_1w_RepV_5


title: C181_B6_L5_1w_RepV_18


title: C181_B12_L5_1w_RepV_24


title: C181_B4_L5_1w_RepV_16


title: C181_B3_L5_1w_RepV_15


title: C181_B11_L5_1w_RepV_23


title: C181_A7_L5_1w_RepV_7


title: C181_A2_L5_1w_RepV_2


title: C181_A9_L5_1w_RepV_9


title: C181_B5_L5_1w_RepV_17


title: C181_B1_L5_1w_RepV_13


title: C181_B10_L5_1w_RepV_22


title: C180_H8_L5_1w_RepU_92


title: C181_A6_L5_1w_RepV_6


title: C181_A8_L5_1w_RepV_8


title: C181_A3_L5_1w_RepV_3


title: C180_G7_L5_1w_RepU_79


title: C180_H11_L5_1w_RepU_95


title: C180_G4_L5_1w_RepU_76


title: C180_H10_L5_1w_RepU_94


title: C181_C1_L5_1w_RepV_25


title: C180_G6_L5_1w_RepU_78


title: C180_G9_L5_1w_RepU_81


title: C181_A10_L5_1w_RepV_10


title: C181_A11_L5_1w_RepV_11


title: C180_G8_L5_1w_RepU_80


title: C180_G10_L5_1w_RepU_82


title: C180_G3_L5_1w_RepU_75


title: C180_G1_L5_1w_RepU_73


title: C180_G12_L5_1w_RepU_84


title: C180_G2_L5_1w_RepU_74


title: C180_G11_L5_1w_RepU_83


title: C180_F5_L5_1w_RepU_65


title: C180_F6_L5_1w_RepU_66


title: C180_F4_L5_1w_RepU_64


title: C180_F9_L5_1w_RepU_69


title: C180_F3_L5_1w_RepU_63


title: C180_E7_L5_1w_RepU_55


title: C180_F11_L5_1w_RepU_71


title: C180_F7_L5_1w_RepU_67


title: C180_E6_L5_1w_RepU_54


title: C180_F2_L5_1w_RepU_62


title: C180_E4_L5_1w_RepU_52


title: C180_F10_L5_1w_RepU_70


title: C180_E5_L5_1w_RepU_53


title: C180_F12_L5_1w_RepU_72


title: C180_F1_L5_1w_RepU_61


title: C180_E9_L5_1w_RepU_57


title: C180_E2_L5_1w_RepU_50


title: C180_E10_L5_1w_RepU_58


title: C180_E3_L5_1w_RepU_51


title: C180_E11_L5_1w_RepU_59


title: C180_E12_L5_1w_RepU_60


title: C180_E1_L5_1w_RepU_49


title: C180_F8_L5_1w_RepU_68


title: C180_E8_L5_1w_RepU_56


title: C180_D4_L5_1w_RepU_40


title: C180_D7_L5_1w_RepU_43


title: C180_D5_L5_1w_RepU_41


title: C180_D8_L5_1w_RepU_44


title: C180_D3_L5_1w_RepU_39


title: C180_D2_L5_1w_RepU_38


title: C180_D1_L5_1w_RepU_37


title: C180_D11_L5_1w_RepU_47


title: C180_C6_L5_1w_RepU_30


title: C180_C7_L5_1w_RepU_31


title: C180_D10_L5_1w_RepU_46


title: C180_C11_L5_1w_RepU_35


title: C180_C1_L5_1w_RepU_25


title: C180_C5_L5_1w_RepU_29


title: C180_C10_L5_1w_RepU_34


title: C180_C12_L5_1w_RepU_36


title: C180_C8_L5_1w_RepU_32


title: C180_C4_L5_1w_RepU_28


title: C180_B9_L5_1w_RepU_21


title: C180_B5_L5_1w_RepU_17


title: C180_C3_L5_1w_RepU_27


title: C180_B7_L5_1w_RepU_19


title: C180_B8_L5_1w_RepU_20


title: C180_C2_L5_1w_RepU_26


title: C180_B6_L5_1w_RepU_18


title: C180_B4_L5_1w_RepU_16


title: C180_B3_L5_1w_RepU_15


title: C180_C9_L5_1w_RepU_33


title: C180_B2_L5_1w_RepU_14


title: C180_B11_L5_1w_RepU_23


title: C180_A8_L5_1w_RepU_8


title: C180_B1_L5_1w_RepU_13


title: C180_A9_L5_1w_RepU_9


title: C180_B10_L5_1w_RepU_22


title: C180_A7_L5_1w_RepU_7


title: C180_A6_L5_1w_RepU_6


title: C180_A5_L5_1w_RepU_5


title: C180_A3_L5_1w_RepU_3


title: C175_H7_L5_9w_RepT_91

value: RepT


title: C175_H2_L5_9w_RepT_86


title: C180_D12_L5_1w_RepU_48


title: C175_H8_L5_9w_RepT_92


title: C180_A12_L5_1w_RepU_12


title: C180_A11_L5_1w_RepU_11


title: C175_H1_L5_9w_RepT_85


title: C175_H3_L5_9w_RepT_87


title: C175_H10_L5_9w_RepT_94


title: C175_H6_L5_9w_RepT_90


title: C175_H4_L5_9w_RepT_88


title: C180_A2_L5_1w_RepU_2


title: C175_G8_L5_9w_RepT_80


title: C175_H5_L5_9w_RepT_89


title: C180_B12_L5_1w_RepU_24


title: C175_G9_L5_9w_RepT_81


title: C175_G7_L5_9w_RepT_79


title: C175_G6_L5_9w_RepT_78


title: C175_G3_L5_9w_RepT_75


title: C175_G2_L5_9w_RepT_74


title: C180_A4_L5_1w_RepU_4


title: C180_A10_L5_1w_RepU_10


title: C175_H9_L5_9w_RepT_93


title: C175_H11_L5_9w_RepT_95


title: C175_G11_L5_9w_RepT_83


title: C175_G12_L5_9w_RepT_84


title: C175_G10_L5_9w_RepT_82


title: C175_F8_L5_9w_RepT_68


title: C175_G5_L5_9w_RepT_77


title: C175_F12_L5_9w_RepT_72


title: C175_E7_L5_9w_RepT_55


title: C175_F1_L5_9w_RepT_61


title: C175_E9_L5_9w_RepT_57


title: C175_F5_L5_9w_RepT_65


title: C175_E8_L5_9w_RepT_56


title: C175_G4_L5_9w_RepT_76


title: C175_F6_L5_9w_RepT_66


title: C175_F4_L5_9w_RepT_64


title: C175_F2_L5_9w_RepT_62


title: C175_F9_L5_9w_RepT_69


title: C175_F7_L5_9w_RepT_67


title: C175_E12_L5_9w_RepT_60


title: C175_F11_L5_9w_RepT_71


title: C175_E2_L5_9w_RepT_50


title: C175_E3_L5_9w_RepT_51


title: C175_E11_L5_9w_RepT_59


title: C175_E10_L5_9w_RepT_58


title: C175_D9_L5_9w_RepT_45


title: C175_D8_L5_9w_RepT_44


title: C175_E1_L5_9w_RepT_49


title: C175_G1_L5_9w_RepT_73


title: C175_D6_L5_9w_RepT_42


title: C175_D5_L5_9w_RepT_41


title: C175_D4_L5_9w_RepT_40


title: C175_E5_L5_9w_RepT_53


title: C175_D1_L5_9w_RepT_37


title: C175_C1_L5_9w_RepT_25


title: C175_C4_L5_9w_RepT_28


title: C175_C2_L5_9w_RepT_26


title: C175_C6_L5_9w_RepT_30


title: C175_D12_L5_9w_RepT_48


title: C175_D2_L5_9w_RepT_38


title: C175_B7_L5_9w_RepT_19


title: C175_C3_L5_9w_RepT_27


title: C175_D11_L5_9w_RepT_47


title: C175_B9_L5_9w_RepT_21


title: C175_C11_L5_9w_RepT_35


title: C175_B5_L5_9w_RepT_17


title: C175_B3_L5_9w_RepT_15


title: C175_B12_L5_9w_RepT_24


title: C175_B2_L5_9w_RepT_14


title: C175_B6_L5_9w_RepT_18


title: C175_B11_L5_9w_RepT_23


title: C175_C12_L5_9w_RepT_36


title: C175_C8_L5_9w_RepT_32


title: C175_C9_L5_9w_RepT_33


title: C175_A8_L5_9w_RepT_8


title: C175_A5_L5_9w_RepT_5


title: C175_A2_L5_9w_RepT_2


title: C175_A7_L5_9w_RepT_7


title: C175_A11_L5_9w_RepT_11


title: C175_A10_L5_9w_RepT_10


title: C175_A4_L5_9w_RepT_4


title: C175_A3_L5_9w_RepT_3


title: C171_H7_L5_9w_RepS_91


title: C175_B10_L5_9w_RepT_22


title: C175_A9_L5_9w_RepT_9


title: C175_A12_L5_9w_RepT_12


title: C171_H5_L5_9w_RepS_89


title: C171_H9_L5_9w_RepS_93


title: C171_H6_L5_9w_RepS_90


title: C171_H8_L5_9w_RepS_92


title: C171_H3_L5_9w_RepS_87


title: C171_G5_L5_9w_RepS_77


title: C171_G8_L5_9w_RepS_80


title: C171_G7_L5_9w_RepS_79


title: C171_G6_L5_9w_RepS_78


title: C171_H11_L5_9w_RepS_95


title: C171_G3_L5_9w_RepS_75


title: C171_G4_L5_9w_RepS_76


title: C171_G11_L5_9w_RepS_83


title: C171_G10_L5_9w_RepS_82


title: C171_F9_L5_9w_RepS_69


title: C171_G1_L5_9w_RepS_73


title: C171_F7_L5_9w_RepS_67


title: C171_F6_L5_9w_RepS_66


title: C171_F8_L5_9w_RepS_68


title: C171_G12_L5_9w_RepS_84


title: C171_F3_L5_9w_RepS_63


title: C171_G2_L5_9w_RepS_74


title: C171_F12_L5_9w_RepS_72


title: C171_F4_L5_9w_RepS_64


title: C171_F5_L5_9w_RepS_65


title: C171_G9_L5_9w_RepS_81


title: C171_H10_L5_9w_RepS_94


title: C171_F2_L5_9w_RepS_62


title: C171_F11_L5_9w_RepS_71


title: C171_E9_L5_9w_RepS_57


title: C171_F1_L5_9w_RepS_61


title: C171_E8_L5_9w_RepS_56


title: C171_F10_L5_9w_RepS_70


title: C171_E7_L5_9w_RepS_55


title: C171_E6_L5_9w_RepS_54


title: C171_E3_L5_9w_RepS_51


title: C171_E2_L5_9w_RepS_50


title: C171_E11_L5_9w_RepS_59


title: C171_E12_L5_9w_RepS_60


title: C171_E1_L5_9w_RepS_49


title: C171_E10_L5_9w_RepS_58


title: C171_D9_L5_9w_RepS_45


title: C171_D7_L5_9w_RepS_43


title: V83_H6_Batch2

description: Cells collected from Distal memory region


title: V83_F4_Batch2


title: V83_F8_Batch2


title: V83_F7_Batch2


title: V83_F11_Batch2


title: V83_F2_Batch2


title: V83_G11_Batch2


title: V83_F3_Batch2


title: C171_E4_L5_9w_RepS_52


title: V83_F6_Batch2


title: V83_G12_Batch2


title: V83_E7_Batch2


title: C171_D8_L5_9w_RepS_44


title: V83_F10_Batch2


title: V83_E11_Batch2


title: V83_E5_Batch2


title: V83_E4_Batch2


title: V83_H10_Batch2


title: V83_E1_Batch2


title: V83_E12_Batch2


title: V83_E10_Batch2


title: C175_C5_L5_9w_RepT_29


title: V83_D9_Batch2


title: V83_D8_Batch2


title: V83_C8_Batch2


title: V83_D6_Batch2


title: V83_D10_Batch2


title: V83_D7_Batch2


title: V83_C7_Batch2


title: V83_D12_Batch2


title: V83_D2_Batch2


title: V83_D1_Batch2


title: V83_D3_Batch2


title: V83_E6_Batch2


title: V83_E2_Batch2


title: V83_C6_Batch2


title: V83_C4_Batch2


title: V83_C11_Batch2


title: V83_B8_Batch2


title: V83_B9_Batch2


title: V83_C10_Batch2


title: V83_B4_Batch2


title: V83_B3_Batch2


title: V83_B7_Batch2


title: V83_B10_Batch2


title: V83_A5_Batch2


title: V83_A10_Batch2


title: V83_A7_Batch2


title: V81_H8_Batch1


title: V83_A8_Batch2


title: V81_H6_Batch1


title: V83_A3_Batch2


title: V81_H4_Batch1


title: V81_H5_Batch1


title: V81_H11_Batch1


title: C175_E4_L5_9w_RepT_52


title: V81_G7_Batch1


title: V81_H3_Batch1


title: V81_G2_Batch1


title: V83_B11_Batch2


title: V81_F11_Batch1


title: V81_E3_Batch1


title: V81_F4_Batch1


title: C175_B8_L5_9w_RepT_20


title: V81_G10_Batch1


title: V81_F1_Batch1


title: V81_E7_Batch1


title: V83_A4_Batch2


title: C175_D3_L5_9w_RepT_39


title: V81_G5_Batch1


title: V81_D8_Batch1


title: V81_D9_Batch1


title: C175_D10_L5_9w_RepT_46


title: V81_E2_Batch1


title: V81_D3_Batch1


title: V81_D6_Batch1


title: V81_E1_Batch1


title: V81_C7_Batch1


title: V81_C5_Batch1


title: V81_D1_Batch1


title: V81_C8_Batch1


title: V81_B2_Batch1


title: V81_C6_Batch1


title: V81_D2_Batch1


title: V75_H9_Batch2

description: Cells collected from wound bed region


title: V81_B11_Batch1


title: V75_H3_Batch2

description: Cells collected from wound bed region


title: V81_E9_Batch1


title: V75_H11_Batch2

description: Cells collected from wound bed region


title: V81_G1_Batch1


title: V81_A12_Batch1


title: V75_H12_Batch2

description: Cells collected from wound bed region


title: V75_G6_Batch2

description: Cells collected from wound bed region


title: V75_H8_Batch2

description: Cells collected from wound bed region


title: V75_H10_Batch2

description: Cells collected from wound bed region


title: V75_G4_Batch2

description: Cells collected from wound bed region


title: V75_G5_Batch2

description: Cells collected from wound bed region


title: V75_G1_Batch2

description: Cells collected from wound bed region


title: V75_F5_Batch2

description: Cells collected from wound bed region


title: V75_G2_Batch2

description: Cells collected from wound bed region


title: V75_F8_Batch2

description: Cells collected from wound bed region


title: V75_G10_Batch2

description: Cells collected from wound bed region


title: V75_F10_Batch2

description: Cells collected from wound bed region


title: V75_H7_Batch2

description: Cells collected from wound bed region


title: V75_E9_Batch2

description: Cells collected from wound bed region


title: V75_E3_Batch2

description: Cells collected from wound bed region


title: V75_E8_Batch2

description: Cells collected from wound bed region


title: V75_F3_Batch2

description: Cells collected from wound bed region


title: V75_E2_Batch2

description: Cells collected from wound bed region


title: C171_H4_L5_9w_RepS_88


title: V75_E12_Batch2

description: Cells collected from wound bed region


title: V75_D9_Batch2

description: Cells collected from wound bed region


title: V75_F11_Batch2

description: Cells collected from wound bed region


title: V75_E10_Batch2

description: Cells collected from wound bed region


title: V75_F6_Batch2

description: Cells collected from wound bed region


title: V75_D3_Batch2

description: Cells collected from wound bed region


title: V75_E11_Batch2

description: Cells collected from wound bed region


title: V75_E4_Batch2

description: Cells collected from wound bed region


title: V75_D2_Batch2

description: Cells collected from wound bed region


title: V75_D1_Batch2

description: Cells collected from wound bed region


title: V75_C9_Batch2

description: Cells collected from wound bed region


title: V75_D11_Batch2

description: Cells collected from wound bed region


title: V75_C8_Batch2

description: Cells collected from wound bed region


title: V75_C3_Batch2

description: Cells collected from wound bed region


title: V75_C4_Batch2

description: Cells collected from wound bed region


title: V75_C11_Batch2

description: Cells collected from wound bed region


title: V75_C2_Batch2

description: Cells collected from wound bed region


title: V75_C6_Batch2

description: Cells collected from wound bed region


title: V75_C10_Batch2

description: Cells collected from wound bed region


title: V75_B6_Batch2

description: Cells collected from wound bed region


title: V75_B5_Batch2

description: Cells collected from wound bed region


title: V75_B1_Batch2

description: Cells collected from wound bed region


title: V75_B4_Batch2

description: Cells collected from wound bed region


title: V75_B10_Batch2

description: Cells collected from wound bed region


title: V75_B11_Batch2

description: Cells collected from wound bed region


title: V75_B2_Batch2

description: Cells collected from wound bed region


title: V75_A5_Batch2

description: Cells collected from wound bed region


title: V75_A8_Batch2

description: Cells collected from wound bed region


title: V75_A10_Batch2

description: Cells collected from wound bed region


title: V75_A9_Batch2

description: Cells collected from wound bed region


title: V75_A7_Batch2

description: Cells collected from wound bed region


title: V75_A11_Batch2

description: Cells collected from wound bed region


title: V73_H6_Batch1

description: Cells collected from wound bed region


title: V73_H2_Batch1

description: Cells collected from wound bed region


title: V73_G1_Batch1

description: Cells collected from wound bed region


title: V73_F4_Batch1

description: Cells collected from wound bed region


title: V73_F1_Batch1

description: Cells collected from wound bed region


title: V73_H1_Batch1

description: Cells collected from wound bed region


title: V73_F11_Batch1

description: Cells collected from wound bed region


title: V73_D9_Batch1

description: Cells collected from wound bed region


title: V73_F10_Batch1

description: Cells collected from wound bed region


title: V73_D5_Batch1

description: Cells collected from wound bed region


title: V73_E7_Batch1

description: Cells collected from wound bed region


title: V73_D12_Batch1

description: Cells collected from wound bed region


title: V73_D2_Batch1

description: Cells collected from wound bed region


title: V73_C5_Batch1

description: Cells collected from wound bed region


title: V73_D1_Batch1

description: Cells collected from wound bed region


title: V73_B9_Batch1

description: Cells collected from wound bed region


title: V73_B8_Batch1

description: Cells collected from wound bed region


title: V73_B3_Batch1

description: Cells collected from wound bed region


title: V73_B7_Batch1

description: Cells collected from wound bed region


title: V75_F2_Batch2

description: Cells collected from wound bed region


title: V73_B2_Batch1

description: Cells collected from wound bed region


title: C171_D6_L5_9w_RepS_42


title: V73_B12_Batch1

description: Cells collected from wound bed region


title: C171_D4_L5_9w_RepS_40


title: C171_D2_L5_9w_RepS_38


title: C171_D5_L5_9w_RepS_41


title: V73_F12_Batch1

description: Cells collected from wound bed region


title: C171_D11_L5_9w_RepS_47


title: C171_D1_L5_9w_RepS_37


title: C171_D10_L5_9w_RepS_46


title: V73_D8_Batch1

description: Cells collected from wound bed region


title: V75_D6_Batch2

description: Cells collected from wound bed region


title: C171_C6_L5_9w_RepS_30


title: C171_C7_L5_9w_RepS_31


title: C175_D7_L5_9w_RepT_43


title: V73_C12_Batch1

description: Cells collected from wound bed region


title: C171_C4_L5_9w_RepS_28


title: C171_C5_L5_9w_RepS_29


title: V73_A7_Batch1

description: Cells collected from wound bed region


title: C171_B8_L5_9w_RepS_20


title: C171_B9_L5_9w_RepS_21


title: C171_C10_L5_9w_RepS_34


title: C171_C2_L5_9w_RepS_26


title: C171_C12_L5_9w_RepS_36


title: C171_C3_L5_9w_RepS_27


title: C171_C1_L5_9w_RepS_25


title: C171_C11_L5_9w_RepS_35


title: C171_C9_L5_9w_RepS_33


title: C171_C8_L5_9w_RepS_32


title: C171_A5_L5_9w_RepS_5


title: C171_B2_L5_9w_RepS_14


title: C171_B1_L5_9w_RepS_13


title: C171_B5_L5_9w_RepS_17


title: C171_A9_L5_9w_RepS_9


title: C171_A6_L5_9w_RepS_6


title: C171_B6_L5_9w_RepS_18


title: C171_B3_L5_9w_RepS_15


title: C171_B11_L5_9w_RepS_23


title: C171_B7_L5_9w_RepS_19


title: C171_B10_L5_9w_RepS_22


title: C171_B12_L5_9w_RepS_24


title: C171_B4_L5_9w_RepS_16


title: C171_A7_L5_9w_RepS_7


title: C171_A3_L5_9w_RepS_3


title: C171_A2_L5_9w_RepS_2


title: C171_A11_L5_9w_RepS_11


title: C129_H8_L1_38wUW_RepN

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior to wounding.

value: RepN


title: C171_A10_L5_9w_RepS_10


title: C171_A8_L5_9w_RepS_8


title: C129_H4_L1_38wUW_RepN


title: C129_H2_L1_38wUW_RepN


title: C129_H5_L1_38wUW_RepN


title: C129_H7_L1_38wUW_RepN


title: C129_H3_L1_38wUW_RepN


title: C171_A4_L5_9w_RepS_4


title: C129_H12_L1_38wUW_RepN_MBULK


title: C129_H10_L1_38wUW_RepN


title: C129_H1_L1_38wUW_RepN


title: C129_G2_L1_38wUW_RepN


title: C129_G4_L1_38wUW_RepN


title: C129_G8_L1_38wUW_RepN


title: C129_G6_L1_38wUW_RepN


title: C129_G7_L1_38wUW_RepN


title: C129_H11_L1_38wUW_RepN


title: C129_G12_L1_38wUW_RepN


title: C171_A12_L5_9w_RepS_12


title: C129_G3_L1_38wUW_RepN


title: C129_G5_L1_38wUW_RepN


title: C129_H6_L1_38wUW_RepN


title: C129_F5_L1_38wUW_RepN


title: C129_G1_L1_38wUW_RepN


title: C129_F8_L1_38wUW_RepN


title: C129_F6_L1_38wUW_RepN


title: C129_F7_L1_38wUW_RepN


title: C129_G11_L1_38wUW_RepN


title: C129_G10_L1_38wUW_RepN


title: C129_E7_L1_38wUW_RepN


title: C129_E8_L1_38wUW_RepN


title: C129_F4_L1_38wUW_RepN


title: C129_F2_L1_38wUW_RepN


title: C129_F3_L1_38wUW_RepN


title: C129_F12_L1_38wUW_RepN


title: C129_F11_L1_38wUW_RepN


title: C129_F1_L1_38wUW_RepN


title: C129_E12_L1_38wUW_RepN


title: C129_E6_L1_38wUW_RepN


title: C129_E3_L1_38wUW_RepN


title: C129_E10_L1_38wUW_RepN


title: C129_E1_L1_38wUW_RepN


title: C129_E11_L1_38wUW_RepN


title: C129_D2_L1_38wUW_RepN


title: C129_D6_L1_38wUW_RepN


title: C129_D7_L1_38wUW_RepN


title: C129_D12_L1_38wUW_RepN


title: C129_D11_L1_38wUW_RepN


title: C129_D5_L1_38wUW_RepN


title: C129_E4_L1_38wUW_RepN


title: C129_E5_L1_38wUW_RepN


title: C129_D1_L1_38wUW_RepN


title: C129_C7_L1_38wUW_RepN


title: C129_E2_L1_38wUW_RepN


title: C129_C6_L1_38wUW_RepN


title: C129_C5_L1_38wUW_RepN


title: C129_C4_L1_38wUW_RepN


title: C129_C3_L1_38wUW_RepN


title: C129_C12_L1_38wUW_RepN


title: C129_C10_L1_38wUW_RepN


title: C129_C1_L1_38wUW_RepN


title: C129_D8_L1_38wUW_RepN


title: C129_D10_L1_38wUW_RepN


title: C129_B7_L1_38wUW_RepN


title: C129_B8_L1_38wUW_RepN


title: C129_B12_L1_38wUW_RepN


title: C129_B2_L1_38wUW_RepN


title: C129_A8_L1_38wUW_RepN


title: C129_B4_L1_38wUW_RepN


title: C129_C11_L1_38wUW_RepN


title: C129_B1_L1_38wUW_RepN


title: C129_A7_L1_38wUW_RepN


title: C129_B11_L1_38wUW_RepN


title: C129_A6_L1_38wUW_RepN


title: C129_A11_L1_38wUW_RepN


title: C129_A3_L1_38wUW_RepN


title: C129_A2_L1_38wUW_RepN


title: C129_A4_L1_38wUW_RepN


title: C129_A5_L1_38wUW_RepN


title: C129_A10_L1_38wUW_RepN


title: C129_A12_L1_38wUW_RepN


title: C129_B3_L1_38wUW_RepN


title: C128_H9_L1_38wUW_RepM

value: RepM


title: C128_H6_L1_38wUW_RepM


title: C128_G9_L1_38wUW_RepM


title: C128_H10_L1_38wUW_RepM


title: C128_H4_L1_38wUW_RepM


title: C128_H2_L1_38wUW_RepM


title: C128_H1_L1_38wUW_RepM


title: C128_G8_L1_38wUW_RepM


title: V73_C10_Batch1

description: Cells collected from wound bed region


title: C171_D12_L5_9w_RepS_48


title: C128_F12_L1_38wUW_RepM


title: C128_E8_L1_38wUW_RepM


title: C128_F8_L1_38wUW_RepM


title: C128_G4_L1_38wUW_RepM


title: C128_F2_L1_38wUW_RepM


title: C128_F11_L1_38wUW_RepM


title: C128_G10_L1_38wUW_RepM


title: C128_G7_L1_38wUW_RepM


title: C129_C8_L1_38wUW_RepN


title: C128_G11_L1_38wUW_RepM


title: C128_F4_L1_38wUW_RepM


title: C128_G5_L1_38wUW_RepM


title: C128_F6_L1_38wUW_RepM


title: C128_F9_L1_38wUW_RepM


title: C128_G6_L1_38wUW_RepM


title: C128_G12_L1_38wUW_RepM


title: C128_F5_L1_38wUW_RepM


title: C128_G2_L1_38wUW_RepM


title: C128_E7_L1_38wUW_RepM


title: C128_G3_L1_38wUW_RepM


title: C128_G1_L1_38wUW_RepM


title: C128_E9_L1_38wUW_RepM


title: C128_F1_L1_38wUW_RepM


title: C128_F7_L1_38wUW_RepM


title: C128_F3_L1_38wUW_RepM


title: C128_E6_L1_38wUW_RepM


title: C128_F10_L1_38wUW_RepM


title: C128_E3_L1_38wUW_RepM


title: C128_E4_L1_38wUW_RepM


title: C128_E2_L1_38wUW_RepM


title: C128_E5_L1_38wUW_RepM


title: C128_E12_L1_38wUW_RepM


title: C128_E11_L1_38wUW_RepM


title: C128_D9_L1_38wUW_RepM


title: C128_E10_L1_38wUW_RepM


title: C128_D8_L1_38wUW_RepM


title: C128_D6_L1_38wUW_RepM


title: C128_D7_L1_38wUW_RepM


title: C128_D4_L1_38wUW_RepM


title: C128_D5_L1_38wUW_RepM


title: C128_C8_L1_38wUW_RepM


title: C128_C4_L1_38wUW_RepM


title: C128_C11_L1_38wUW_RepM


title: C128_D12_L1_38wUW_RepM


title: C128_C12_L1_38wUW_RepM


title: C128_D11_L1_38wUW_RepM


title: C128_D10_L1_38wUW_RepM


title: C128_D2_L1_38wUW_RepM


title: C128_C7_L1_38wUW_RepM


title: C128_C5_L1_38wUW_RepM


title: C128_C6_L1_38wUW_RepM


title: C128_C3_L1_38wUW_RepM


title: C128_C9_L1_38wUW_RepM


title: C128_D1_L1_38wUW_RepM


title: C128_C10_L1_38wUW_RepM


title: C128_B9_L1_38wUW_RepM


title: C128_B8_L1_38wUW_RepM


title: C128_B6_L1_38wUW_RepM


title: C128_B7_L1_38wUW_RepM


title: C128_B4_L1_38wUW_RepM


title: C128_B12_L1_38wUW_RepM


title: C128_B3_L1_38wUW_RepM


title: C128_B10_L1_38wUW_RepM


title: C128_B2_L1_38wUW_RepM


title: C128_B11_L1_38wUW_RepM


title: C128_B1_L1_38wUW_RepM


title: C128_A6_L1_38wUW_RepM


title: C128_A8_L1_38wUW_RepM