title: Jurkat Safe Harbor RNA-seq rep1


title: Liver, Rage-KO, replicate 4

status: Public on Jan 07 2025

type: SRA

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

country: Germany

institute: University of Tuebingen

description:
Treatment batch 4
QSFPA016AU

library_source: transcriptomic

data_processing:
Raw data analysis was performed with the Nextflow-based nf-core/rnaseq (version 1.4.2) pipeline. Quality control of the raw data was performed using FastQC (version 0.11.8) and RSeQC (version 3.0.1). Adapter trimming was conducted with Trim Galore (version 0.6.4). Reads were mapped to the reference genome using the STAR aligner (version 2.6.1d) and the quantification of raw gene expression was performed with featureCounts (version 1.6.4).
Differential expression analysis was performed using the featureCounts raw read count table as input for the rnadeseq (version 1.3.2) pipeline, used with the R package (version 3.5.1). The integrated DESeq2 tool (version 1.22.1) utilized normalized counts to calculate the log2 fold change and assess its statistical significance using the Wald test, reported as a p-value. Adjusted p-values (padj) were calculated using the Benjamini-Hochberg correction for multiple testing. Genes with a padj ≤0.05 were considered differentially expressed.
Pathway analysis was performed with the R packages gprofiler2 (version 0.1.8) and AnnotationDbi (version 1.44.0). The DEG lists, together with their associated log2FC were used as input for the pathway analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: The CDE diet was employed to investigate the effect of BEC-specific Rage activity on diet-induced cholestasis and its influence on ductular reaction and fibrosis. After tamoxifen injection, the mice were maintained for two weeks of wash-out period prior to the start of the injury model. The control mice (R26Tom Hnf1b-CreER Rage+/fl) were fed with normal chow diet and drinking water. To induce chronic liver injury and cholestasis, the experimental mice (R26Tom Hnf1b-CreER Ragefl/fl) were fed with choline-deficient (CD) diet and 0.165% DL-ethionine in drinking water by ad libitum access for three weeks.

extract_protocol:
During FACS, the biliary epithelial cells sorted directly into RNA lysis buffer for subsequent RNA isolation. RNeasy Mini Kit was used to isolate the total RNA.
Total RNA was subjected to an initial quality and quantity check using the BioAnalyzer by Agilent Technologies (RNA Pico Kit). Starting with 8.35 ng of input material total RNA was converted to cDNA using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.) according to the manufacturer’s instructions: During first-strand synthesis the product was primed by the 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide was used for template switching at the 5’ end of the transcript. The cDNA was then amplified by long distance PCR using 9 PCR cycles. The BioAnalyzer was used to check for successful cDNA synthesis and amplification (High Sensitivity DNA Kit). On the Covaris LE200 the amplified double-stranded cDNA was sheared to 150-250bp fragments. Successful fragmentation was verified on the TapeStation by Agilent Technologies (HS DNA 1000 Kit). For subsequent library preparation the NEBNext® ChIP-Seq Library Prep Master Mix Kit was used. After end repair, dA-Tailing and adaptor-ligation the cDNA was subjected to PCR amplification introducing i5 and i7 primers using 12 PCR cycles. Library quality was assessed on the TapeStation (DNA 1000 Kit). Sequencing was performed on the HiSeq 4000 platform (Illumina) in 100bp paired end mode, which resulted in at least 40 Mio reads/sample.

treatment_protocol: The animals were annesthetized with the anesthesia cocktail comprising 100 mg/kg KETASET (Ketamine hydrochloride) and 10 mg/kg Rompun® 2% (Xylazine hydrochloride) by intraperitoneal injection. The livers of the animals were perfused with a two-step colleagenase protocol, followed by protease digestion. The digested cell suspensions were filtered, and the non-parenchymal cells (NPCs) were isolated using a 20%/50% Percoll gradient centrifuged at 1400 x g for 20 mins at 4 degree celcius. The NPCs  were subjected to FACS. Cell sorting was gated for tdTomato and GFP expression. For NPCs isolated from R26Tom Hnf1b-CreER Rage+/∆BEC animals, tdTomato positive cells were sorted. For R26Tom Hnf1b-CreER Rage∆BEC animals, toTomato- and GFP-double positive cells were sorted.

tag: tissue

value: Liver

tag: cell type

value: Biliary epithelial cells (BECs)

tag: genotype

value: Rage-KO

tag: treatment

value: Choline-deficient, ethionine-supplemented (CDE) diet


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Library name: G2_119

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.10.0) was used to map the cleaned reads to the GRCm39 mouse genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M33). Salmon parameters used: -i ./salmon_index_M33  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximeta to estimate gene level counts.
Assembly: GRCm39
Supplementary files format and content: Matrix table (TxiMeta.GeneLevel.counts.GEO.txt) with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (gse.counts.annotated.v2.Rdata; exported tximeta object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (gse.lengthScaledTPM.annotated.v2.Rdata; exported tximeta object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: liver

growth_protocol: Six- to seven-week-old male wildtype C57BL/J mice were purchased from Envigo. Mice were housed individually at the animal facility of Wageningen University under specific pathogen-free conditions and housed on a 12:12 hour light-dark cycle. Mice had ad libitum access to food and water throughout the study. Normal bedding and cage enrichment were provided. The experiment received approval from the central committee on animal experimentation and the local animal welfare committee of Wageningen University (AVD10400202115283, 2021.W-0016.006).

extract_protocol:
Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 100bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: After two weeks of acclimatization, mice (in the age of eight to nine weeks) were randomly divided into four groups (N = 15) and placed on a HFD (45% energy derived from fat; D12451, Research Diets, USA) for 20 weeks to induce MASLD, obesity and insulin resistance. After 10 weeks on HFD, mice were subsequently treated with either vehicle or three doses of propiconazole through oral gavage (100 µl olive oil + 6.5% EtOH) three times per week. The administrated doses of propiconazole were calculated to achieve daily doses of 0.04, 30, or 100 mg/kg bw/day propiconazole (Sigma-Aldrich, purity ≥98.0%). Prior to starting the administration of propiconazole, two mice per group with atypical growth curves (either fast or slow body weight gainers) were excluded from analysis, finally resulting in 13 mice per group. Body weight and food intake were assessed weekly. Five mice (three mice in the control group and two mice in the 100 mg/kg bw/day dose group) were prematurely euthanized during the study period due to problems emerging shortly after the oral gavage. These mice were inspected after sacrifice, and it was concluded that problems were likely caused by the technical aspects of the procedure. Mice were euthanized after 20 weeks of HFD and 10 weeks of administration of propiconazole or vehicle. Mice were euthanized three days after the final administration of propiconazole at Zeitgeber Time (ZT) 8. Mice were anesthetized with isoflurane inhalation followed by blood collection by orbital puncture and euthanized by cervical dislocation. Livers were weighed, and subsequently snap frozen in liquid nitrogen. Samples were stored at -80 °C before further analyses. Samples from 6 mice per treatment group were used for RNA-sequencing.

value: liver

tag: strain

tag: background diet

value: high-fat diet (45% energy derived from fat; D12451, Research Diets, USA)

value: propiconazole

tag: dose (mg/kg_body_weight)

tag: mouseid

tag: Sex

value: male

tag: section day_(day1_or_day2)

value: Day 1


title: Jurkat sg4 RNA-seq rep1

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

country: USA

institute: Broad Institute

data_processing:
Fastqs were processed using Kallisto v0.46.1 with default parameters. GTF and transcriptome index were taken from https://github.com/pachterlab/kallisto-transcriptome-indices/releases.
Assembly: hg38
Supplementary files format and content: .h5 files that contain raw counts and TPM normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Jurkat cells were continuously cultured in RPMI 1640 supplemented with 10% FBS and penicilin/streptomycin. A375 cells were cultured in GlutaMAX High Glucose DMEM (Gibco) + 10% FBS supplemented with 1% penicillin/streptomycin

extract_protocol:
RNA was isolated with Qiagen RNeasy Plus Micro kit according to the manufacturer's protocol and ensuring RIN values were greater than 7.
Libraries were prepared first with Poly-A enrichment using magnetic oligo(dT)-beads (Invitrogen), then ligated to RNA adaptors for sequencing.

treatment_protocol: CRISPRi guide

value: peripheral blood

tag: cell line

value: Jurkat

value: T lymphoblast


title: RNA_RRP001_Pt4_Week11_PBMC

city: Plymouth Meeting

first: Elisabeth

last: Gillespie

state: PA

address: 660 W Germantown Pike, Suite 110

institute: Inovio Pharmaceuticals

data_processing:
Data were processed as per ImmunoID Next Analysis Pipeline from Personalis (www.personalis.com)
Aligment was perfomred with STAR (Spliced Transcripts Aligment to a Refernce)
Normalized gene and transcript expression were derived from propietery tools from Personalis and Salmon
Immune repertorie analysis was conducted with MIXCR
Raw count  normalization was conducted in EdgeR
Assembly: hs37d5
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing TCR sequences and  counts for each sample

source_name: PBMC

extract_protocol:
Dual isolation of nucleic acids was performed utilizing the AllPrep DNA/RNA FFPE Tissue kit (Qiagen).
Libraries were prepared using the Stranded RNA Sequencing kit (Kapa Biosystems).

tag: individual

value: PBMC

value: Male

tag: time


title: AsPC1_CDK9i_Rep1_H3K4me3_HiChIP

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

library_source: other

data_processing:
HiChIP data were analyzed using the HiC-Pro pipeline. Briefly, sequencing reads were mapped with HiC-Pro/3.1.01 and FitHiChIP/11.0 was utilized to generate bedpe file format. For HiC-Pro, we used MIN_CIS_DIST = 20000 and BIN_SIZE = 2000. We generated an in-house script (https://github.com/bhc-rbct/Filter-A2A-loops-for-active-genes.git) which extracts the active TSS of target genes using a cell line specific H3K4me3 bed file (anchor 1) which interacts with (enhancer) regions of interest (anchor 2). Resulting bedpe files and .hic files (generated from hicpro2juicebox.sh) were used to generate aggregate peak analysis (APA) plots and contact maps utilizing the Tinker Box platform (Morgan et al. manuscript in preparation, https://docs.axiotl.com/). Counts per million were used to normalize samples.
Assembly: hg38
Supplementary files format and content: All-to-all bedpe files for each condition
Supplementary files format and content: bedpe files of control AsPC1 or L36pl cells for active TSS regions to intergenic open (ATAC positive) and active (H3K27ac positive) regions in each cell line.

molecule: other

source_name: cell line

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
H3K4me3 HiChIP was performed as previously described with a few modifications (PMID: 32051612, PMID: 33658703). Briefly, cells were trypsinized, counted, and 10 million cells were used for each condition. Pertinent modifications are digestion was carried out by incubating with 200 U each of MboI, DpnII, and HinfI (NEB) at 37°C for 2 hr and samples were sonicated for 8 cycles 30 sec on/off. 6 µg of H3K4me3 and Protein A beads were added to the samples. DNA was purified as described above for ChIP-seq and on-bead libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).
Libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).

value: cell line

value: PDAC


title: L36pl_siTP63_Pol2pSer2_Rep3_ChIPseq

library_source: genomic

data_processing:
Paired or single end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.11) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: merged bigiwg file for each conditiion
Supplementary files format and content: 3 column bed file

molecule: genomic DNA

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep), GöCDX5 (keratinocyte-SFM media, 10% FBS, 1% Pen-Strep, recombinant epidermal growth factor, bovine pituitary extract) were maintained in humidified 5% CO2 incubator at 37C. GöCDX5, a GöPDX5-derived cell line, was thawed on collagen coated plates and after the first trypsinization were transferred to a normal cell culture plate. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.


title: RNA_RRP001_Pt4_Week9_PBMC


title: L36pl_siTP63_Pol2pSer2_Rep2_ChIPseq


title: Liver, Rage-KO, replicate 2

description:
Treatment batch 2
QSFPA014AE


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 2

description: Library name: G2_116


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 3

description: Library name: G2_117


title: Liver, Rage-KO, replicate 1

description:
Treatment batch 1
QSFPA013A6


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 2

description: Library name: G3_129


title: RNA_RRP001_Pt4_Week6_PBMC


title: RNA_RRP001_Pt4_Day0_PBMC


title: Liver, Rage-control, replicate 4

description:
Treatment batch 4
QSFPA012AW

value: Rage-HET


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 1

description: Library name: G2_115


title: L36pl_siTP63_Pol2pSer2_Rep1_ChIPseq


title: Liver, Rage-control, replicate 3

description:
Treatment batch 3
QSFPA011AO

value: Liver


title: L36pl_siTP63_Pol2_Rep3_ChIPseq


title: liver, high-fat diet, control treatment, replicate 6

description: Library name: G1_113

value: control

value: Day 2


title: RNA_RRP001_Pt3_Week52_PBMC


title: RNA_RRP001_Pt4_Week26_PBMC


title: Liver, Rage-KO, replicate 3

description:
Treatment batch 3
QSFPA015AM

value: Biliary epithelial cells (BECs)

value: Rage-KO

value: Choline-deficient, ethionine-supplemented (CDE) diet


title: L36pl_siTP63_Pol2_Rep2_ChIPseq


title: Liver, Rage-control, replicate 2

description:
Treatment batch 2
QSFPA010AG


title: liver, high-fat diet, control treatment, replicate 5

description: Library name: G1_112

value: liver

value: high-fat diet (45% energy derived from fat; D12451, Research Diets, USA)


title: RNA_RRP001_Pt3_Week26_PBMC


title: liver, high-fat diet, control treatment, replicate 4

description: Library name: G1_111

value: male


title: L36pl_siTP63_Pol2_Rep1_ChIPseq


title: Liver, Rage-control, replicate 1

description:
Treatment batch 1
QSFPA009AD


title: liver, high-fat diet, control treatment, replicate 3

description: Library name: G1_109

value: Day 1


title: Retina,  RNase H treated, sample 4

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
DNA/RNA immunoprecipitation
RNAseH_treated_plus_std.bw
RNAseH_treated_minus_std.bw
R_loops_both_std
R_loops_std_spe

data_processing:
After trimming adaptor sequences, low-complexity tails were removed by further trimming 10 bps from each read on the 3’ end of the first read in the pair and 5’ end of the second read in the pair.
Reads were aligned to the mouse genome (mm10) using Bowtie2. Duplicated reads, reads with score < 20 (including multi-mapping reads) and reads mapping ENCODE consortium blacklisted regions of mm10 genome (github.com/Boyle-Lab/Blacklist/) were removed. Mapped reads were split by strand using samtools.
R-loops calling has been performed using MACS2. First all R-loops (without regard of any strand specificity) have been called on all reads, using the merged RNAseH treated samples as control dataset using MACS2 with the default parameters (narrow peaks) and using the broad peaks option. R-loops found in at least 3 samples with a q-value < 0.001 in the narrow call or in the broad call were merged.
Then, strand specific enriched peaks (including strand-specific R-loops and non-specific signal) have been called on reads split by strand, using the reads mapping the opposite strand as control dataset using MACS2 with the default parameters (narrow peaks) and using the broad peaks option. Strand-specific peaks found in at least 3 samples with a q-value < 0.001 in the narrow call or in the broad call were merged.
Finally, from these two lists of peaks (total R-loops and strand-specific peaks), we selected the unstranded R-loops as the R-loops not found in the strand-specific peaks and the stranded R-loops as the peaks present in both the R-loops list and the strand-specific peak.
Assembly: mm10
Supplementary files format and content: Bigwig files containing locations of strand specific R loops for individual samples
Supplementary files format and content: Bed files containing merged locations of strand specific and non-strand specific loops identified in at least 3 samples.
Library strategy: DRIP-seq

source_name: Retina

extract_protocol:
Single strand DNA/RNA immunoprecipitation followed by sequencing (DRIP-Seq) was performed in retinas from four adult mice (P28). Briefly, Genomic DNA from one retina was enzymatically digested, treated with RNase III with or without RNase H and immunoprecipitated with the DNA/RNA hybrid antibody S9.6.
After elution, gDNA was further sonicated. Libraries were constructed using the Accel-NGS 1S Plus DNA Library Kit (IDT technologies Coralville, IA, USA). One library was prepared per mouse (n = 4).

treatment_protocol: Samples were divided into two before immunoprecipitation, one group was treated with RNase H as negative control.

value: Retina

value: Wild type

value: IP with S9.9 antibody, age P28, Treated with RNase H


title: RNA_RRP001_Pt3_Week9_PBMC

value: PBMC

value: Male


title: RNA_RRP001_Pt3_Week11_PBMC


title: L36pl_siNT5_Pol2pSer5_Rep2_ChIPseq

value: cell line

value: PDAC


title: liver, high-fat diet, control treatment, replicate 2

description: Library name: G1_108


title: L36pl_siNT5_Pol2pSer5_Rep3_ChIPseq


title: Retina,  RNase H treated, sample 3


title: RNA_RRP001_Pt3_Week6_PBMC


title: liver, high-fat diet, control treatment, replicate 1

description: Library name: G1_104


title: L36pl_siNT5_Pol2pSer5_Rep1_ChIPseq


title: RNA_RRP001_Pt3_Day0_PBMC


title: Retina,  RNase H treated, sample 2


title: Retina,  RNase H treated, sample 1


title: L36pl_siNT5_Pol2pSer2_Rep3_ChIPseq


title: RNA_RRP001_Pt2_Week52_PBMC


title: caco2 cells, DSS+polydatin

city: Guangzhou

first: Ting

last: Zhang

address: 183 Zhongshan Avenue West

country: China

institute: the third affiliated hospital of southern medical university

description:
Library name: sample 3
DSS+polydatin

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: caco-2 cells

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: caco-2 cells

value: colon carcinoma cells

value: WT

value: DSS+polydatin


title: caco2 cells, DSS

description:
Library name: sample 2
DSS

value: DSS


title: L36pl_siNT5_Pol2pSer2_Rep2_ChIPseq


title: RNA_RRP001_Pt2_Week26_PBMC


title: L36pl_siNT5_Pol2pSer2_Rep1_ChIPseq


title: caco2 cells, control

description:
Library name: sample1
NC

value: control


title: RNA_RRP001_Pt2_Week11_PBMC


title: Retina,  sample 3

description:
DNA/RNA immunoprecipitation
R_loops_both_std
R_loops_std_spe

value: IP with S9.9 antibody, age P28


title: L36pl_siNT5_Pol2_Rep3_ChIPseq


title: WT-Tail-T3_3

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Short reads mapping (Bowtie2 v2.3.4.1)
Peak calling (MACS2 v2.1.1.20160309)
Genome_build: Xenbase v9.1
Supplementary_files_format_and_content: peak xls files

organism: Xenopus tropicalis

growth_protocol: Tail samples were collected from WT and TRα (-/-) tadpoles which born from same parents.

extract_protocol:
Tail chromatin DNA was extracted and IP was performed with TR antibody (non-commercial; PMID: 18635662). After purification of ChIP-DNA, all purified DNA was used for the construction of sequencing libraries.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to around stage 54, tadpoles of T3 groups were treated with 10nM T3 for 18 hours.

tag: genotype/variation

value: 10nM T3 for 18 hours

value: Tail


title: Retina,  sample 2


title: RNA_RRP001_Pt2_Week9_PBMC


title: WT-Tail-T3_2


title: L36pl_siNT5_Pol2_Rep2_ChIPseq


title: RNA_RRP001_Pt2_Week6_PBMC


title: Retina,  sample 1


title: WT-Tail-control_3

source_name: WT-Tail-control


title: RNA_RRP001_Pt1_Week52_PBMC


title: Mouse lungs, post-injury day 14, scATAC-seq

city: Stanford

first: Jason

last: Guo

state: CA

address: 257 Campus Dr

institute: Stanford University

library_source: genomic single cell

data_processing:
Raw base call (BCL) files were demultiplexed to fastq files using the 10x Genomics Cell Ranger tool cellranger-atac mkfastq. These files were then aligned to the mouse genome (mm10) using cellranger-atac count with default parameters.
Quality control for scATAC-seq included restriction to 1000-20000 fragments in peaks, blacklist ratio less than 0.05, over 9% of fragments in peaks, mononucleosomal:nucleosome-free fragment ratio less than 4, and transcriptional start site enrichment score greater than 2. Batch correction was performed at the sample-level using Harmony.
Differentially accessible peaks were calculated with a log fold change threshold of 0.25 and a minimum percentage of 10% using the recommended logistic regression framework for scATAC-seq data in Signac. Cell populations were manually annotated as described in the main text.
Assembly: mm10
Supplementary files format and content: filtered peak matrix files and filtered transcription factor (tf) matrix files in 10X format

source_name: lungs

extract_protocol:
Lung samples were minced, digested in 5 mg/mL each of collagenase II and IV (ThermoFisher Scientific, cat# 17101015 and 17104019) in serum-free Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher Scientific, cat# 11965092) at 37 oC for 30 min with gentle agitation, neutralized in DMEM with 10% v/v fetal bovine serum (FBS) (GeminiBio, cat# 100-106), and filtered at 100 μm. The resulting suspensions were centrifuged at 500g for 5 min to isolate cell pellets, incubated in RBC lysis buffer (Millipore Sigma, cat# 11814389001) for 5 min, neutralized in DMEM with 10% FBS, centrifuged, resuspended in PBS, and filtered at 40 μm to yield single-cell suspensions.
Epigenomic samples were prepared from pooled single-nuclei suspensions using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, Chromium Next GEM Chip H Single Cell Kit, and Single Index Kit N, Set A (10X Genomics, cat# 1000175, 1000161, and 1000212) according to kit instructions.
Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: lungs

value: post-injury day 14

value: all cells (unsorted)

value: black 6

value: bleomycin


title: RNA_RRP001_Pt2_Day0_PBMC

value: PBMC

value: Male


title: Mouse lungs, post-injury day 35, scATAC-seq

value: post-injury day 35


title: L36pl_dNp63_Rep2_ChIPseq

value: cell line

value: PDAC


title: L36pl_siNT5_Pol2_Rep1_ChIPseq


title: WT-Tail-T3_1

value: WT


title: WT-Tail-control_2


title: Retina,  sample 4

value: Retina

value: Wild type


title: L36pl_dNp63_Rep1_ChIPseq


title: Mouse lungs, post-injury day 0, scATAC-seq

value: post-injury day 0

value: none (control)


title: Mouse lungs, post-injury day 35, scRNA-seq

library_source: transcriptomic single cell

data_processing:
Base calls were converted to reads using the 10X Cell Ranger implementation of mkfastq and then aligned against the mm10 reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/.
For quality control, scRNA-seq cell barcodes were restricted to those with 500-5000 reads and less than 10% of their transcriptome from mitochondrial genes, and reads for Gm42418 and AY036118, representing ribosomal RNA contamination, were removed. Batch correction was performed at the sample-level using Harmony.
Differentially expressed genes were calculated with a log fold change threshold of 0.25 and a minimum expression percentage of 25% using the default Wilcoxon Rank Sum test for scRNA-seq data in Seurat, with exclusion of unannotated transcripts (i.e., Gm, Rik transcripts) and mitochondrial genes. Cell populations were manually annotated as described in the main text.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Lung samples were minced, digested in 5 mg/mL each of collagenase II and IV (ThermoFisher Scientific, cat# 17101015 and 17104019) in serum-free Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher Scientific, cat# 11965092) at 37 oC for 30 min with gentle agitation, neutralized in DMEM with 10% v/v fetal bovine serum (FBS) (GeminiBio, cat# 100-106), and filtered at 100 μm. The resulting suspensions were centrifuged at 500g for 5 min to isolate cell pellets, incubated in RBC lysis buffer (Millipore Sigma, cat# 11814389001) for 5 min, neutralized in DMEM with 10% FBS, centrifuged, resuspended in PBS, and filtered at 40 μm to yield single-cell suspensions.
Transcriptomic samples were prepared from pooled single-cell suspensions using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, Chromium Single Cell B Chip Kit, and Chromium i7 Multiplex Kit (10X Genomics, cat# 1000075, 1000073, and 120262).
Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.


title: L36pl_dNp63_Rep3_ChIPseq


title: L36pl_DMSO_Pol2_Rep3_ChIPseq


title: TRaKO-Tail-T3_3

value: TRaKO

value: 10nM T3 for 18 hours


title: RNA_RRP001_Pt1_Week26_PBMC


title: RNA_RRP001_Pt1_Week11_PBMC


title: RNA_RRP001_Pt1_Week9_PBMC


title: L36pl_DMSO_Pol2_Rep2_ChIPseq


title: Mouse lungs, post-injury day 14, scRNA-seq

value: lungs


title: RNA_RRP001_Pt1_Week6_PBMC


title: L36pl_DMSO_Pol2_Rep1_ChIPseq


title: TRaKO-Tail-T3_1

value: Tail


title: L36pl_CDK9i_Pol2_Rep3_ChIPseq


title: TRaKO-Tail-control_3

source_name: TRaKO-Tail-control

value: control


title: RNA_RRP001+B52:B88_Pt1_Day0_PBMC


title: TRaKO-Tail-T3_2


title: WT-Tail-control_1


title: ARMS92-infect-28days

city: Groningen

first: Xiaofang

last: Li

address: Hanzeplein 1

institute: University of Groningen

description:
Library name: Sample 23-B3I28D
T3I28D_FPKM

data_processing:
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. These clean data were further mapped to pre-defined reference genome generating mapped data. Assessment on insert size and sequencing randomness were processed on mapped data as library quality control. Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization
Assembly: Reference genome was pre-defined for the analysis. Version information of the reference genome is: Homo_sapiens.GRCh38_release95.genome.fa.  HISAT2[2] is a highly efficient system for mapping RNA-seq reads, which is a more advanced version of TopHat2/Bowtie2.HISAT2 uses a Burrows-Wheeler Transform and Ferragina-Manzini（FM）index based search. HISAT2 uses one global graph FM index (GFM) to represent general population, as well as small indexes (local indexes) combined with several alignment strategies in order to achieve more efficient alignment.  StringTie[3] was applied to assemble the mapped reads. The algorithm is established based on optimality theory. It utilizes a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantify transcripts representing multiple spliced variants for each gene locus
Supplementary files format and content: ref_trans_full_table.xls

source_name: Lung

extract_protocol:
the extract protocol of mRNA sequencing includes sample preparation, library construction, library quality control and sequencing.
Qualified RNA were processed for library construction. The procedures are described as follow:  (1) mRNA was isolated by Oligo(dT)-attached magnetic beads.  (2) mRNA was then randomly fragmented in fragmentation buffer.  (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.  (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.  (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: Lung

value: epithelial cell


title: L36pl_CDK9i_Pol2_Rep2_ChIPseq


title: BC36, MAIT, TetIL23

city: Paris

first: Hélène

last: Lopez-Maestre

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were mapped to the reference human genome (hg38) using STAR v2.7.10a.
FeatureCounts (from Subread, version 2.0.0) was used to estimate genes expression for each sample.
Assembly: hg38
Supplementary files format and content: Raw counts per sample, from FeatureCounts

source_name: MAIT cells isolated from PBMC

growth_protocol: Freshly isolated PBMC were cultured in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin and 20UI/mL.

extract_protocol:
Nuclei from 90000 sorted MAIT cells were isolated using ATAC-lysis buffer from the Active Motif ATAC-seq Kit following manufacturer's instructions.
Libraries were prepared using the ATAC-seq kit from Active motif according to manufacturer’s instructions. After centrifugation (2800 rpm, 10 min 4°C), nuclei were incubated with the tagmentation master mix in a shaking heat block for 30min at 37°C with agitation at 800rpm. DNA was then purified and amplified for 10 cycles using indexed primers, and size-selected using SPRI bead solution.

treatment_protocol: MR1/5-OP-RU tetramers (NIH) were added the first day of culture at 40pM, and cells were cultured for 6 days. IL-23 or IL-12 (Miltenyi Biotec) were added at the concentration of 20 ng/mL and renewed after 3 days.

value: MAIT cells isolated from PBMC

value: MR1 5-OP-RU + IL-23


title: BC36, MAIT, Tet

value: MR1 5-OP-RU


title: L36pl_CDK9i_Pol2_Rep1_ChIPseq

value: cell line


title: TRaKO-Tail-control_2


title: HPAFII_Input_Rep3_ChIPseq

value: HPAFII

value: PDAC


title: TRaKO-Tail-control_1


title: ARMS92-control-7days

description:
Library name: Sample 22-B3C7D
T3C7D_FPKM


title: MG5 cells, CTRL2

city: Nagoya

first: Makoto

last: Inoue

address: 1-100 Kusumoto-cho, Chikusa-ku, Nagoya

department: School of Pharmacy

country: Japan

institute: Aichi Gakuin University

description: Library name: Sample 4

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 version 2.1.0 by incorporating both HISAT2 and Bowtie2 for alignment. Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases. Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM, TPM values for each Sample

growth_protocol: Mouse astrocyte-like A1 cells were cultured in DMEM supplemeted with 10% FBS, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in a humidified atmosphere of 5% CO2 in air.  MG5 cells were cultured in a mixture of 30% DMEM supplemented with 10% FBS, 50 U/ml penicillin, and 50 µg/ml streptomycin, and 70% A1 cell-conditioned medium at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa Bio Inc., Kusatsu, Japan).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: MG5 cells were treated with 6OHA or Bex at a concentration of 10 µM for 6 h.

value: microglial cells

value: WT

value: untreated


title: ARMS92-infect-7days

description:
Library name: Sample 21-B3I7D
T3C28D_FPKM


title: HPAFII_Input_Rep2_ChIPseq


title: MG5 cells, CTRL1

description: Library name: Sample 3


title: Mouse lungs, post-injury day 0, scRNA-seq

value: post-injury day 0

value: all cells (unsorted)

value: black 6

value: none (control)


title: ARMS92-control-28days

description:
Library name: Sample 24-B3C28D
T3I7D_FPKM


title: BC35, MAIT, TetIL12

value: MR1 5-OP-RU + IL-12


title: ARMS132-infect-28days

description:
Library name: Sample 19-B2I28D
T2I28D_FPKM


title: BC35, MAIT, Tet


title: MG5 cells, 6OHA1

description: Library name: Sample 1

value: treated with 6OHA


title: HPAFII_Input_Rep1_ChIPseq


title: MG5 cells, 6OHA3

description: Library name: Sample 2


title: BC36, MAIT, TetIL12


title: ARMS132-control-7days

description:
Library name: Sample 18-B2C7D
T2C7D_FPKM

value: Lung


title: ARMS132-infect-7days

description:
Library name: Sample 17-B2I7D
T2C28D_FPKM

value: epithelial cell


title: HPAFII_GATA6_Rep3_ChIPseq


title: BC33, MAIT, TetIL23

value: MAIT cells isolated from PBMC


title: HPAFII_GATA6_Rep2_ChIPseq


title: pulmonary endothelial cells_LPS3

city: Shanghai

first: Jian

last: Xu

address: 180 Fenglin Road

institute: Zhongshan hospital

description: Library name: Sample6

data_processing:
Raw data of FASTQ format were firstly processed through in-house perl scripts and obtained clean data. Then, map the clean reads to the silva database to remove the rRNA. Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene. EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: mm10; GRCh38
Supplementary files format and content: Gene counts or fpkm for each sample.

extract_protocol:
Total RNA was extracted using TRIzol reagent. Total RNA was qualified and quantified: (1) RNA purity and concentration were examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Libraries were constructed by enriching mRNA with polyT, synthesizing cDNA, adding adapters, and amplifying via PCR. Libraries were sequenced on an Illumina NovaSeq 6000 platform, generating paired-end 150 bp reads.

value: LPS


title: ARMS132-control-28days

description:
Library name: Sample 20-B2C28D
T2I7D_FPKM


title: pulmonary endothelial cells_LPS2

description: Library name: Sample5


title: ARMS126-infect-28days

description:
Library name: Sample 15-B1I28D
T1I28D_FPKM


title: BC33, MAIT, Tet

value: MR1 5-OP-RU


title: BC35, MAIT, TetIL23

value: MR1 5-OP-RU + IL-23


title: GoPdx8_GATA6_ChIPseq

source_name: PDX

value: PDX


title: HPAFII_GATA6_Rep1_ChIPseq

value: cell line

value: HPAFII

value: PDAC


title: BC30, MAIT, TetIL23


title: pulmonary endothelial cells_PBS3

description: Library name: Sample3

value: WT

value: PBS


title: ARMS126-control-7days

description:
Library name: Sample 14-B1C7D
T1C7D_FPKM


title: GoPdx8_Pol2_ChIPseq


title: pulmonary endothelial cells_LPS1

description: Library name: Sample4


title: BC30, MAIT, Tet


title: ARMS126-infect-7days

description:
Library name: Sample 13-B1I7D
T1C28D_FPKM


title: BC26, MAIT, TetIL23


title: GoPdx5_GATA6_ChIPseq


title: pulmonary endothelial cells_PBS2

description: Library name: Sample2


title: BC26, MAIT, TetIL12


title: GoPdx5_Pol2_ChIPseq


title: pulmonary endothelial cells_PBS1

description: Library name: Sample1


title: BC26, MAIT, Tet


title: 200718-infect-28days

description:
Library name: Sample 11-T3I28D
B3I28D_FPKM


title: 200718-control-28days

description:
Library name: Sample 12-T3C28D
B3I7D_FPKM


title: LPS/KO2

first: Michael

last: Sack

address: 10 Center Drive

institute: NHLBI

data_processing:
Trimmomatic tool (V0.33; https://github.com/timflutre/trimmomatic) was used to remove adapters, followed by quality trimming and alignment to the mouse genome (GRCm38) using HISAT2.40 (https://daehwankimlab.github.io/hisat2/). Gene expression levels were quantified using Stringtie (https://github.com/gpertea/stringtie). Differentially expressed genes were evaluated using Ballgown (http://bioconductor.org/packages/release/bioc/html/ballgown.html).
Assembly: GRCm38
Supplementary files format and content: text file includes raw counts for each sample

growth_protocol: J774A.1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted with the NucleoSpin® RNA kit (Takara) and RNA integrity was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent).
Dual index libraries were constructed with at least one unique index per each library using NEB Next® Ultra™ II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: WT and ACAT1 KO J774A.1 cells were either untreated or treated with 100ng/mL Lipopolysaccharide (LPS) for 2 hr.

value: mouse macrophage

value: ACAT1 KO


title: GoCdx5_Pol2_Rep2_ChIPseq


title: LPS/KO3


title: ARMS126-control-28days

description:
Library name: Sample 16-B1C28D
T1I7D_FPKM


title: BC22, MAIT, TetIL12


title: GoCdx5_Input_Rep2_ChIPseq


title: 200718-control-7days

description:
Library name: Sample 10-T3C7D
B3C7D_FPKM


title: 190619-control-28days

description:
Library name: Sample 8-T2C28D
B2I7D_FPKM


title: BC22, MAIT, TetIL23


title: 190619-infect-28days

description:
Library name: Sample 7-T2I28D
B2I28D_FPKM


title: GoCdx5_Pol2_Rep1_ChIPseq


title: 200718-infect-7days

description:
Library name: Sample 9-T3I7D
B3C28D_FPKM


title: LPS/KO1


title: 190619-control-7days

description:
Library name: Sample 6-T2C7D
B2C7D_FPKM


title: BC22, MAIT, Tet


title: GoCdx5_GATA6_Rep1_ChIPseq


title: BC21, MAIT, TetIL23


title: LPS/WT2


title: BC21, MAIT, Tet


title: 190619-infect-7days

description:
Library name: Sample 5-T2I7D
B2C28D_FPKM


title: BC20, MAIT, TetIL23


title: LPS/WT1


title: 130122-control-28days

description:
Library name: Sample 4-T1C28D
B1I7D_FPKM


title: BC20, MAIT, TetIL12


title: AsPC1_siNT5_Pol2pSer5_Rep3_ChIPseq


title: AsPC1_siNT5_Pol2pSer5_Rep2_ChIPseq


title: GoCdx5_Input_Rep1_ChIPseq


title: P96_AD5 (scTCR-seq)

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids); filtered_contig_annotations.csv and clonotypes.csv (information about TCR sequencing)

source_name: Skin

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 and v2 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin

value: mixture of isolated cells

tag: condition

value: AD


title: GoCdx5_GATA6_Rep2_ChIPseq


title: KO2

value: no treatment


title: P81_AD4 (scTCR-seq)


title: BC20, MAIT, Tet


title: AsPC1_siNT5_Pol2pSer2_Rep1_ChIPseq


title: KO3


title: 130122-infect-28days

description:
Library name: Sample 3-T1I28D
B1I28D_FPKM

value: Lung

value: epithelial cell


title: P121_HC4 (scTCR-seq)

value: HC


title: AsPC1_siNT5_Pol2pSer5_Rep1_ChIPseq


title: AsPC1_siGATA6_Pol2pSer2_Rep1_ChIPseq


title: LPS/WT3

value: LPS


title: KO1


title: 130122-control-7days

description:
Library name: Sample 2-T1C7D
B1C7D_FPKM


title: AsPC1_siNT5_Pol2pSer2_Rep3_ChIPseq


title: P116_HC3 (scTCR-seq)


title: P112_HC1 (scTCR-seq)


title: 130122-infect-7days

description:
Library name: Sample 1-T1I7D
B1C28D_FPKM


title: AsPC1_Ctrl_GATA6_Rep1_ChIPseq


title: WT3


title: AsPC1_siNT5_Pol2pSer2_Rep2_ChIPseq


title: Mum-2b, NC2

city: shenzhen

first: huan

last: wan

address: huaqiangnan road

institute: shenzhen aier eye hospital

description: Library name: NC2

data_processing:
Raw reads were filtered using fastp57 (version 0.13.1, default parameters) and mapped to hg38, using HISAT263 (version 2.1.0) with parameters “--rna-strandness RF –dta”.
Read counts per gene were calculated in strand-specific manner using featureCounts64.
Differential expression analysis was performed using DESeq265, and genes with mean TPM ≥ 1, FDR < 0.05, and fold change > 1.5 were identified as significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: FPKM and count

source_name: Uveal melanoma

extract_protocol:
RNA was extracted from cells using TRNzol Universal Reagent (TIANGEN, cat. no. DP424) or Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054) by following the manufacturers’ protocols
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols

value: Uveal melanoma


title: Mum-2b, NC1

description: Library name: NC1


title: AsPC1_siGATA6_Pol2pSer2_Rep2_ChIPseq


title: WT2


title: Mouse lungs, post-injury day 0, replicate 2, Visium

data_processing:
Raw FASTQ files and histology images were processed by sample with the Space Ranger software, which uses STAR v.2.5.1b (Dobin et al., 2013) for genome alignment, against the Cell Ranger mm10 reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/ (Dobin et al., 2013).
Analysis was performed using the standard Visium pipeline in Seurat. To impute cell type probabilities in each Visium “spot”, a scRNA-seq reference manifold was integrated in Seurat by anchor label transfer using the default PCA projection pipeline. RBC’s and related genes (i.e., Hba, Hbb) were excluded from downstream analyses, to minimize effects of variability in RBC removal during tissue processing, and unannotated transcripts (i.e., Gm, Rik genes) and mitochondrial genes were also excluded.
Assembly: mm10
Supplementary files format and content: Aligned and spatially processed Visium data in standard 10X format
Library strategy: Visium

extract_protocol:
Lung tissues were flash frozen in OCT using an isopentane bath with liquid N2. 8 µm sections were acquired directly onto Visium gene expression slides.
Visium gene expression slides were processed using the Visium Spatial Gene Expression Slide & Reagent Kit (10X Genomics, cat# 1000184) by the Stanford Functional Genomics Facility.
The Gene Expression Slide & Reagent kit was followed per protocol, and used to produce sequencing libraries. The libraries were then sequenced using NextSeq (Illumina), and Bcl files were demultiplexed.

value: lungs

value: post-injury day 0

value: all cells (unsorted)

value: black 6

value: none (control)


title: WT1

value: WT


title: P77_AD3 (scTCR-seq)


title: P197_Blood (scTCR-seq)

source_name: Blood

value: Blood

value: CIE


title: Mum-2b, shRNA1_3

description: Library name: shRNA1_3


title: Mouse lungs, post-injury day 14, replicate 3, Visium

value: post-injury day 14

value: bleomycin


title: P75_AD2 (scTCR-seq)

value: Skin

value: mixture of isolated cells

value: AD


title: P197_Skin (scTCR-seq)


title: Mum-2b, shRNA1_1

description: Library name: shRNA1_1


title: AsPC1_siGATA6_Pol2pSer2_Rep3_ChIPseq

value: cell line

value: PDAC


title: Mum-2b, shRNA1_2

description: Library name: shRNA1_2


title: AsPC1_BI653048_GATA6_Rep2_ChIPseq


title: CD8 T cells KO2 48h

first: Xiaohan

last: Song

state: Shanghai

address: South ChongQing Road 227

institute: Shanghai Jiao Tong University School of Medicine

description:
KO-48-2
KO2_48h

data_processing:
The libraries were sequenced on an llumina Hiseq platform and 150 bp paired-end reads were generated. About 40-60 million raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 6.53~7.16 G clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
fastp 0.20.1
RseQC 4.0.0
fastqc v0.11.9
hisat2 2.1.0
samtools 1.9
htseq-count 0.11.2
Assembly: GRCm39
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: spleen

extract_protocol:
Total RNA was isolated from CD8+ T cells with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNextUltra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations, and index codes were added to attribute sequences for each sample.

value: spleen

tag: strain background

value: primary CD8 T cells


title: Mum-2b, NC3

description: Library name: NC3

value: Uveal melanoma


title: P91_Skin (scTCR-seq)


title: L36pl_ATAC_Rep3

data_processing:
Paired end sequencing reads were filtered for adapter contamination with cutadapt/2.8 and mapped to the reference genome assembly hg38 using bowtie2 with --dovetail. BamTools Filter was used for removing low quality (mapQ >= 30) and mitochondrial reads. Resulting bam file was converted to a bed file with bedtools/2.30.0 bamtobed. Peak calling and bedgraph generation was performed using macs2 callpeak using shift and extend method to center peaks at 5’ cut site (shift -100 extension size 200). The data was visualized by using bedGraphToBigWig (ucscbigtools/11-Aug-2023).
Assembly: hg38
Supplementary files format and content: bigwigs for each condition
Supplementary files format and content: 3 column bed file

extract_protocol:
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.


title: CD8 T cells KO1 48h

description:
KO-48-1
KO1_48h


title: Mouse lungs, post-injury day 0, replicate 1, Visium

value: lungs

value: post-injury day 0


title: P86_Blood (scTCR-seq)


title: AsPC1_Ctrl_GATA6_Rep3_ChIPseq


title: P74_AD1 (scTCR-seq)


title: P115_HC2 (scTCR-seq)

value: HC


title: AsPC1_Ctrl_GATA6_Rep2_ChIPseq


title: L36pl_ATAC_Rep1


title: CD8 T cells WT2 48h

description:
WT-48-2
WT3_48h


title: AsPC1_BI653048_GATA6_Rep3_ChIPseq


title: CD8 T cells KO3 48h

description:
KO-48-3
KO3_48h


title: P119_Blood (scTCR-seq)


title: Mouse lungs, post-injury day 14, replicate 1, Visium

value: all cells (unsorted)

value: black 6


title: RNA-Seq of Leptinotarsa decemlineata: yellow fat body larva Sample4

city: Mainz

first: Shuqing

address: Hanns-Dieter-Hüsch-Weg 15

institute: University of Mainz

description: Library name: YFB4

data_processing:
Trimmomatic was used to remove the Illumina adapters, drop the reads with a low quality or a short length (SLIDINGWINDOW:4:15 MINLEN:36) and remove the first ten bases of the reads (HEADCROP:10). To assess the quality both before and after this filtering process, we utilized FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were mapped to a chromosome-level genome assembly 31 using STAR 35 (version 2.7.8a). FeatureCounts (Subread 2.0.5) was used to count the reads mapped to the annotated genes, with the parameters "-p –countReadPairs" which indicates that the reads are paired. The genes that were not expressed were filtered out based on their transcript per million (TPM) values. We kept only the transcript having a TPM value above one in at least two samples (https://github.com/Xu-lab-Evolution/CPB_gene_expression_atlas/blob/main/TPMfiltration.R).
Assembly: JANJPO000000000, https://cpb-atlas.uni-mainz.de/media/genome_annotation/Leptinotarsa_decemlineata_01.fa
Supplementary files format and content: tab-delimited text file includes counts in transcript per million (TPM) information for each gene and each Sample

organism: Leptinotarsa decemlineata

source_name: white fat body

growth_protocol: The insects were maintained in a climate chamber with 24°C, 70% humidity and a photoperiod of 16 h light and 8 h dark per day. Larvae as well as adults were fed with leaves from organically grown potato plants (Annabelle variety, purchased from Ellenberg´s Kartoffelvielfalt GmbH & Co. KG, Barum, Germany).

extract_protocol:
RNA was extracted using the RNeasy Mini kit from Qiagen (Venlo, The Netherlands), following the manufacturer’s protocol. Lysis was performed with micro pestles.
For RNA-seq library preparation, the Novogene NGS RNA Library Prep Set (PT042) was used. The magnetic beads of oligos d(T)25 were used to enrich the mRNA. Subsequently, mRNA was randomly fragmented and cDNA synthesis was carried out using random hexamers and the reverse transcriptase enzyme. The second chain was synthesized with the addition of an Illumina buffer (non-directional library preparation). The resulting products were purified, end-repaired, and ligated with adapters. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The libraries were checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection.

treatment_protocol: Tissues from fourth instar larvae (L4) and adults, as well as the whole body from different stages, from egg to third instar larva (figure 2) were collected. The tissues were dissected in PBS under a stereoscopic microscope. Dissection time was limited to 10 min to avoid RNA degradation and the tissues were subsequently snap-frozen in liquid nitrogen and stored in a -80°C freezer. The whole-body samples were similarly snap-frozen before being stored to ensure identical processing of the entire dataset. The eggs were pooled into groups of five. Three L1, L2, and L3 larvae were pooled to create each sample, respectively. We pool individuals because the extracted RNA from each individual was not sufficient for sequencing. The L4 larvae and adult tissues are from single individuals. The L4 larvae were dissected on the 19th day of development from egg laying. Adults were kept in individual petri dishes from emergence and dissected seven days later.

value: white fat body

value: WT

value: No treatment


title: AsPC1_ATAC_Rep3


title: AsPC1_ATAC_Rep2


title: P91_Blood (scTCR-seq)

value: Blood

value: CIE


title: Mouse lungs, post-injury day 35, replicate 2, Visium

value: post-injury day 35

value: bleomycin


title: CD8 T cells WT3 48h

description:
WT-48-3
WT6_48h


title: Mouse lungs, post-injury day 14, replicate 2, Visium

value: post-injury day 14


title: P86_Skin (scTCR-seq)

value: Skin

value: mixture of isolated cells


title: RNA-Seq of Leptinotarsa decemlineata: white fat body larva Sample3

description: Library name: WFB3

source_name: testis

value: testis


title: AsPC1_BI653048_GATA6_Rep1_ChIPseq

data_processing:
Paired or single end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.11) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: merged bigiwg file for each conditiion
Supplementary files format and content: 3 column bed file

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

value: cell line

value: PDAC


title: P152_Skin (scTCR-seq)


title: UOK124-ARID2_KO-03

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

data_processing:
Trim Galore! (version 0.6.6, incorporating cutadapt version 2.5) was used to remove adapter sequences and trim low-quality ends.
The trimmed reads were aligned to the human genome (UCSC hg38 assembly) using STAR (version 2.7.9a).
Assembly: hg38
Supplementary files format and content: tsv

source_name: Kidney

growth_protocol: UOK124-WT and UOK124-ARID2_KO cells were cultured with DMEM supplemented with 10% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent, and its quality was assessed using a BioAnalyzer 2100.
Library preparation was performed using the TruSeq Stranded mRNA Library Prep kit, following the manufacturer's protocol.

value: Kidney


title: L36pl_ATAC_Rep2


title: Mouse lungs, post-injury day 35, replicate 1, Visium

value: lungs


title: Mouse lungs, post-injury day 35, replicate 3, Visium

value: all cells (unsorted)


title: CD8 T cells WT3 0h

description:
WT-0-3
WT6

value: spleen

value: primary CD8 T cells


title: CD8 T cells WT2 0h

description:
WT-0-2
WT3

value: WT


title: CD8 T cells WT1 48h

description:
WT-48-1
WT1_48h


title: PGS_Blood (scTCR-seq)

value: Erythrodermic CTCL


title: CD8 T cells KO3 0h

description:
KO-0-3
KO3


title: P152_Blood (scTCR-seq)

value: Blood


title: RNA-Seq of Leptinotarsa decemlineata: yellow fat body larva Sample2

description: Library name: YFB2

value: No treatment


title: UOK124-ARID2_KO-01


title: CD8 T cells KO2 0h

description:
KO-0-2
KO2


title: AsPC1_ATAC_Rep1


title: CD8 T cells WT1 0h

description:
WT-0-1
WT1


title: CD8 T cells KO1 0h

description:
KO-0-1
KO1


title: RNA-Seq of Leptinotarsa decemlineata: testis Sample2

description: Library name: T2

source_name: ovaries

value: ovaries


title: P178_Blood (scTCR-seq)


title: P119_Skin (scTCR-seq)

value: CIE


title: PGS_Skin (scTCR-seq)


title: UOK124-WT-03

value: parental


title: RNA-Seq of Leptinotarsa decemlineata: testis Sample1

description: Library name: T1

source_name: malpighian tubules male

value: malpighian tubules male


title: RNA-Seq of Leptinotarsa decemlineata: white fat body larva Sample1

description: Library name: WFB1


title: P94_Skin (scTCR-seq)

value: Skin

value: mixture of isolated cells


title: UOK124-WT-02


title: Optic cup, AAV8-GFP, rep9

city: Pozzuoli

first: Santiago

last: Negueruela

address: Via Campi Flegrei, 34

department: Genetic Medicie

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

data_processing:
Adapter trimming and filtering was performed using TrimGalore v0.6.7 with default parameters
Trimmed sequence reads were mapped to GRCm39 genome using STAR v2.7.10a with default parameters
Feature quantification was performed using HTSeq-count v2.0.2 with Gencode reference annotation vM31
Assembly: GRCm39
Supplementary files format and content: counts.tsv: A tab delimited file containing raw counts for all samples

source_name: Optic cup

growth_protocol: Maintenance of the mice was on a regular 12/12-h light/dark cycle, temperature of 20–24°C, and humidity of 54–65%, with ad libitum access to food and water.

extract_protocol:
Eye samples were processed in QIAzol Lysis Reagent (QIAGEN). RNA was extracted using the miRNeasy extraction kit (QIAGEN), according to the manufacturer's instructions.
RNAseq libraries were prepared according to manufacturer's instructions (TruSeq RNA Sample Preparation kit, Illumina, San Diego, CA) with an initial amount of 150 ng of total RNA

treatment_protocol: Retinal injection of viral vectors

value: Optic cup

tag: subject


title: RNA-Seq of Leptinotarsa decemlineata: ovaries Sample2

description: Library name: O2

tag: tissue


title: Optic cup, AAV8-miR-429, rep8


title: UOK124-ARID2_KO-02

tag: cell type


title: Optic cup, AAV8-miR-429, rep9

tag: genotype


title: UOK124-WT-01


title: RNA-Seq of Leptinotarsa decemlineata: testis Sample4

description: Library name: T4

tag: treatment


title: HK-2 cells, PRCC-TFE3_2_Doxy+

growth_protocol: HA-PRCC-TFE3-inducible HK-2 cell lines which express HA-PRCC-TFE3 in a doxycycline-dependent manner were cultured with advanced DMEM/F-12 supplemented with 1.5% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

treatment_protocol: HA-PRCC-TFE3-inducible HK-2 cells were cultured with or without 0.2 microg/ml of doxycycline for 24hr.

value: HA-PRCC-TFE3-inducible cell

value: Doxycycline +


title: RNA-Seq of Leptinotarsa decemlineata: ovaries Sample4

description: Library name: O4


title: P87_Skin (scTCR-seq)


title: Optic cup, AAV8-GFP, rep8


title: P303_Blood (scTCR-seq)


title: HK-2 cells, PRCC-TFE3_2_Doxy-

value: Kidney

value: Doxycycline -


title: Optic cup, AAV8-miR-429, rep7


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule male Sample5

description: Library name: MTM5

source_name: malpighian tubules female

value: malpighian tubules female


title: HK-2 cells, PRCC-TFE3_1_Doxy+


title: P94_Blood (scTCR-seq)


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule male Sample4

description: Library name: MTM4

source_name: midgutmale

value: midgutmale


title: P303_Skin (scTCR-seq)


title: HK-2 cells, PRCC-TFE3_1_Doxy-


title: P196_Blood (scTCR-seq)


title: Optic cup, AAV8-miR-429, rep6


title: P87_Blood (scTCR-seq)


title: Optic cup, AAV8-GFP, rep7


title: P196_Skin (scTCR-seq)


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule male Sample3

description: Library name: MTM3

value: WT


title: Jurkat Safe Harbor WCE for dCas9 rep1

first: Fadi

last: Najm

address: 415 Main Street 6043

institute: Broad Institute

data_processing:
Fastqs were processed using ENCODE ChIP-seq pipeline v2.2.0 with default parameters. The parameter pipeline_type was set to "tf" for CTCF and Cas9 and "histone" for H3K9me3 respectively.
Bigwigs were generated from the BAMs from the ENCODE pipeline using bamCoverage -b <input.bam> -o <output.bw> -bs 50 -p 4 --effectiveGenomeSize 2913022398 --normalizeUsing BPM
Assembly: hg38
Supplementary files format and content: bigwig

source_name: peripheral blood

growth_protocol: Jurkat cells were continuously cultured in RPMI 1640 supplemented with 10% FBS and penicilin/streptomycin.

extract_protocol:
Frozen crosslinked cell pellets were suspended in cell lysis buffer, sonicated, treated with antibody, and cleaned up for sequencing.
Libraries with 6 µg of input were prepared using the KAPA Hyper Prep Kit.

value: peripheral blood

value: Jurkat

value: T lymphoblast

tag: antibody


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule female Sample2

description: Library name: MTF2

source_name: midgutlarva

value: midgutlarva

value: No treatment


title: Optic cup, AAV8-GFP, rep6


title: Optic cup, AAV8-GFP, rep5


title: P192_Skin (scTCR-seq)

value: Erythrodermic CTCL


title: Optic cup, AAV8-miR-429, rep5


title: P192_Blood (scTCR-seq)

value: Blood


title: Jurkat Safe Harbor WCE for dCas9 rep2


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule female Sample1

description: Library name: MTF1


title: Optic cup, AAV8-miR-429, rep4


title: Jurkat Safe Harbor dCas9 rep2

value: Diagenode C15310263


title: RNA-Seq of Leptinotarsa decemlineata: ovaries Sample1

description: Library name: O1


title: P105_Blood (scTCR-seq)

value: mixture of isolated cells


title: Optic cup, AAV8-GFP, rep4

value: Optic cup


title: P105_Skin (scTCR-seq)

value: Skin


title: Jurkat Safe Harbor dCas9 rep1

value: Diagenode C15310262


title: RNA-Seq of Leptinotarsa decemlineata: midgut male Sample4

description: Library name: MM4

source_name: midgutfemale

value: midgutfemale


title: Jurkat sg4 WCE for dCas9 rep1


title: RNA-Seq of Leptinotarsa decemlineata: malpighian tubule female Sample3

description: Library name: MTF3


title: RNA-Seq of Leptinotarsa decemlineata: midgut male Sample2

description: Library name: MM2


title: P96_AD5 (scRNA-seq)

value: AD


title: Optic cup, AAV8-GFP, rep3


title: Optic cup, AAV8-miR-429, rep3


title: RNA-Seq of Leptinotarsa decemlineata: midgut larva Sample5

description: Library name: ML5


title: Jurkat sg4 dCas9 rep2

value: Diagenode C15310259


title: P77_AD3 (scRNA-seq)


title: Optic cup, AAV8-miR-429, rep2


title: Jurkat sg4 dCas9 rep1

value: Diagenode C15310258


title: P75_AD2 (scRNA-seq)


title: RNA-Seq of Leptinotarsa decemlineata: midgut larva Sample3

description: Library name: ML3

value: WT


title: MDA-MB-231, Doxorubicin-Resistant, shIMPDH2, Replicate 2

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Raw reads that passed the Illumina RTA quality filter were demultiplexed and pre-processed using FastQC for sequencing base quality control.
Genome alignment of raw reads to the human reference genome (GRCh38.p13) using STAR
Mapped reads were quantified at the gene level as a raw counts matrix using featureCounts from Subread
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited .txt file includes raw counts for each sample

source_name: Mammary

growth_protocol: MDA-MB-231 were cultured in DMEM media (Invitrogen).Media was supplemented with 10% fetal bovine serum (Invitrogen) and 1% antibiotic-antimycotic (Invitrogen), in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total cellular RNA was isolated using the PureLink RNA Mini kit with on-column DNase treatment (Thermo Fisher Sceintific)
sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina) from 500 ng total RNA following manufacturer’s instructions

value: Mammary

value: Mammary Epithelial Cells

value: Doxorubicin Resistant, IMPDH2 knockdown

value: proliferation


title: MDA-MB-231, Doxorubicin-Resistant, shIMPDH2, Replicate 3


title: RNA-Seq of Leptinotarsa decemlineata: midgut larva Sample4

description: Library name: ML4

value: No treatment


title: Optic cup, AAV8-miR-429, rep1


title: Jurkat sg4 WCE for dCas9 rep2

value: peripheral blood

value: Jurkat

value: T lymphoblast


title: RNA-Seq of Leptinotarsa decemlineata: midgut male Sample5

description: Library name: MM5

value: midgutlarva


title: P74_AD1 (scRNA-seq)

value: mixture of isolated cells


title: MDA-MB-231, Doxorubicin-Resistant, shIMPDH2, Replicate 1


title: Optic cup, AAV8-GFP, rep1

value: Optic cup


title: RNA-Seq of Leptinotarsa decemlineata: midgut female Sample3

description: Library name: MF3


title: RNA-Seq of Leptinotarsa decemlineata: midgut female Sample4

description: Library name: MF4


title: P121_HC4 (scRNA-seq)

value: Skin

value: HC


title: MDA-MB-231, Doxorubicin-Resistant, PLKO-GFP Replicate 3

value: Doxorubicin Resistant


title: Meibomian Gland Awat2 KO

city: Irvine

first: Julie

last: Wiedemann

state: California

address: Sprague Hall

institute: UCI

description: 10X Genomics

data_processing:
Raw sequencing data were demultiplexed and processed using Cellranger (10× Genomics version 3.1.0) using a mm10-2020-A reference provided by 10× Genomics.
Assembly: mm10
Supplementary files format and content: Matrices in the Hierarchical Data Format  (H5) which were obtained with Cellranger v3.1.0.

source_name: Eyelid

extract_protocol:
We collected eyelids and placed them in ice cold, sterile, phosphate buffered saline with a pH of 7.2. Individual eyelids were then dissected to remove the tarsal plate using a number 11 Bard-Parker scalpel to separate the tarsus from the underlying muscle and epidermis. After isolation, the tissue was minced and then placed in 500 ml of PBS containing 0.2% collagenase (Gibco, cat# 17028-029) and 0.05% hyaluronidase (Worthington, Cat# LS02592) in DMEM (Gibco, Cat# 31600-026). Tissues were nutated for 2 hours at 37oC, spun down at 700cf for 5 minutes and then resuspended in 500 ml of 0.25% Trypsin-EDTA (Gibco, Cat# 25200-056), nutated for another 5 minutes at 37oC, and then blocked using 500 ml of 0.25% soybean trypsin inhibitor (Gibco, Cat# 17075-029) in PBS. Single cells were then spun down at 700cf and resuspended in 500 ml of DMEM. Finally, cells were filtered through a 250 mm filter, washed with DMEM, transferred to Eppendorf tubes on ice, and submitted to the UCI Genomics Core.
The UCI Genomics Core team constructed libraries using a 10× Genomics Chromium instrument and then used a Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads.

value: Eyelid

value: Meibomian gland

tag: breed

value: Awat2 KO

tag: age

value: 6 month

value: Male


title: RNA-Seq of Leptinotarsa decemlineata: midgut female Sample2

description: Library name: MF2

value: WT


title: MDA-MB-231, Doxorubicin-Resistant, PLKO-GFP Replicate 2

value: Mammary

value: Mammary Epithelial Cells

value: proliferation


title: P116_HC3 (scRNA-seq)

source_name: Skin


title: RNA-Seq of Leptinotarsa decemlineata: l3 instar larva Sample5

description: Library name: L3rep5

value: No treatment


title: P115_HC2 (scRNA-seq)


title: P81_AD4 (scRNA-seq)

value: AD


title: MDA-MB-231, Doxorubicin-Resistant, PLKO-GFP Replicate 1


title: RNA-Seq of Leptinotarsa decemlineata: l3 instar larva Sample4

description: Library name: L3rep4


title: Meibomian Gland WT replicate 2

description: 10X Genomics


title: Optic cup, AAV8-GFP, rep2


title: P112_HC1 (scRNA-seq)


title: Meibomian Gland WT replicate 1

description: 10X Genomics


title: RNA-Seq of Leptinotarsa decemlineata: l3 instar larva Sample3

description: Library name: L3rep3


title: MDA-MB-231, PLKO-GFP,Replicate 2

value: GFP-PLKO


title: RNA-Seq of Leptinotarsa decemlineata: l2 instar larva Sample5

description: Library name: L2rep5

source_name: hemolymph larva

value: hemolymph larva


title: P197_Blood (scRNA-seq)

source_name: Blood

value: Blood

value: mixture of isolated cells

value: CIE


title: Pgr cre/+ Grb2 f/f 3

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description:
Gene expression data from uterus at gestation day 3.5
GRB3

data_processing:
Raw reads were trimmed with cutadapt v1.18 and Trim Galore! v0.6.4_dev.
Quality control analysis was performed using FastQC v0.11.9.
Trimmed reads were aligned to the GRCm38 genome assembly using STAR v2.7.3a, and feature counting was performed using the command ‘--quantMode GeneCounts’.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

source_name: Uterus

growth_protocol: Collect uteri from intact adult female mice on the third morning after detection of a vaginal mucus plug (gestation day 3.5).

extract_protocol:
RNA was extracted from the uterine tissues using the RNeasy Mini Kit for total RNA isolation (Qiagen, Valencia, CA, USA).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT Illumina UDI dual Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNF-474 HS fragment kit (Agilent Technologies, Inc.) using a Fragment Analyzer (Agilent Technologies, Inc.), and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 50M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: Uterus

tag: developmental stage

value: adult mouse at gestation day 3.5

value: Pgr cre/+ Grb2 f/f


title: Pgr cre/+ Grb2 f/f 4

description:
Gene expression data from uterus at gestation day 3.5
GRB4


title: P91_Blood (scRNA-seq)


title: Jurkat Untransduced CTCF rep2

city: Cambridge

data_processing:
Fastqs were processed using ENCODE ChIP-seq pipeline v2.2.0 with default parameters. The parameter pipeline_type was set to "tf" and "histone" for CTCF and H3K9me3 respectively.
CTCF bigwig files were created using bamCoverage from ENCODE ChIP-seq pipeline BAM outputs, using the following command: bamCoverage -b $1 -o "$2.bw" -bs 50 -p 4 --effectiveGenomeSize 2913022398 -- normalizeUsing BPM
CTCF count matrix was calculated using featureCounts and a .saf file of JASPAR CTCF motifs (MA0139) with the following command: featureCounts(files, allowMultiOverlap = T, largestOverlap = T, annot.ext = "jaspar_motifs.saf", readExtension3 = 200, ignoreDup = T
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: count matrix in tab separated file (tsv) provided as supplementary files

value: peripheral blood

value: Jurkat

value: T lymphoblast

value: Diagenode C15410210


title: MDA-MB-231, PLKO-GFP, Replicate 1

value: Mammary


title: RNA-Seq of Leptinotarsa decemlineata: l2 instar larva Sample1

description: Library name: L2rep1

value: WT


title: P91_Skin (scRNA-seq)

value: Skin


title: Jurkat Untransduced CTCF rep1


title: Pgr cre/+ Grb2 f/f 2

description:
Gene expression data from uterus at gestation day 3.5
GRB2


title: Pgr cre/+ Grb2 f/f 1

description:
Gene expression data from uterus at gestation day 3.5
GRB1


title: RNA-Seq of Leptinotarsa decemlineata: L1 instar larva Sample5

description: Library name: L1rep5

source_name: hindgut male

value: hindgut male

value: No treatment


title: Meibomian Gland WT replicate 3

description: 10X Genomics

value: Eyelid

value: Meibomian gland

value: 6 month

tag: Sex

value: Male


title: RNA-Seq of Leptinotarsa decemlineata: L1 instar larva Sample2

description: Library name: L1rep2


title: P86_Blood (scRNA-seq)

value: Blood

value: mixture of isolated cells

value: CIE


title: Jurkat Untransduced WCE rep2


title: P86_Skin (scRNA-seq)


title: Jurkat Untransduced WCE rep1


title: Grb2 f/f 4

description:
Gene expression data from uterus at gestation day 3.5
WT4

value: Uterus

value: adult mouse at gestation day 3.5

value: Grb2 f/f


title: RNA-Seq of Leptinotarsa decemlineata: L1 instar larva Sample1

description: Library name: L1rep1

source_name: hindgut larva

value: hindgut larva


title: Grb2 f/f 3

description:
Gene expression data from uterus at gestation day 3.5
WT3


title: P119_Blood (scRNA-seq)


title: MDA-MB-231, PLKO-GFP, Replicate 3

value: Mammary Epithelial Cells

value: GFP-PLKO

value: proliferation


title: Grb2 f/f 2

description:
Gene expression data from uterus at gestation day 3.5
WT2


title: Jurkat sg8 WCE rep2

value: peripheral blood

value: Jurkat

value: T lymphoblast


title: P197_Skin (scRNA-seq)

value: Skin


title: RNA-Seq of Leptinotarsa decemlineata: l2 instar larva Sample4

description: Library name: L2rep4

value: hemolymph larva

value: WT

value: No treatment


title: P152_Blood (scRNA-seq)

value: Blood


title: Jurkat sg8 CTCF rep2

value: Diagenode C15410210


title: RNA-Seq of Leptinotarsa decemlineata: hemolymph Sample5

description: Library name: HmK5


title: RNA-Seq of Leptinotarsa decemlineata: hemolymph Sample4

description: Library name: HmK4


title: 630Δerm perRWT_5, 60 min O2

city: Madison

first: Anna

last: Gregory

state: WI

address: 1550 Linden Dr., MSB Rm3435

department: Department of Gastroenterology and Department of Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

data_processing:
Quality control and adapter trimming was performed with bcl2fastq (version 2.20.0.445). Read mapping was performed with HISAT2 (version 2.2.0). Read quantification was performed using Subread’s featureCounts (version 2.0.1) functionality. Read counts loaded into R (version 4.0.2) and were normalized using edgeR’s. Trimmed Mean of M values (TMM) algorithm (version 1.14.5). Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1. Transcript level quantification, count normalization, and differential expression analysis were provided using C. difficile 630Δerm (GCA_002080065.1) as the reference genome.
Assembly: GCA_002080065.1
Supplementary files format and content: text file includes raw counts and fold change

organism: Clostridioides difficile 630

extract_protocol:
At indicated timepoints, 5 mL aliquots were diluted 1:1 in chilled 1:1 ethanol:acetone and stored at -20° to preserve RNA. RNA was extracted by centrifuging samples at 3,000 xg for 5 minutes at 4°C. Pellets were washed with 5 mL cold, nuclease free PBS, and centrifuged at 3,000 xg for 5 minutes at 4°C. The supernatant was removed, and remaining pellets were resuspended in 1 mL TRIzol and processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment. Purified RNA integrity was confirmed via 2100 Agilent BioAnalyzer and frozen at -80°C.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

value: perR corrected (perRWT)

value: 60 min O2


title: RNA-Seq of Leptinotarsa decemlineata: hemolymph Sample3

description: Library name: HmK3

source_name: hindgut female

value: hindgut female


title: P152_Skin (scRNA-seq)

value: mixture of isolated cells

value: CIE


title: P119_Skin (scRNA-seq)


title: P178_Blood (scRNA-seq)

value: Erythrodermic CTCL


title: Jurkat sg8 WCE rep1


title: Grb2 f/f 1

description:
Gene expression data from uterus at gestation day 3.5
WT1

value: Uterus

value: adult mouse at gestation day 3.5

value: Grb2 f/f


title: RNA-Seq of Leptinotarsa decemlineata: hindgut male Sample5

description: Library name: HM5


title: 630Δerm perRWT_5, 0 min O2

value: 0 min O2


title: PGS_Blood (scRNA-seq)


title: Jurkat sg4 H3K9me3 rep2

value: peripheral blood

value: Jurkat

value: T lymphoblast

value: Abcam ab176916


title: 630Δerm perRWT_3, 60 min O2


title: RNA-Seq of Leptinotarsa decemlineata: hindgut male Sample4

description: Library name: HM4

value: WT

value: No treatment


title: Jurkat sg4 H3K9me3 rep1


title: 630Δerm perRWT_3, 0 min O2


title: Jurkat Safe Harbor H3K9me3 rep2


title: P94_Blood (scRNA-seq)

value: Blood


title: RNA-Seq of Leptinotarsa decemlineata: hindgut larva Sample5

description: Library name: HL5

source_name: fertilized egg

value: fertilized egg


title: 630Δerm perRWT_2, 0 min O2

value: perR corrected (perRWT)


title: 630Δerm perRWT_2, 60 min O2

value: 60 min O2


title: Jurkat Safe Harbor H3K9me3 rep1


title: RNA-Seq of Leptinotarsa decemlineata: hindgut larva Sample4

description: Library name: HL4

source_name: fat body male

value: fat body male


title: P94_Skin (scRNA-seq)

value: Skin

value: mixture of isolated cells


title: 630Δerm perRWT_1, 60 min O2


title: Jurkat sg8 CTCF rep1

value: Diagenode C15410210


title: P87_Skin (scRNA-seq)

value: Erythrodermic CTCL


title: P87_Blood (scRNA-seq)


title: Jurkat [aag]sg4 WCE rep1


title: RNA-Seq of Leptinotarsa decemlineata: hindgut female Sample5

description: Library name: HF5


title: RNA-Seq of Leptinotarsa decemlineata: hindgut female Sample4

description: Library name: HF4

source_name: fat body female

value: fat body female


title: Jurkat [aag]sg4 CTCF rep2


title: PGS_Skin (scRNA-seq)


title: P303_Blood (scRNA-seq)


title: Jurkat [aag]sg4 CTCF rep1


title: P303_Skin (scRNA-seq)


title: RNA-Seq of Leptinotarsa decemlineata: hindgut larva Sample1

description: Library name: HL1


title: 630Δerm_4, 60 min O2


title: Jurkat sg4 WCE rep2


title: RNA-Seq of Leptinotarsa decemlineata: fertilized egg Sample4

description: Library name: FE4


title: 630Δerm perRWT_1, 0 min O2

value: 0 min O2


title: P196_Blood (scRNA-seq)


title: Jurkat sg4 WCE rep1

value: peripheral blood


title: 630Δerm_5, 60 min O2


title: 630Δerm_4, 0 min  O2


title: RNA-Seq of Leptinotarsa decemlineata: hindgut male Sample3

description: Library name: HM3


title: 630Δerm_5, 0 min O2


title: P196_Skin (scRNA-seq)


title: RNA-Seq of Leptinotarsa decemlineata: fertilized egg Sample2

description: Library name: FE2

source_name: genital ducts

value: genital ducts


title: Jurkat [aag]sg4 WCE rep2

value: Jurkat

value: T lymphoblast


title: Jurkat sg4 CTCF rep2


title: RNA-Seq of Leptinotarsa decemlineata: fertilized egg Sample1

description: Library name: FE1

value: WT


title: P192_Blood (scRNA-seq)


title: RNA-Seq of Leptinotarsa decemlineata: hindgut female Sample1

description: Library name: HF1

value: No treatment


title: Jurkat sg4 CTCF rep1


title: 630Δerm_2, 60 min O2


title: P192_Skin (scRNA-seq)


title: Jurkat Safe Harbor WCE rep2


title: 630Δerm_2, 0 min O2


title: 630Δerm_1, 60 min O2


title: RNA-Seq of Leptinotarsa decemlineata: fat body male Sample5

description: Library name: FbM5

source_name: aedeagus

value: aedeagus


title: 630Δerm_1, 0 min O2


title: RNA-Seq of Leptinotarsa decemlineata: fat body male Sample7

description: Library name: FbM7


title: P105_Blood (scRNA-seq)

value: Blood


title: P105_Skin (scRNA-seq)


title: Jurkat Safe Harbor WCE rep1

source_name: peripheral blood


title: RNA-Seq of Leptinotarsa decemlineata: fat body male Sample1

description: Library name: FBM1

source_name: yellow fat body

value: yellow fat body


title: Jurkat Safe Harbor CTCF rep2


title: RNA-Seq of Leptinotarsa decemlineata: fat body female Sample6

description: Library name: FbF6


title: Motor neurons, healthy control,  Day 52, rep 3

city: Trondheim

middle: Mikalsen

last: Kollstrøm

address: Edvard Griegs gate 8

department: Department of Neuromedicine and Movement Science

country: Norway

institute: NTNU

data_processing:
FASTQ files quality controlled with fastqc (v0.11.9), and filtered and trimmed by fastp (v0.20.0).
Trimmed sequence reads were aligned to the human GRCh38 reference genome using STAR (v2.7.3).
Read counts and normalization were performed using Salmon (v1.3.0) and R statistical software.
Assembly: GRCh38
Supplementary files format and content: tab-separated text file containing raw gene counts for each sample
Supplementary files format and content: tab-separated text file containing TPM normalized gene counts for each sample

source_name: human fibroblasts

growth_protocol: hiPSCs were differentiated to motor neurons according to the protocol by Nijssen et al. (2019), and maintained on PEI and laminin-coated dishes in Neurobasal medium supplemented with 1% PenStrep, 10 ng/mL BDNF and GDNF, and 200 uM L-Ascorbic Acid.

extract_protocol:
Qiagen RNeasy Mini Kit.
Illumina Stranded mRNA Prep kit

value: human fibroblasts

value: hiPSC-derived motor neurons

tag: disease

value: Healthy control


title: WT2

city: Dallas

first: Xing

last: Yang

state: TX

address: 5323 Harry Hines Blvd

department: Physiology

institute: University of Texas Southwestwen Mdeical Center

description:
Library name: Sample8
Column name in gene_count_WT2

data_processing:
Data Quality Control: Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Readsmapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Quantification of gene expression level: featureCount v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimation gene expression levels.

source_name: tumor

extract_protocol:
Total RNA from the sorted M-MDSCs was purified using the PurelinkTM RNA Mini Kit (Thermo Fisher Scientific, #12183025). 200ng of total RNA was used for the construction of sequencing libraries.
Directional (Strand Specific) Prep, Poly-A selection. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the secone strand cDNA synthesis using dUTP for directional library. For the sirectional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: tumor

tag: cell line

value: M-MDSCs

value: monocytic myeloid-derived suppressor cells

value: MC38 cell tumor bearing


title: Jurkat Safe Harbor CTCF rep1

value: Diagenode C15410210


title: RNA-Seq of Leptinotarsa decemlineata: fat body female Sample3

description: Library name: FbF3

source_name: white fat body

value: white fat body


title: Motor neurons, healthy control,  Day 52, rep 2


title: ht CBh>FLEX[Ascl1] (2w)

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

institute: University of Washington

description:
Library name: SCR215
Chromium Next GEM single Cell 3’ Reagent kits v3.1

data_processing:
fastq files were generated using cellranegr mkfastq
fastq files were aligned to custom mm10 reference genome using cellranger 7.2 or 8.0
Assembly: Custom mm10 genome containing TurboGFP sequence
Supplementary files format and content: filtered_feature_bc_matrix.h5, expression matrix with feature names and barcodes generated by cellranger in h5 format

source_name: retina

extract_protocol:
Following euthanasia, pools of >4 retinas were dissociated using the Worthington Papain Dissociation System (catalog no. LK003150) according to the manufacturer’s instructions. Cells were then spun at 4 °C at 400 × g for 10 min and resuspended in neurobasal medium (Gibco no. 21103049), 10% fetal bovine serum (Clontech), B27 (Invitrogen), N2 (Invitrogen), 1 mM l-glutamine (Invitrogen), and 1% penicillin-streptomycin (Invitrogen). The cell suspension was passed through a 35-μm filter and then sorted using a BD FACSAria III cell sorter (BD Bioscience) to retrieve TdT+ cells.
Following FACS purification, TdT+ cells were centrifuged at 300g at 4ºC for 5 mins. Supernatant was removed to achieve an approximate concentration of 1000 cells per µl. scRNA-seq libraries were constructed with a targeted cell recovery of 6,000-8,000 cells using the Chromium Next GEM single Cell 3’ Reagent kits v3.1 (Dual Index) following the manufacturer’s instructions.

value: retina

value: FACS TdT+ cells


title: RB3

description:
Library name: Sample6
Column name in gene_count_RB3


title: Ef1a>FLEX[Ascl1] (2w)

description:
Library name: SCR204
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: WT1

description:
Library name: Sample7
Column name in gene_count_WT1


title: WT3

description:
Library name: Sample9
Column name in gene_count_WT3


title: Motor neurons, healthy control,  Day 38, rep 3


title: RNA-Seq of Leptinotarsa decemlineata: genital ducts Sample4

description: Library name: D4


title: RB2

description:
Library name: Sample5
Column name in gene_count_RB2


title: CBh>FLEX[GFP] (2w)

description:
Library name: SCR203
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: Motor neurons, healthy control,  Day 38, rep 2


title: RNA-Seq of Leptinotarsa decemlineata: genital ducts Sample5

description: Library name: D5

source_name: malpighian tubules female

value: malpighian tubules female


title: RNA-Seq of Leptinotarsa decemlineata:  genital ducts Sample1

description: Library name: D1

value: hindgut male

value: WT


title: CBh>FLEX[Ascl1-Atoh1] (6w) no injury

description:
Library name: SCR182
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: RB1

description:
Library name: Sample4
Column name in gene_count_RB1


title: RNA-Seq of Leptinotarsa decemlineata: aedeagus Sample5

description: Library name: A5

value: fertilized egg

value: No treatment


title: Motor neurons, healthy control,  Day 38, rep 1


title: KO3

description:
Library name: Sample3
Column name in gene_count_KO3

value: LILRB4+/+ SCG2-/-


title: Motor neurons, healthy control,  Day 18, rep 3

value: human fibroblasts


title: KO2

description:
Library name: Sample2
Column name in gene_count_KO2


title: RNA-Seq of Leptinotarsa decemlineata: aedeagus Sample4

description: Library name: A4

value: aedeagus


title: Motor neurons, healthy control,  Day 18, rep 2

value: hiPSC-derived motor neurons

value: Healthy control


title: CBh>FLEX[Ascl1-Atoh7] (2w)

description:
Library name: SCR176
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: RNA-Seq of Leptinotarsa decemlineata: aedeagus Sample2

description: Library name: A2


title: KO1

description:
Library name: Sample1
Column name in gene_count_KO1

value: tumor

value: M-MDSCs


title: Motor neurons, healthy control,  Day 52, rep 1


title: Motor neurons, healthy control,  Day 18, rep 1


title: CBh>FLEX[Ascl1-Atoh1] (2w)

description:
Library name: SCR175
Chromium Next GEM single Cell 3’ Reagent kits v3.1