title: T0330339-02_non-res

description:
Library name: DSP-1001660021595-E-B04
FFPE sample Spatial transcriptome sequencing


title: T0330339-03_non-res

status: Public on Jan 08 2026

type: SRA

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

description:
Library name: DSP-1001660021595-E-B06
FFPE sample Spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
FASTQ files for GeoMx were aggregated into count matrices using GeoMx NGS pipeline.
Hs_R_NGS_WTA_v1.0.zip file include probe information, which was used for transform from fastq to dcc.
Assembly: GRCh38
Supplementary files format and content: DCC files which contain raw read counts along with RTS_IDs (probe barcodes).
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Formalin-fixed, paraffin-embedde (FFPE) tissues (5 µm) were baked at 60 °C for 30 min, deparaffinized, rehydrated, and processed using a Leica BOND Rx system according to the manufacturer’s protocol.
The GeoMx Human Whole Transcriptome Atlas Human RNA for Illumina Systems (GMX-RNA-NGSHuWTA-4) was used in this study. All tumor samples were processed and stained according to the manufacturer’s protocol. Single 5-μm formalin-fixed, paraffin-embedded (FFPE) tissue sections were deparaffinized and subjected to antigen retrieval procedures.

tag: tissue

value: Lung

tag: treatment

value: non-responder


title: AKPS P5 16d MRTX1133 mouse #38_rep3

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

country: USA

institute: Genentech Inc.

description:
Library name: SAM24462145
EpCam+ cells sorted from AKPS P5 tumor treated for 16d MRTX1133 mouse #38_rep3

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the mouse reference genome (GRCm38.p5) using GSNAP version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (mouse: GENCODE M15). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Trimmed mean of M-values (TMM) normalization was performed on the read counts using the "edgeR" package (Robinson et al., 2010), then the normalized counts were transformed to log counts per million (log-CPM) values.
Differential expression analysis on the normalized and transformed count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting MRTX1133 treated samples respectively with vehicle samples.
Assembly: mouse genome (GRCm38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log-CPM values for each sample

organism: Mus musculus

source_name: Colon tumor

extract_protocol:
RNA from sorted tumor epithelial cells from in vivo colon tumors was extracted using the RNeasy Plus Micro kit (Qiagen, 74034 ) with on column DNAse digestion (Qiagen 12023460) according to manufacturer’s instructions
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For low-input RNA-sequencing library generation (2 nanograms), the cDNA library was using Smart-Seq V4 Ultra Low Input RNA Kit (Takara). 150 picograms of cDNA were used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: Colon tumor

tag: cell type

value: Epithelial cell

value: MRTX1133_16 days


title: Il33 Deleted

city: Philadelphia

first: Kang

last: Ko

state: Pennsylvania

address: 240 S. 40th Street

department: Department of Periodontics

institute: University of Pennsylvania

description:
Library name: Experimental
10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were fabricated using cellranger-6.1.2 software
Assembly: mm10
Supplementary files format and content: tab separated matrix and value files

source_name: oral palate

extract_protocol:
Oral wound samples were collected after 2 d of healing as above, from bilateral sites such that control group had 14 wounds whereas experimental group had 16 wounds pooled together. Single cells were prepared as above and sorted on FACSAria II SORPinstrument such that 1-to-1 ratio of FSClow SSClow CD45+ DAPI- lymphoid cells and FSCmid-hi SSCmid-hi CD45+ DAPI- myeloid/granulocytes were collected prior to single cell barcode capture
library was prepared according to manufacturer's instrutions (Single Cell 3' v3)

treatment_protocol: tamoxifen injection (1 mg/ 25g daily for 5 days) or corn oil injection with oral wound induced with 1 mm^2 biopsy punch.

value: oral palate

value: CD45+ leukocytes

tag: genotype

value: Tamoxifen

tag: batch

value: batch 1


title: AKPS P5 16d MRTX1133 mouse #36_rep2

description:
Library name: SAM24462144
EpCam+ cells sorted from AKPS P5 tumor treated for 16d MRTX1133 mouse #36_rep2


title: AKPS P5 3d vehicle mouse #29_rep1

description:
Library name: SAM24462135
EpCam+ cells sorted from AKPS P5 tumor treated for 3d vehicle mouse #29_rep1

value: Vehicle_3 days


title: T0330339-07_non-res

description:
Library name: DSP-1001660021595-E-C02
FFPE sample Spatial transcriptome sequencing


title: S03545-1-05_non-res

description:
Library name: DSP-1001660021518-D-A10
FFPE sample Spatial transcriptome sequencing

source_name: Lymph node

value: Lymph node


title: AKPS P5 3d MRTX1133 mouse #30_rep3

description:
Library name: SAM24462141
EpCam+ cells sorted from AKPS P5 tumor treated for 3d MRTX1133 mouse #30_rep3

value: MRTX1133_3 days


title: S03545-1-02_non-res

description:
Library name: DSP-1001660021518-D-A04
FFPE sample Spatial transcriptome sequencing


title: AKPS P5 mouse #816_rep2

description:
Library name: SAM24420036
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #816

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the mouse reference genome (GRCm38.p5) using GSNAP version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (mouse: GENCODE M15). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Trimmed mean of M-values (TMM) normalization was performed on the read counts using the "edgeR" package (Robinson et al., 2010), then the normalized counts were  transformed to log counts per million (log-CPM) values.
Differential expression analysis on the normalized count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting P5 samples with P1 samples.
Assembly: mouse genome (GRCm38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log-CPM values for each sample

growth_protocol: 1x10^4 AKPS P1 (m4) organoids and or AKPS P5 (m484) organoids were orthotopically injected into the colon of C57BL/6N mice. 5 weeks post orthotopic injection colon tumors were harvested and digested into single cells.

extract_protocol:
RNA from sorted tumor epithelial cells from in vivo colon tumors was extracted using the RNeasy Plus Mini kit (Qiagen, 74134) with on column DNAse digestion (Qiagen 12023460) according to manufacturer’s instructions
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For sequencing library generation of more than 100 nanogramms of RNA, the Truseq Stranded mRNA kit (Illumina) was used. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: no treatment


title: AKPS P5 mouse #817_rep3

description:
Library name: SAM24420037
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #817


title: AKPS P5 3d MRTX1133 mouse #28_rep2

description:
Library name: SAM24462140
EpCam+ cells sorted from AKPS P5 tumor treated for 3d MRTX1133 mouse #28_rep2


title: T0268363-2_res

description:
Library name: DSP-1001660021518-D-C08
FFPE sample Spatial transcriptome sequencing

value: responder


title: AKPS P1 mouse #804_rep4

description:
Library name: SAM24420034
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #804


title: AKPS P1 mouse #802_rep2

description:
Library name: SAM24420032
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #802


title: AKPS P5 3d vehicle mouse #31_rep2

description:
Library name: SAM24462136
EpCam+ cells sorted from AKPS P5 tumor treated for 3d vehicle mouse #31_rep2


title: S03545-1-03_non-res

description:
Library name: DSP-1001660021518-D-A06
FFPE sample Spatial transcriptome sequencing


title: MDAPCA2B, 1% ethanol (control), input rep2

city: San Francisco

first: Franklin

last: Huang

address: 513 Parnassus Ave

department: Hematology and Oncology

institute: UCSF

description: Library name: CTRLIGG_2

library_source: genomic

data_processing:
FASTQ alignment, QC, and peak-calling were performed using the Nextflow (v22.10.6) nf-core pipeline for ChIP-seq data (v2.1.0)
Differential peak calling was performed using DESeq2 (v1.40.1). ChIP-seq tracks and peaks were normalized and visualized using deepTools (v3.5.2) and SparK (v2.6.2, bioRxiv 845529).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Prostate

growth_protocol: MDA PCa 2b cells (ATCC CRL-2422, RRID:CVCL_4748) were cultured in BRFF-HPC-1 media (Athena #0403).

extract_protocol:
Cells were harvested in suspension and prepared for ChIP-seq according to the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology #9003). 0.75 µl of micrococcal nuclease and 5 sonication cycles of 125 W, 20 khz, in 20 second intervals were used to digest chromatin. H3K27ac and IgG ChIP were performed in paired R1881-treated and ethanol-treated samples. ChIPs were run in duplicate. 5 µg H3K27ac (Active Motif 39133, RRID:AB_2561016), and 1 µg Rabbit IgG (Cell Signaling Technology #2729, RRID:AB_1031062) were used as ChIP antibodies.
20 ng samples were submitted to Novogene for DNA library preparation and sequencing with Illumina PE150 NovaSeq 6000.

treatment_protocol: MDA PCa 2b cells were seeded at 4 million cells in a 15 cm dish per chromatin immunoprecipitation (ChIP). Cells were hormone deprived for 3 days in BRFF-HPC-1 media with 10% charcoal-stripped serum before treatment for 16 hours with either 1% ethanol (control) or 10 nM of methyltrienolone (R1881) dissolved in 1% ethanol.

value: Prostate

tag: cell line

value: prostate adenocarcinoma cells

value: 1% ethanol (control)


title: AKPS P5 mouse #815_rep1

description:
Library name: SAM24420035
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #815


title: S03545-1-07_non-res

description:
Library name: DSP-1001660021518-D-B01
FFPE sample Spatial transcriptome sequencing


title: T0330339-06_non-res

description:
Library name: DSP-1001660021595-E-B12
FFPE sample Spatial transcriptome sequencing

value: Lung


title: MDAPCA2B, R1881 (treatment), H3K27ac ChIP rep2

description: Library name: R1881H3K27_2

value: R1881 (treatment)


title: T0330339-05_non-res

description:
Library name: DSP-1001660021595-E-B10
FFPE sample Spatial transcriptome sequencing

value: non-responder


title: MDAPCA2B, R1881 (treatment), input rep2

description: Library name: R1881IGG_2


title: S03545-1-01_non-res

description:
Library name: DSP-1001660021518-D-A02
FFPE sample Spatial transcriptome sequencing


title: AKPS P1 mouse #801_rep1

description:
Library name: SAM24420031
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #801

value: Colon tumor

value: Epithelial cell


title: MDAPCA2B, R1881 (treatment), input rep1

description: Library name: R1881IGG_1


title: MDAPCA2B, 1% ethanol (control), H3K27ac ChIP rep1

description: Library name: CTRLH3K27_1


title: LNCaP cells, R1881 (treatment) rep1

description: Library name: LNCAP_R1

data_processing:
FASTQ files were obtained, then data QC and filtering were performed using fastp (v0.24.0)
Transcript-level abundances were quantified using kallisto (v0.51.1)
Gene-level TPM counts were generated using tximport
Assembly: hg38
Supplementary files format and content: csv file with gene-level TPM counts for each sample

growth_protocol: LNCaP cells were cultured in RPMI (Gibco) with 10% FBS (Thermo Fisher) and 1% HyClone penicillin-streptomycin (Cytiva)

extract_protocol:
Total RNA was isolated using an RNAeasy Kit (Qiagen) according to the manufacturer's instructions. At least 10,000 ng total RNA dissolved in ddH2O was extracted.
Libraries were prepared externally by NovoGene

treatment_protocol: LNCaP cells were hormone deprived for 3 days in phenol red-free medium with 5% charcoal-stripped serum, before treatment for 16 hrs with either 1% ethanol (control) or 10 nM of methyltrienolone (R1881, NEN Life Science Products) dissolved in ethanol. Bulk RNA-seq was performed on 3 pairs of R1881-treated and ethanol-treated samples.

value: LNCaP


title: 2612935_NICD_BTH845

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description:
Library name: sample 8
NICD OE

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR(v2.7.9a) using parameters " --genomeLoad NoSharedMemory --readFilesCommand unpigz -c -p 4 --limitBAMsortRAM 67108864000 --outReadsUnmapped None --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMmapqUnique 60 --outSAMmultNmax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions WithinBAM SoftClip --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic".
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: mm10
Supplementary files format and content: gene-based raw counts and TPM tsv file

source_name: tumor

extract_protocol:
TRIzol based total RNA Extraction
Follow commercial protocols: KAPA RNA HyperPrep Kit with RiboErase (HMR) (Fisher Scientific Cat#50-196-5257)

value: tumor

value: tumor associated macrophages

value: lysm cre+; lox-stop-lox NICD


title: 1953904_WT_UVAC_2

description: Library name: sample 6

data_processing:
Single-end reads of 100bp reads obtained from all samples were trimming for adapter by cutadapt(version 1.9, default parameter with “ -m 25 -O 6 ”).
Then aligned to hybrid reference genome hg38(GRCh38.p13) and mm10(GRCm38.p6) by SLAMDUNK (version 0.4.0, parameters “-5 12 -n 100 -c 2 -mv 0.2 -m -rl 100”).
3’UTR bed file for Gencode v31 and vM22(for each gene, 3’UTR regions from different isoforms were merged to avoid duplicated counting) were used for counting reads and collapse into gene-based counts (SLAMDUNK collapse function).
All samples achieved > 100M reads (median 120M) and > 98.4% mapping rate. Quality control results from SLAMDUNK (alleyoop function, all default parameters except “-mq 2” for rates subfunction) were extensively reviewed, that we conformed they were comparable to the published data from SLAM-seq paper.
Assembly: mm10
Supplementary files format and content: 3UTR based counts summed by gene for both nascent RNA(T to C, "tccount") and total ("count") tsv file

source_name: Bone marrow

extract_protocol:
TRIzol based total RNA Extraction
Follow commercial protocols: SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen Cat#061.24)

value: Bone marrow

value: Bone marrow derived macrophages

value: WT

value: fed apoptotic cells


title: AKPS P5 3d vehicle mouse #39_rep4

description:
Library name: SAM24462138
EpCam+ cells sorted from AKPS P5 tumor treated for 3d vehicle mouse #39_rep4

value: Vehicle_3 days


title: AKPS P5 3d vehicle mouse #37_rep3

description:
Library name: SAM24462137
EpCam+ cells sorted from AKPS P5 tumor treated for 3d vehicle mouse #37_rep3


title: 2612934_NICD_BTH839

description:
Library name: sample 7
NICD OE


title: LNCaP cells, 1% ethanol (control) rep3

description: Library name: LNCAP_C3

value: Prostate

value: 1% ethanol


title: S03545-1-04_non-res

description:
Library name: DSP-1001660021518-D-A08
FFPE sample Spatial transcriptome sequencing

value: Lymph node


title: LNCaP cells, 1% ethanol (control) rep2

description: Library name: LNCAP_C2

value: prostate adenocarcinoma cells


title: 2612932_NICD_BTH866

description:
Library name: sample 5
NICD OE


title: LNCaP cells, ACSM1 overexpression rep3

description:
Library name: ACSM1_3
Columns in processed data file: ACSM1_3

treatment_protocol: Lentiviruses containing an ORF construct for Acyl-CoA Synthetase Medium Chain Family Member 1 (ACSM1, GeneCopoeia, Cat: EX-OL09432-LX304) or LacZ were produced in 293T cells using established protocols. LNCaP cells were seeded at 2 x 105 per well of a 6-well and transduced with the lentivirus to overexpress ACSM1 or LacZ. Following incubation, blasticidin (5 μg/ml) was used to select cells.

value: Lentiviral transduction to overexpress ACSM1


title: 1953908_RubKO_UVAC_2

description: Library name: sample 8

value: Rubcn-/-


title: MDAPCA2B, 1% ethanol (control), H3K27ac ChIP rep2

description: Library name: CTRLH3K27_2

value: 1% ethanol (control)


title: 2612931_WT_BTH841

description:
Library name: sample 4
WT

value: lysm cre-; lox-stop-lox NICD


title: MDAPCA2B, 1% ethanol (control), input rep1

description: Library name: CTRLIGG_1


title: LNCaP cells, ACSM1 overexpression rep1

description:
Library name: ACSM1_1
Columns in processed data file: ACSM1_1

value: LNCaP


title: AKPS P1 mouse #803_rep3

description:
Library name: SAM24420033
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #803

value: Colon tumor

value: Epithelial cell

value: no treatment


title: 1953907_RubKO_UVAC_1

description: Library name: sample 7

value: Bone marrow


title: 1953903_WT_UVAC_1

description: Library name: sample 5

value: Bone marrow derived macrophages


title: 2612929_WT_BTH864

description:
Library name: sample 2
WT

value: tumor

value: tumor associated macrophages


title: LNCaP cells, ACSM1 overexpression rep2

description:
Library name: ACSM1_2
Columns in processed data file: ACSM1_2


title: 1953900_RubKO_BMDM_2

description: Library name: sample 4


title: LNCaP cells, LacZ overexpression rep1

description:
Library name: LacZ_1
Columns in processed data file: LacZ_1

value: Lentiviral transduction to overexpress LacZ


title: LNCaP cells, LacZ overexpression rep3

description:
Library name: LacZ_3
Columns in processed data file: LacZ_3

value: Prostate


title: LNCaP cells, 1% ethanol (control) rep1

description: Library name: LNCAP_C1

value: 1% ethanol


title: RNA-CytoD_DC_4-3215214

description:
Library name: sample 40
apoptotic Jurkat and Cytochalasin D

data_processing:
Paired-end 100-cycle sequencing was performed on Illumina NovaSeq sequencers, per the manufacturer’s directions (Illumina).
Reads were first trimmed for adapters using fastp (version 0.20.0, paired-end mode, parameter as “--detect_adapter_for_pe --trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 ”)1. Then alignment to the hybrid reference genome hg38(GRCh38.p13) and mm10(GRCm38.p6) by STAR (version 2.7.1a, parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1").
Gene level quantification was determined by HTSeq(v0.11.2, union mode)3 based on GENCODE v31 and vM22 gene annotation.
After confirmed the samples with human dead cells have significantly more human reads, mice gene counts were extracted for downstream analysis.
Assembly: mm10
Supplementary files format and content: gene-based raw counts included both human and mice genes(prefix mm10_) tsv file

source_name: macrophages

extract_protocol:
TRIzol based total RNA Extraction
Follow commercial protocols: KAPA RNA HyperPrep Kit with RiboErase (HMR) (Fisher Scientific Cat#50-196-5257) and SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen Cat#061.24)

value: macrophages

value: WT

value: apoptotic Human Jurkat and Cytochalasin D


title: Resistant, dKO, rep2

city: Incheon

first: So Hee

last: Kwon

address: 85, Songdogwahak-ro, Yeonsu-gu

department: Pharmacy

country: South Korea

institute: Yonsei University

description:
Library name: Sample 11
Column name in rawcount.txt and rawcount.csv: CDDP_dKO_2

data_processing:
Adapter trimming and quality filtering were performed using Trim Galore v0.6.10 with parameters: --paired --phred33 --length 30 --gzip
Quality-controlled reads were aligned to the GRCh38 reference genome using STAR v2.7.10a with parameters: --sjdbOverhang 150 --readFilesCommand zcat --outSAMtype BAM Unsorted
Aligned BAM files were processed with featureCounts v2.0.1 to quantify gene-level expression, using -T 6 -p -t exon -g gene_id
Gene annotation was based on GTF file: Homo_sapiens.GRCh38.102.gtf (Ensembl release 102).
Only uniquely mapped, properly paired reads were used for quantification.
Assembly: Genome: Homo sapiens (GRCh38), Annotation: Ensembl release 102.
Supplementary files format and content: Count matrices in comma-separated .csv format containing Ensembl gene IDs and raw integer counts for each samples.

growth_protocol: SKOV-3 and SKOV-3 CDDP were cultured in RMPI medium supplemented with 10% FBS and 1% penicillin-streptomycin. All cells were incubated in humidified chambers with temeperature maintained at 37 ℃with 5% CO2.

extract_protocol:
Total RNA was extracted using the FavorPrep™ Total RNA Isolation Kit (Favorgen, Vienna, Austria) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760S), incorporating poly(A) mRNA magnetic isolation, according to the manufacturer’s instructions.500 ng of total RNA was enriched for polyadenylated transcripts using oligo-dT magnetic beads.

value: epithelial ovarian adenocarcinoma

value: KDM5A, KDM5B double-knockout

tag: drug resistance

value: cisplatin


title: Resistant, rep2

description:
Library name: Sample 8
Column name in rawcount.txt and rawcount.csv: CDDP_NT_2


title: LNCaP cells, R1881 (treatment) rep3

description: Library name: LNCAP_R3

value: LNCaP

value: prostate adenocarcinoma cells


title: RNA-PLD_DC_3-3215205

description:
Library name: sample 35
apoptotic Jurkat and PLD inhibitors

value: apoptotic Human Jurkat and PLD inhibitors


title: 1953899_RubKO_BMDM_1

description: Library name: sample 3

value: Rubcn-/-


title: Resistant, rep1

description:
Library name: Sample 7
Column name in rawcount.txt and rawcount.csv: CDDP_NT_1


title: LNCaP cells, LacZ overexpression rep2

description:
Library name: LacZ_2
Columns in processed data file: LacZ_2


title: RNA-PLD_DC_1-3215203

description:
Library name: sample 33
apoptotic Jurkat and PLD inhibitors


title: LNCaP cells, R1881 (treatment) rep2

description: Library name: LNCAP_R2


title: Parental, dKO, rep3

description:
Library name: Sample 6
Column name in rawcount.txt and rawcount.csv: dKO_3


title: 2612933_NICD_BTH835

description:
Library name: sample 6
NICD OE

value: lysm cre+; lox-stop-lox NICD


title: 2612928_WT_BTH862

description:
Library name: sample 1
WT

value: lysm cre-; lox-stop-lox NICD


title: 1953896_WT_BMDM_2

description: Library name: sample 2

value: Bone marrow

value: Bone marrow derived macrophages


title: RNA-CytoD_DC_3-3215213

description:
Library name: sample 39
apoptotic Jurkat and Cytochalasin D


title: Resistant, dKO, rep3

description:
Library name: Sample 12
Column name in rawcount.txt and rawcount.csv: CDDP_dKO_3


title: Parental, dKO, rep1

description:
Library name: Sample 4
Column name in rawcount.txt and rawcount.csv: dKO_1


title: 2612930_WT_BTH837

description:
Library name: sample 3
WT

value: tumor

value: tumor associated macrophages


title: 1953895_WT_BMDM_1

description: Library name: sample 1


title: RNA-ATG5KO_BMDM_DC_2-2657613

description:
Library name: sample 27
apoptotic Jurkat were fed to macrophages

value: apoptotic Human Jurkat


title: RNA-CytoD_DC_1-3215211

description:
Library name: sample 37
apoptotic Jurkat and Cytochalasin D

value: macrophages


title: RNA-CytoD_DC_2-3215212

description:
Library name: sample 38
apoptotic Jurkat and Cytochalasin D

value: WT


title: RNA-PLD_DC_2-3215204

description:
Library name: sample 34
apoptotic Jurkat and PLD inhibitors


title: Resistant, dKO, rep1

description:
Library name: Sample 10
Column name in rawcount.txt and rawcount.csv: CDDP_dKO_1


title: MDAPCA2B, R1881 (treatment), H3K27ac ChIP rep1

description: Library name: R1881H3K27_1

value: Prostate

value: R1881 (treatment)


title: RNA-control_DC_3-3215197

description:
Library name: sample 31
apoptotic Jurkat and DMSO (vehicle)

value: apoptotic Human Jurkat and DMSO (vehicle)


title: RNA-PLD_DC_4-3215206

description:
Library name: sample 36
apoptotic Jurkat and PLD inhibitors


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-DE7, Replicate 3

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

description: Library name: TGP_RNA-seq_siNT+NRF1-∆E7_Replicate3

data_processing:
Raw sequencing reads were trimmed for adapters and low-quality bases using Cutadapt 1.18, and processed reads were aligned to the human reference genome (hg38) and annotated transcripts using the STAR 2.7.0f alignment tool. Raw counts for individual samples were calculated, gene expression levels were quantified from read normalized counts, and differential gene expression analysis was performed using the Deseq2 pipeline (version 1.46.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw files for each sample

molecule: polyA RNA

source_name: Hek293 FLP-in

growth_protocol: HEK293 Flp-In cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose and pyruvate (Gibco #11995073) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (Gibco #16140071) and 1% penicillin-streptomycin (Gibco #15140122). All cells were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from HEK293 Flp-In cells of NRF1 isoform rescue experiments (see above) using the RNeasy Plus Mini Kit (Qiagen #74136).
The library was prepared using the Illumina® Stranded mRNA Prep kit

treatment_protocol: HEK293 Flp-In cells were transfected with NRF1 siRNA using Lipofectamine RNAiMAX (ThermoFisher Scientific #13778150). After 24 hours, doxycycline was added to induce expression of siRNA-resistant NRF1 isoforms: NRF1-FL or NRF1-ΔEx7.

value: Hek293 FLP-in

value: Human embryonic kidney

value: siRNA+dox


title: RNA-ATG5KO_BMDM_noDC_1-2657609

description: Library name: sample 23


title: RNA-WT_BMDM_DC_2-2657607

description:
Library name: sample 21
apoptotic Jurkat were fed to macrophages


title: Parental, rep2

description:
Library name: Sample 2
Column name in rawcount.txt and rawcount.csv: dKO_NT_2

value: epithelial ovarian adenocarcinoma


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-DE7, Replicate 2

description: Library name: TGP_RNA-seq_siNRF1+NRF1-∆E7_Replicate2


title: mRNA-seq of Hek293 FLP-in cells with siNRF1, Replicate 3

description: Library name: TGP_RNA-seq_siNRF1_Replicate3


title: Resistant, rep3

description:
Library name: Sample 9
Column name in rawcount.txt and rawcount.csv: CDDP_NT_3

value: cisplatin


title: RNA-control_DC_2-3215196

description:
Library name: sample 30
apoptotic Jurkat and DMSO (vehicle)


title: RNA-ATG5KO_BMDM_DC_1-2657612

description:
Library name: sample 26
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-FL, Replicate 3

description: Library name: TGP_RNA-seq_NRF1-FL_siNT_Replicate3


title: Parental, dKO, rep2

description:
Library name: Sample 5
Column name in rawcount.txt and rawcount.csv: dKO_2

value: KDM5A, KDM5B double-knockout


title: RNA-ATG5KO_BMDM_noDC_3-2657611

description: Library name: sample 25


title: RNA-ATG5KO_BMDM_noDC_2-2657610

description: Library name: sample 24


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-DE7, Replicate 3

description: Library name: TGP_RNA-seq_siNRF1+NRF1-∆E7_Replicate3


title: RNA-ATG5KO_BMDM_DC_3-2657614

description:
Library name: sample 28
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-FL, Replicate 3

description: Library name: TGP_RNA-seq_siNRF1+NRF1-FL_Replicate3


title: RNA-control_DC_4-3215198

description:
Library name: sample 32
apoptotic Jurkat and DMSO (vehicle)


title: RNA-WT_BMDM_noDC_1-2657603

description: Library name: sample 17


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-DE7, Replicate 2

description: Library name: TGP_RNA-seq_siNT+NRF1-∆E7_Replicate2


title: RNA-control_DC_1-3215195

description:
Library name: sample 29
apoptotic Jurkat and DMSO (vehicle)


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-DE7, Replicate 1

description: Library name: TGP_RNA-seq_siNRF1+NRF1-∆E7_Replicate1


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-FL, Replicate 1

description: Library name: TGP_RNA-seq_siNRF1+NRF1-FL_Replicate1


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate 2

description: Library name: TGP_RNA-seq_siNT_Replicate2


title: RNA-WT_BMDM_DC_3-2657608

description:
Library name: sample 22
apoptotic Jurkat were fed to macrophages


title: RNA-RubcnKO_engfulfDC_4-2461053

description:
Library name: sample 12
apoptotic Jurkat were fed to macrophages

value: Rubcn-/-


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate 3

description: Library name: TGP_RNA-seq_siNT_Replicate3


title: RNA-WT_BMDM_DC_1-2657606

description:
Library name: sample 20
apoptotic Jurkat were fed to macrophages


title: Parental, rep1

description:
Library name: Sample 1
Column name in rawcount.txt and rawcount.csv: dKO_NT_1


title: Parental, rep3

description:
Library name: Sample 3
Column name in rawcount.txt and rawcount.csv: dKO_NT_3


title: RNA-RubcnKO_engfulfDC_3-2461052

description:
Library name: sample 11
apoptotic Jurkat were fed to macrophages


title: RNA-RubcnKO_noDC_1-2461054

description: Library name: sample 13


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-FL, Replicate 2

description: Library name: TGP_RNA-seq_NRF1-FL_siNT_Replicate2


title: RNA-WT_BMDM_noDC_3-2657605

description: Library name: sample 19


title: RNA-WT_BMDM_noDC_2-2657604

description: Library name: sample 18


title: RNA-WT_noDC_3-2461064

description: Library name: sample 7


title: mRNA-seq of Hek293 FLP-in cells with siNRF1+NRF1-FL, Replicate 2

description: Library name: TGP_RNA-seq_siNRF1+NRF1-FL_Replicate2


title: RNA-RubcnKO_noDC_3-2461056

description: Library name: sample 15


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-DE7, Replicate 1

description: Library name: TGP_RNA-seq_siNT+NRF1-∆E7_Replicate1


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting NRF1, Replicate3

description: Library name: TGP_SpCas9_CBE_NRF1_Replicate3

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose and pyruvate (Gibco #11995073) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (Gibco #16140071) and 1% penicillin-streptomycin (Gibco #15140122). All cells were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from HEK293T of NRF1 Base Editor experiments (see above) using the RNeasy Plus Mini Kit (Qiagen #74136).
The library was prepared using the Illumina® Stranded mRNA Prep kit

treatment_protocol: A total of 750,000 HEK293T cells were transfected with one of the following vectors: pX461-ABE8e-nSpCas9-Intergenic, pX461-evoCDA1-nSpCas9-Intergenic, pX462-ABE8e-nSaCas9-Intergenic, pX461-ABE8e-nSpCas9-NRF1-ss-sgRNA, pX461-evoCDA1-nSpCas9-NRF1-ss-sgRNA, or pX462-ABE8e-nSaCas9-NRF1-ss-sgRNA, using X-tremeGENE 9. Following transfection, cells were selected with puromycin for 48 hours. At 72 hours post-transfection, cells were lysed for RNA extraction.

value: Plasmid+Puromycin


title: RNA-RubcnKO_engfulfDC_1-2461050

description:
Library name: sample 9
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting intergenic control, Replicate3

description: Library name: TGP_SpCas9_CBE_intergenic_Replicate3


title: RNA-WT_noDC_4-2461065

description: Library name: sample 8


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting NRF1, Replicate2

description: Library name: TGP_SpCas9_CBE_NRF1_Replicate2


title: RNA-RubcnKO_noDC_4-2461057

description: Library name: sample 16


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting NRF1, Replicate1

description: Library name: TGP_SpCas9_CBE_NRF1_Replicate1


title: mRNA-seq of Hek293 FLP-in cells with siNRF1, Replicate 2

description: Library name: TGP_RNA-seq_siNRF1_Replicate2


title: RNA-WT_engulfDC_3-2461060

description:
Library name: sample 3
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293 FLP-in cells with siNT, Replicate 1

description: Library name: TGP_RNA-seq_siNT_Replicate1


title: RNA-RubcnKO_noDC_2-2461055

description: Library name: sample 14


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting intergenic control, Replicate3

description: Library name: TGP_SpCas9_ABE_intergenic_Replicate3


title: mRNA-seq of Hek293 FLP-in cells with siNT+NRF1-FL, Replicate 1

description: Library name: TGP_RNA-seq_NRF1-FL_siNT_Replicate1


title: mRNA-seq of Hek293 FLP-in cells with siNRF1, Replicate 1

description: Library name: TGP_RNA-seq_siNRF1_Replicate1


title: RNA-WT_noDC_1-2461062

description: Library name: sample 5


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting intergenic control, Replicate2

description: Library name: TGP_SpCas9_CBE_intergenic_Replicate2


title: RNA-WT_noDC_2-2461063

description: Library name: sample 6


title: RNA-WT_engulfDC_1-2461058

description:
Library name: sample 1
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting NRF1, Replicate3

description: Library name: TGP_SpCas9_ABE_NRF1_Replicate3


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting intergenic control, Replicate2

description: Library name: TGP_SpCas9_ABE_intergenic_Replicate2


title: CTRL_1_SC_Chatneg

city: Leuven

first: Sandrine

last: Da Cruz

address: Herestraat 49 |

country: Belgium

institute: VIB-KUL Center for Brain & Disease Research

description:
DSP-1005580000422-D-D11
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

data_processing:
raw sequencing data was aligned to Nanostring in situ hybridization probes.
Raw Nanostring .dcc and .pkc counts and configuration files were read using the R packages NanoStringNCTools v1.6.1, GeomxTools v3.2.0 and GeoMxWorkflows v1.4.0 within R v4.2.0 environment to produce a non-normalized count matrix with target names which were converted to GENEIDs.
The following targets were not included in the annotation file and were excluded from the final count matrix: Gm10406, LOC118568634, D830030K20Rik, and NegProbe-WTX.
Assembly: mm10
Supplementary files format and content: processed count matrix in TSV format, dcc files, sample metadata in CSV format and Positive Key Count .pkc file

source_name: mouse spinal cord tissue

extract_protocol:
UV-photocleavable oligos were detached from RNA probes in the selected regions of interest through a UV-light beam. The oligos were collected in a test tube and further processed.
Processing of the samples was performed according to available protocols from the manufacturer (Manual MAN-10153-01 GeoMx DSP NGS Readout User Manual, Nanostring).
GeoMx spatial transcriptomics

value: mouse spinal cord tissue

value: Non-motor neurons

tag: area of_interest

value: Chatneg


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting NRF1, Replicate1

description: Library name: TGP_SpCas9_ABE_NRF1_Replicate1


title: FUSR521H_2_SC_ChaTpos

description:
DSP-1005580000422-D-D04
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Motor neurons

value: ChaTpos


title: RNA-WT_engulfDC_2-2461059

description:
Library name: sample 2
apoptotic Jurkat were fed to macrophages

value: macrophages

value: WT

value: apoptotic Human Jurkat


title: mRNA-seq of Hek293T cells with ABE SaCAs9 targeting NRF1, Replicate1

description: Library name: TGP_SaCas9_ABE_NRF1_Replicate1


title: mRNA-seq of Hek293T cells with ABE SaCas9 targeting NRF1, Replicate3

description: Library name: TGP_SaCas9_ABE_NRF1_Replicate3


title: mRNA-seq of Hek293T cells with CBE SpCas9 targeting intergenic control, Replicate1

description: Library name: TGP_SpCas9_CBE_intergenic_Replicate1


title: RNA-RubcnKO_engfulfDC_2-2461051

description:
Library name: sample 10
apoptotic Jurkat were fed to macrophages


title: FUSR521H_4_SC_ChaTneg

description:
DSP-1005580000422-D-D09
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: ChaTneg


title: CTRL_4_SC_Chatpos

description:
DSP-1005580000422-D-D12
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Chatpos


title: mRNA-seq of Hek293T cells with ABE SaCas9 targeting intergenic control, Replicate3

description: Library name: TGP_SaCas9_ABE_intergenic_Replicate3

value: Human embryonic kidney


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting intergenic control, Replicate1

description: Library name: TGP_SpCas9_ABE_intergenic_Replicate1


title: FUSR521H_1_SC_ChaTneg

description:
DSP-1005580000422-D-C07
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: CTRL_3_SC_Chatpos

description:
DSP-1005580000422-D-C10
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: mRNA-seq of Hek293T cells with ABE SaCas9 targeting NRF1, Replicate2

description: Library name: TGP_SaCas9_ABE_NRF1_Replicate2


title: FUSR521H_2_SC_ChaTneg

description:
DSP-1005580000422-D-D05
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: FUSR521H_3_SC_ChaTpos

description:
DSP-1005580000422-D-C12
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: mRNA-seq of Hek293T cells with ABE SaCas9 targeting intergenic control, Replicate1

description: Library name: TGP_SaCas9_ABE_intergenic_Replicate1


title: ChIP_NRF1-dE7_Replicate1

description:
Library name: TGP_ChIP_NRF1-dE7_Replicate1
NRF1-dE7.bw

data_processing:
Demultiplexing was performed using Bcl2fastq 2.20
Adatpter and quality trimming was performed by Cutadapt 1.18 to select bases with quality score  ≥ 30
Processed ChIP-seq reads were mapped to the human genome hg38 using the Software Bowtie2 (version 2.3.4.1)
bigWig files were generated for NRF1 full length and NRF1-∆E7, and EGFP normalized to the Input samples. For this Deeptools (version 3.5.2) bamCompare was used with the options "--binSize 50 --smoothLength 500 --effectiveGenomeSize 2913022398
bigwig for Input were generated by Deeptools (version 3.5.2) bamCoverage. Selected options were: --binSize 50 --smoothLength 500 --effectiveGenomeSize 2913022398
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were crosslinked in 1% formaldehyde (Pierce #28908) for 10 minutes, quenched with 125 mM glycine (Sigma #G8898) for 5 minutes, washed with cold PBS, and collected by scraping. Nuclei were isolated in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) with protease inhibitors, then lysed in ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1). Chromatin was sheared (Diagenode Bioruptor Plus) for 15 cycles (30 sec on/off) to 200-500 bp fragments. Chromatin (50 µg per IP) was diluted in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl) and incubated overnight at 4°C with 6 µg anti-FLAG M2 (Sigma #F1804) and 40 µL Dynabeads Protein G (ThermoFisher Scientific #10004D). Beads were washed sequentially with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), high salt buffer (same with 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted in 1% SDS, 100 mM NaHCO₃ at 65°C for 30 minutes. Crosslinks were reversed overnight at 65°C, followed by RNase A and Proteinase K treatment. DNA was purified using the phenol:chloroform:isoamyl alcohol.
The sequencing library was prepared from 11.5 ng of purified DNA using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences # 21096)

treatment_protocol: HEK293 Flp-In cells expressing FLAG-tagged NRF1-FL, NRF1-ΔEx7, or EGFP were induced with doxycycline for 48 hours.

value: Hek293 FLP-in

tag: chip antibody

value: Anti-Flag M2

value: Dox


title: CTRL_1_SC_Chatpos

description:
DSP-1005580000422-D-D10
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: CTRL_3_SC_Chatneg

description:
DSP-1005580000422-D-C11
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: FUSR521H_4_SC_ChaTpos

description:
DSP-1005580000422-D-D08
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: RNA-WT_engulfDC_4-2461061

description:
Library name: sample 4
apoptotic Jurkat were fed to macrophages


title: mRNA-seq of Hek293T cells with ABE SpCas9 targeting NRF1, Replicate2

description: Library name: TGP_SpCas9_ABE_NRF1_Replicate2


title: CTRL_3_SN_ChaTneg

description:
DSP-1005580000422-D-C01
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

source_name: mouse sciatic nerve tissue

value: mouse sciatic nerve tissue

value: Non-motor axons


title: ChIP_NRF1-dE7_Replicate2

description:
Library name: TGP_ChIP_NRF1-dE7_Replicate2
NRF1-dE7.bw


title: CTRL_4_SC_Chatneg

description:
DSP-1005580000422-D-E01
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: CTRL_3_SN_ChaTpos

description:
DSP-1005580000422-D-B12
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Motor axons


title: ChIP_NRF1-FL_Replicate1

description:
Library name: TGP_ChIP_NRF1-FL_Replicate1
NRF1-FL.bw


title: Input_NRF1-FL_Replicate1

description:
Library name: TGP_Input_NRF1-FL_Replicate1
NRF1-FL.bw


title: Input_EGFP_Replicate2

description:
Library name: TGP_Input_EGFP_Replicate2
EGFP.bw


title: ChIP_NRF1-FL_Replicate2

description:
Library name: TGP_ChIP_NRF1-FL_Replicate2
NRF1-FL.bw


title: FUSR521H_1_SC_ChaTpos

description:
DSP-1005580000422-D-C06
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: mouse spinal cord tissue


title: ChIP_EGFP_Replicate2

description:
Library name: TGP_ChIP_EGFP_Replicate2
EGFP.bw


title: CTRL_4_SN_ChaTpos

description:
DSP-1005580000422-D-B10
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: mRNA-seq of Hek293T cells with ABE SaCas9 targeting intergenic control, Replicate2

description: Library name: TGP_SaCas9_ABE_intergenic_Replicate2

value: Plasmid+Puromycin


title: ChIP_EGFP_Replicate1

description:
Library name: TGP_ChIP_EGFP_Replicate1
EGFP.bw


title: FUSR521H_3_SC_ChaTneg

description:
DSP-1005580000422-D-D01
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Non-motor neurons


title: Input_NRF1-FL_Replicate2

description:
Library name: TGP_Input_NRF1-FL_Replicate2
NRF1-FL.bw


title: Input_NRF1-dE7_Replicate2

description:
Library name: TGP_Input_NRF1-dE7_Replicate2
NRF1-dE7.bw


title: Input_EGFP_Replicate1

description:
Library name: TGP_Input_EGFP_Replicate1
EGFP.bw


title: Input_NRF1-dE7_Replicate1

description:
Library name: TGP Input_NRF1-dE7_Replicate1
NRF1-dE7.bw


title: CTRL_4_SN_ChaTneg

description:
DSP-1005580000422-D-B11
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: FUSR521H_2_SN_ChaTneg

description:
DSP-1005580000422-D-B01
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: Dami cells_heterozygous mutant CYCS_Mutant biol rep5

city: Athens

first: Eleni

last: Katsantoni

state: Attiki

address: Soranou tou Efesiou 4

department: Basic Research Department

country: Greece

institute: Biomedica Research Foundation Academy of Athens

description: Library name: Sample 13

data_processing:
Fastq files containing 100bp single-end reads have been generated by all sequenced samples and have been QCed using FastQC v.0.11.9. Trimming was considered not to be essential and  alignment to the human genome (hg38) using the STAR RNA Sequencing aligner (V. 2.7.7a) has been performed
The count files for each sample were generated by the featureCounts tool (V. 2.0.1)
Assembly: Hg38
Supplementary files format and content: Csv (comma separated value) files includes raw counts for each Sample

source_name: Dami

growth_protocol: Dami cells have been cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with glutamine, 10% Horse serum and 1% Penicillin-Streptomycin 10.000U/ml.

extract_protocol:
RNA has been extracted using TRI Reagent according to the manufacturer’s instructions.
Approximately 1 ug of RNA has been used for library preparation with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs (NEB), Massachusetts, USA), according to the manufacturer’s instruction, after the mRNA isolation with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)

treatment_protocol: The novel variant has been inserted in Dami cells using the CRISPR-Cas9 method. Alt-R CRISPR-Cas9 crRNA and HDR Donor oligo have been designed in the IDT Alt-R CRISPR HDR Designing Tool (Supplemental Table 1). Alt-R CRISPR-Cas9 tracrRNA, Alt-R S.p HiFi Cas9 Nuclease V3 and Alt-R HDR Enhancer V2 have been purchased from IDT. The preparation of the CRISPR reagents, the gRNA complex and the culture media have been performed according to the IDT protocol. Nucleofection of Dami cells has been performed in Nucleofector 2b Device, using the Amaxa Cell Line Nucleofector Kit V (Lonza, Switzerland). 48h after nucleofection, genomic DNA has been extracted using the Quick-gDNA MiniPrep Kit (ZymoResearch, USA) and tested by Sanger sequencing. The nucleofected Dami cells have then been sorted as single cells, using FACSAria IIu (BD Biosciences, USA) in 96-well plates, for the isolation of the homozygous (C/C), heterozygous (T/C), and wild-type (WT) clones.

value: Dami

value: Megakaryocytic

value: heterozygous mutant

value: Heterozygous CYCS variant ((NM_018947.6):c.292T>C (p.Tyr98His)


title: FUSR521H_3_SN_ChaTneg

description:
DSP-1005580000422-D-B07
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: CTRL_2_SC_Chatneg

description:
DSP-1005580000422-D-C05
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: WT

value: Chatneg


title: Dami cells_heterozygous mutant CYCS_Mutant biol rep2

description: Library name: Sample 10


title: CTRL_2_SC_Chatpos

description:
DSP-1005580000422-D-C04
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Motor neurons

value: Chatpos


title: FUSR521H_4_SN_ChaTneg

description:
DSP-1005580000422-D-B09
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: ChaTneg


title: FUSR521H_2_SN_ChaTpos

description:
DSP-1005580000422-D-A12
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: ChaTpos


title: Dami cells_heterozygous mutant CYCS_Mutant biol rep4

description: Library name: Sample 12


title: FUSR521H_3_SN_ChaTpos

description:
DSP-1005580000422-D-B06
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: CTRL_2_SN_ChaTneg

description:
DSP-1005580000422-D-A11
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: Dami cells_heterozygous mutant CYCS_Mutant biol rep3

description: Library name: Sample 11


title: Dami cells_heterozygous mutant CYCS_Mutant biol rep1

description: Library name: Sample 9


title: CTRL_2_SN_ChaTpos

description:
DSP-1005580000422-D-A10
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: Dami cells_homozygous mutant CYCS_Mutant biol rep4

description: Library name: Sample 8

value: homozygous mutant

value: Homozygous CYCS variant ((NM_018947.6):c.292T>C (p.Tyr98His)


title: FUSR521H_1_SN_ChaTpos

description:
DSP-1005580000422-D-A08
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: mouse sciatic nerve tissue


title: Dami cells_homozygous mutant CYCS_Mutant biol rep1

description: Library name: Sample 5


title: FUSR521H_1_SN_ChaTneg

description:
DSP-1005580000422-D-A09
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: Non-motor axons


title: Dami cells_homozygous mutant CYCS_Mutant biol rep3

description: Library name: Sample 7


title: Dami cells_homozygous mutant CYCS_Mutant biol rep2

description: Library name: Sample 6


title: Dami cells_WT_Control biol rep4

description: Library name: Sample 4


title: 3013

city: New York

first: yu

last: liu

state: NY

address: 1428 Madison Ave

institute: Mount Sinai

data_processing:
Raw 10× read processing and quality control Raw sequence reads were quality-checked using FastQC software. The CellRanger version 7.0 software suite from 10× Genomics was used to process, align and summarize unique molecular identifier (UMI) counts against the mouse GRCm38 assembly reference genome analysis set, obtained from https://www.10xgenomics.com. Filtered count matrices from CellRanger were imported into R for further processing. Low quality cells are filtered, such as cell for which a high percentage of UMIs originated from mitochondrial features (more than 20%) and cell with fewer than 200 expressed genes. Three methods (doubletfinder, scds and scDblFinder) are applied to detect doublets, doublets cells identified by at least two methods are filtered. Median absolute deviation method is used to derive a cutoff for the maximum number of genes in cell. After filtering, 34,417 cells are left, used for further analysis. The Seurat R package (version 5.0) is used to normalization, integration using harmony, and plotting. Slingshot is used for trajectory and psudotime analysis. Cellchat is used for cell-cell communication between macrophage and neurons.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: colon

extract_protocol:
Wild-type mice were anesthetized by isoflurane after which they were sacrificed by cervical dislocation. The GI tract was harvested with care to prevent nicking major blood vessels. The mesenteric fat was removed as much as possible. The colonic bowel contents were flushed out with ice-cold 1X PBS (which did not contain RNase inhibitor or Actinomycin D). After cleaning the tissue was transferred to a petri-dish containing ice-cold Opti-MEM (with 2uM Actinomycin D). The LM-MP tissue was peeled on a sterile 1 ml pipette and placed in sterile RNase free tubes containing maintenance media (composition given below) and kept on ice. After all the animals have been sacrificed and LM-MP isolated, using new single edged blade, the LM-MP was chopped into minute pieces. The chopped tissues were digested in 50ml conical tubes with digestion media (composition given below) for 35 mins at 37C with shaking. The tubes were then vortexed for 30 sec at the highest speed followed by trituration with 1ml pipette tips. Samples were centrifuged for 7mins at 200g at temperature of 4C. Supernatants were aspirated gently and re-suspended in 4-5ml of Maintenance Buffer. The re-suspended pellets were passed through a 100 micron cell sieve after which the eluents were triturated with fire polished glass pipettes. The samples were centrifuged for 7mins at 200g, the supernatants aspirated, and the pellets resuspended in 3-4ml of Maintenance Buffer followed by trituration with glass pipettes. The washing process was repeated once more tand the pellets finally re-suspended in 1ml Maintenance Buffer and filtered through 40micron cell sieve and submitted to Hopkins Single Cell Sequencing Core.
Upon submission, the quality of the samples (viability and cell count) was assessed with Trypan Blue and Cell Countess (Invitrogen). The library was made using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X genomics). The depth of reads was 20,000/cell and the sequencing was carried out by NovaSeq 6000 (Illumina).

value: colon

tag: strain

value: wt

tag: dob

tag: date experiment

tag: Sex

value: F


title: CTRL_1_SN_ChaTneg

description:
DSP-1005580000422-D-A03
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc


title: Dami cells_WT_Control biol rep1

description: Library name: Sample 1

value: Dami


title: Dami cells_WT_Control biol rep3

description: Library name: Sample 3

value: Megakaryocytic


title: 2771


title: U2OS,  RNaseH1-D210N mutant stable expression cell line without Doxycycline added, rep2

city: Beijing

first: weibin

last: wang

address: No. 38 Academy Road

country: China

institute: Peking University Health Science Center

data_processing:
The raw data were trimmed for adaptor and low-quality sequence by Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
DRIP-seq reads were aligned to the genome using the Hisat2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
Duplicate reads were removed using Sambamba version 0.8.2, and sorted using SAMtools version 1.17, transferred to bigWig files by bamCoverage of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
The narrowPeak files and called peaks were generated by MACS2 version 2.1.0.20150731 (parameters: -q 0.2).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Bone

growth_protocol: Human U2OS cells were incubated in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (ExCell Bio) and 1% penicillin-streptomycin (MAC Gene) at 37°C (5% CO2).

extract_protocol:
Briefly, for each IP, U2OS cells (four 100 mm dishes per biological replicate for sequencing) were washed twice with cold PBS and cross-linked with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine for 5 min at room temperature. Cells were lysed sequentially with buffer1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TritonX-100) containing protease inhibitors including 1 mM PMSF (Amresco), 1 μg/ml Aprotinin (Targetmol) and 1× cocktail (Cwbio) and buffer2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl) containing protease inhibitors as described above on a rotative shaker at 4°C for 10 min. After centrifugation, cell pellets were resuspended in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) containing protease inhibitors as described above, followed by sonicating to appropriate fragment (250~500 bp). After sonication, the lysate was centrifuged at 14000 rpm for 10 min to collect the supernatant. Next, 2% of the supernatant was saved as input and the remaining was diluted with NETN buffer containing protease inhibitors as described above. For ChIP-seq using tet-on stable expression cell lines of nuclease-dead mutant REXO4-D386A and RNaseH1-D210N, the samples were incubated with anti-Flag M2 affinity beads (Sigma-Aldrich) on a rotative shaker overnight at 4°C. Then the beads were washed with the following buffers successively: once with low salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA; 20 mM Tris-HCl, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl) and twice with TE buffer. The protein-chromatin complex bound to beads was eluted using elution buffer (10 mM Tris-HCl, 1% SDS, 1 mM EDTA) supplemented with protease K and incubated with input overnight at 65°C shaking to revert crosslinking. After sequential RNaseA and Proteinase K treatment, The DNA samples were purified using phenol chloroform extract assay. The precipitated DNA samples were subjected to library preparation.
The library was prepared by using NEBNext Ultra II DNA Library Prep Kit (NEB).

treatment_protocol: Dox 1 μg/ml added or not added  for ~60h

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells

value: Tet-on stable expression cell line of  nuclease-dead mutant RNaseH1-D210N

value: No doxycycline added


title: macrophage exosomes_2

city: Guangzhou

first: Xi

last: Ming

state: Guangdong

address: No. 48 Xinhua Road, Xinhua Street, Huadu District, Guangzhou

institute: Guangzhou Huadu District People's Hospital

description:
Library name: Sample 2
Exosomes were isolated from the CM of macrophages . Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system

data_processing:
Raw data were generated and then subjected to initial quality control to retain sequences 16 to 35 nt in length.
Human miRNA sequences were referenced from the miRbase database, Differential expression analysis was conducted with DESeq package in R (version 4.2.2), identifying differentially expressed miRNAs through fold change filtering (fold change > 2 with P < 0.05).
Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis was conducted on target gene candidates of differentially expressed miRNAs using miRanda and RNAhybrid software.
Assembly: Homo_sapiens_Ensembl_106
Supplementary files format and content: Readcount_TPM

source_name: Peripheral blood

growth_protocol: Human monocyte cells (THP-1) were obtained from American Type Culture Collection (ATCC), Chinese Academy. Cells were cultured in RPMI-1640 medium (Gibco, USA) with 10% exosome-depleted FBS (Gibco, USA), 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were cultured in an incubator set at 37 °C with 5% CO2.

extract_protocol:
Exosomes were harvested from approximately 250 mL of conditioned medium (CM) collected from macrophage or M2 macrophage polarization through polymerization precipitation, ultrafiltration, and ultracentrifugation. The CM underwent sequential centrifugation at 1,000×g for 10 min, 2,000×g for 10 min, and 18,000×g for 30 min to eliminate cell fragments, debris, and large extracellular vesicles.  Exosomal total RNA were extracted following exosome characterization.
Small RNA sequencing was performed in an Illumina Novaseq system
30 ng of RNA was ligated with RNA 3′ and 5′ adapters, converted to cDNA, and amplified using Illumina primers.

treatment_protocol: THP-1 cells (1 x 10^6) were treated with 100 ng/mL phorbol 12-mphorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich, St. Loius, USA) for 48 h. Cell attachment and morphological changes were documented using light microscopy. Macrophages are induced to M2-polarized alternatively activated macrophages using either 20 ng/ml IL-4 (AF-200-04, PeproTech) and 20 ng/ml IL-13 (AF-200-13, PeproTech) or 10 ng/mL or 20 ng/mL TGF-β (R&D Systems, Minnesota, USA) for 48 h. The M2 polarization is confirmed through flow cytometry and western blotting. CM from macrophage or M2 macrophage polarization was obtained after culturing in serum-free medium for another 30 h.

value: Peripheral blood

value: Human monocyte cells (THP-1)

value: Macrophage-like cells


title: macrophage exosomes_1

description:
Library name: Sample 1
Exosomes were isolated from the CM of macrophages . Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system

value: THP-1 cells (1 x 10^6) were treated with 100 ng/mL phorbol 12-mphorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich, St. Loius, USA) for 48 h


title: Ccr2+MHCII+ DSS3

data_processing:
fastQC(v0.11.9) was usd to compute basic statistic and check QC, trimmomatic(v0.36) was used to trim low quality parts of reads. STAR (v2.7.5b) was used to align reads to GRCm39. Reads counts for each gene summarized using RNA-SeQC(v2.1.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: macrophage

growth_protocol: 8-9 week-old female Cx3Cr1+/GFP Ccr2+/RFP littermates were used to identify and sort different macrophage subsets present in the colonic muscularis during colitis.

extract_protocol:
Total RNA was isolated from sorted cell populations using Trizol protocol as described previously (PMID: 15284119 and PMID: 32276965)
RNA-seq libraries were prepared in the Penn State College of Medicine Genome Sciences core (RRID:SCR_021123) using Lexogen’s QuantSeq 3’ mRNA-Seq V2 Library Prep Kit Forward (FWD) with 12 nucleotide Unique Dual Indices (UDIs) following the manufacturer’s instructions for low input RNA library prep. Briefly, 1 ng of total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming followed by cDNA purification and library amplification using Lexogen’s 12 nt Unique Dual Indices and 24 cycles. The libraries were analyzed for size distribution and concentration using BioAnalyzer High Sensitivity DNA kit (Agilent technologies, Santa Clara, CA). Libraries were pooled at equimolar concentrations and sequenced on Novaseq6000 (Illumina) to get approximately 5 million paired end 50 bp reads.

treatment_protocol: Mice received sterile 3% dextran sodium sulfate (DSS) in drinking water for 5 consecutive days followed by sterile water till they reached peak of inflammation. Control mice received sterile water throughout the experiment. DSS treated mice were euthanized at the peak of inflammation i.e. D7-8 along with control mice (n=3 to 4, per group).

value: macrophage

value: Cx3Cr1+/GFP Ccr2+/RFP

value: DSS

value: female


title: M2 macrophage exosomes_2

description:
Library name: Sample 5
Exosomes were isolated from the CM of  M2 macrophages. Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system

value: Monocyte M2-like cells

value: Macrophages are induced to M2-polarized alternatively activated macrophages using either 20 ng/ml IL-4 (AF-200-04, PeproTech) and 20 ng/ml IL-13 (AF-200-13, PeproTech)  or 20 ng/mL TGF-β (R&D Systems, Minnesota, USA) for 48 h.


title: Ccr2+MHCII+ DSS5


title: 3263

value: colon

value: wt

value: M


title: 3268

value: F


title: macrophage exosomes_3

description:
Library name: Sample 3
Exosomes were isolated from the CM of macrophages . Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system


title: M2 macrophage exosomes_1

description:
Library name: Sample 4
Exosomes were isolated from the CM of  M2 macrophages. Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system

value: Macrophage M2-like cells


title: M2 macrophage exosomes_3

description:
Library name: Sample 6
Exosomes were isolated from the CM of  M2 macrophages. Exosomal total RNA were extracted following exosome characterization. Small RNA sequencing was performed in an Illumina Novaseq system


title: U2OS,  RNaseH1-D210N mutant stable expression cell line without Doxycycline added, rep1

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells

value: Tet-on stable expression cell line of  nuclease-dead mutant RNaseH1-D210N


title: Ccr2+MHCII+ DSS1


title: Ccr2+Ly6c+MHCII+ DSS4


title: U2OS,  RNaseH1-D210N mutant stable expression cell line without Doxycycline added, input

value: No doxycycline added


title: CTRL_1_SN_ChaTpos

description:
DSP-1005580000422-D-A02
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

value: mouse sciatic nerve tissue

value: Motor axons

value: WT

value: ChaTpos


title: Dami cells_WT_Control biol rep2

description: Library name: Sample 2

value: Dami

value: Megakaryocytic


title: Ccr2+MHCII+ DSS2

value: macrophage

value: Cx3Cr1+/GFP Ccr2+/RFP

value: DSS

value: female


title: 3262

value: colon

value: wt

value: M


title: 3272

value: F


title: Ccr2+MHCII+ DSS4


title: Ccr2+Ly6c+MHCII+ DSS5


title: U2OS,  RNaseH1-D210N mutant stable expression cell line with Doxycycline added, rep1

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells

value: Doxycycline added


title: U2OS,  RNaseH1-D210N mutant stable expression cell line with Doxycycline added, rep2

value: Tet-on stable expression cell line of  nuclease-dead mutant RNaseH1-D210N


title: Section A 3 dpf rep 3

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

description: Library name: trout_1000_cells_A_3

data_processing:
Low-quality reads and adaptor sequences were removed using fastp (v0.23.4) . Ribosomal RNA sequences were removed using Ribodetector  (v0.3.1) and mitochondrial reads with SortMeRNA (v4.3.6). The reads were then aligned to the Oncorhynchus mykiss genome (NCBI: GCF_013265735.2, access date: Feb 2024) and Salvelinus fontinalis genome (NCBI: GCF_029448725.1_ASM2944872, access date: Mar 2025) using STAR (v2.7.11). Library strandedness was verified using checkstrandedness (v1.0.1) and alignment quality using Qualimap (v2.3). Gene-level counts were generated with HTSeq-count (v2.0.4).
Normalized number of reads was generated using DESeq2.
Raw counts were initially filtered to keep transcripts with counts greater than 30 in at least one sample.
Ortholog mapping was done using a combination of ProteinOrtho (v6.0.31), Ensembl BioMart (v.2.56.1), orthogene (v.1.6.1) and gene symbol matching.
Assembly: USDA_OmykA_1.1 (GCF_013265735.2) & ASM2944872v1 (GCF_029448725.1)
Supplementary files format and content: The Excel files contain non-normalized and normalized read counts for each sample (rows contain genes, columns contain samples), and include only data from samples processed after outlier removal.
Supplementary files format and content: - "01_sfontinalis_all_samples_non_normalized.xlsx" contains the non-normalized reads for all samples.
Supplementary files format and content: - "02_sfontinalis_Stage_A_normalized.xlsx" contains the normalized reads for section A (animal portion) of all samples.
Supplementary files format and content: - "03_sfontinalis_Stage_B_normalized.xlsx" contains the normalized reads for section B (vegetal portion) of all samples.
Supplementary files format and content: - "04_ortholog_analysis_gene_symbols.xlsx" contains the ortholog mapping between Oncorhynchus mykiss, Salvelinus fontinalis and Danio rerio for differentially localized transcripts.

organism: Oncorhynchus mykiss

source_name: 1000 cells

extract_protocol:
The samples were homogenized in 1000 μl of TRIReagent® (Sigma-Aldrich, USA) and total RNA was extracted according to the manufacturer’s protocol. LiCl precipitation was performed to remove inhibitors present in the yolky vegetal hemisphere. The concentration of RNA was measured using NanoDrop-2000 (ThermoFisher, USA) and sample quality was assessed using 5200 Fragment Analyzer (Agilent, USA).
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, USA) and NEBNext® Multiplex Oligos for Illumina® (96 Index Primers) (New England Biolabs, USA). 70 ng of a total RNA was used for library preparation. Ribosomal RNA depletion was performed using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs, USA).

value: 3 dpf (mid-blastula, ~1000 cells)

tag: section

value: Section A

tag: biological replicate


title: Ccr2+Ly6c+MHCII+ DSS3


title: U2OS,  RNaseH1-D210N mutant stable expression cell line with Doxycycline added, input


title: Section B 3 dpf rep 2

description: Library name: trout_1000_cells_B_2

value: Section B


title: Section B 3 dpf rep 1

description: Library name: trout_1000_cells_B_1


title: Section B 1 dpf rep 3

description: Library name: trout_64_cells_B_3

source_name: 64 cells

value: 1 dpf (early blastula stage, ~32-64 cells)


title: Ccr2+Ly6c+MHCII+ DSS1


title: Section A 3 dpf rep 2

description: Library name: trout_1000_cells_A_2


title: U2OS,  REXO4-D386A mutant stable expression cell line without Doxycycline added, rep2

value: Tet-on stable expression cell line of  nuclease-dead mutant REXO4-D386A

value: No doxycycline added


title: Ccr2+Ly6c+MHCII+ DSS2

value: macrophage

value: Cx3Cr1+/GFP Ccr2+/RFP


title: U2OS,  REXO4-D386A mutant stable expression cell line with Doxycycline added, rep2


title: Section A 3 dpf rep 1

description: Library name: trout_1000_cells_A_1


title: Section A 1 dpf rep 1

description: Library name: trout_64_cells_A_1


title: Section B 1 dpf rep 1

description: Library name: trout_64_cells_B_1


title: Ccr2+ DSS3

value: DSS

value: female


title: U2OS,  REXO4-D386A mutant stable expression cell line without Doxycycline added, rep1


title: Section B 3 dpf rep 3

description: Library name: trout_1000_cells_B_3


title: Section B 1 dpf rep 2

description: Library name: trout_64_cells_B_2


title: Section A 1 dpf rep 3

description: Library name: trout_64_cells_A_3


title: U2OS,  REXO4-D386A mutant stable expression cell line with Doxycycline added, rep1


title: Section A 1 dpf rep 2

description: Library name: trout_64_cells_A_2


title: Section B 1 hpf rep 3

description: Library name: trout_1_cell_B_3

source_name: fertilized egg (1-cell)

value: 1 hpf (early cleavage stage)


title: Ccr2+ DSS2


title: Section A 1 hpf rep 3

description: Library name: trout_1_cell_A_3


title: Ccr2+ DSS1


title: Ccr2+ DSS4


title: Section B 1 hpf rep 2

description: Library name: trout_1_cell_B_2


title: Ccr2+ DSS5


title: U2OS,  REXO4-D386A mutant stable expression cell line without Doxycycline added, input


title: Section A 1 hpf rep 2

description: Library name: trout_1_cell_A_2


title: U2OS,  REXO4-D386A mutant stable expression cell line with Doxycycline added, input


title: U2OS, siRNaseH1, IP_rep3

library_source: other

data_processing:
The raw data were trimmed for adaptor and low-quality sequence by Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
DRIP-seq reads were aligned to the genome using the Hisat2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
Duplicate reads were removed using Sambamba version 0.8.2, and sorted using SAMtools version 1.17, transferred to bigWig files by bamCoverage of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
The narrowPeak files and called peaks were generated by MACS2 version 2.1.0.20150731 (parameters: -q 0.05).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: DRIP-seq

molecule: other

extract_protocol:
Cell pellets for DRIP were resuspended in TE, followed by the addition of 20% SDS and proteinase K (10 mg/ml). Subsequently, cells were sonicated on ice to fragment genomic DNA, resulting in an average fragment size of ~500 bp. Then, the samples were incubated at 37°C overnight. Next, DNA was gently extracted using phenol-chloroform. After reserving 10% for input DNA, the rest of the DNA was mixed with binding buffer (10 mM sodium phosphate, pH 7.0, 140 mM NaCl, 0.05% Triton X-100), followed by the addition of S9.6 antibody or mouse IgG control and incubation on a rotative shaker at 4°C overnight. Then, the samples containing DNA/antibody complex were further incubated with Protein G beads (GE Healthcare) for 5 h at 4°C. After washing beads four times with binding buffer at 4°C for 7 min each, the DNA binding to beads were eluted using elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS) with proteinase K (10 mg/ml) at 55°C for 1 h. Finally, the eluted DNA was gently extracted using phenol-chloroform, resuspended in TE, and subjected to library preparation and sequencing.
The samples were subjected to 2nd strand synthesis using Hieff NGS® ds-cDNA Synthesis Kit (Yeasen, 13488) and the library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645L) based on the ChIP library construction method by Novogene (China).

treatment_protocol: Transfected with REXO4 or RNaseH1 siRNA

value: RNaseH1 knockdown

value: S9.6 (Kerafast, #ENH001)


title: Section A 1 hpf rep 1

description: Library name: trout_1_cell_A_1


title: Section A 0 hpf rep 2

description: Library name: trout_NF_egg_A_2

source_name: non-fertilized egg

value: 0 hpf (freshly fertilized egg/zygote)


title: U2OS, siRNaseH1, IP_rep2

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells


title: MHCII+ DSS5


title: Section B 0 hpf rep 3

description: Library name: trout_NF_egg_B_3


title: U2OS, siRNaseH1, Input

value: input


title: MHCII+ DSS2


title: Section A 0 hpf rep 1

description: Library name: trout_NF_egg_A_1


title: Section D 3 dpf rep 3

description: Library name: trout_1000_cells_D_3

data_processing:
Low-quality reads and adaptor sequences were removed using fastp (v0.23.4) . Ribosomal RNA sequences were removed using Ribodetector (v0.3.1) and mitochondrial reads with SortMeRNA (v4.3.6). The reads were then aligned to the Oncorhynchus mykiss genome (NCBI: GCF_013265735.2, access date: Feb 2024) using STAR (v2.7.11). Library strandedness was verified using checkstrandedness (v1.0.1) and alignment quality using Qualimap (v2.3). Gene-level counts were generated with HTSeq-count (v2.0.4).
Normalized number of reads was generated using DESeq2.
Raw counts were initially filtered to keep transcripts with counts greater than 30 in at least one sample.
Ortholog mapping was done using a combination of ProteinOrtho (v6.0.31), Ensembl BioMart (v.2.56.1), orthogene (v.1.6.1) and gene symbol matching.
Assembly: USDA_OmykA_1.1 (GCF_013265735.2)
Supplementary files format and content: The Excel files contain non-normalized and normalized read counts for each sample (rows contain genes, columns contain samples), and include only data from samples processed after outlier removal.
Supplementary files format and content: - "01_omykiss_all_samples_non_normalized.xlsx" contains the non-normalized reads for all samples.
Supplementary files format and content: - "02_omykiss_all_samples_normalized.xlsx" contains the normalized reads for all samples.
Supplementary files format and content: - "03_omykiss_total_altered_counts_per_stage_non_normalized.xlsx"  contains the non-normalized reads for the summarized total transcripts per stage.
Supplementary files format and content: - "04_omykiss_total_altered_counts_per_stage_normalized.xlsx" contains the normalized reads for the summarized total transcripts per stage.
Supplementary files format and content: - "05_omykiss_alteration_between_the_sections_at_NF_egg_stage_normalized.xlsx" contains the normalized reads for non-fertilized (NF) stage samples.
Supplementary files format and content: - "06_omykiss_alteration_between_the_sections_at_1_cell_stage_normalized.xlsx" contains the normalized reads for 1-cell (fertilized egg) stage samples.
Supplementary files format and content: - "07_omykiss_alteration_between_the_sections_at_64_cells_stage_normalized.xlsx" contains the normalized reads for 64-cells stage samples.
Supplementary files format and content: - "08_omykiss_alteration_between_the_sections_at_1000_cells_stage_normalized.xlsx" contains the normalized reads for 1000-cells stage samples.
Supplementary files format and content: - "09_ortholog_analysis_gene_symbols.xlsx" contains the ortholog mapping between Oncorhynchus mykiss, Salvelinus fontinalis and Danio rerio for differentially localized transcripts.

source_name: 1000 cell stage

extract_protocol:
The samples were homogenized in 1000 μl of TRIReagent® (Sigma-Aldrich, USA) and total RNA was extracted according to the manufacturer’s protocol. LiCl precipitation was performed to remove inhibitors present in the yolky vegetal hemisphere. The concentration of RNA was measured using NanoDrop-2000 (ThermoFisher, USA) and sample quality was assessed using 5200 Fragment Analyzer (Agilent, USA).
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, USA) and adaptors and indexes were provided with NEBNext® Multiplex Oligos for Illumina® (96 Index Primers) (New England Biolabs, USA). 30 ng of a total RNA was used for library preparation. Ribosomal RNA depletion was performed using Ribocop rRNA Depletion Kit V1.3 (Lexogen, Austria).

value: 3 dpf (mid-blastula, ~1000 cells)

value: Section D


title: Section E 3 dpf rep 3

description: Library name: trout_1000_cells_E_3

value: Section E


title: MHCII+ DSS4


title: MHCII+ Tap4

value: water


title: Section B 0 hpf rep 2

description: Library name: trout_NF_egg_B_2

value: Section B


title: U2OS, siRNaseH1, IP_rep1


title: U2OS, siREXO4, IP_rep1

value: REXO4 knockdown


title: Section D 3 dpf rep 2

description: Library name: trout_1000_cells_D_2


title: Section B 0 hpf rep 1

description: Library name: trout_NF_egg_B_1


title: U2OS, siREXO4, IP_rep2


title: Section B 1 hpf rep 1

description: Library name: trout_1_cell_B_1


title: Section B 3 dpf rep 3

description: Library name: trout_1000_cells_B_3


title: MHCII+ Tap3

value: macrophage


title: Section C 3 dpf rep 3

description: Library name: trout_1000_cells_C_3

value: Section C


title: Section A 3 dpf rep 3

description: Library name: trout_1000_cells_A_3

value: Section A


title: U2OS, siCtrl, IP_rep3

value: WT


title: Ccr2+MHCII+ Tap5

value: Cx3Cr1+/GFP Ccr2+/RFP

value: female


title: U2OS, siCtrl, IP_rep2

value: S9.6 (Kerafast, #ENH001)


title: Section E 3 dpf rep 2

description: Library name: trout_1000_cells_E_2


title: U2OS, siREXO4, IP_rep3


title: U2OS, siREXO4, Input


title: MHCII+ Tap2


title: MHCII+ DSS3

value: DSS


title: Section E 3 dpf rep 1

description: Library name: trout_1000_cells_E_1


title: Section D 3 dpf rep 1

description: Library name: trout_1000_cells_D_1


title: Section C 3 dpf rep 2

description: Library name: trout_1000_cells_C_2


title: Section B 3 dpf rep 2

description: Library name: trout_1000_cells_B_2


title: MHCII+ Tap1


title: Section A 0 hpf rep 3

description: Library name: trout_NF_egg_A_3

value: 0 hpf (freshly fertilized egg/zygote)


title: Section A 3 dpf rep 1

description: Library name: trout_1000_cells_A_1


title: U2OS, siCtrl, Input

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells


title: U2OS, siCtrl, IP_rep1


title: Ccr2+MHCII+ Tap2


title: Section B 3 dpf rep 1

description: Library name: trout_1000_cells_B_1

value: 3 dpf (mid-blastula, ~1000 cells)


title: U2OS, siCtrl, IgG

value: Mouse IgG (Bioss, #bs-0296P)


title: Ccr2+MHCII+ Tap3


title: Section C 3 dpf rep 1

description: Library name: trout_1000_cells_C_1


title: Section D 1 dpf rep 3

description: Library name: trout_64_cells_D_3

source_name: 64 cell stage

value: 1 dpf (early blastula stage, ~32-64 cells)

value: Section D


title: Section A 3 dpf rep 2

description: Library name: trout_1000_cells_A_2


title: Section E 1 dpf rep 3

description: Library name: trout_64_cells_E_3

value: Section E


title: Ccr2+MHCII+ Tap4

value: water


title: 56 year old sarcoidosis female

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pre-processed using the umi_homopolymer.py script (https://github.com/jwfoley/3SEQtools) followed by alignment to human genome assembly GRCh38.p14 with HISAT2 version 2.2.1. Gene counts were obtained using featurecounts in the Subread software package version 1.6.4.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated text file gene ID, chromosome, start position, end position, strand, length, and count

source_name: nasal epithelium

growth_protocol: Nasal airway epithelial cells were differentiated at the air-liquid interface

extract_protocol:
RNA was isolated in-lysis using Igepal
Sequencing-ready libraries were prepared using SMART-3SEQ

treatment_protocol: Cells were treated with cell culture media

value: nasal epithelium

tag: age

tag: disease

value: sarcoidosis


title: Ccr2+Ly6c+MHCII+ Tap1+2+ half of 5

value: macrophage


title: Section E 1 dpf rep 2

description: Library name: trout_64_cells_E_2

tag: tissue


title: 47 year old sarcoidosis male

value: male


title: Section A 1 dpf rep 3

description: Library name: trout_64_cells_A_3

value: Section A


title: Section B 1 dpf rep 2

description: Library name: trout_64_cells_B_2

value: Section B


title: Section C 1 dpf rep 2

description: Library name: trout_64_cells_C_2

value: Section C


title: MHCII+ Tap5

value: Cx3Cr1+/GFP Ccr2+/RFP

tag: treatment

value: female


title: 53 year old control male

value: control


title: Section B 1 dpf rep 3

description: Library name: trout_64_cells_B_3


title: Section C 1 dpf rep 1

description: Library name: trout_64_cells_C_1


title: Section C 1 dpf rep 3

description: Library name: trout_64_cells_C_3


title: Ccr2+Ly6c+MHCII+ Tap3+4+ half of 5

tag: cell type


title: Section A 1 dpf rep 1

description: Library name: trout_64_cells_A_1


title: ΔORF heart snRNA-seq

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
snRNA-seq and snATAC-seq reads were demultiplexed and aligned to mouse reference genome mm10 by 10x Genomics Cell Ranger ARC 2.0.2. For snRNA-seq, a count a count matrix was created by summarizing reads mapped to both exon and intron regions of each gene in each nucleus. For snATAC-seq, fragment files were generated containing all unique properly paired and aligned fragments. Each unique fragment was associated with a single cell barcode. A gene accessibility matrix was generated by summarizing fragments mapped to the promoter and gene body of each gene in each nucleus.
Only nuclei with more than 200 snRNA-seq reads and snATAC-seq fragments were included in the analysis. Potential doublets were eliminated using DoubletFinder, with an estimated doublet rate of 5%. Dimension reduction and clustering were primarily reliant on the the top 3000 variant features in snRNA-seq data. Prior to these processes, data from WT and delta uORF hearts were integrated together, utilizing SCTransformed counts and relevant functions in Seruat v4 in a R-4.2.2 environment. Dimension reduction was initiated with a PCA test, with a subsequent UMAP test utilizing the first 20 PCs. Clustering was performed via the k-nearest neighbors algorithm and Shared Nearest Neighbor (SNN) algorithm. Cluster annotations were initially established by comparing gene expression profiles to publicly available annotated datasets using SingleR, with gene expression counts being normalized and scaled prior to these comparisons. Reference datasets from Tabula Muris, containing snRNA-seq data from mouse heart and aorta, were employed for this annotation, and additional refinement was undertaken by considering normalized RNA expression and gene accessibility data for well-established cardiac cell-type-specific markers. To identify differentially expressed genes (DEGs) within each cluster, a logistic regression model, known for its robust performance in previous publications, was applied to the normalized counts, with variations in sequencing depth among nucleus being treated as latent variables.
snATAC-seq Peaks were called separately in WT and delta uORF hearts using MACS2. Putative cis-regulatory elements (pCREs) were identified using Signac v1.131 following the developer’s manual.
Assembly: mouse reference genome mm10
Supplementary files format and content: WT_atac_fragments.tsv.gz: gene-barcode matrix in h5 format; ΔORF_atac_fragments.tsv.gz: gene-barcode matrix in h5 format; WT_atac_fragments.tsv.gz: The ATAC per-fragment information file and index; ΔORF_atac_fragments.tsv.gz: The ATAC per-fragment information file and index
Supplementary files format and content: single.integrated.rds: summarizedexperiment object (seurat) containing all processed data including clustering, celltype annotation, and DEGs

molecule: nuclear RNA

source_name: heart

extract_protocol:
Whole hearts were harvested from both wildtype and ΔuORF mice, which were at an age of 2 month (n = 3), and were fast frozen in liquid nitrogen. Nuclei were isolated from the frozen mouse heart tissue using the 10x Genomics single nuclei isolation kit, adhering to the manufacturer's instructions.
We isolated nuclei from frozen mouse heart tissue and constructed single nuclei gene expression libraries and single nuclei ATAC libraries on the 10x Genomics Chromium System using the 10x Chromium Multiome kit. Each library was sequenced with ~200 million pair end reads (PE150) on Illumina NovaSeq 6000

value: heart

tag: genotype

value: delta-ORF


title: Section E 1 hpf rep 3

description: Library name: trout_1_cell_E_3

value: 1 hpf (early cleavage stage)


title: Section D 1 dpf rep 2

description: Library name: trout_64_cells_D_2

value: 1 dpf (early blastula stage, ~32-64 cells)


title: 56 year old sarcoidosis male


title: Section D 1 hpf rep 3

description: Library name: trout_1_cell_D_3

value: Section D


title: 59 year old control male


title: COTC022-2202-M-F-Liver

type: RNA

city: Bethesda

first: Christina

last: Mazcko

address: 10 Center Drive Room 1B58

department: CCR

institute: NCI

description: RNA was profiled using the Canine IO Panel

hyb_protocol: Gene expression profiling was performed using NanoString Canine Immuno-Oncology panel and nCounter instrument according to the manufacturer’s instructions.

data_processing: Normalization was accomplished using the nanostringr platform using the positive control normalization approach. Sample-specific correlation within each sample lane was also performed using CodeSet context (housekeeping gene) normalization

organism: Canis lupus familiaris

source_name: FFPE

extract_protocol: RNA was extracted using RNeasy Mini reagents and protocol. RNA quality was determined by Agilent 2100 Bioanalyzer’s DV200 analysis.

treatment_protocol: Dogs with osteosarcoma were enrolled in COTC021/022 and received standard of care with or without adjuvant sirolimus (LeBlanc et al., Clinical Cancer Research 2021)

tag: sample site

value: Liver

tag: primary tumor or met

value: Metastatic Tumor Tissue


title: Section E 1 hpf rep 2

description: Library name: trout_1_cell_E_2

value: Section E


title: COTC022-2202-M-F-Brain

value: Brain


title: Section D 1 dpf rep 1

description: Library name: trout_64_cells_D_1


title: Section A 1 dpf rep 2

description: Library name: trout_64_cells_A_2


title: Double- Tap4

value: macrophage

value: water


title: WT heart snRNA-seq

value: WT


title: Double- Tap2


title: Double- Tap5


title: Section E 1 dpf rep 1

description: Library name: trout_64_cells_E_1


title: Section D 1 hpf rep 2

description: Library name: trout_1_cell_D_2


title: Smit1-/- two weeks post TAC 5

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm39.cdna.all.fa file.
Assembly: Mus_musculus.GRCm39.cdna.all.fa
Supplementary files format and content: Matrix of Raw counts

source_name: Heart

extract_protocol:
Total RNA was isolated from mouse left ventricle using the Qiagen RNeasy Mini Kit for mRNA analyses (Qiagen, 74106).
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase following the manufacturer’s recommendations. Libraries were equimolarly pooled and sequenced on a single lane on an Illumina NovaSeq 6000 platform

value: Heart

value: TAC surgery

tag: time

value: 2 weeks


title: ΔORF heart snATAC-seq


title: WT heart snATAC-seq


title: Section A 1 hpf rep 3

description: Library name: trout_1_cell_A_3

value: Section A


title: Section E 1 hpf rep 1

description: Library name: trout_1_cell_E_1


title: Section D 1 hpf rep 1

description: Library name: trout_1_cell_D_1


title: Smit1-/- two weeks post TAC 3


title: Section B 1 hpf rep 3

description: Library name: trout_1_cell_B_3

value: Section B


title: COTC022-2006-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Section B 1 dpf rep 1

description: Library name: trout_64_cells_B_1


title: 47 year old control male

value: nasal epithelium

value: male

value: control


title: Smit1-/- two weeks post TAC 1


title: COTC022-1402-M-F-Lung

value: Lung


title: COTC022-1022-T

source_name: RNAlater


title: COTC022-1022-M-S-Omentum

source_name: Snap Frozen

value: Omentum

value: Metastatic Tumor Tissue


title: Section E 0 hpf rep 3

description: Library name: trout_NF_egg_E_3

value: 0 hpf (freshly fertilized egg/zygote)

value: Section E


title: FUSR521H_4_SN_ChaTpos

description:
DSP-1005580000422-D-B08
GeoMX DSP probe target file
processed_count_matrix.tsv
Mm_R_NGS_WTA_v1.0.pkc

source_name: mouse sciatic nerve tissue

value: mouse sciatic nerve tissue

value: Motor axons

tag: area of_interest

value: ChaTpos


title: Section C 1 hpf rep 2

description: Library name: trout_1_cell_C_2

value: 1 hpf (early cleavage stage)

value: Section C


title: Section D 0 hpf rep 3

description: Library name: trout_NF_egg_D_3

value: Section D


title: Section C 1 hpf rep 3

description: Library name: trout_1_cell_C_3


title: Smit1-/- two weeks post TAC 4

value: Heart

value: TAC surgery

value: 2 weeks


title: WT two weeks post TAC 5

value: WT


title: COTC022-2006-M-F-Lung 2


title: COTC022-1022-M-S-Lung-2


title: COTC022-1022-M-S-Lung-1


title: Section B 1 hpf rep 2

description: Library name: trout_1_cell_B_2

value: Section B


title: WT two weeks post TAC 3


title: Smit1-/- two weeks post TAC 2


title: WT two weeks post TAC 1


title: COTC022-1022-M-F-Diaphragm

value: Diaphragm


title: Section A 1 hpf rep 2

description: Library name: trout_1_cell_A_2

value: Section A


title: COTC022-1022-M-F-Colon

value: Colon


title: SEVO3

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  Ø MT% < 30%;   Ø Cell Gene Number < Median Gene Number * 2;  Ø Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mmu10(Ensembl release 100)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: hippocampus

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

value: hippocampus

value: sevoflurane


title: Section C 0 hpf rep 3

description: Library name: trout_NF_egg_C_3

value: 0 hpf (freshly fertilized egg/zygote)


title: Section D 0 hpf rep 2

description: Library name: trout_NF_egg_D_2


title: Section C 1 hpf rep 1

description: Library name: trout_1_cell_C_1


title: Section B 1 hpf rep 1

description: Library name: trout_1_cell_B_1


title: Section A 1 hpf rep 1

description: Library name: trout_1_cell_A_1


title: SEVO2

description: 10x Genomics


title: WT two weeks post TAC 2


title: WT two weeks post TAC 4


title: Section B 0 hpf rep 3

description: Library name: trout_NF_egg_B_3


title: COTC022-1012-M-F-T11T13

value: T11/T13 Vertebrae

value: Metastatic Tumor Tissue


title: Section A 0 hpf rep 3

description: Library name: trout_NF_egg_A_3


title: Section C 0 hpf rep 2

description: Library name: trout_NF_egg_C_2


title: COTC022-1012-M-F-Rib

value: Rib


title: Section D 0 hpf rep 1

description: Library name: trout_NF_egg_D_1


title: Section B 0 hpf rep 2

description: Library name: trout_NF_egg_B_2


title: Section E 0 hpf rep 2

description: Library name: trout_NF_egg_E_2

value: Section E


title: Section A 0 hpf rep 2

description: Library name: trout_NF_egg_A_2


title: OSRC-2 cells,si-KLHDC4,day2,biol rep 3

first: Qingjiang

address: Senior Department of Urology, Chinese PLA General Hospital, Beijing, China.

institute: Chinese PLA General Hospital

description:
Library name: sample6
SI_3

data_processing:
CLC Genomics Workbenchv 11.0.1
Assembly: GRCH38
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Homo

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep Ligation following manufacturer's prolocols.

tag: cell line

value: epithelial cell

value: KLHDC4 Knockdown


title: Section E 0 hpf rep 1

description: Library name: trout_NF_egg_E_1


title: COTC022-2006-M-F-Lung 1

value: Lung


title: COTC022-1012-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Section C 0 hpf rep 1

description: Library name: trout_NF_egg_C_1

value: Section C


title: Section A 0 hpf rep 1

description: Library name: trout_NF_egg_A_1


title: SEVO1

description: 10x Genomics


title: OSRC-2 cells,si-KLHDC4,day2,biol rep 2

description:
Library name: sample5
SI_2


title: Section B 0 hpf rep 1

description: Library name: trout_NF_egg_B_1

value: Section B


title: COTC022-1022-M-F-Stomach

value: Stomach


title: COTC022-1006-T


title: COTC022-1006-M-S-Lung