title: 98

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and assessed on a Nanodrop, Qubit, and Bioanalyzer
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one S4 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000.  Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome

value: Forager


title: mir-80(cdb530) III, , replicate 2

status: Public on Jul 20 2025

type: SRA

city: Chevy Chase

first: Katherine

last: McJunkin

state: Maryland

address: 3714 Cardiff Court

country: USA

institute: NIH/NIDDK Intramural Research Program

description:
Library name: sBY402
bias_minimized_processed_2.xlsx

library_source: other

data_processing:
Adapters were removed using fastq. Bowtiew was used to map reads to the WS235 genome. htseq was used to count reads using gff files from mirGeneDB.
Assembly: WS280
Supplementary files format and content: raw counts from htseq

molecule: other

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans strains grown at 20 degrees.

extract_protocol:
Total RNA was extracted form whole worms using Trizol.
bias-minimized small RNA cloning protocol with adaptors containing degenerate bases for unbiased ligations

tag: tissue

value: whole worm

tag: genotype

value: mir-80(cdb530) III


title: ATAC_LCMV_4h_R2_1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Base calling was performed by Illumina Real Time Analysis (2.7.7) software and the base calls were converted to short reads using the IlluminaBasecallsToSam tool from the Picard toolkit (2.19.2). Sequencing adapters were removed using the software fastp (0.20.1). Bowtie2 (2.4.4) was used for the alignment of the short reads (representing locations of transposition events) to the GRCm38 (mm10) assembly of the mouse genome using the “–very-sensitive” parameter. PCR duplicates were marked using samblaster (0.1.24). Aligned BAM files were then sorted, filtered using ENCODE blacklisted regions, and indexed using samtools (1.12).
To detect the open chromatin regions, peak calling was performed using MACS2 (2.2.7.1) using the “–nomodel”, “–keep-dup auto” and “–extsize 147” options on each sample. A consensus region set was generated by merging the identified peak summits, extended by 250 bp on both sides using the slop function from bedtools (2.27.1) and pybedtools (0.8.1), across all samples while again discarding peaks overlapping blacklisted features as defined by the ENCODE project. A total of 142,831 genomic regions were obtained and were annotated using the annotatePeaks function from Homer (4.11).
The consensus region set was used to quantify the chromatin accessibility in each sample by summing the number of reads overlapping each consensus region. The consensus region set, and sample-wise quantification of accessibility was performed using bedtools (2.27.1) and pybedtools (0.8.1). The data processing was performed using a Snakemake workflow publicly shared on GitHub (https://github.com/epigen/atacseq_pipeline).
Assembly: mm10
Supplementary files format and content: ATAC_raw_counts.csv: comma-separated read count file of the ATAC-seq data
Supplementary files format and content: ATAC_region_annotation.csv: comma-separated annotation on the genomic location and HOMER gene annotation of each consensus region in the ATAC-seq data

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Femur and tibia were obtained from 8-12 week old female Cas9-mice (Jackson Laboratory cat. No. 024858) and washed with PBS. The bones were crushed in PBS with a sterile mortar and pestle and the bone marrow containing supernatant was filtered through a 100 µm and subsequently a 45 µm filter. The cells were counted, centrifuged at 4 °C for 5 min at 400 rcf and resuspended in DMEM-GlutaMAX (Gibco cat. No. 31966047) with 40% FBS. The cell suspension was mixed with an equal volume of DMEM GlutaMAX with 40% FBS and 30% DMSO (Sigma cat. No. 1019001000) and frozen in 50 million/ml aliquots and stored at -80 °C (short-term) or in liquid nitrogen (long-term storage). Bone marrow aliquots were thawed, once washed with media to remove excess DMSO, and seeded on three 15 cm dishes (non-cell culture treated, VWR cat. No. 734-2797) in 20 ml standard media (DMEM-GlutaMAX (Gibco cat. No. 31966047) with 10% FBS and 1x penicillin-streptomycin (Gibco cat. No. 15140122)) supplemented with 200 ng/ml murine-mCSF (Peprotech cat. No. 315-02). After four days, 5 ml of the media was exchanged with fresh media supplemented with murine-mCSF to reach a total concentration of 100 ng/ml in the dish, and the media substitution was repeated after an additional 3 days

extract_protocol:
At the end of the treatment period, cells were washed with PBS and then scraped in 0.5 ml PBS per million cells. 50,000 cells were directly used for ATAC-seq. Cells were centrifuged at 4 °C and 500 rcf for 5 minutes. The supernatant was removed, and cells were lysed and tagmented at 37 °C for 30 minutes in the following mixture (per sample): 9.75 µl water, 2x transposase buffer (Illumina cat. No. 20034197), 0.5 µl PIC (Roche cat. No. 11873580001), 2 µl TDE1 DNA Enzyme (Illumina cat. No. 20034197), and 0.25 µl 1% Digitonin (Promega cat. No. G9441). The DNA was cleaned using the Qiagen MinElute kit (Qiagen cat. No. 28006) according to the manufacturer’s recommendations and eluted in 12 µl EB buffer.
To estimate the enrichment cycle number, a qPCR was set up using 2.9 µl water, 0.5 µl index primer 1 noMX and Index primer 2.1 barcode, respectively, 0.1 µl 100x SYBR green (Invitrogen cat. No. S7563), 5 µl NEBnext HF 2x MM (NEB cat. No. M0541L), and 1 µl eluted sample, and run as follows: 5 min at 72 °C, 30 seconds at 98 °C, 25x cycles of (10 sec at 98 °C, 30 sec at 63 °C and 1 min at 72 °C). The cycle number was determined based on the amplification entering the early exponential phase. Subsequently, an enrichment PCR was set up with 10 µl water, 2.5 µl Index primer 1 noMX and Index primer 2 barcode, respectively, 25 µl NEBnext HF 2x MM (NEB cat. No. M0541L), and 10 µl eluted sample (see Buenrostro et al. 2013 for primer sequences https://doi.org/10.1038/nmeth.2688). A left-sided 1.6x clean-up was performed using AMPure XP beads (Beckman Coulter cat. No. A63881). To that end, 80 µl beads were added and the sample incubated for 10 minutes at room temperature, followed by 10 minutes on a magnetic rack at room temperature. The beads were washed twice with 80% EtOH, air-dried for 2 minutes and the DNA eluted in 50 µl EB buffer. A second 0.5/1.4 double-sided clean-up was performed. 25 µl beads were added and the sample incubated 10 minutes at room temperature followed by 10 minutes on a magnetic rack as before. The supernatant was transferred to a new well and mixed with additional 45 µl beads, and the left-sided clean-up continued as described above. The DNA was eluted in 15 µl EB buffer

treatment_protocol: On day 9, cells were scraped, counted, and seeded into 6 well plates (non-cell culture treated, Fischer Scientific cat. No. 10284901) with fresh standard media (without penicillin-streptomycin antibiotic) plus 100 ng/ml mCSF, at 1-2 million cells per well. The following day, wells were treated in a staggered manner by adding the respective stimulus for the stated duration, such that all treatments (except the 24 hour timepoint) could be stopped and harvested at the same time to minimize technical variability. UV-killed Candida albi-cans SC5314 were added at a multiplicity of infection (MOI) of 2, LCMV Cl13 at an MOI of 3, Listeria monocytogenes LO28 at an MOI of 20, LPS (Merck cat. No. L4641) at a final concentration of 10 ng/ml, IFN-β (Pbl Assay Science cat. No. 12401-1) at a final concentration of 500 U/ml, and IFN-γ (Peprotech cat. No. 315-05) at a final concentration of 240 U/ml. 50 µg/ml Gentamicin (MP Biomedicals cat. No. 1676045) was added to Listeria monocytogenes LO28 treated wells after one hour. Two hours after infection, the media was exchanged to standard media without antibiotics supplemented with 100 ng/ml mCSF and 5 µg/ml gentamicin.

tag: cell type

value: bone marrow-derived macrophages

tag: protocol

value: ATAC-seq

tag: timepoint after_thawing

tag: stimulus

value: LCMV

tag: time point

tag: Sex

value: female

tag: bio-replicate

tag: batch


title: mir-80(cdb530) III, , replicate 1

description:
Library name: sBY401
bias_minimized_processed_2.xlsx


title: 57

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

library_source: transcriptomic

data_processing:
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used the first 33nt for adaptor trimming).
fastq.gz files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
Assembly: HAv3.1
Supplementary files format and content: featureCounts output files: gene names in column 1, gene counts in column 7

molecule: polyA RNA

organism: Apis mellifera

source_name: Mushroom bodies (brain region)

growth_protocol: Honey bees were flash frozen in liquid nitrogen and stored at -80C until processing

treatment_protocol: Heads were chipped, incubated in RNA-laterICE for ~16 hr, and the mushroom body was dissected.

value: Mushroom bodies (brain region)

tag: input reads

tag: mapped reads

tag: assigned reads

tag: replicate (note

tag: treatment

value: Non-Responder


title: ATAC_LCMV_2h_R2_1


title: 100

tag: reads aligned_to_dwv_genome


title: 203

tag: reads aligned_to_vdv_genome


title: mir-80(cdb494) III, , replicate 2

description:
Library name: sBY379
bias_minimized_processed_2.xlsx

tag: tissue

value: mir-80(cdb494) III


title: mir-80(cdb494) III, , replicate 1

description:
Library name: sBY378
bias_minimized_processed_2.xlsx

tag: genotype


title: drsh-1(cdb263 cdb328) I; mir-80(cdb494) III, , replicate 3

description:
Library name: sBY376
bias_minimized_processed_2.xlsx


title: ATAC_IFNgamma_8h_R2_1

tag: cell type

value: IFNgamma


title: 137


title: drsh-1(cdb263 cdb328) I; mir-80(cdb494) III, , replicate 2

description:
Library name: sBY375
bias_minimized_processed_2.xlsx


title: ATAC_IFNgamma_6h_R2_1

tag: protocol


title: drsh-1(cdb263 cdb328) I; mir-80(cdb494) III, , replicate 1

description:
Library name: sBY374
bias_minimized_processed_2.xlsx


title: 73


title: mir-80(cdb496) III, , replicate 3

description:
Library name: sBY370
bias_minimized_processed_2.xlsx

value: mir-80(cdb496) III


title: mir-80(cdb496) III, , replicate 2

description:
Library name: sBY369
bias_minimized_processed_2.xlsx


title: ATAC_IFNgamma_4h_R2_1

tag: timepoint after_thawing


title: 60


title: ATAC_IFNgamma_2h_R2_1

tag: stimulus


title: drsh-1(cdb263 cdb328) I; mir-80(cdb496) III, , replicate 3

description:
Library name: sBY367
bias_minimized_processed_2.xlsx


title: drsh-1(cdb263 cdb328) I; mir-80(cdb496) III, , replicate 2

description:
Library name: sBY366
bias_minimized_processed_2.xlsx


title: 182


title: mir-80(cdb496) III, , replicate 1

description:
Library name: sBY368
bias_minimized_processed_2.xlsx


title: drsh-1(cdb263 cdb328) I; mir-80(cdb496) III, , replicate 1

description:
Library name: sBY365
bias_minimized_processed_2.xlsx


title: 228

value: Generalist


title: ATAC_IFNbeta_8h_R2_1

value: IFNbeta

tag: time point


title: mir-80(cdb495) III, , replicate 1

description:
Library name: sBY362
bias_minimized_processed_2.xlsx

value: mir-80(cdb495) III


title: ATAC_IFNbeta_6h_R2_1

tag: Sex


title: 103


title: drsh-1(cdb263 cdb328) I; mir-80(cdb495) III, , replicate 3

description:
Library name: sBY361
bias_minimized_processed_2.xlsx


title: ATAC_IFNbeta_4h_R2_1

tag: bio-replicate


title: drsh-1(cdb263 cdb328) I; mir-80(cdb495) III, , replicate 2

description:
Library name: sBY360
bias_minimized_processed_2.xlsx


title: ATAC_IFNbeta_2h_R2_1

tag: batch


title: drsh-1(cdb263 cdb328) I; mir-80(cdb495) III, , replicate 1

description:
Library name: sBY359
bias_minimized_processed_2.xlsx


title: 129

tag: input reads


title: 90

tag: mapped reads


title: ATAC_Candida_8h_R2_1

value: Candida


title: drsh-1(cdb 263 cdb328) I, , replicate 2

description:
Library name: sBY351
bias_minimized_processed_2.xlsx

value: drsh-1(cdb 263 cdb328) I


title: THP-1 treated with CART+Raji supernatant rep1

city: Changchun

first: lei

last: qian

state: Jilin

address: Number 71,Xinmin Street,

department: cancer center

country: China

institute: First Hospital of Jilin Unniversity

description: Library name: Samlpe 10

data_processing:
1.Data quality control Use fastp to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads. 2. Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT to construct the index, and compare clean reads to the reference genome. 3. New transcript prediction Use StringTie for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster. 4. Quantification of gene expression levels Use featureCounts to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels. 5. Difference analysis DESeq2 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression. 6. Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: THP-1 cells were maintained in 1640 supplemented with 10% fetabovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was were extracted by Trizol method
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection，Finally, the effective concentration of the library was accurately quantified using Q-PCR;

treatment_protocol: THP-1 cell line was stimulated with PBS, LPS, Mock T+Raji or CART+Raji supernatant

value: cell line

tag: cell line

value: monocytic cell line

value: WT

value: CART+Raji supernatant rep1


title: THP-1 treated with CART+Raji supernatant rep2

description: Library name: Samlpe 11

value: CART+Raji supernatant rep2


title: THP-1 treated with Mock T+Raji supernatant rep3

description: Library name: Samlpe 9

value: Mock T+Raji supernatant rep3


title: THP-1 treated with CART+Raji supernatant rep3

description: Library name: Samlpe 12

value: CART+Raji supernatant rep3


title: ATAC_Candida_6h_R2_1

value: bone marrow-derived macrophages

value: ATAC-seq

value: female


title: drsh-1(cdb 263 cdb328) I, , replicate 1

description:
Library name: sBY350
bias_minimized_processed_2.xlsx

value: whole worm


title: 165

value: Mushroom bodies (brain region)

tag: assigned reads

tag: replicate (note


title: wild type, , replicate 3

description:
Library name: sBY349
bias_minimized_processed_2.xlsx

value: wild type


title: ATAC_Candida_4h_R2_1


title: 187

tag: reads aligned_to_dwv_genome

tag: treatment

value: Non-Responder


title: 99

tag: tissue

tag: reads aligned_to_vdv_genome

value: Forager


title: 50

tag: genotype


title: THP-1 treated with LPS rep3

description: Library name: Samlpe 6

tag: cell type

value: LPS  rep3


title: wild type, , replicate 2

description:
Library name: sBY348
bias_minimized_processed_2.xlsx


title: wild type, , replicate 1

description:
Library name: sBY347
bias_minimized_processed_2.xlsx


title: ATAC_Candida_2h_R2_1

tag: protocol

tag: timepoint after_thawing

value: Candida


title: ATAC_LPS_8h_R1_1

tag: stimulus

value: LPS

tag: time point


title: 109

value: Generalist


title: drsh-1(cdb 263 cdb328) I, , replicate 3

description:
Library name: sBY352
bias_minimized_processed_2.xlsx

value: drsh-1(cdb 263 cdb328) I


title: THP-1 treated with LPS rep2

description: Library name: Samlpe 5

value: cell line

value: monocytic cell line

value: WT

value: LPS  rep2


title: ATAC_untreated_0h_R2_1

value: bone marrow-derived macrophages

value: untreated

tag: Sex

tag: bio-replicate


title: 139

tag: input reads

value: Guard


title: drsh-1(cdb263 cdb328) I; mir-80(cdb493) III, , replicate 2

description:
Library name: sBY346
bias_minimized_processed_2.xlsx

value: whole worm


title: THP-1 treated with LPS rep1

description: Library name: Samlpe 4

value: LPS  rep1


title: 240

value: Mushroom bodies (brain region)

tag: mapped reads


title: THP-1 treated with Mock T+Raji supernatant rep2

description: Library name: Samlpe 8

tag: cell line

value: Mock T+Raji supernatant rep2


title: ATAC_LPS_4h_R1_1

value: ATAC-seq

value: female

tag: batch


title: ATAC_LPS_2h_R1_1


title: THP-1 treated with PBS rep3

description: Library name: Samlpe 3

value: PBS rep3


title: mir-80(cdb493) III, , replicate 3

description:
Library name: sBY343
bias_minimized_processed_2.xlsx

value: mir-80(cdb493) III


title: 87

tag: assigned reads

tag: replicate (note

value: Forager


title: THP-1 treated with Mock T+Raji supernatant rep1

description: Library name: Samlpe 7

tag: treatment

value: Mock T+Raji supernatant rep1


title: ATAC_Listeria_8h_R1_1

value: Listeria


title: drsh-1::gfp;tdp-1::mScarlet/drsh-1(null) , Adult , replicate 2

description: Library name: sBY340

data_processing:
Adapters were removed using fastq. Bowtiew was used to map reads to the WS235 genome. htseq was used to count reads using gff files from mirGeneDB and pirdb.org.
Assembly: WS280
Supplementary files format and content: raw counts from htseq

extract_protocol:
Total RNA was extracted form whole worms using Trizol.
NEBNext small RNA cloning kit was used to clone small RNA.

tag: tissue


title: THP-1 treated with PBS rep2

description: Library name: Samlpe 2

value: cell line

value: monocytic cell line

value: PBS rep2


title: drsh-1::gfp;tdp-1::mScarlet/drsh-1(null) , Adult , replicate 1

description: Library name: sBY339


title: mir-80(cdb493) III, , replicate 2

description:
Library name: sBY342
bias_minimized_processed_2.xlsx


title: THP-1 treated with PBS rep1

description: Library name: Samlpe 1

value: WT

value: PBS rep1


title: ATAC_Listeria_4h_R1_1

value: bone marrow-derived macrophages


title: ATAC_LPS_6h_R1_1

value: LPS


title: drsh-1::gfp;tdp-1::mScarlet, Adult, replicate 2

description: Library name: sBY336

value: whole worm


title: drsh-1 (cdb330) I, Adult, replicate 3

description:
Library name: sBY298_2
bias_minimized_processed_2.xlsx

value: drsh-1 (cdb330) I


title: SV-HUC-1 cells, DCBQ treatment, oxRRBS, rep3

city: Hangzhou

first: Xinran

last: Zhao

address: Yuhangtang Road

institute: Zhejiang University

description: Library name: oxRRBS_DCBQ3

data_processing:
Raw bisulfite sequencing data were filtered by cutadapt and trimgalore.
Then clean data were mapped to reference hg38 using BSMAP (v2.90).
The methratio.py provided by BSMAP was used for calculating the methylation level in the cleaned bam file.
The hydroxymethylation level of each site was calculated by subtracting the oxRRBS-seq methylation level from the RRBS-seq methylation level.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include methylation and hydroxymethylation rates for each RRBS and oxRRBS Sample

extract_protocol:
Genomic DNA was extracted from the harvested cells using a QIAamp DNA mini kit (Qiagen, Germany).
The RRBS and oxRRBS libraries were prepared by Ovation RRBS Methyl-Seq with the TrueMethyl oxBS kit according to the manufacturer’s instructions.

value: epithelial cell


title: ATAC_Listeria_2h_R1_1

value: ATAC-seq


title: drsh-1::gfp;tdp-1::mScarlet, Adult, replicate 1

description: Library name: sBY335


title: SV-HUC-1 cells, DCBQ treatment, oxRRBS, rep2

description: Library name: oxRRBS_DCBQ2


title: drsh-1 (cdb330) I, Adult, replicate 2

description:
Library name: sBY297_2
bias_minimized_processed_2.xlsx


title: drsh-1 (cdb330) I, Adult, replicate 3

description: Library name: sBY298


title: SV-HUC-1 cells, DCBQ treatment, oxRRBS, rep1

description: Library name: oxRRBS_DCBQ1


title: ATAC_LCMV_8h_R1_1

value: LCMV

value: female


title: drsh-1(cdb263 cdb328) I; mir-80(cdb493) III, , replicate 1

description:
Library name: sBY344
bias_minimized_processed_2.xlsx


title: SV-HUC-1 cells, control, oxRRBS, rep3

description: Library name: oxRRBS_Control3


title: drsh-1 (cdb330) I, Adult, replicate 1

description: Library name: sBY296


title: SV-HUC-1 cells, control, oxRRBS, rep2

description: Library name: oxRRBS_Control2


title: mir-80(cdb493) III, , replicate 1

description:
Library name: sBY341
bias_minimized_processed_2.xlsx

value: mir-80(cdb493) III


title: drsh-1 (cdb330) I, L4, replicate 3

description: Library name: sBY295


title: drsh-1 (cdb328) I, Adult, replicate 2

description:
Library name: sBY291_2
bias_minimized_processed_2.xlsx

value: drsh-1 (cdb328) I


title: ATAC_Listeria_6h_R1_1


title: ATAC_LCMV_4h_R1_1


title: SV-HUC-1 cells, control, oxRRBS, rep1

description: Library name: oxRRBS_Control1


title: ATAC_LCMV_2h_R1_1


title: ATAC_LCMV_6h_R1_1


title: drsh-1 (cdb328) I, Adult, replicate 3

description:
Library name: sBY292_2
bias_minimized_processed_2.xlsx


title: CROPseq_KO150_B1_GEX

description:
polyA RNA
CROPseq_KO150_B1_raw_feature_bc_matrix.h5
CROPseq_KO150_B1_filtered_feature_bc_matrix.h5

data_processing:
Raw basecalls from the sequencer were demultiplexed and converted to FASTQ format using the 10x Genomics' Cell Ranger (3.0.2) command “mkfastq”.
FASTQ files were then aligned to the mouse reference genome assembly GRCm38 (mm10), and count matrices were generated for each sample based on genome annotation v93 using the Cell Ranger command “count”.
Assembly: mm10
Supplementary files format and content: raw and filtered feature barcode matrices: .h5 archives of CellRanger output
Supplementary files format and content: feature_reference.csv: comma-separated feature reference file for ADT, HTO, GDO quantification and annotation
Library strategy: CROP-seq

growth_protocol: RAW264.7-Cas9 (transduced with vector from Addgene #52962) cell lines were cultivated in standard media (DMEM-GlutaMAX (Gibco cat. No. 31966047) with 10% FBS and 1x penicillin-streptomycin (Gibco cat. No. 15140122)) supplemented with 20 µg/ml blasticidin (InvivoGen cat. No. ant-bl-1). The cell line was split every 3-4 days after detachment with 0.05x Trypsin-EDTA (Gibco cat. No. 25300054) and kept at low passage number. All cells were grown at 37 °C, 5% CO2 and regularly tested for potential contamination with mycoplasma (Lonza cat. No. LT07-318)

extract_protocol:
Cells were washed with ice cold FACS buffer, scraped without trypsin, and centrifuged at 4 °C for 5 min at 500 rcf. The cells were resuspended in 100 µl FACS buffer with 1 µg TrueStain FcX PLUS (Biozym cat. No. 156604) per 1 million cells and incubated on ice for 10 minutes. Afterward, 100 µl FACS buffer containing CITE-seq antibodies (see Table S6; 1 µl per antibody per 10 million cells for KO15; 0.33 µl per 10 million cells for KO150) as well as TotalSeq-C hashing antibodies (BioLegend; 1 µl antibody per per 10 million cells) were added, and the incubation continued at 4 °C for 30 minutes. Cells were washed twice with FACS buffer and resuspended in fresh FACS buffer with Zombie NIR viability staining (BioLegend cat. No. 423105) at a 1:1000 dilution. Cells were sorted on a FACS Aria by selecting NIR negative (live) cells that were mCherry positive. The replicates of the same condition for the KO150 library were sorted, with 50,000 cells each going into three tubes. Superfluous supernatant was reduced using the VRNxT machine and processed according to the Chromium Next GEM Single Cell 5’ v2 Dual Indexing kit with Feature Barcoding (10x Genomics cat. No. 1000263), with the following modifications. At the GEM generation, step 1.1, an additional 0.5 µl of a 10 µM stock CROPseq-3P5P_gRNA_RT primer (5'-AAGCAGTGGTATCAACGCAGAGTACCAAGTTGTTAACGGTCTAGCC-3') were added to the master mix.  To limit technical bias/batch effects we sorted each of the three RAW264.7 thaws (individually hashtagged) together (1:1:1) for a total of three tubes per treatment (3 tubes x 3 treatments = 9 samples). One tube per treatment was processed on a 10x chip resulting in a total of 3 chips being used. The treatment is indicated by the letter in the library name, the chip/tube number is indicated by the number (e.g. "_A1_").
The cDNA amplification was performed for 11 cycles, and during the SPRI select clean-up, the remaining 80 µl supernatant were mixed with 30 µl beads to perform a 1.2x clean-up, otherwise following the 2.3B Cell Surface Protein protocol. 5 µl of the guide RNA fraction were amplified with the following PCR mix: 3 µl of a 10 µM fwd/rev CROPseq-3P5P i7/i5 primer mix (see Table S6), 2x Kapa HIFI MM (Roche cat. No. 7958935001), 0.5 µl SYBR green (Life Technologies cat. No. S7563) and 16.5 µl water. The PCR was run for 30 sec at 98 °C, 7 to 8 cycles of (10 sec at 98 °C, 30 sec at 70 °C and 20 sec at 72 °C), followed by 1 min at 72 °C. The amount of amplification cycles was determined by inspecting the fluorescence signal. The reaction was stopped once the amplification has reached the early exponential phase. A left-sided 0.9x SPRI bead clean-up was performed, and the DNA was eluted in 15 µl EB buffer. Correct amplification was determined using a Bioanalyzer HS chip, confirming a peak around 272 bp for the guide RNA library. For the KO15 and KO150 experiments, cell surface and guide RNA libraries were added to the gene expression library at 10% and 15% of the final concentration, respectively.

treatment_protocol: 12 million RAW264.7 cells were seeded per 10 cm dish in triplicates at least three hours before transduction start. For the scaled-up screen (KO150) we used cells from three independent frozen vials thawed at different days. To transduce the cells, 8 µg/ml polybrene (Sigma Aldrich, cat. No. H9268-5G) and virus dilutions were added to achieve an MOI of 0.1. After 24 hours, the cells were detached, and 95% of these cells were seeded in fresh media without polybrene on 15 cm dishes. The remaining 5% of cells were seeded in a 6-well plate and kept for MOI assessment via FACS after three days, for which cells were scraped in FACS buffer with 1x DAPI stain (BioLegend, cat. No. 422801). mCherry signal (i.e., guide RNA positive) among DAPI negative cells (live gate) was measured to confirm MOI. Five days after transduction, the cells were detached and single-cell filtered through a 45 µm filter, and 25-30 million cells per treatment condition were seeded in standard media without antibiotics (no penicillin/streptomycin and blasticidin). Three hours after cell seeding, Listeria monocytogenes LO28 were added for the 24 hour time point with an MOI of 20, while the other time points were started the next day, in order to finish at a single shared time point. All treatments were harvested at the same time at 6 days after transduction. Gentamicin addition was added to Listeria monocytogenes LO28 treated wells after 1 hour. Two hours later, the media was exchanged to standard media without antibiotics supplemented with 5 µg/ml gentamicin.

value: Listeria 6h

tag: library type

value: mRNA


title: drsh-1 (cdb328) I, Adult, replicate 1

description:
Library name: sBY290_2
bias_minimized_processed_2.xlsx

tag: genotype


title: wildtype, Adult, replicate 3

description:
Library name: sBY286_2
bias_minimized_processed_2.xlsx

value: wildtype


title: drsh-1 (cdb330) I, Adult, replicate 1

description:
Library name: sBY296_2
bias_minimized_processed_2.xlsx


title: drsh-1 (cdb330) I, L4, replicate 2

description: Library name: sBY294


title: SV-HUC-1 cells, DCBQ treatment, RRBS, rep3

description: Library name: RRBS_DCBQ3

tag: cell type


title: drsh-1 (cdb330) I, L4, replicate 1

description: Library name: sBY293


title: ATAC_IFNgamma_8h_R1_1

tag: protocol

value: IFNgamma


title: wildtype, Adult, replicate 2

description:
Library name: sBY285_2
bias_minimized_processed_2.xlsx


title: SV-HUC-1 cells, DCBQ treatment, RRBS, rep2

description: Library name: RRBS_DCBQ2


title: ATAC_IFNgamma_6h_R1_1

tag: timepoint after_thawing


title: drsh-1 (cdb328) I, Adult, replicate 3

description: Library name: sBY292


title: ATAC_IFNgamma_4h_R1_1

tag: stimulus


title: SV-HUC-1 cells, DCBQ treatment, RRBS, rep1

description: Library name: RRBS_DCBQ1


title: mir-80(cdb495) III, , replicate 2

description:
Library name: sBY363
bias_minimized_processed_2.xlsx

value: mir-80(cdb495) III


title: wildtype, Adult, replicate 1

description:
Library name: sBY284_2
bias_minimized_processed_2.xlsx


title: drsh-1 (cdb328) I, Adult, replicate 2

description: Library name: sBY291


title: drsh-1 (cdb330) I, Adult, replicate 2

description: Library name: sBY297


title: ATAC_IFNgamma_2h_R1_1

tag: time point


title: drsh-1 (cdb328) I, Adult, replicate 1

description: Library name: sBY290


title: SV-HUC-1 cells, control, RRBS, rep2

description: Library name: RRBS_Control2


title: L1_D4_JMJD1A

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

country: Japan

institute: Akita University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome using STAR2.
The FPKM tables of RNA-seq were assessed using GFOLD with the GENCODE comprehensive gene annotation set M1 release.
As for ChIP-seq, all bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used for H3K27ac and H3K27me3 under the following parameters: window size 200 bp; gap size 400 bp ; E-value threshold, 100. The FindPeaks function of HOMER was used for H3K9me2 and JMJD1A with histone mode. MACS3 program was used for NFIC with default setting.
Assembly: mm9
Supplementary files format and content: tab files (RNA-seq)
Supplementary files format and content: bigwig and txt files (ChIP-seq)

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. Immortalized stromal vascular fraction (imSVF) cells were maintained in Dulbecco's modified Eagle's medium/F12 supplemented with 10% fetal bovine serum at 37 °C. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 g/ml), 0.25 M dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail).

extract_protocol:
Total RNA was isolated using ISOGEN (Nippongene) following manufacturer's protocol. Sonicated nuclear fraction was incubated with each antibody and protein-DNA complexes were isolated.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Duplexes of each small interfering RNA (siRNA) against Jmjd1a and control siRNA were transfected into cells using the Lipofectamine RNAi MAX reagent (Thrmo Fisher Scientific).

tag: time

value: Day 4

tag: chip antibody


title: ATAC_IFNbeta_8h_R1_1

value: IFNbeta

tag: Sex

tag: bio-replicate


title: SV-HUC-1 cells, control, RRBS, rep1

description: Library name: RRBS_Control1

tag: cell line


title: drsh-1 (cdb328) I, L4, replicate 2

description: Library name: sBY288


title: ATAC_IFNbeta_6h_R1_1

value: bone marrow-derived macrophages

tag: batch


title: ATAC_IFNbeta_4h_R1_1


title: SV-HUC-1 cells, DCBQ treatment, RNA, rep3

description: Library name: RNA_DCBQ3

data_processing:
For RNA-seq, quality control of raw reads was performed using FastQC, and clean reads were obtained following the removal of low-quality reads with Trimmomatic (v0.38).
Hisat2 (v2.2.1) was employed for performing read mapping to hg38 genome reference, and gene expression profiling was based on the number of reads.
TPM values were calculated by StringTie (v2.1.7), and were used to estimate the expressed values.
Differential expression genes were obtained using DESeq2 (v1.34.0) with an adjusted P-value< 0.05 and an absolute log2(fold-change) > 1.
Assembly: hg38
Supplementary files format and content: csv file includes TPM values for each RNA-seq Sample

extract_protocol:
The total RNA of each sample was extracted using the TRIzol reagent (Invitrogen, USA).
The RNA was treated with RNase-free DNase I for 30 min. The poly(A) containing mRNA were purified using Oligo (dT) Beads from about 1 ug total RNA. The captured mRNA was firstly fragmented into 100-200 nt using divalent cations at elevated temperature. The fragmented mRNA was reverse-transcribed with SuperScript II and then converted to double-stranded cDNA using RNaseH and DNA Polymerase I by random priming. After purification, the double-stranded cDNA was subjected to blunt-ending, dA addition to 3'-end and adapter ligation.


title: L1_D0_JMJD1A

value: Day 0


title: drsh-1 (cdb328) I, L4, replicate 1

description: Library name: sBY287

value: whole worm


title: L1_D6_H3K27me3

value: Day 6


title: SV-HUC-1 cells, DCBQ treatment, RNA, rep2

description: Library name: RNA_DCBQ2

value: epithelial cell


title: wildtype, Adult, replicate 3

description: Library name: sBY286


title: imSVF_D0_NFIC

description: Library name: Sample 14

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome using STAR2.
The FPKM tables of RNA-seq were assessed using GFOLD with the GENCODE comprehensive gene annotation set M1 release.
As for ChIP-seq, all bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used for H3K27ac and H3K27me3 under the following parameters: window size 200 bp; gap size 400 bp ; E-value threshold, 100. The FindPeaks function of HOMER was used for H3K9me2 and JMJD1A with histone mode. MACS3 program was used for NFIC with default setting. MACS3 program was used for NFIC with default setting.
Assembly: mm9
Supplementary files format and content: tab files (RNA-seq)
Supplementary files format and content: bigwig and txt files (ChIP-seq)

source_name: imSVF

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. Immortalized stromal vascular fraction (imSVF) cells were maintained in Dulbecco's modified Eagle's medium/F12 supplemented with 10% fetal bovine serum at 37 °C. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 μg/ml), 0.25 μM dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail).

value: imSVF

value: anti-NFIC


title: ATAC_IFNbeta_2h_R1_1

value: ATAC-seq

value: female


title: ATAC_untreated_0h_R1_1

value: untreated


title: ATAC_Candida_8h_R1_1

value: Candida


title: SV-HUC-1 cells, control, RNA, rep3

description: Library name: RNA_Control3


title: L1_D6_H3K9me2


title: L1_D0_H3K9me2


title: wildtype, Adult, replicate 2

description: Library name: sBY285


title: SV-HUC-1 cells, control, RRBS, rep3

description: Library name: RRBS_Control3


title: SV-HUC-1 cells, control, RNA, rep2

description: Library name: RNA_Control2


title: ATAC_Candida_6h_R1_1


title: wildtype, Adult, replicate 1

description: Library name: sBY284


title: drsh-1 (cdb328) I, L4, replicate 3

description: Library name: sBY289

value: drsh-1 (cdb328) I


title: L1_D8_RNA-seq

value: Day 8


title: SV-HUC-1 cells, control, RNA, rep1

description: Library name: RNA_Control1


title: ATAC_Candida_4h_R1_1


title: wildtype, L4, replicate 3

description: Library name: sBY283

value: wildtype


title: L1_D4_RNA-seq


title: ATAC_Candida_2h_R1_1


title: wildtype, L4, replicate 1

description: Library name: sBY281


title: MC205R, scRNAseq

status: Public on Jul 19 2025

city: Stockholm

first: Hui

last: Wan

address: Biomedicum, Solnavägen 9, floor 9D

country: Sweden

institute: Karolinska Institutet

description:
Library name: MC205R
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were preprocessed using Cell Ranger (version 7.0.0) with default parameters.
Assembly: GRCh38
Supplementary files format and content: HDF5 files

source_name: Lymph node

extract_protocol:
Sample processing: Mononuclear cells were isolated from bone marrow samples by standard density centrifugation using Lymphoprep (Axis-Shield) following the manufacturer’s instructions. Intestinal, tonsillar, and lymphoid tissues were processed into single-cell suspensions using mechanical dissociation and then filtered through 70 μm containers. Single cells were cryopreserved in fetal bovine serum (FBS) supplemented with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen before use.  Cell sorting: The cells used for flow cytometry were thawed in RPMI 1640 cell medium (Gibco). The cells were blocked with human FcR Blocking Reagent (Miltenyi Biotec) for 10 min and subsequently stained with anti-CD19 BV421 and anti-CD235a FITC in FACS buffer (PBS with 2% FBS) for 20 min on ice. Immediately before sorting, the cells were briefly incubated with propidium iodide staining solution. For the MCL samples, live CD235a- cells, CD235a-CD19+ cells, and CD235a-CD19- cells were sorted in FACS buffer using a BD FACSAria Fusion Sorter (BD Biosciences). Live CD235a- cells were used for single-cell sequencing, while live CD235a- CD19+ and CD235a- CD19- cells were used to extract DNA for tumor and germline WGS, respectively. For the control sample, live CD19- cells and live CD19+ cells were sorted separately and then mixed at a 3:7 ratio for single-cell sequencing.
scRNA-seq sequencing and data analysis: Using the Chromium Next GEM Single-Cell 5′ Reagent Kit v2 (10x Genomics), the cells were loaded onto separate lanes of the Next GEM Chromium Controller (10x Genomics) for encapsulation (target recovery of 10,000 cells for each sample). Single-cell gene expression (GEX) libraries were constructed following the manufacturer’s protocols.

value: Lymph node

tag: diagnosis

value: mantle cell lymphoma (MCL)


title: MC206R, scRNAseq

description:
Library name: MC206R
10x Genomics

source_name: Bone marrow

value: Bone marrow


title: L1_D0_RNA-seq


title: MC206P, scRNAseq

description:
Library name: MC206P
10x Genomics


title: L1_D0_H3K27me3


title: SV-HUC-1 cells, DCBQ treatment, RNA, rep1

description: Library name: RNA_DCBQ1


title: MC205P, scRNAseq

description:
Library name: MC205P
10x Genomics


title: MC204P, scRNAseq

description:
Library name: MC204P
10x Genomics


title: T_Mycn

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

description: Library name: Sample3

data_processing:
Raw reads were trimmed, aligned to the mouse genome (GRCm38) using Bowtie2, and normalized coverage tracks were generated using deepTools (bamCoverage). Peak calling was performed using MACS2, and peaks were annotated relative to TSS using HOMER.
Assembly: mm10
Supplementary files format and content: CSV file includes peak annotations relative to input controls
Library strategy: CUT&Run

source_name: liver

extract_protocol:
DNA was extracted by phenol–chloroform, ethanol-precipitated, and resuspended in nuclease-free water.
Library was prepared using the DNA Library Prep Kit for Illumina (Cell Signaling Technology, 56795) and dual-index primers (Cell Signaling Technology, 47538).

value: liver

value: Tumor


title: T_input

description: Library name: Sample4


title: MC203P2, scRNAseq

description:
Library name: MC203P2
10x Genomics


title: SOL5

first: Xuesong

last: Shan

address: 2888 Xingcheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description: Library name: Sample 17

data_processing:
Transcript expression was quantified as FPKM using RSEQC (v4.0.0). Differentially expressed lncRNAs were identified using DESeq (|log2FoldChange|>1, P<0.05). Cis-target genes were defined as mRNAs located within ±100kb of each lncRNA.
Assembly: Ovis_aries_rambouillet.Oar_rambouillet_v1.0.dna.toplevel.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Ovis aries

source_name: Skeletal muscle

extract_protocol:
total RNA was isolated using TRIzol reagent. RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent, CA, USA). Ribosomal RNA was depleted, and RNA fragments (about 300bp) were generated by fragmentation. First-strand and second-strand cDNA synthesis was performed using random hexamers.
Libraries were PCR-amplified and sequenced on the Illumina platform (Illumina, CA, USA). Raw reads were filtered using DASTQ (v0.11.9) and Cutadapt to remove adapters and low-quality reads (Q≤ 20). Clean reads were aligned to the sheep reference genome using HISAT2 (v2.2.1), and transcript assembly was performed with StringTie (v2.2.0). Transcripts with length ≥200bp and ≥2 exons were retained. Coding potential was assessed using PLEK, CNCI, and Pfamscan; only transcripts lacking coding potential across all tools were classified as high confidence lncRNAs.

value: Skeletal muscle

value: soleus


title: SOL3

description: Library name: Sample 15


title: SOL6

description: Library name: Sample 18


title: SOL2

description: Library name: Sample 14


title: NT_input

description: Library name: Sample2

value: Non-tumor


title: SOL1

description: Library name: Sample 13


title: SOL4

description: Library name: Sample 16


title: MC203P1, scRNAseq

description:
Library name: MC203P1
10x Genomics


title: LL6

description: Library name: Sample 12

value: longissimus lumborum


title: MC202R, scRNAseq

description:
Library name: MC202R
10x Genomics


title: LL5

description: Library name: Sample 11


title: NT_Mync

description: Library name: Sample1


title: wildtype, L4, replicate 2

description: Library name: sBY282

value: whole worm


title: LL4

description: Library name: Sample 10


title: IU 21-019-2

city: Indianapolis

first: Tarek

last: Ashkar

state: IN

address: 950 W Walnut St.

department: Nephrology

institute: Indiana University

description: Library name: IU 21-019-2

data_processing:
Expression counts determined by spaceranger and reference genome hg38.
The remaining processing and normalization steps described on the paper were not performed on the provided processed data.
Assembly: Hg38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5 : counts matrix on H5 format
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
One reference tissues was provided by the Kidney Precision Medicine Project. The samples was frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to the manufacturer's protocol. CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics
Spatial trasncriptomics sequensing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

tag: disease state

value: Reference

value: Kidney

tag: tissue source

value: Nephrectomy

tag: storage

value: OCT at -80

tag: gender

value: M

tag: median umis_per_spot

tag: median genes_per_spot


title: MC202P, scRNAseq

description:
Library name: MC202P
10x Genomics

tag: tissue


title: LL1

description: Library name: Sample 7

tag: cell type


title: MC201P2, scRNAseq

description:
Library name: MC201P2
10x Genomics

source_name: Tonsil

value: Tonsil


title: PM6

description: Library name: Sample 6

value: psoas major


title: LL3

description: Library name: Sample 9


title: GW2-3

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

description:
Library name: GW2-3
replicate 3

data_processing:
Adapter trimming and removal of undetermined or low-quality bases were performed using Cutadapt and an LC Science in house perl script.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for sequence quality control
Reads were mapped to the reference genome of Dracunculus medinensis from WormBase using HISAT2
Mapped read assembly was performed using StringTie, followed by the merging of all transcriptomes to reconstruct a comprehensive transcriptome using Perl scripts and gffcompare
To estimate the expression levels of all transcripts, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used.
Assembly: https://parasite.wormbase.org/Dracunculus_medinensis_prjeb500/Info/Index/ (D_medinensis_Ghana_v2_0_4, GCA_000946415.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Dracunculus medinensis

source_name: Adult female

extract_protocol:
Total RNA was extracted using the Total RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada) according to the manufacturer's instructions.
Illumina’s TruSeq-stranded-mRNA sample preparation protocol

value: Whole organism


title: GW2-1

description:
Library name: GW2-1
replicate 1


title: GW2-2

description:
Library name: GW2-2
replicate 2


title: MC201P1, scRNAseq

description:
Library name: MC201P1
10x Genomics

value: Lymph node

value: mantle cell lymphoma (MCL)


title: PM4

description: Library name: Sample 4


title: MC4R2, scRNAseq

description:
Library name: MC4R2
10x Genomics

value: Bone marrow


title: GW1-3

description:
Library name: GW1-3
replicate 3

source_name: Adult female, Ferret's front leg


title: PM1

description: Library name: Sample 1


title: PM2

description: Library name: Sample 2


title: GW1-2

description:
Library name: GW1-2
replicate 2


title: PM3

description: Library name: Sample 3


title: PM5

description: Library name: Sample 5


title: GW1-1

description:
Library name: GW1-1
replicate 1


title: MC4R1, scRNAseq

description:
Library name: MC4R1
10x Genomics


title: MC3Ri, scRNAseq

description:
Library name: MC3Ri
10x Genomics

source_name: Intestine

value: Intestine


title: MC3R, scRNAseq

description:
Library name: MC3R
10x Genomics


title: GW2-L1-3

description:
Library name: GW2-L1-3
replicate 3_4800L1

source_name: L1, Ferret's rear leg


title: Chip-seq of Tbet 3

city: Suzhou

first: Qiang

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 33

data_processing:
Library construction and the quality inspection was carried out using Illumina HiSeq 4000 for sequencing
Assembly: T-bet,Runx3
Supplementary files format and content: .txt
Supplementary files format and content: .bw

source_name: CD8+T cells

extract_protocol:
T-bet and Runx3 CUT&RUN:We adopted Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for genome-wide mapping of Runx3 in WT and Tbx21–/–.In brief, FACS-sorted live cells (1 × 105 cells per reaction) were bound to concanavalin A-coated magnetic beads (Bangs Laboratories) and permeabilized with 0.05% (w/v) digitonin and then incubated with anti-Runx3 antibody (Active Motif, 1 µl per reaction) or IgG overnight. After removal of unbounded antibodies with proper washing, the nuclei were incubated with protein A/G-micrococcal nuclease (MNase) fusion protein (plasmid obtained from Addgene) for 1hr at 4 °C. CaCl2 was then added to activate MNase activity and incubated on ice for 30 min. ATAC-seq:WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells cells were sorted on 4 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described71. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific). RNA-seq:Total RNA was extracted from the sorted WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells on 4 dpi, and triplicates were obtained for each genotype. cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA Kit (Clontech).
T-bet and Runx3 CUT&RUN:The reaction was quenched with stopping buffer and the DNA fragments were purified with MinElute Reaction Cleanup kit (QIAGEN) and then amplified by PCR for 10–14 cycles with barcoded Nextera primers (Illumina). ATAC-seq:The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health. RNA-seq:Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

value: CD8+T cells


title: LL2

description: Library name: Sample 8

value: Skeletal muscle


title: Chip-seq of Runx3 with Tbet KO 3

description: Library name: Sample 36


title: Chip-seq of Runx3 with Tbet KO 1

description: Library name: Sample 34


title: Chip-seq of Tbet 2

description: Library name: Sample 32


title: Chip-seq of Tbet 1

description: Library name: Sample 31


title: GW2-L1-2

description:
Library name: GW2-L1-2
replicate 2_1600 L1


title: Chip-seq of Runx3 3

description: Library name: Sample 27


title: GW2-L1-1

description:
Library name: GW2-L1-1
replicate 1_1100 L1


title: MC3P1, scRNAseq

description:
Library name: MC3P1
10x Genomics


title: Chip-seq of Runx3 2

description: Library name: Sample 26


title: Chip-seq of Runx3 1

description: Library name: Sample 25


title: GW1-L1-2

description:
Library name: GW1-L1-2
replicate 2_1600 L1

source_name: L1, Ferret's front leg


title: MC2P, scRNAseq

description:
Library name: MC2P
10x Genomics


title: ATAC-seq of Tbet KO 3

description: Library name: Sample 24


title: GW1-L1-1

description:
Library name: GW1-L1-1
replicate 1_1100 L1


title: ATAC-seq of Tbet KO 2

description: Library name: Sample 23


title: ATAC-seq of Cpntrol 3

description: Library name: Sample 15


title: ATAC-seq of Tbet KO 1

description: Library name: Sample 22


title: ATAC-seq of Cpntrol 2

description: Library name: Sample 14


title: TPC-1 cells, RRM2 overexpression strain, OE_RRM2_3

city: Fuzhou

first: Bo Wang

last: Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

institute: Fujian Medical University Union Hospital

description: Library name: Sample 6

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-hous eperl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q3 0 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selectedHisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level. Mapped reads were counted against gene features using FeatureCounts (v1.5.0‑p3). Gene expression levels were normalized to fragments per kilobase of transcript per million mapped reads (FPKM) by dividing the read counts by the gene length and sequencing depth.
Differential Expression Analysis Each cell line was assayed in biological triplicate. Differential expression between two conditions was determined using DESeq2 (v1.20.0). P values were adjusted for multiple testing using the Benjamini–Hochberg procedure to control the false discovery rate (FDR). Genes with an adjusted P ≤ 0.05 were considered significantly differentially expressed.
Functional Enrichment Analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of differentially expressed genes were performed using ClusterProfiler (v3.8.1). Terms with an adjusted P < 0.05 were deemed significantly enriched.
Assembly: GRCh38.p14
Supplementary files format and content: Text file include FRKM values for each sample.

source_name: Thyroid

extract_protocol:
Ribosomal RNA was removed by Epicentre Ribozer rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA.
The sequencing libraries were generated by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370-420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy, according to effective library concentration and data amount required.

value: Thyroid

value: TPC-1 cells

value: Papillary Thyroid Carcinoma cells

tag: genotype

value: RRM4 overexpression


title: Chip-seq of Runx3 with Tbet KO 2

description: Library name: Sample 35


title: ATAC-seq of Cpntrol 1

description: Library name: Sample 13


title: Dusp2 KO

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

institute: Peking University

description: Library name: KO

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 6000 or less than 500 were removed.
Normalization of the count matrix was performed, and dataset integration was achieved using Harmony.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for UMAP. UAMP were performed by R package Seurat (version 4.0.4)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: tumor

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

value: tumor

value: murine tumor infiltration lymphocytes


title: Dusp2 WT

description: Library name: WT


title: TPC-1 cells, RRM2 overexpression strain, OE_RRM2_2

description: Library name: Sample 5

value: RRM3 overexpression


title: MC3P2, scRNAseq

description:
Library name: MC3P2
10x Genomics


title: poplar stem rep 2

city: GAINESVILLE

first: Henry

middle: W

last: Schmidt

state: FL

address: 2033 Mowry road

institute: University of Florida

description: Library name: poplar stem rep 2

data_processing:
Raw sequencing data were preprocessed using CellRanger (v 5.0)
Assembly: NCBI:txid3694
Supplementary files format and content: When using the 10× Genomics Chromium single-cell RNA-seq technology, sequencing data are initially preprocessed by the Cell Ranger v3.1.0 pipeline. Cell Ranger integrates a series of bioinformatic tools that align sequencing reads, generate feature-barcode matrices, and the output files for further clustering and gene expression analysis.
Supplementary files format and content: The processed data files correpsond with the 3 outputs of the Cell Ranger pipeline: barcodes.tsv, features.tsv, and matrix.mtx

molecule: nuclear RNA

organism: Populus trichocarpa

source_name: Stem internode 4-5

growth_protocol: Rooted cuttings of Populus trichocarpa were grown in a greenhouse with Peters Professional 20-20-20 Fertilizer (The Scotts Company, Marysvillle, OH) adjusted to 5mM with respect to nitrogen, in a flood irrigation system of ebb-and-flow benches. The ebb-and-flow benches were flooded once daily for approximately 30 minutes. Temperatures in the fan and pad cooled greenhouse ranged between 22°C and 24°C, and interior photosynthetically active radiation ranged up to 1200 μmol s-1 m-2 photosynthetic photon flux (over the waveband 400–700 nm) during the daily 14 hours of natural irradiance. After six weeks of growth, the whole stem (xylem, phloem and bark) internode interval between leaf plastochron index 4 and 5 was collected for nuclei isolation.

extract_protocol:
To perform nuclei isolation, we followed the protocol that we previously developed for extraction of high quality nuclei from plant tissues (https://doi.org/10.1371/journal.pone.0251149). 20k nuclei were loaded to the 10X Genomics Chromium to generate the snRNA-seq library following the 10X Genomics Chromium Single Cell v3.1 protocol. The cDNA reaction was prepared as described previously (https://doi.org/10.1371/journal.pone.0251149). Prior to full-scale sample sequencing, a preliminary run was performed in an Illumina iSeq (~ 4M reads) to allow the evaluation of parameters that are indicative of the quality of the single-cell RNA-seq library, including the estimated number of cells captured and the fraction of reads in cells (i.e., percentage of ambient or "leaked" RNA). The sequencing was performed using a standard program as follows: 28 bp (Cell barcode and UMI) for read 1, 90 bp (cDNA) for read 2, 10 bp for I7 Index, and 10 bp for I5 Index. The assessment of RNA leakage was derived from the profile of the relationship between UMI counts and cell barcodes detected. If the library was considered suitable for full-scale sequencing (reads in cells > 50% and at least 3,000 cells captured at low sequencing depth) we proceeded to sequencing in an Illumina NovaSeq6000. For full-scale sequencing we targeted 150-200M reads mapped to the genome per sample, which in our experience resulted in a sequencing saturation >70% and an average of 43,000 reads per nucleus.
The 10x Genomics Single Cell v3.1 Dual Index Gene Expression protocol was followed

value: Stem internode 4-5


title: TPC-1 cells, RRM2 overexpression strain, OE_RRM2_1

description: Library name: Sample 4

value: RRM2 overexpression


title: poplar stem rep 1

description: Library name: poplar stem rep 1


title: Telencephalon, Replicate2

city: Paris

first: Laure

last: Bally-Cuif

address: 25 Rue du Docteur Roux

department: Developmental and stem cell biology department

country: France

institute: Institut Pasteur

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Telencephalon

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Telencephalon

tag: age

value: 12 weeks


title: spr-5; met-2_lin-35 RNAi_Rep3

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

institute: Kennesaw State University

description:
Library name: Sample 12
replicate 12

data_processing:
Raw RNAseq reads were checked for quality using FastQC (Andrews 2010), filtered using Trimmomatic (Bolger et al. 2014)
Trimmed reads emapped to the C. elegans transcriptome (ce11, WBcel235) using HISAT2 (Kim et al., 2015b)
Read count by gene was obtained by FeatureCounts (Yang liao et al 2014)
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) (Love et al 2014)
Assembly: ce11
Supplementary files format and content: FeatureCounts files are in tabular format and include Read count by gene
Supplementary files format and content: Processed files from DESEQ2 analysis are in tabular format and contain a list of differentially expressed genes compared to WT (N2 strain on control RNAi)

source_name: whole animal L1 Larvae

growth_protocol: Animals were cultured with OP50 on 10-cm NGM agar plates at 20C.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from 500-1000 starved L1 larvae born at 20°C overnight on unseeded NGM plates. Total RNA was sent to Georgia Genomics and Bioinformatics Core (University of Georgia, Athens, Georgia) for standard Poly-A RNA-seq services (Illumina Nextseq, 50bp paired-end reads)
Libraries were prepared by HAIB-GSL (for HiSeq).

treatment_protocol: Feeding experiments were performed on RNAi plates (NGM plates containing 100 ug/ml ampicillin, 0.4mM IPTG, and 12.5ug/ml tetracycline). F0 worms were placed on RNAi plates as L2 larvae and then moved to fresh RNAi plates 48hrs later where they were allowed to lay embryos for 2-4 hrs. F0 worms were then removed from plates and sacrificed or placed on unseeded RNAi plates overnight so that starved L1 progeny could be isolated for RNAseq experiments. F1 progeny were scored 72hrs after the synchronized lay for L1 larval arrest. For each RNAi experiment, pos-1 RNAi was used as a positive control. Each RNAi experiment reported here pos-1 RNAi resulted in >95% embryonic lethality, indicating that RNAi plates were optimal.

value: whole animal L1 Larvae


title: H3K27-2(ChIP-seq)

city: Shanghai

first: Jieyu

last: Guo

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

description: Library name: Sample 6

data_processing:
Basecalls were performed using bcl2fastg v2.17 for Novaseg output
ChlP-seg reads were trimmed from 3' end until the final base had a quality score > 30 using Trimmomatic v0.39
ChlP-seg reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.4.5.
ChlP-seg coverage was created by deepTools and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.5
Assembly: mm10
Supplementary files format and content: bigWig

source_name: E14Tg2A line

growth_protocol: WT and BACH1-KO mESC maintained in a culture medium for 2 days. The culture mediumconsisting of 90% Dulbecco's modified Eagle's medium (DMEM), 10% fetal bovine serum (FBS) , 1% non-essential amino acids (NEAA), 0.1 mM β-mercaptoethanol , and 200 Units/ml murine leukemia inhibitory factor (mLIF) . Bach1-KO mESCs were generated by using CRISPR/Cas9 genome editing technology. sgRNAs targeting the genomic regions of interest were designed with the CRISPR Design Tool . Annealed sgRNA oligos were cloned into LentiCRISPR V2, transiently transfected into mESCs with Lipofectamine 2000 , and then selected with puromycin ; single-cell clones were sorted 7 days later.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis.chromatin was sonicated using a Q800R2  DNA shearing sonicator (thermocube).
ChlP-seg libraries were prepared using the DNA Library Preparation Kit (nd607-01) complemented with VAHTSTM DNA adapters set2 for Illumina (N802-00) from Vazyme. 25 ng of DNA wasused as starting material for input and ip samples. Libraries were amplified using 13cycles on the thermocycler. Post amplification libraries were size selected at 250-450bpin length using VAHTS DNA clean beads from Beckman Coulter. Libraries were sequenced on Illumina Hiseq X Ten by Basepair Company (Suzhou, China).

value: E14Tg2A line

value: mouse embryonic stem cells

value: WT

tag: chip-antibody

value: H3K27ac (Millipore,#MABE670)


title: H3K27-1(ChIP-seq)

description: Library name: Sample 5


title: Telencephalon, Replicate1

description: 10x Genomics


title: TPC-1 cells, wild strain, TPC_1_2

description: Library name: Sample 2


title: spr-5; met-2_lin-35 RNAi_Rep2

description:
Library name: Sample 11
replicate 11


title: BACH2-ko2(ChIP-seq)

description: Library name: Sample 4

value: BACH1 (#sc-271211, Santa Cruz Biotechnology, Santa Cruz, CA, USA)


title: Combined treatment

city: Taipei

first: Yu Chiu

last: Kao

address: Academia Road

country: Taiwan

institute: Academia Sinica

description:
Library name: Red Light_EF_SHSY5Y
SH-SY5Y cells treated with combined dcEF and red light stimulation in 3D collagen.
E_R2

data_processing:
Raw reads were quality-checked and trimmed using CLC Genomics Workbench v10 (QV ≥ 20, no ambiguous bases, adapter removal).
Trimmed reads were aligned to the human reference genome (hg38) with minimum length fraction = 0.5 and similarity fraction = 0.8.
Only reads with up to 10 hits were retained; strand-specific mapping was set to forwardOnly reads with up to 10 hits were retained; strand-specific mapping was set to forward.
Gene expression levels were quantified using the FPKM method.
Assembly: Homo sapiens genome build GRCh38 (hg38)
Supplementary files format and content: Processed data are provided in Excel (.xlsx) format. Each file contains gene-level expression values (FPKM) for each sample. Columns include gene identifiers (Ensembl Gene ID or Gene Symbol) and FPKM values.

source_name: neuroblastoma

growth_protocol: SH-SY5Y cells were cultured in 3D collagen scaffolds (1 mg/mL) with a cell density of 1 × 10⁶ cells/mL under standard conditions (37°C, 5% CO₂).

extract_protocol:
Total RNA was extracted using TRIzol Reagent and BCP Reagent (Invitrogen) according to the manufacturer's protocol.
Poly(A)+ RNA was enriched from total RNA using oligo(dT) selection, followed by RNA fragmentation, first and second strand cDNA synthesis, end repair, adapter ligation, and PCR amplification. Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant kit (TECAN) according to the manufacturer's instructions.

treatment_protocol: Cells were divided into four groups: (1) Control (no treatment), (2) direct current electric field (dcEF, 175 mV/mm, 3 hours), (3) red light (620 nm, 2 mW/cm², 45 hours), and (4) combined dcEF and red light.

value: neuroblastoma

value: neuroblastoma cell

tag: treatment

value: dcEF+red light

value: Batch 1


title: MC1R, scRNAseq

description:
Library name: MC1R
10x Genomics

source_name: Pleural fluid

value: Pleural fluid

value: mantle cell lymphoma (MCL)


title: spr-5; met-2_lin-35 RNAi_Rep1

description:
Library name: Sample 10
replicate 10


title: Red light only

description:
Library name: Red Light_SHSY5Y
SH-SY5Y cells exposed to red light (620 nm, 2 mW/cm２, 45 h) in 3D collagen.
R2

value: red light


title: spr-5; met-2_control RNAi_Rep3

description:
Library name: Sample 9
replicate 9


title: BACH1WT2(ChIP-seq)

description: Library name: Sample 2


title: TPC-1 cells, wild strain, TPC_1_1

description: Library name: Sample 1

value: Thyroid

value: TPC-1 cells

value: Papillary Thyroid Carcinoma cells


title: OAA3

city: Guangzhou, Guangdong

first: Shouheng

last: Jin

address: School of Life Sciences, Sun Yat-sen University, No.135, Xingang West Road

department: School of Life Sciences

institute: Sun Yat-sen University

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

source_name: PBMC

growth_protocol: PBMC cells were cultured in 1640 with 1% sodium pyruvate and 10% (vol/vol) fetal bovine serum.

extract_protocol:
The nucleus was collected from 5 × 10^4 cells (plated in a 12-well plate that the density reached 80% with a good growth state) and treated by transposase reaction mix (22.5 μL of nuclease-free water, 25 μL 2 × TD buffer, and 2.5 μL Transposase (Illumina)) at 37 °C for 30 minutes.
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit. The library products were enriched, quantified and finally sequenced on a Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: PBMCs were treated with diethyl-ester OAA (1 mM).

value: PBMC

value: OAA


title: spr-5; met-2_control RNAi_Rep2

description:
Library name: Sample 8
replicate 8

value: whole animal L1 Larvae


title: BACH1WT1(ChIP-seq)

description: Library name: Sample 1

value: E14Tg2A line

value: mouse embryonic stem cells


title: OAA2


title: Telencephalon, Replicate3

description: 10x Genomics

value: Telencephalon

value: 12 weeks


title: spr-5; met-2_control RNAi_Rep1

description:
Library name: Sample 7
replicate 7


title: Control group

description:
Library name: Ctrl_SHSY5Y
SH-SY5Y cells cultured in 3D collagen matrix with treatment: nan
C2

value: neuroblastoma


title: OAA1


title: TPC-1 cells, wild strain, TPC_1_3

description: Library name: Sample 3

value: WT


title: ko10326

description: Library name: Sample 5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hista2 V2.2.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene FPKM for every gene and every sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: total RNA


title: Normal3

city: Shenzhen

first: Ziyu

last: Chen

state: Guangdong

address: 1120 Lianhua Rd

institute: Peking University Shenzhen Hospital

description:
Library name: Sample8
FPKM.Normal_3

data_processing:
Fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo sapiens ensembl v107
Supplementary files format and content: xlsx file include FPKM and count values for each sample

source_name: subcutaneous tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: subcutaneous tissue


title: WT_lin-35 RNAi_Rep3

description:
Library name: Sample 6
replicate 6

value: N2; (lin-35 RNAi)


title: Normal2

description:
Library name: Sample7
FPKM.Normal_2


title: WT_lin-35 RNAi_Rep2

description:
Library name: Sample 5
replicate 5


title: Mock3


title: Mock2


title: Normal1

description:
Library name: Sample6
FPKM.Normal_1


title: WT40402

description: Library name: Sample 3


title: WT_lin-35 RNAi_Rep1

description:
Library name: Sample 4
replicate 4


title: Mock1


title: WT40326

description: Library name: Sample 2


title: dcEF only

description:
Library name: EF_SHSY5Y
SH-SY5Y cells treated with direct current electric field (175 mV/mm, 3 h) in 3D collagen.
E2

value: neuroblastoma cell

value: dcEF

value: Batch 1


title: Lymphedema4

description:
Library name: Sample4
FPKM.Lymphedema_4


title: MDA-MB-231 cells, W23-1006, 24h, rep2

city: Guangzhou

first: Xianyuan

last: Yang

address: No.132 East Ring Road

institute: Sun Yat-Sen University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each 2 gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: The resulting data table file, separated by a Tab.

extract_protocol:
Total RNA was extracted from Trizol reagent. Then, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the librar


title: WT_control RNAi_Rep2

description:
Library name: Sample 2
replicate 2


title: WT_control RNAi_Rep3

description:
Library name: Sample 3
replicate 3


title: MDA-MB-231 cells, W23-1006, 24h, rep1


title: Lymphedema3

description:
Library name: Sample3
FPKM.Lymphedema_3


title: WT30326

description: Library name: Sample 1


title: ko10402

description: Library name: Sample 6


title: Dorsal skin tissue from aged C57BL/6 mice (18-20 months old), after red light irradiation

first: Haocai

last: Chang

address: 55 Zhongshan Avenue West, Tianhe District

institute: South China Normal University

description: Library name: Sample2

data_processing:
RSEM software, statistical software R (v.4.3.1), DESeq2 (v.1.40.2)
Assembly: Short reads alignment tool Bowtie2 (version 2.2.8)
Supplementary files format and content: Tab-delimited Text File Includes FPKM  for Each Sample

source_name: skin

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: skin

tag: strain

value: red light irradiation


title: DMS-MaPseq of E. coli DH10b, exponential phase, 37°C (mRNA)

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

data_processing:
*library strategy: DMS-MaPseq
Following sequencing, sequencing adapters were clipped using Cutadapt v4.4 (parameters: -a AGATCGGAAG -m 100 -O 1). Reads were then mapped to the reference genome (U00096.3) using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed using RNA Framework’s rf-count-genome to generate genome-level RC files (containing per-base mutations and coverage). Aligned reads spanning less than 100 nt, as well as reads having more than 10% mutated bases, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1).
Assembly: U00096.3
Supplementary files format and content: Wiggle files of bulk raw DMS-MaPseq mutation frequencies, separated by genomic strand

molecule: cytoplasmic RNA

organism: Escherichia coli

growth_protocol: E. coli K-12 MG1655 derivative strain DH10b was streaked on LB plates, and a single colony was picked, inoculated in 4 mL LB broth, and grown overnight at 37°C with shaking. The day after, the culture was diluted to an OD600 = 0.05 in 25 mL LB broth and grown at 37°C until OD600 ≈ 0.5 (~2 h).

extract_protocol:
Cell pellets were resuspended in 62.5 μl Resuspension Buffer [20 mM Tris-HCl pH 8.0; 80 mM NaCl; 10 mM EDTA pH 8.0], supplemented with 100 μg/mL final Lysozyme (cat. L6876, Merck) and 20 U SUPERase•In™ RNase Inhibitor (cat. A2696, ThermoFisher Scientific), by vigorous vortexing. Samples were incubated at room temperature for 1 min, followed by addition of 62.5 μl Lysis Buffer [0.5% Tween-20; 0.4% Sodium deoxycholate; 2 M NaCl; 10 mM EDTA]. Samples were then inverted 5-10 times and incubated at room temperature for 2 min, followed by additional 2 min on ice. 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific) was then added, samples were vigorously vortexed for 15 sec, and RNA was extracted as per manufacturer instructions.
Prior to library preparation, highly abundant short RNA species, such as tRNAs, were depleted on Monarch® RNA Cleanup columns by loading a 1:1:1 mixture of total RNA in nuclease-free water, RNA binding buffer and 100% ethanol. rRNA depletion was performed on 1.1 μg total RNA using the RiboCop for Bacteria kit (cat. 126, Lexogen), with two minor changes to the manufacturer’s protocol: denaturation temperature was increased to 95°C, and probe annealing temperature was lowered to 55°C. Following rRNA depletion, RNA was cleaned up on Monarch® RNA Cleanup columns, eluted in 8 μl nuclease-free water, and supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50) and 25 ng/μl Actinomycin D (to increase strand-specificity; cat. A1410, Merck), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: For dimethyl sulfate (DMS; cat. D186309, Merck) probing, DMS from a fresh 1:4 dilution in ethanol (~2.64 M) was added to the bacteria at a final concentration of 200 mM. Probing was conducted for 2 min at 37°C, with moderate shaking (800 RPM). Bacteria were collected by centrifugation at 17,000g for 1 min. Supernatant was discarded, the pellet was washed twice with 0.5 M DTT, and then immediately subjected to RNA extraction.


title: ko1411

description: Library name: Sample 4


title: DICER OE  WT

status: Public on Jul 18 2025

city: Frederick

first: Sharan

last: Malagobadan

address: 1050 Boyles Street, Building 560, Room 11-2

institute: National Institutes of Health

description: Library name: DICER OE  WT

data_processing:
Reads were trimmed for adapter sequence and processed by QuagmiR to map and quantify miRNA reads using a custom motif file for mouse miRNA
For total RNA miR-seq data, reads were normalized to spike-in. For AGO2-IP miR-seq, reads were normalized to total miRNA.
Assembly: Mus musculus and homo sapiens custom motif file for miRNA quantification by QuagmiR
Supplementary files format and content: Tab-delimited text file with RPM for each group

source_name: embryonic kidney

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
Small RNA libraries for miR-seq were generated using the QIAseq miRNA Library Kit (Qiagen, 331502) according to the manufacturer's instructions. For normalization of total RNA samples, 1ul of QIAseq miRNA Library QC Spike-ins (Qiagen, 331535) was added to 500 ng of RNA before library preparation. The library was size-selected and purified on a native 6% (w/v) acrylamide gel and ethanol precipitation, respectively. The library was sequenced on the Illumina Nextseq 1000 platform.

value: embryonic kidney

value: Dicer KO

value: Dicer (-/-)

value: WT Dicer overexpression


title: WT_control RNAi_Rep1

description:
Library name: Sample 1
replicate 1

value: whole animal L1 Larvae


title: MDA-MB-231 cells, DMSO, 24h, rep2

value: DMSO


title: tumor in boundary of the lesser curvature of cardia, bio rep3

first: Shanqiang

last: Zhou

state: Fujian

address: 32 No. 29 Xinquan Road

department: Department of Gastric Surgery

description:
Library name: JM017
Column name in rawCount.csv: JM017

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96,  Mouse:GRCm38.p6) using kallisto (0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38.p6
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: stomach

extract_protocol:
Total RNA was extracted from the tissue using RNeasy Mini Kit (QIAGEN).
Libraries are sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: Mice were administered tamoxifen via intraperitoneal injection at a dose of 50 mg/kg (20 mg/mL) for one day.

value: stomach

value: 7-8 weeks old

value: Pou2f3-CreERT; Rb1fl/fl; Trp53fl/fl; LSL-MycT58A

value: tamoxifen induction

tag: time

value: 5 weeks


title: tumor in boundary of the greater curvatureof cardia, bio rep3

description:
Library name: JM016
Column name in rawCount.csv: JM016


title: tumor in corpus, bio rep3

description:
Library name: JM018
Column name in rawCount.csv: JM018


title: Lymphedema2

description:
Library name: Sample2
FPKM.Lymphedema_2

value: subcutaneous tissue


title: Lymphedema1

description:
Library name: Sample1
FPKM.Lymphedema_1


title: DICER OE D1320A

description: Library name: DICER OE D1320A

tag: cell line

value: D1320A Dicer overexpression


title: tumor in corpus, bio rep2

description:
Library name: JM012
Column name in rawCount.csv: JM012


title: MDA-MB-231 cells, DMSO, 24h, rep1

value: WT


title: Lymphedema5

description:
Library name: Sample5
FPKM.Lymphedema_5


title: Dorsal skin tissue from untreated aged C57BL/6 mice (18-20 months old)

description: Library name: Sample1


title: MC207R, scRNAseq

city: Stockholm

first: Hui

last: Wan

address: Biomedicum, Solnavägen 9, floor 9D

institute: Karolinska Institutet

description:
Library name: MC207R
10x Genomics

data_processing:
The raw sequencing data were preprocessed using Cell Ranger (version 7.0.0) with default parameters.
Assembly: GRCh38
Supplementary files format and content: HDF5 files

source_name: Lymph node

extract_protocol:
Sample processing: Mononuclear cells were isolated from bone marrow samples by standard density centrifugation using Lymphoprep (Axis-Shield) following the manufacturer’s instructions. Intestinal, tonsillar, and lymphoid tissues were processed into single-cell suspensions using mechanical dissociation and then filtered through 70 μm containers. Single cells were cryopreserved in fetal bovine serum (FBS) supplemented with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen before use.  Cell sorting: The cells used for flow cytometry were thawed in RPMI 1640 cell medium (Gibco). The cells were blocked with human FcR Blocking Reagent (Miltenyi Biotec) for 10 min and subsequently stained with anti-CD19 BV421 and anti-CD235a FITC in FACS buffer (PBS with 2% FBS) for 20 min on ice. Immediately before sorting, the cells were briefly incubated with propidium iodide staining solution. For the MCL samples, live CD235a- cells, CD235a-CD19+ cells, and CD235a-CD19- cells were sorted in FACS buffer using a BD FACSAria Fusion Sorter (BD Biosciences). Live CD235a- cells were used for single-cell sequencing, while live CD235a- CD19+ and CD235a- CD19- cells were used to extract DNA for tumor and germline WGS, respectively. For the control sample, live CD19- cells and live CD19+ cells were sorted separately and then mixed at a 3:7 ratio for single-cell sequencing.
scRNA-seq sequencing and data analysis: Using the Chromium Next GEM Single-Cell 5′ Reagent Kit v2 (10x Genomics), the cells were loaded onto separate lanes of the Next GEM Chromium Controller (10x Genomics) for encapsulation (target recovery of 10,000 cells for each sample). Single-cell gene expression (GEX) libraries were constructed following the manufacturer’s protocols.

value: Lymph node

value: mantle cell lymphoma (MCL)


title: normal tissue, bio rep3

description:
Library name: JM014
Column name in rawCount.csv: JM014


title: tumor in antrum, bio rep2

description:
Library name: JM009
Column name in rawCount.csv: JM009


title: tumor in corpus, bio rep1

description:
Library name: JM006
Column name in rawCount.csv: JM006


title: tumor in antrum, bio rep1

description:
Library name: JM003
Column name in rawCount.csv: JM003


title: Stomach_ML01

description:
Library name: Sample1
10x Genomics

data_processing:
Gene counts were made by CellRanger 7.1.0
Assembly: Assembly:Mouse mm10
Supplementary files format and content: Tap-separated values file and matrix file

extract_protocol:
Gastric tissues were collected, digested with collagenase, and processed into single-cell suspensions. After erythrocyte lysis, cell suspensions were centrifuged at 300 × g for 5 minutes. The supernatant was discarded, and pellets were resuspended in FACS buffer. Cells were incubated with APC-conjugated anti-EPCAM and PE-CY7-conjugated anti-CD45 antibodies (room temperature, protected from light, 10 minutes), followed by centrifugation (300 × g, 5 minutes). Pellets were resuspended in 500 μL FACS buffer containing DAPI. Cell suspensions (500 μL) were transferred to flow tubes for analysis. TdTomato+ cells were sorted and pooled from multiple mice. TdTomato−, EpCAM+, CD45− gastric epithelial cells were mixed at a 1:1 ratio with sorted TdTomato+ cells for single-cell RNA sequencing (scRNA-seq).
The 10x Genomics Single Cell Gene Expression 3’ and 5’ workflows are both high-throughput, scalable technologies that encapsulate thousands of individual cells (or nuclei) in droplets for lysis and reverse transcription from up to 8 samples in parallel. The droplets contain primers for cell- and and molecule-specific barcoding of cDNA. We can prepare libraries for CITE-Seq/feature barcoding, CRISPR, or cell hashing. Using our 5’ workflow, we can profile the full length V(D)J regions from T-cell or B-cell receptors from human and mouse samples. The resulting libraries are typically sequenced on an Illumina NovaSeq 6000. Users must deliver live cells (or nuclei) in suspension to the Core.

treatment_protocol: Three Pou2f3-CreERT; Rosa26-tdTomato transgenic mice were induced with tamoxifen for 2 weeks.

value: epithelium cells

value: 7-8 weeks

value: Pou2f3-CreERT; Rosa26-tdTomato

value: 2 weeks