title: RNA-seq of NIH-H146 cells with KIFC1 siRNA, biological replicate 3

city: Bunkyo-ku

first: Natsuki

last: Nakagawa

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

description: Library name: KD_2_3

data_processing:
Raw RNA-seq reads in FASTQ format were aligned to the human reference genome using HISAT2 (v2.2.1) with default parameters.
Gene-level read counts were generated using featureCounts (v2.0.8).
Differential expression analysis was performed using DESeq2 (v1.46.0) in R (v4.4.2).
Assembly: GRCh38 (human reference genome)
Supplementary files format and content: Processed data files consist of a comma-separated values (CSV) matrix containing raw gene-level read counts for all samples. Rows correspond to genes and columns correspond to individual samples. Gene identifiers (Geneid) represent Ensembl Gene IDs based on the GRCh38 reference annotation.

extract_protocol:
Total RNA from cultured cells was extracted using RNAiso Plus according to the instructions of the manufacturer (Takara Bio). The purity and concentration of RNA were determined by NanoDrop ONE (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: small-cell lung cancer

value: KIFC1 knockdown

value: KIFC1 siRNA was transfected

value: day 2


title: Single-cell sequencing WT 1

status: Public on Feb 06 2026

type: SRA

city: Tianjin

first: Wanyi

last: Xiao

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District Tianjin

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

description: Library name: WT_scRNA_1

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger for alignment and gene counting. Downstream quality control, normalization, dimensionality reduction, clustering, and differential expression analyses were performed using Seurat.
Assembly: hg19
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Single-cell suspensions were prepared from cultured cells with viability greater than 90% prior to loading onto the 10x Genomics Chromium platform.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ library preparation kit according to the manufacturer’s instructions.

tag: cell line


title: Single-cell sequencing WT 2

description: Library name: WT_scRNA_2


title: MII_smRNA-seq_1

city: Shanghai

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description:
Library name: Sample 42
MII stage oocyte (MII)

library_source: transcriptomic

data_processing:
For small RNA-seq, raw read1 sequences were processed using the fastx_toolkit (v.0.0.14) for quality filtering and adapters trimming. Reads lacking the 3’ adapter sequence or shorter than 17 bp post-trimming were discarded. Reads of 17-40 bp were mapped to the human genome (hg19) using Bowtie (v.1.2) with parameters --k=100 --v=0.
For long RNA-seq, raw pair-end reads were processed using TrimGalore (v.0.5.0) for adapter trimming and quality filtering. The remaining reads were mapped to the human genome (hg19) and representative TE sequences using STAR (v2.7.1a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. Gene abundance was quantified using RSEM (v.1.2.31) with default settings.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include useful reads count of smRNAs and each gene count.

source_name: oocyte

extract_protocol:
Total RNAs were extracted from mouse oocytes and cultured cells using TRIzol reagent (Ambion), respectively. The quantity of isolated RNA was measured with Qubit 2.0 Fluorometer (Invitrogen).
Lysates from the single oocyte were incubated at 72 °C for 3 minutes to release and unfold the small RNAs. After 3′ adapter ligation, 5 U of lambda exonuclease and 25 U of 5′ deadenylates were used to remove the excess 3′ adapter. Subsequently, 5′ adapter was ligated, followed by reverse transcription and pre-amplification. For final amplification, 1 μL of the pre-amplified product was used as a template. Libraries were size-selected by electrophoresis on a 6% polyacrylamide gel, and 130–160 bp DNA fragments were extracted to recover small RNA libraries. Single-oocyte mRNA was captured and amplified using Smart-seq2, as previously described, 69. 2 ng of purified cDNA was subjected to a tagmentation reaction with Tn5 transposase70.

treatment_protocol: Human follicles were isolated from fresh ovarian cortex obtained from patients undergoing ovarian cyst or cystic teratoma resection, following previously described procedures67. Briefly, ovarian cortical tissues were fragmented into pieces measuring 30–600 μm and digested with 1 mg/mL collagenase type IA (Sigma-Aldrich) and 8 IU/mL DNase I (Sigma-Aldrich) in 10 mL of M199 medium (Gibco) at 37°C for 30 minutes with gentle agitation. Follicles were subsequently isolated and evaluated under a stereomicroscope (Nikon SMZ 1000), and their diameters were measured using an inverted microscope (Nikon Ti2). Ovarian stimulation and oocyte collection was performed as previously describe39, 67. GV and MI stage oocytes were collected following stimulation. MII stage oocytes were obtained after overnight incubation to facilitate maturation, conforming by the presence of a distinct first polar body under microscope observation. Granulosa cells were removed via incubation with trypsin-EDTA solution (Gibco) and 1 mg/mL hyaluronidase. The zona pellucida was eliminated using Acidic Tyrode's Solution (Millipore), yielding denuded oocytes which were then washed and transferred to PCR tubes containing 4 μL of cell lysis buffer (0.2% Triton X-100, Sigma; 1 U/μL RiboLock RNase inhibitor, Thermo Fisher). The oocytes were stored at -80°C until further processing.

tag: tissue

value: oocyte

tag: genotype

value: wild type


title: RNA-seq of NIH-H146 cells with KIFC1 siRNA, biological replicate 2

description: Library name: KD_2_2

tag: cell type

tag: treatment

tag: time


title: WT_1,PD7

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Raw reads were trimmed to remove low-quality bases and adaptor sequences using Trim Galore v0.6.7. Reads were further mapped to the mouse (mm9) genomes using STAR v2.7.10a.
Uniquely mapped reads were applied for gene expression quantification using FeatureCounts v2.0.2.
Biotinylated gene transcript abundance was further analyzed using the DESeq2 R package. An adjusted p-value of < 0.05, and fold change (FC) of APEXflox/+;Gdf9-Cre/WT > 2 were considered statistically significant to identify primordial follicle oocyte mRNAs.
Transcripts per million mapped reads (TPM) was calculated to validate gene expression and normalized to gene length and sequencing depth.
Assembly: mm9
Supplementary files format and content: countlist.xlsx includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: ovary

extract_protocol:
The whole ovary was lysed and then RNA was enriched for sequencing.
RNAs were diluted to 0.2 ng/μL and 2.5 μL samples were performed library constructions. The samples were incubated with oligo(dT) primers (a deoxynucleoside triphosphate mixture) for 3 min at 72 °C, and cDNA pools were obtained by Smart-seq2 reverse transcription reactions. After the first-strand reaction, the cDNAs were pre-amplified with limited cycles (~ 12 cycles). Sequencing libraries were then constructed with 0.5 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503; Vazyme, Nanjing, China) according to the manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform in the 151 bp paired-end mode.

value: ovary


title: RNA-seq of NIH-H146 cells with KIFC1 siRNA, biological replicate 1

description: Library name: KD_2_1


title: GV_smRNA-seq_3

description:
Library name: Sample 40
germinal vesicle stage oocyte (GV)


title: GV_smRNA-seq_1

description:
Library name: Sample 38
germinal vesicle stage oocyte (GV)


title: GV_smRNA-seq_4

description:
Library name: Sample 41
germinal vesicle stage oocyte (GV)


title: PF_smRNA-seq_9

description:
Library name: Sample 37
primary follicle stage oocyte (PF)


title: cardiac mitochondria, db/db, 5

city: Wuhan

first: zhan

last: jiabing

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Majorbio self-developed software and Fastx-Toolkit was first filtered to obtain high quality sequencing data (clean data) including remove reads of too short length (<18nt) or too long length (>32nt).
Clean data (reads) are compared with the reference genome (GRCm39) to obtain mapped data (reads) for subsequent analysis.
Mapped reads were compared with miRbase and Rfam databases to obtain known miRNA and ncRNA annotation information, respectively. Novel miRNAs were predicted using miRDeep2 (animal) or miReap (plant) software for reads for which no annotation information was obtained.
The expression of known miRNAs and new miRNAs in each sample were counted and homogenized the expression using TPM.
Assembly: GRCm39
Supplementary files format and content: WT-DB miRNA-seq TPM.txt

source_name: Heart

extract_protocol:
Total RNA was extracted from cells or frozen tissues using RNAiso Plus reagent (Takara Bio, Japan) according to the manufacturer’s instructions.  1 ug of total RNA was used for the construction of sequencing libraries
Total RNA was ligateed with the 3' end junction and the 5' end junction, respectively. First strand of cDNA synthesis was performed using random primer, followed by library enrichment (11-12 cycles of PCR) and library purification (6% Novex TBE PAGE gel, 1.0 mm, 10 well). Quantification was performed with TBS380 (Picogreen). Then samples were mixed on the machine in proportion to the quantitative data, followed by bridge PCR amplification on cBot to generate clusters.

value: Heart

value: db/db

tag: fraction

value: mitochondrial microRNA


title: cardiac mitochondria, db/db, 4


title: RNA-seq of NIH-H146 cells with negative control siRNA, biological replicate 2

description: Library name: sinega_2

value: WT

value: negative control siRNA was transfected


title: RNA-seq of NIH-H146 cells with negative control siRNA, biological replicate 1

description: Library name: sinega_1


title: PF_smRNA-seq_7

description:
Library name: Sample 35
primary follicle stage oocyte (PF)


title: GV_smRNA-seq_2

description:
Library name: Sample 39
germinal vesicle stage oocyte (GV)


title: cardiac mitochondria, db/db, 6


title: MII_smRNA-seq_2

description:
Library name: Sample 43
MII stage oocyte (MII)


title: PF_smRNA-seq_6

description:
Library name: Sample 34
primary follicle stage oocyte (PF)


title: MII_smRNA-seq_4

description:
Library name: Sample 45
MII stage oocyte (MII)


title: PF_smRNA-seq_8

description:
Library name: Sample 36
primary follicle stage oocyte (PF)


title: PF_smRNA-seq_5

description:
Library name: Sample 33
primary follicle stage oocyte (PF)


title: cardiac mitochondria, db/db, 3


title: PF_smRNA-seq_3

description:
Library name: Sample 31
primary follicle stage oocyte (PF)


title: cardiac mitochondria, db/db, 2


title: coculture with T cells, Day 3 collection gDNA , rep1

description: Library name: Tcell_Treat_rep1

library_source: genomic

data_processing:
Raw sequencing reads were demultiplexed and quality-checked. sgRNA abundance was quantified and differential representation was analyzed using the MAGeCK-VISPR pipeline(v0.5.4).
Assembly: Not applicable.
Supplementary files format and content: Processed data files are provided as tab-delimited text files containing sgRNA-level abundance from a pooled CRISPR screen targeting miRNAs. Rows correspond to individual sgRNAs, and columns represent raw read counts for different experimental conditions and biological replicates. Each sgRNA is annotated with its corresponding target miRNA.
Library strategy: CRISPR Screen

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted from harvested cells using standard phenol-chloroform extraction or commercial genomic DNA purification kits according to the manufacturer’s instructions.
sgRNA cassettes were PCR-amplified from genomic DNA using primers flanking the sgRNA region. PCR products were purified, indexed, and prepared for Illumina sequencing according to standard amplicon sequencing protocols.


title: PF_smRNA-seq_4

description:
Library name: Sample 32
primary follicle stage oocyte (PF)


title: PF_smRNA-seq_2

description:
Library name: Sample 30
primary follicle stage oocyte (PF)


title: RNA-seq of NIH-H146 cells with negative control siRNA, biological replicate 3

description: Library name: sinega_3


title: cardiac mitochondria, db/db, 1


title: PF_smRNA-seq_1

description:
Library name: Sample 29
primary follicle stage oocyte (PF)


title: coculture with T cells, Day 3 collection gDNA , rep2

description: Library name: Tcell_Treat_rep2


title: cardiac mitochondria, WT, 6


title: coculture with T cells, Day 0 collection gDNA, rep2

description: Library name: Tcell_Day0_rep2


title: PrF_smRNA-seq_4

description:
Library name: Sample 27
primordial follicle stage oocyte (PrF)


title: coculture with T cells, Day 0 collection gDNA, rep1

description: Library name: Tcell_Day0_rep1


title: PrF_smRNA-seq_3

description:
Library name: Sample 26
primordial follicle stage oocyte (PrF)


title: PrF_smRNA-seq_1

description:
Library name: Sample 24
primordial follicle stage oocyte (PrF)


title: MII_longRNA-seq_5

description:
Library name: Sample 23
MII stage oocyte (MII)


title: cardiac mitochondria, WT, 4


title: PrF_smRNA-seq_5

description:
Library name: Sample 28
primordial follicle stage oocyte (PrF)


title: MII_longRNA-seq_4

description:
Library name: Sample 22
MII stage oocyte (MII)


title: MII_longRNA-seq_3

description:
Library name: Sample 21
MII stage oocyte (MII)


title: cardiac mitochondria, WT, 3


title: MII_longRNA-seq_2

description:
Library name: Sample 20
MII stage oocyte (MII)


title: PrF_smRNA-seq_2

description:
Library name: Sample 25
primordial follicle stage oocyte (PrF)


title: MII_longRNA-seq_1

description:
Library name: Sample 19
MII stage oocyte (MII)


title: cardiac mitochondria, WT, 5


title: control, Day 3 collection gDNA, rep2

description: Library name: Tcell_Con_rep2


title: PF_longRNA-seq_9

description:
Library name: Sample 14
primary follicle stage oocyte (PF)


title: cardiac mitochondria, WT, 1


title: cardiac mitochondria, WT, 2


title: vemurafenib selection, day 23 collection gDNA, rep3

description: Library name: vf_rep3


title: GV_longRNA-seq_3

description:
Library name: Sample 17
germinal vesicle stage oocyte (GV)


title: GV_longRNA-seq_2

description:
Library name: Sample 16
germinal vesicle stage oocyte (GV)


title: control, Day 3 collection gDNA, rep1

description: Library name: Tcell_Con_rep1


title: GV_longRNA-seq_1

description:
Library name: Sample 15
germinal vesicle stage oocyte (GV)


title: GV_longRNA-seq_4

description:
Library name: Sample 18
germinal vesicle stage oocyte (GV)


title: SS082

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

country: USA

institute: Columbia University Medical Center

description: C57BL/6 female mouse

data_processing:
We used 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 (Mouse: GRCm38) using kallisto (version 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: Mouse: GRCm38
Supplementary files format and content: xslx
Supplementary files format and content: xslx

extract_protocol:
Animals were euthanized by IP injection of Euthasol (diluted with  sterile saline solution) Blood samples were  collected immediately after euthanasia by cardiac puncture in a sterile  hood. Blood (400–500 ll) was added to PAXgenet RNA solution  (Becton, Dickinson and Co., Franklin Lakes, NJ) at a 1:5 ratio and  inverted _x0003_10 times to mix. Samples were stored at –80C for the  length of the study. RNA samples were prepared  using the PAXgene protocol, globin-depleted using the mouse  Ambiont GLOBINclear kit (Ambiont; Thermo Fisher Scientifice  Inc., Waltham, MA), and quantified using a NanoDrope One  spectrophotometer (Thermo Fisher Scientific). RNA quality was  determined using the Agilent 2100 Bioanalyzer (Santa Clara, CA), and  RIN values ranged from 8.0 to 9.5 across all samples.
RNA sequencing analysis for gene expression was performed according to standard RNA-seq pipeline at the Columbia University Medical Center Genome Center. We used the RIBOZERO workflow in which ribosomal depletion was performed to remove rRNAs from globin cleared total RNA. RINs of globin cleared RNA (catalog number AM1981 from Thermofisher) were in the acceptable range for 40-million reads RNAseq (75% of samples had RIN values >7.5).
After rRNA depletion, library construction was performed using Illumina TruSeq Stranded Total RNA kit.

value: Whole blood

value: sham irradiation

tag: dose (gy)

value: 0 Gy

tag: dose, mode

value: Acute

tag: dose rate

tag: time (day)


title: control, day 23 collection gDNA , rep3

description: Library name: day23_rep3


title: vemurafenib selection, day 23 collection gDNA, rep2

description: Library name: vf_rep2


title: vemurafenib selection, day 23 collection gDNA, rep1

description: Library name: vf_rep1


title: SS080

description: C57BL/6 female mouse


title: PF_longRNA-seq_8

description:
Library name: Sample 13
primary follicle stage oocyte (PF)


title: PF_longRNA-seq_7

description:
Library name: Sample 12
primary follicle stage oocyte (PF)


title: SS081

description: C57BL/6 female mouse


title: PF_longRNA-seq_5

description:
Library name: Sample 10
primary follicle stage oocyte (PF)


title: SS079

description: C57BL/6 female mouse


title: PF_longRNA-seq_4

description:
Library name: Sample 9
primary follicle stage oocyte (PF)


title: control, day 23 collection gDNA , rep1

description: Library name: day23_rep1


title: SS078

description: C57BL/6 female mouse


title: control, day 23 collection gDNA , rep2

description: Library name: day23_rep2


title: vemurafenib selection, day 0 collection gDNA, rep3

description: Library name: day0_rep3


title: PF_longRNA-seq_3

description:
Library name: Sample 8
primary follicle stage oocyte (PF)


title: PF_longRNA-seq_6

description:
Library name: Sample 11
primary follicle stage oocyte (PF)


title: PF_longRNA-seq_2

description:
Library name: Sample 7
primary follicle stage oocyte (PF)


title: PF_longRNA-seq_1

description:
Library name: Sample 6
primary follicle stage oocyte (PF)


title: PrF_longRNA-seq_3

description:
Library name: Sample 3
primordial follicle stage oocyte (PrF)


title: SS077

description: C57BL/6 female mouse


title: PrF_longRNA-seq_5

description:
Library name: Sample 5
primordial follicle stage oocyte (PrF)


title: SS076

description: C57BL/6 female mouse


title: PrF_longRNA-seq_4

description:
Library name: Sample 4
primordial follicle stage oocyte (PrF)


title: vemurafenib selection, day 0 collection gDNA, rep1

description: Library name: day0_rep1


title: PrF_longRNA-seq_1

description:
Library name: Sample 1
primordial follicle stage oocyte (PrF)


title: SS075

description: C57BL/6 female mouse


title: PrF_longRNA-seq_2

description:
Library name: Sample 2
primordial follicle stage oocyte (PrF)


title: vemurafenib selection, day 0 collection gDNA, rep2

description: Library name: day0_rep2


title: Control 6

city: Seoul

first: Soonhyo

last: Kwon

address: 892 Dongnam-ro, Gangdong-gu

country: South Korea

institute: Kyung Hee University Hospital at Gangdong

description: Library name: Lib_sample6_control

data_processing:
Paired-end sequencing reads were generated using the Illumina NovaSeq sequencing platform. Before analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim low-quality bases. The cleaned reads were aligned to the human reference genome (GRCh38) using HISAT v2.1.0 (Kim et al. 2015) and Bowtie2 implementations. Reference ge- nome sequences and gene annotation data were obtained from the NCBI genome assembly and RefSeq databases, respec- tively. The aligned data in the SAM file format were sorted and indexed using SAMtools v1.9. Post-alignment, transcripts were assembled and quantified using StringTie v2.1.3b (Pertea et al. 2016; Pertea et al. 2015).
Assembly: GRCh38
Supplementary files format and content: Gene-level and transcript-level quantifications were acquired as raw read counts and tran- scripts per million (TPM).

source_name: Skin

extract_protocol:
The total RNA concentration was measured using the Quant-IT RiboGreen assay (Invitrogen). The RNA integrity was assessed by determining the DV200 value, which indicates the percentage of RNA fragments longer than 200bp, using the TapeStation RNA Screentape System (Agilent).
For sequencing library construction, 100ng of total RNA was processed using an Agilent SureSelect RNA Direct kit according to the manufacturer's instructions.

value: Skin


title: SS074

description: C57BL/6 female mouse


title: NKR87_AGN_L962

city: Philadelphia

first: Brian

last: Capell

state: PA

address: 421 Curie Blvd

department: Dermatology

institute: University of Pennsylvania

description: Library name: Sample 14

data_processing:
75bp single end reads
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: DESeq2 output

source_name: Epidermis

extract_protocol:
Tissue was homogenized in Trizol followed by RNA processing/extraction using chlorofom and the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina

treatment_protocol: C57BL/6 mice from Jax Lab were shaved and dorsal back treated with DMSO, LSD1i, LSD1i + RARi, or RARi once daily for 15 days

value: Epidermis

value: RARi

tag: Sex

value: female


title: Control 5

description: Library name: Lib_sample5_control


title: SS073

description: C57BL/6 female mouse


title: NKR88_AGN_G921

description: Library name: Sample 15

value: male


title: Control 7

description: Library name: Lib_sample7_control


title: NKR86_AGN_L960

description: Library name: Sample 13


title: Control 4

description: Library name: Lib_sample4_control


title: NKR84_ORYAGN_G918

description: Library name: Sample 11

value: LSD1i + RARi


title: NKR83_ORYAGN_L943

description: Library name: Sample 10


title: Control 3

description: Library name: Lib_sample3_control


title: NKR85_ORYAGN_G919

description: Library name: Sample 12


title: NKR82_ORYAGN_L941

description: Library name: Sample 9


title: Control 2

description: Library name: Lib_sample2_control


title: NKR81_ORY_L956

description: Library name: Sample 8


title: NKR80_ORY_G908

description: Library name: Sample 7


title: Control 1

description: Library name: Lib_sample1_control


title: SS070

description: C57BL/6 female mouse


title: NKR78_ORY_G911

description: Library name: Sample 5


title: SS071

description: C57BL/6 female mouse


title: NKR79_ORY_L940

description: Library name: Sample 6


title: SS069

description: C57BL/6 female mouse


title: Lentigo 7

description: Library name: Lib_sample7_lentigo


title: SS067

description: C57BL/6 female mouse


title: NKR74_DMSO_G902

description: Library name: Sample 1

value: DMSO


title: SS072

description: C57BL/6 female mouse


title: NKR76_DMSO_G906

description: Library name: Sample 3


title: Lentigo 5

description: Library name: Lib_sample5_lentigo


title: IgG_ORY3_NKC082

description: Library name: Sample 12

data_processing:
37-37bp paired-end reads
Aligned using bowtie2 with following parameters: –local–very-sensitive-local–end-to-end–no-unal–no-mixed–no-discordant–phred33-I 10-X 700– dovetail
Converted to BAM, filtered using samtools and converted to BED files with bedtools
BED files were sorted, converted to bedGraph format and spike-in normalization applied with bedtools
Peak identification was performed with SICER2 and differential expression was performed using sicer_df function with resolution window size 200 bp (--w 200) and the minimum length of “gap” such that the neighboring window is an “island” sized to be 600 bp (--f 600). Significant differential H3K4me2 regions were defined as padj or FDR < 0.01.
Assembly: Mus musculus GRCm38/mm10 and SacCer3 (for spike-in)
Supplementary files format and content: Sicer_df output
Library strategy: CUT&Run

extract_protocol:
Single cell suspensions from generated from mouse epidermis using Liberase and 300K cells per sample were taken for Cut&Run using Cell Signaling Kit 86652S according to manufacturer's instructions
NEBNext Ultra Directional DNA library prep kit (NEBE7645S) for Illumina following CellSignaling Cut&Run library prep protocols

treatment_protocol: C57BL/6 mice from Jax Lab were shaved and dorsal back treated with H2O or LSD1i once daily for 48h

tag: number of_cells

tag: number of_mice_pooled

tag: antibody

value: IgG

tag: antibody catalog

value: CST 66362S, Lot 3


title: SS068

description: C57BL/6 female mouse


title: Lentigo 6

description: Library name: Lib_sample6_lentigo


title: NKR75_DMSO_G907

description: Library name: Sample 2


title: H3K4me2_ORY3_NKC076

description: Library name: Sample 9


title: SS065

description: C57BL/6 female mouse


title: IgG_ORY1_NKC080

description: Library name: Sample 10


title: SS064

description: C57BL/6 female mouse

value: 4.1 Gy delivered acutely

value: 0.73 Gy/min


title: SS066

description: C57BL/6 female mouse


title: H3K4me2_ORY1_NKC074

description: Library name: Sample 7


title: Lentigo 2

description: Library name: Lib_sample2_lentigo


title: Lentigo 3

description: Library name: Lib_sample3_lentigo


title: IgG_H2O2_NKC069

description: Library name: Sample 5


title: SS063

description: C57BL/6 female mouse


title: IgG_ORY2_NKC081

description: Library name: Sample 11


title: IgG_H2O1_NKC068

description: Library name: Sample 4


title: NKR77_DMSO_G910

description: Library name: Sample 4


title: Lentigo 1

description: Library name: Lib_sample1_lentigo


title: IgG_H2O3_NKC070

description: Library name: Sample 6


title: H3K4me2_H2O2_NKC063

description: Library name: Sample 2


title: H3K4me2_H2O3_NKC064

description: Library name: Sample 3


title: SS062

description: C57BL/6 female mouse


title: SS061

description: C57BL/6 female mouse


title: PLC cells, HNRNPA1_IP

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

description:
Library name: SAMPLE7
IgG.bam

data_processing:
For mecciRNAs, reads from the differentially expressed RNAs of HCC tissues were mapped to the hg38 genome using find_circ. For linear RNAs, reads from the differentially expressed RNAs after mecciRNR2 knockdown and from the RNAs enriched in the HNRNPA1 RIP experiment were mapped to the hg38 genome using HISAT2 (v2.2.1). We then carried out differential expression analysis using the R package edgeR. We considered transcripts with P ≤ 0.05 and |log2(foldchange) | ≥ 1 to be significant.
Assembly: hg38
Supplementary files format and content: Table files include counts value for each Sample.

growth_protocol: All fresh HCC tumor tissues were obtained at the operation time and post-surgery, the samples were the rapidly frozen in liquid nitrogen for storage. PLC cell lines were cultured under standard conditions in the DMEM medium supplemented with 10% FBS (CLARK, FB25015) and 1% penicillin/streptomycin (Beyotime, C0222) at 37 °C under 5% CO2.

extract_protocol:
Total RNA was extracted from the exosomes using TRIzol reagent (Invitrogen) following the manufacturer's protocol. RNA concentration and quality were assessed with a Nanodrop spectrophotometer and confirmed by gel electrophoresis.The RNA from anti-HNRNPA1 RIP was extracted with TRIzol reagent according to the protocol.
RNA-seq was conducted on an Illumina platform with 150-bp paired-end reads.For RIP-seq cDNA library preparation, purified RNAs were ligated to adapters, reverse transcribed, and PCR-amplified for approximately 25 cycles. The resulting libraries were then subjected to high-throughput sequencing using an Illumina Novoseq platform with a 150-nt run length.

treatment_protocol: For the HCC samples, liver cancer tissues and adjacent tissues were used. For the PLC RNA seq, the mecciRNR2 knockdown group and its control were used. For RIP seq, the RNA enriched by HNRNPA1 and the RNA enriched by the control IgG were used.

value: PLC

value: hepatoma carcinoma cell


title: PLC cells, IgG_IP

institute: University of Science and Technology of China

description:
Library name: SAMPLE8
anti-HNRNPA1.bam


title: NKR72_KO_L563M

description: Library name: Sample 14

treatment_protocol: Control (corn oil or Cre-ERT WT) or LSD1 Knockout (tamoxifen induced) mice were induced at 7wks of age and harvested 6 weeks post induction

value: K14-CreERT +; LSD1 fl/fl

value: Tamoxifen


title: NKR73_KO_L564M

description: Library name: Sample 15


title: NKR70_KO_L602F

description: Library name: Sample 12


title: H3K4me2_ORY2_NKC075

description: Library name: Sample 8


title: Lentigo 4

description: Library name: Lib_sample4_lentigo


title: H3K4me2_H2O1_NKC062

description: Library name: Sample 1


title: SS060

description: C57BL/6 female mouse

value: Whole blood


title: SS059

description: C57BL/6 female mouse

value: Acute


title: NKR69_KO_L600F

description: Library name: Sample 11


title: PLC cells, shmecciRNR2

description:
Library name: SAMPLE6
sh-meccirnr2


title: NKR71_KO_L562M

description: Library name: Sample 13


title: PLC cells, Control

description:
Library name: SAMPLE5
shCOO2

value: shNC


title: NKR68_KO_L549F

description: Library name: Sample 10

value: Epidermis


title: NKR67_Control_L565M

description: Library name: Sample 9

value: Corn Oil


title: HCC/pTumor/mitochondria/S4

description:
Library name: SAMPLE4
C4

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma

value: tissue


title: SS058

description: C57BL/6 female mouse

value: 2.8 Gy delivered acutely


title: SS057

description: C57BL/6 female mouse


title: HCC/Tumor/mitochondria/S3

description:
Library name: SAMPLE3
C3


title: NKR65_Control_L630F

description: Library name: Sample 7

value: K14-CreERT +; LSD1 +/fl

value: female


title: NKR63_Control_L628F

description: Library name: Sample 5

value: K14-CreERT -; LSD1 +/+


title: NKR66_Control_L567M

description: Library name: Sample 8

value: male


title: NKR64_Control_L629F

description: Library name: Sample 6


title: SS056

description: C57BL/6 female mouse

value: 0.73 Gy/min


title: SS053

description: C57BL/6 female mouse

value: 2 Gy delivered acutely

value: 2 Gy


title: NKR62_Control_L627F

description: Library name: Sample 4


title: NKR61_Control_L605F

description: Library name: Sample 3

value: K14-CreERT +; LSD1 fl/fl


title: HCC/Tumor/mitochondria/S1

description:
Library name: SAMPLE1
C1


title: HCC/pTumor/mitochondria/S2

description:
Library name: SAMPLE2
C2


title: NKR59_Control_L548F

description: Library name: Sample 1


title: EpiVaginal tissue, 15 nM DHT, D3

city: Boston

first: Robin

middle: R.

last: Ingalls

state: MA

address: 650 Albany St, EBRC 610

department: Infectious Disease

institute: Boston Medical Center

description: Library name: D3

data_processing:
After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered < 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group >/= 0.5.
Assembly: GRCh37
Supplementary files format and content: fastq.gz raw sequencing files

source_name: vaginal

extract_protocol:
Total RNA was extracted using the RNAqueous Micro Kit (Invitrogen).  Modifications to the manufacturer’s protocol for the MatTek tissues were as follows.  The microporous membrane from the cell culture inserts was cut away using sharp forceps.  It was added to lysis buffer and homogenized using a pellet pestle mixer tip.  RNA extraction was then performed according to the manufacturer’s instructions.  Total RNA samples are quantified using Nanodrop and qualified by agarose gel electrophoresis.
Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the
integrality of total RNA samples. 1 - 2 ug total RNA of each sample was taken for RNA-seq library preparation.
Briefly, mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Alternatively, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched mRNA
or rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library
Prep Kit (Roche). The library preparation procedure included:
1) Fragmentation of the RNA molecules;
2) Reverse transcription to synthesis first strand cDNA;
3) Second strand cDNA synthesis incorporating dUTP;
4) End-repair and A-tailing of the double stranded cDNA;
5) Illumina compatible adapter ligation;
6) PCR amplification and purification for the final RNA-seq library.
The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400-600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.

value: vaginal

value: epithelial

value: WT

value: 15 nM DHT

tag: batch


title: SS051

description: C57BL/6 female mouse

tag: cell line

value: Whole blood

value: Acute


title: NKC45_H3K4me3_KO3

description: Library name: Sample 14

extract_protocol:
Single cell suspensions from generated from mouse epidermis using Liberase and 200K cells per sample were taken for Cut&Run using Cell Signaling Kit 86652S according to manufacturer's instructions
NEBNext Ultra Directional DNA library prep kit (NEBE7645S) for Illumina following CellSignaling Cut&Run library prep protocols

treatment_protocol: Control (corn oil or Cre-ERT WT) or Lsd1 Knockout (tamoxifen induced) mice were induced at 7wks of age and harvested 6 weeks post induction. Note: multiple mice were pooled together to make a single sample (ie. WT1 contained dorsal epidermis from 2 mice)

tag: tissue

value: Epidermis

value: Tamoxifen

value: CST 9751T, Lot 16


title: NKR60_Control_L604F

description: Library name: Sample 2

tag: genotype

value: Corn Oil


title: SS052

description: C57BL/6 female mouse

tag: cell type


title: EpiVaginal tissue, 15 nM DHT, D1

description: Library name: D1

tag: treatment


title: NKC46_IgG_KO3

description: Library name: Sample 15

value: IgG

value: CST 66362S, Lot 3


title: EpiVaginal tissue, 150 nM testosterone, T3

description: Library name: T3

value: 150 nM testosterone


title: EpiVaginal tissue, 150 nM testosterone, T2

description: Library name: T2


title: SS050

description: C57BL/6 female mouse

value: 0.73 Gy/min


title: NKC38_H3K4me2_KO1

description: Library name: Sample 7


title: NKC44_H3K4me2_KO3

description: Library name: Sample 13


title: SS047

description: C57BL/6 female mouse

value: sham irradiation

value: 0 Gy

value: VarDR


title: EpiVaginal tissue, 15 nM DHT, D2

description: Library name: D2

value: vaginal


title: NKC42_H3K4me3_KO2

description: Library name: Sample 11

value: K14-CreERT +; LSD1 fl/fl


title: EpiVaginal tissue, 150 nM testosterone, T1

description: Library name: T1

value: epithelial

value: WT


title: NKC37_IgG_WT2

description: Library name: Sample 6


title: SS049

description: C57BL/6 female mouse

value: Whole blood

value: 2 Gy delivered acutely

value: 2 Gy


title: EpiVaginal tissue, 10 nM estradiol, E3

description: Library name: E3

value: 10 nM estradiol


title: NKC41_H3K4me2_KO2

description: Library name: Sample 10

value: Epidermis

value: Tamoxifen


title: NKC40_IgG_KO1

description: Library name: Sample 9

value: IgG


title: NKC43_IgG_KO2

description: Library name: Sample 12

value: CST 66362S, Lot 3


title: SS048

description: C57BL/6 female mouse

value: Acute


title: NKC39_H3K4me3_KO1

description: Library name: Sample 8

value: CST 9751T, Lot 16


title: TR, rep3

description: Library name: TR_rep3

data_processing:
Raw reads were processed using the TOPMed RNA-seq pipeline. Reads were aligned to the human reference genome, and gene-level counts and TPM values were generated. Differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: Gene-level expression matrix from bulk RNA-seq data. Rows represent genes and columns represent biological replicates. Values are TPM-normalized expression levels.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s protocol. RNA quality and concentration were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using poly(A) selection and strand-specific library construction according to standard Illumina protocols.


title: NKC36_H3K4me3_WT2

description: Library name: Sample 5

value: Corn Oil


title: SS044

description: C57BL/6 female mouse

value: sham irradiation

value: 0 Gy


title: SS046

description: C57BL/6 female mouse

value: VarDR


title: NKC35_H3K4me2_WT2

description: Library name: Sample 4

value: K14-CreERT +; LSD1 fl/fl


title: NKC33_H3K4me3_WT1

description: Library name: Sample 2


title: NKC34_IgG_WT1

description: Library name: Sample 3


title: VR, RNA-seq, rep2

description: Library name: VR_RNA_rep2


title: EpiVaginal tissue, 10 nM estradiol, E2

description: Library name: E2

value: vaginal

value: epithelial


title: VR, RNA-seq, rep1

description: Library name: VR_RNA_rep1


title: EpiVaginal tissue, 10 nM estradiol, E1

description: Library name: E1

value: WT


title: SS045

description: C57BL/6 female mouse

value: Whole blood


title: NKC32_H3K4me2_WT1

description: Library name: Sample 1


title: TR, rep2

description: Library name: TR_rep2


title: SS043

description: C57BL/6 female mouse


title: SS039

description: C57BL/6 female mouse


title: 10687-JF-9

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 10687-JF-9

data_processing:
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Assembly: hg38
Supplementary files format and content: cellranger output format

source_name: human skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin

value: mixed (single cell)

tag: disease

value: Healthy control(scalp)


title: TR, rep1

description: Library name: TR_rep1


title: T cell, miR-18a KO, replicate 1

description: Library name: TcellKO_rep1


title: SS042

description: C57BL/6 female mouse


title: miR-18a KO, Vemurafenib, replicate 2

description: Library name: VEMKO_rep2


title: EpiVaginal tissue, no hormone, N3

description: Library name: N3

value: none (control)


title: EpiVaginal tissue, no hormone, N2

description: Library name: N2


title: T cell, replicate 2

description: Library name: Tcell_rep2


title: SS041

description: C57BL/6 female mouse


title: SS040

description: C57BL/6 female mouse


title: T cell, replicate 1

description: Library name: Tcell_rep1


title: EpiVaginal tissue, no hormone, N1

description: Library name: N1


title: miR-18a KO, replicate 2

description: Library name: KO_rep2


title: 10687-JF-8

description: Library name: 10687-JF-8


title: Vemurafenib, replicate 2

description: Library name: VEM_rep2


title: 10687-JF-7

description: Library name: 10687-JF-7


title: T cell, miR-18a KO, replicate 2

description: Library name: TcellKO_rep2


title: SS038

description: C57BL/6 female mouse


title: miR-18a KO, Vemurafenib, replicate 1

description: Library name: VEMKO_rep1


title: miR-18a KO, replicate 1

description: Library name: KO_rep1


title: SS037

description: C57BL/6 female mouse


title: HCT116 WT H3K9me3 [CUT&Tag]

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

address: 1300 Jefferson Park Avenue

department: Genome Sciences

institute: University of Virginia

description: Library name: Sample1

data_processing:
Raw sequencing reads were aligned to the GRCh38 (hg38) reference genome with bowtie2 (v2.2.9) (-X 2000 for paired-end data). Low-quality reads (MAPQ < 30) were discarded. For paired-end sequencing data, reads with two ends aligned to different chromosomes (chimeric reads) were discarded. For paired-end data, reads with identical 5’ end positions for both ends were regarded as redundant reads and discarded. Reads mapped to mitochondrial DNA (mtDNA reads) were discarded. To generate the genome-wide signal track for downstream analysis, we extended reads from their 5’end to 146 base pair (bp), piled them up and normalized the piled-up signal by total reads count in the sample (i.e., RPM).
Assembly: hg38
Supplementary files format and content: BigWig file for sequencing depth normalzed signals .
Library strategy: CUT&Tag

growth_protocol: HCT116 p53-/- cell (referred to as wild-type, RRID: CVCL_S744) was a generous gift from Fred Bunz (Johns Hopkins) (Bunz et al., 1998). HCT116 cell lines were maintained in McCoy’s 5A-modified medium (Corning, no. 10-050-CV) supplemented with 10% fetal bovine serum.

extract_protocol: CUT&Tag Assay Kit  (Active Motif, no. 2200) was used to perform CUT&Tag according to the manufacturer's instructions. Anti-H3K9me3 (Diagenode, C15410193) was used.

value: wild-type


title: SS036

description: C57BL/6 female mouse


title: control, replicate 2

description: Library name: WT_rep2


title: control, replicate 1

description: Library name: WT_rep1


title: Vemurafenib, replicate 1

description: Library name: VEM_rep1


title: 10687-JF-6

description: Library name: 10687-JF-6


title: 10687-JF-5

description: Library name: 10687-JF-5

value: Healthy control(skin)


title: 10687-JF-4

description: Library name: 10687-JF-4


title: ATOH8 knockdown rep4

city: Maebashi

first: Hiroko

last: Hamatani

state: Gunma

department: Nephrology and Rheumatology

institute: Gunma University

description: Library name: ATOH8sh_rep4

data_processing:
Quality control was performed using FastQC. Reads were aligned to the human reference genome (hg19) using STAR. Gene expression levels were quantified using featureCounts, and differential expression analysis was performed with DESeq2.
Assembly: hg19
Supplementary files format and content: Processed data are provided as a tab-delimited matrix containing raw counts for all genes and samples. Column headers correspond to sample library names.

source_name: ATOH8 knockdown in human podocytes

growth_protocol: Human podocytes (AB8/13) were cultured at 33°C for proliferation and shifted to 37°C for 5 days to induce differentiation.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer, and samples with RIN > 7.0 were used for library preparation.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Poly(A) mRNA was enriched, fragmented, and reverse-transcribed into cDNA, followed by adaptor ligation and PCR amplification.

treatment_protocol: ATOH8 knockdown was achieved using shRNA transfection with Lipofectamine 3000. Control samples were transfected with non-targeting shRNA.

value: Kidney tissue

value: Podocytes

value: ATOH8 knockdown


title: SS034

description: C57BL/6 female mouse

value: 9.7 Gy delivered at variable dose rate in 30 days


title: SS035

description: C57BL/6 female mouse


title: ATOH8 knockdown rep3

description: Library name: ATOH8sh_rep3


title: 10687-JF-2

description: Library name: 10687-JF-2


title: ATOH8 knockdown rep2

description: Library name: ATOH8sh_rep2


title: SS032

description: C57BL/6 female mouse


title: 10687-JF-3

description: Library name: 10687-JF-3


title: ATOH8 knockdown rep1

description: Library name: ATOH8sh_rep1


title: SS033

description: C57BL/6 female mouse


title: 10687-JF-1

description: Library name: 10687-JF-1


title: Control replicate 2

description: Library name: control_rep2

source_name: Control condition in human podocytes

value: Non-targeting shRNA control


title: EXP713RNA116

city: TAmpa

first: Yonghong

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

description: Library name: EXP713RNA116

data_processing:
Sequence reads were aligned to the human reference genome (hs37d5) in a splice-aware fashion using Tophat261, allowing for accurate alignments of sequences across introns. Aligned sequences were assigned to exons using the HTseq package against RefSeq gene models to generate initial counts by region62.
Paired-end RNA-seq reads were aligned to the GRCh38 human reference genome using STAR v2.5.3a following adaptor trimming by cutadapt v1.8.1.
Gene level expression was quantified using RSEM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files of read count

source_name: patient tissue

extract_protocol:
Qiagen’s AllPrep DNA/RNA Mini kit was used for the simultaneous purification of genomic DNA and total RNA from the homogenized tumor tissue aliquot
RNAseq was performed using the NuGen Ovation Encore Complete RNAseq kit with 100ng of Dnase-treated total RNA.

value: lung tumor

value: squamous cell lung carcinoma


title: 10687-JF-15

description: Library name: 10687-JF-15

value: Healthy control(mucosa)


title: SS031

description: C57BL/6 female mouse

value: VarDR


title: EXP713RNA114

description: Library name: EXP713RNA114


title: SS030

description: C57BL/6 female mouse


title: EXP713RNA115

description: Library name: EXP713RNA115


title: Control replicate 4

description: Library name: control_rep4


title: EXP713RNA113

description: Library name: EXP713RNA113


title: Control replicate 3

description: Library name: control_rep3


title: Control replicate 1

description: Library name: control_rep1


title: EXP713RNA111

description: Library name: EXP713RNA111


title: EXP713RNA112

description: Library name: EXP713RNA112


title: SS029

description: C57BL/6 female mouse

value: 4.1 Gy delivered at variable dose rate in 5 days

value: 0.62 Gy/day


title: EXP713RNA110

description: Library name: EXP713RNA110


title: 10687-JF-13

description: Library name: 10687-JF-13

value: human skin


title: 10687-JF-14

description: Library name: 10687-JF-14

value: mixed (single cell)


title: 10687-JF-11

description: Library name: 10687-JF-11


title: EXP713RNA109

description: Library name: EXP713RNA109


title: SS027

description: C57BL/6 female mouse

value: Whole blood


title: SS028

description: C57BL/6 female mouse


title: SS026

description: C57BL/6 female mouse


title: 10687-JF-10

description: Library name: 10687-JF-10

value: Healthy control(scalp)


title: EXP713RNA107

description: Library name: EXP713RNA107


title: EXP713RNA108

description: Library name: EXP713RNA108


title: EXP713RNA106

description: Library name: EXP713RNA106


title: EXP713RNA103

description: Library name: EXP713RNA103


title: EXP713RNA105

description: Library name: EXP713RNA105


title: 10547-JF-7

description: Library name: 10547-JF-7

value: Lichen planopilaris


title: SS025

description: C57BL/6 female mouse


title: EXP713RNA104

description: Library name: EXP713RNA104


title: 10547-JF-9

description: Library name: 10547-JF-9


title: EXP713RNA102

description: Library name: EXP713RNA102


title: SS024

description: C57BL/6 female mouse


title: EXP713RNA100

description: Library name: EXP713RNA100


title: SS023

description: C57BL/6 female mouse

value: sham irradiation

value: 0 Gy


title: 10547-JF-5

description: Library name: 10547-JF-5

value: Cutaneous lichen planus


title: 10547-JF-6

description: Library name: 10547-JF-6


title: EXP713RNA101

description: Library name: EXP713RNA101


title: SS022

description: C57BL/6 female mouse


title: EXP713RNA098

description: Library name: EXP713RNA098


title: EXP713RNA099

description: Library name: EXP713RNA099


title: EXP713RNA096

description: Library name: EXP713RNA096


title: EXP713RNA095

description: Library name: EXP713RNA095


title: 10547-JF-2

description: Library name: 10547-JF-2


title: EXP713RNA094

description: Library name: EXP713RNA094


title: SS021

description: C57BL/6 female mouse


title: EXP713RNA093

description: Library name: EXP713RNA093


title: EXP713RNA092

description: Library name: EXP713RNA092


title: SS019

description: C57BL/6 female mouse


title: 10547-JF-1

description: Library name: 10547-JF-1


title: 10547-JF-16

description: Library name: 10547-JF-16


title: EXP713RNA091

description: Library name: EXP713RNA091


title: 10547-JF-3

description: Library name: 10547-JF-3


title: EXP713RNA097

description: Library name: EXP713RNA097


title: EXP713RNA090

description: Library name: EXP713RNA090


title: SS020

description: C57BL/6 female mouse


title: EXP713RNA088

description: Library name: EXP713RNA088


title: EXP713RNA089

description: Library name: EXP713RNA089


title: SS017

description: C57BL/6 female mouse


title: EXP713RNA087

description: Library name: EXP713RNA087


title: EXP713RNA086

description: Library name: EXP713RNA086


title: 10547-JF-14

description: Library name: 10547-JF-14


title: SS016

description: C57BL/6 female mouse


title: EXP713RNA084

description: Library name: EXP713RNA084


title: SS015

description: C57BL/6 female mouse


title: SS018

description: C57BL/6 female mouse


title: EXP713RNA085

description: Library name: EXP713RNA085


title: 10547-JF-13

description: Library name: 10547-JF-13


title: 10547-JF-12

description: Library name: 10547-JF-12


title: 10547-JF-15

description: Library name: 10547-JF-15


title: 10547-JF-11

description: Library name: 10547-JF-11


title: EXP713RNA083

description: Library name: EXP713RNA083


title: EXP713RNA082

description: Library name: EXP713RNA082


title: EXP713RNA081

description: Library name: EXP713RNA081


title: EXP713RNA079

description: Library name: EXP713RNA079


title: EXP713RNA080

description: Library name: EXP713RNA080


title: SS012

description: C57BL/6 female mouse


title: EXP713RNA078

description: Library name: EXP713RNA078


title: 10546-JF-9

description: Library name: 10546-JF-9

value: Mucosal lichen planus


title: SS011

description: C57BL/6 female mouse

value: 2.8 Gy delivered at variable dose rate in 3 days

value: 0.77 Gy/day


title: EXP713RNA077

description: Library name: EXP713RNA077

value: lung tumor


title: SS013

description: C57BL/6 female mouse


title: EXP713RNA075

description: Library name: EXP713RNA075

value: squamous cell lung carcinoma


title: SS014

description: C57BL/6 female mouse


title: 10546-JF-6

description: Library name: 10546-JF-6


title: SS009

description: C57BL/6 female mouse


title: SS010

description: C57BL/6 female mouse


title: EXP713RNA073

description: Library name: EXP713RNA073


title: EXP713RNA072

description: Library name: EXP713RNA072


title: 10547-JF-10

description: Library name: 10547-JF-10


title: EXP713RNA070

description: Library name: EXP713RNA070


title: SS008

description: C57BL/6 female mouse


title: 10546-JF-5

description: Library name: 10546-JF-5


title: 10546-JF-4

description: Library name: 10546-JF-4


title: EXP713RNA069

description: Library name: EXP713RNA069


title: EXP713RNA076

description: Library name: EXP713RNA076


title: EXP713RNA071

description: Library name: EXP713RNA071


title: EXP713RNA074

description: Library name: EXP713RNA074


title: 10546-JF-7

description: Library name: 10546-JF-7


title: SS006

description: C57BL/6 female mouse


title: EXP713RNA066

description: Library name: EXP713RNA066


title: EXP713RNA065

description: Library name: EXP713RNA065


title: 10546-JF-3

description: Library name: 10546-JF-3


title: SS005

description: C57BL/6 female mouse

value: 2 Gy delivered at variable dose rate in 2 days

value: 2 Gy

value: 1 Gy/day


title: SS007

description: C57BL/6 female mouse

value: VarDR


title: EXP713RNA067

description: Library name: EXP713RNA067


title: 10546-JF-1

description: Library name: 10546-JF-1

value: human skin


title: EXP713RNA061

description: Library name: EXP713RNA061


title: 10546-JF-2

description: Library name: 10546-JF-2

value: mixed (single cell)


title: 10546-JF-16

description: Library name: 10546-JF-16


title: EXP713RNA064

description: Library name: EXP713RNA064


title: SS004

description: C57BL/6 female mouse

value: Whole blood


title: EXP713RNA068

description: Library name: EXP713RNA068


title: SS002

description: C57BL/6 female mouse


title: EXP713RNA063

description: Library name: EXP713RNA063


title: EXP713RNA059

description: Library name: EXP713RNA059


title: EXP713RNA058

description: Library name: EXP713RNA058


title: EXP713RNA057

description: Library name: EXP713RNA057


title: SS001

description: C57BL/6 female mouse


title: 10546-JF-14

description: Library name: 10546-JF-14


title: 10546-JF-15

description: Library name: 10546-JF-15

value: MLP and CLP


title: EXP713RNA062

description: Library name: EXP713RNA062


title: EXP713RNA060

description: Library name: EXP713RNA060


title: SS003

description: C57BL/6 female mouse


title: 10546-JF-13

description: Library name: 10546-JF-13


title: EXP713RNA054

description: Library name: EXP713RNA054


title: cardiac mitochondria, control, 1

description: mitochondrial microRNA

data_processing:
Majorbio self-developed software and Fastx-Toolkit was first filtered to obtain high quality sequencing data (clean data) including remove reads of too short length (<18nt) or too long length (>32nt).
Clean data (reads) are compared with the reference genome (GRCm39) to obtain mapped data (reads) for subsequent analysis.
Mapped reads were compared with miRbase and Rfam databases to obtain known miRNA and ncRNA annotation information, respectively. Novel miRNAs were predicted using miRDeep2 (animal) or miReap (plant) software for reads for which no annotation information was obtained.
The expression of known miRNAs and new miRNAs in each sample were counted and homogenized the expression using TPM.
Assembly: GRCm39
Supplementary files format and content: Excel files include TPM values for each sample.

extract_protocol:
Total RNA was extracted from cells or frozen tissues using RNAiso Plus reagent (Takara Bio, Japan) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was ligated with the 3' end junction and the 5' end junction, respectively. First strand of cDNA synthesis was performed using random primer, followed by library enrichment (11-12 cycles of PCR) and library purification (6% Novex TBE PAGE gel, 1.0 mm, 10 well). Quantification was performed with TBS380 (Picogreen). Then samples were mixed on the machine in proportion to the quantitative data, followed by bridge PCR amplification on cBot to generate clusters.

value: Heart

tag: organelle

value: Mitochondria

value: Control


title: cardiac mitochondria, STZ, 1

description: mitochondrial microRNA

value: STZ


title: EXP713RNA056

description: Library name: EXP713RNA056


title: EXP713RNA052

description: Library name: EXP713RNA052


title: EXP713RNA051

description: Library name: EXP713RNA051


title: EXP713RNA050

description: Library name: EXP713RNA050


title: Ahr-Liver-12

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
FastQC (v0.11.8) was used to inspect the quality of the raw sequences.
Adapters were trimmed by TrimGalore (v0.6.5).
All sequencing data were aligned using STAR (v2.7.8) to the reference mouse genome sequence GRCm38 primary assembly version and the GENCODE M25 annotation GTF file.
Read counts were quantifiedn using Rsubread (v2.2.6).
Read counts were normalized using variance-stabilizing transformation provided by R package DESeq2 (v1.28.1).
Genome_build: GRCm38 GENCODE M25 (29.04.20)
Supplementary_files_format_and_content: Normalized abundances by DESeq2 variable-stabilizing transformation (vst) and raw read counts

source_name: Apoe-/-AhR-/- Female

extract_protocol:
RNA extraction was performed using Micro Rneasy kit (Qiagen). Average RIN value was 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed a HFD for 12 weeks. After sacrifice, the mice were flushed with PBS and livers were extracted.

tag: age

value: 12 weeks HFD

value: Female

value: Apoe-/-AhR-/-

value: Liver


title: EXP713RNA055

description: Library name: EXP713RNA055

value: lung tumor

value: squamous cell lung carcinoma


title: EXP713RNA053

description: Library name: EXP713RNA053


title: EXP713RNA049

description: Library name: EXP713RNA049


title: 10546-JF-11

description: Library name: 10546-JF-11

value: Cutaneous lichen planus


title: EXP713RNA048

description: Library name: EXP713RNA048


title: U2OS Parental Cell EPZ-719 9days POINTseq rep2

city: Fukuoka

first: Takayuki

last: Nojima

state: Japan

address: Maidashi

department: Medical Sciences

institute: Kyushu University

description: Library name: Sample4

library_source: other

data_processing:
The raw reads were trimmed using TrimGalore (v0.6.6)
Trimmed reads were mapped to hg38 using STAR (v2.7.6a)
Aligned reads were assigned to forward and reverse strand using SAMtools (v1.10)
Coverage files were created using bedtools (v2.31.1) genomecov tool (Quinlan & Hall, 2010). The coverage files were normalized in R to reads per million (RPMs) and DESeq2 (Love et al, 2014) sizing factors based on ReadsPerGene.out.tab STAR output file. Bigwigs were then generated using bedGraphToBigWig tool (Perez et al, 2025)
Assembly: hg38
Supplementary files format and content: stranded bigwig files include read coverage for each sample

molecule: other

growth_protocol: U2OS Parental Cellswere maintained in DMEM and DMSO/EPZ-719 supplemeted with 10% FBS and PS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Pol II boud nascent RNA was extract by POINTseq protocol.
Followed the protocol of NEBNext Ultra II Directional RNA library prep kit

value: Osteosarcoma

value: WT


title: Ahr-Liver-11


title: EXP713RNA047

description: Library name: EXP713RNA047


title: Ahr-Liver-10


title: U2OS Parental Cell EPZ-719 9days POINTseq rep1

description: Library name: Sample3


title: 10546-JF-10

description: Library name: 10546-JF-10

value: human skin


title: Ahr-Liver-9

source_name: Apoe-/-AhR-/- Male

value: Male


title: U2OS Parental Cell DMSO 9days POINTseq rep1

description: Library name: Sample1


title: EXP713RNA045

description: Library name: EXP713RNA045


title: EXP713RNA042

description: Library name: EXP713RNA042


title: Ahr-Liver-8


title: EXP713RNA043

description: Library name: EXP713RNA043


title: EXP713RNA041

description: Library name: EXP713RNA041


title: EXP713RNA046

description: Library name: EXP713RNA046


title: Healthy Donor 3 - ILC2 TrkA-

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
Library name: hILC2_6_S47
TRKAneg_3

data_processing:
Raw reads were pre-processed for quality and adapter sequences were trimmed using fastp (v. 0.23.4). Reads were aligned to the human reference genome using HISAT2 (v. 2.1.0). The number of reads per gene per sample were summarized using StringTie (v. 2.2.1). All these steps were performed using the Subio Platform 64 (v. 1.24.5859).
The raw count matrix was imported into iDEP 2.01 online platform for normalization and differential gene expression analysis.
Assembly: Homo sapiens GRCh38 Ensembl release 110
Supplementary files format and content: Tab-separated file containing raw counts per gene (in rows) per sample (in columns). The first column ("gene_id") contains the Ensembl ID of each gene. The second column ("gene_name") contains the corresponding gene symbol. Genes that don't have a unique gene symbol have "NA" in the gene_name column. The next six columns contain the raw counts per sample.

source_name: Innate lymphoid cells type 2 sorted from PBMCs

growth_protocol: Venous blood was collected from healthy donors (HDs) at the local blood transfusion center. Peripheral blood mononuclear cells (PBMCs) were freshly isolated by Lymphoprep (Promega) centrifugation (1800 rpm, 20 minutes, without break, room temperature). Red blood cell lysis was performed using red blood lysis buffer (Qiagen) and platelets were removed by centrifugation (1000 rpm, 10 minutes without break, room temperature).

extract_protocol:
Total RNA was extracted using the RNEasy Micro Plus Kit (Qiagen) according to the manufacturer’s instructions. Cells were lysed in RLT Plus buffer containing b-mercaptoethanol and genomic DNA was removed using a gDNA Eliminator spin column. RNA was purified via silica membrane spin columns with DNase digestion, washed, and eluted in RNase-free water. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies). The SMART-Seq mRNA kit from Takara was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 2 ng of total RNA as input.
200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.

treatment_protocol: ILCs were isolated from fresh PBMCs using a FACS Aria II (BD Biosciences). Total ILCs were identified as Live CD45+Lineage-CD127+ lymphocytes, after doublets exclusion. Within total ILCs, ILC2s were identified as CRTH2+c-Kit+/-

value: Live CD45+ Lineage- CD127+ CRTH2+ c-Kit+/- lymphocytes

value: ILC2 TrkA-

value: healthy

value: healthy donor 3


title: U2OS Parental Cell DMSO 9days POINTseq rep2

description: Library name: Sample2


title: EXP713RNA039

description: Library name: EXP713RNA039


title: Healthy Donor 3 - ILC2 TrkA+

description:
Library name: hILC2_5_S46
TRKApos_3

value: Innate lymphoid cells type 2 sorted from PBMCs

value: ILC2 TrkA+


title: Ahr-Liver-7

value: 12 weeks HFD


title: EXP713RNA040

description: Library name: EXP713RNA040


title: EXP713RNA038

description: Library name: EXP713RNA038


title: Healthy Donor 2 - ILC2 TrkA-

description:
Library name: hILC2_4_S45
TRKAneg_2

value: healthy donor 2


title: EXP713RNA044

description: Library name: EXP713RNA044


title: EXP713RNA036

description: Library name: EXP713RNA036


title: Ahr-Liver-6

source_name: Apoe-/- control - Female

value: Female

value: Apoe-/-


title: Healthy Donor 2 - ILC2 TrkA+

description:
Library name: hILC2_3_S44
TRKApos_2


title: EXP713RNA037

description: Library name: EXP713RNA037

value: lung tumor


title: Healthy Donor 1 - ILC2 TrkA-

description:
Library name: hILC2_2_S43
TRKAneg_1

value: healthy donor 1


title: EXP713RNA035

description: Library name: EXP713RNA035

value: squamous cell lung carcinoma


title: Ahr-Liver-5

value: Liver


title: Ahr-Liver-4


title: Healthy Donor 1 - ILC2 TrkA+

description:
Library name: hILC2_1_S42
TRKApos_1


title: Ahr-Liver-3

source_name: Apoe-/- control - Male


title: EXP713RNA032

description: Library name: EXP713RNA032


title: EXP713RNA033

description: Library name: EXP713RNA033


title: EXP713RNA029

description: Library name: EXP713RNA029


title: Ahr-Liver-1


title: EXP713RNA031

description: Library name: EXP713RNA031


title: U2OS SETD2 KO Cell POINT5 rep2

description: Library name: Sample4

data_processing:
The raw reads were trimmed using TrimGalore (v0.6.6)
Trimmed reads were mapped to hg38 using STAR (v2.7.6a)
Aligned reads were assigned to forward and reverse strand using SAMtools (v1.10)
The python script developed by Sousa-Luís et al, Mol Cell, 2021 was used to extract the last nucleotide on 5’ end of newly transcribed RNA
Coverage files were created using bedtools (v2.31.1) genomecov tool. The coverage files were normalized in R to reads per million (RPMs) and DESeq2 sizing factors based on ReadsPerGene.out.tab STAR output file. Bigwigs were then generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: stranded bigwig files include read coverage for each sample

growth_protocol: U2OS Parental Cells and U2OS SETD2 KO Cells were maintained in DMEM supplemeted with 10% FBS and PS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Pol II boud nascent RNA was extract by POINTseq protocol. Then nascent RNA was treated with Terminator 5’-Phosphate-Dependent Exonuclease using buffer A (BIOSEARCH TECH, #TER51020)
Followed the protocol of the SMARTer Stranded RNA-seq kit

value: Osteosarcoma

value: SETD2 CRISPR  KO


title: Ahr-Liver-2

value: Male


title: EXP713RNA034

description: Library name: EXP713RNA034


title: U2OS SETD2 KO Cell POINT5 rep1

description: Library name: Sample3


title: EXP713RNA026

description: Library name: EXP713RNA026


title: EXP713RNA025

description: Library name: EXP713RNA025


title: CM4

city: Wilmington

first: Uciel

last: Chorostecki

state: Delaware

address: 251 Little Falls Drive

institute: Kresko RNA Tech

description: Library name: Sample 7

data_processing:
Adapter sequences were trimmed with cutadapt; reads were quality-filtered with FASTQC; alignment was performed using bowtie2 against curated sRNA references (tRNA, yRNA, rRNA, miRNA). Unknown reads were aligned to GRCh38 or Bos taurus genome with HISAT2.
Assembly: GRCh38 (human) and Bos taurus UMD3.1 assemblies.
Supplementary files format and content: All results described in the manuscript were derived from raw sequencing data.

organism: Bos taurus

source_name: Bovine skim milk sample collected at a processing facility

extract_protocol:
Skim milk was centrifuged and filtered to remove cells and fat. Total RNA was extracted from the cell-free supernatant using TRIzol reagent following the manufacturer’s protocol
Small RNA libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit, following the manufacturer’s instructions.

value: milk


title: EXP713RNA027

description: Library name: EXP713RNA027


title: EXP713RNA028

description: Library name: EXP713RNA028


title: U2OS Parental Cell POINT5 rep2

description: Library name: Sample2

value: WT


title: EXP713RNA024

description: Library name: EXP713RNA024


title: EXP713RNA030

description: Library name: EXP713RNA030


title: CM2

description: Library name: Sample 5

source_name: Bovine Cow skim milk pool


title: EXP713RNA023

description: Library name: EXP713RNA023


title: U2OS Parental Cell POINT5 rep1

description: Library name: Sample1


title: EXP713RNA022

description: Library name: EXP713RNA022


title: EXP713RNA019

description: Library name: EXP713RNA019


title: EXP713RNA021

description: Library name: EXP713RNA021


title: U2OS SETD2 KO Cell T4PmNETseq rep1

description: Library name: Sample3

data_processing:
Raw reads were trimmed using TrimGalore (v0.6.6) in pair-end.
Trimmed reads were mapped to hg38 using STAR (v2.7.6a) with an output of one SAM line for each mapped read, including multimappers (--outSAMmultNmax 1).
Aligned reads were assigned to forward and reverse strand using SAMtools (v1.10).
The custom R script was used to extract the last nucleotide on 3’ end of newly transcribed RNA and the coverage files were normalized to reads per million (RPMs) and DESeq2 sizing factors based on ReadsPerGene.out.tab STAR output file. Bigwigs were then generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: stranded bigwig files include read coverage for each sample

extract_protocol:
Pol II boud nascent RNA was extract by mNETseq protocol with T4P Pol II antibodies.
Following the protocol of NEBNext Small RNA Library Prep Set for Illumina (NEB, E7330L)


title: U2OS SETD2 KO Cell T4PmNETseq rep2

description: Library name: Sample4


title: CM3

description: Library name: Sample 6

source_name: Bovine skim milk sample from Jersey cows, collected at farm


title: U2OS Parental Cell T4PmNETseq rep2

description: Library name: Sample2


title: EXP713RNA020

description: Library name: EXP713RNA020


title: EXP713RNA017

description: Library name: EXP713RNA017


title: CM1

description: Library name: Sample 4

source_name: Bovine skim milk sample


title: Fw12_Day3

city: Chicago

first: Joao

last: Barroso-Batista

state: IL

address: The University of Chicago, KCBD room 9220E, 900 E 57th Street

institute: The University of Chicago

description: Library name: SPF5.RFw12.Day3

data_processing:
reads were trimmed with trimmomatic to remove adapter sequence and trailing bases with a quality score less than 20
trimmed reads were mapped to the rhesus macaque genome (RheMac8) using the STAR v2.7.10ac two-pass method
read counts were generated for each gene using HTCseq v2.0 based on overlap of any part of a read with an annotated gene exon
Assembly: RheMac8
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Macaca mulatta

source_name: blood

extract_protocol:
RNA was extracted using miRNAeasy kit (Qiagen). 300 ng of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit (Illumina) according to the manufacturer’s protocol

value: blood

value: PBMCs

value: Influenza vaccination


title: EXP713RNA018

description: Library name: EXP713RNA018


title: U2OS Parental Cell T4PmNETseq rep1

description: Library name: Sample1


title: Fw12_Day1

description: Library name: SPF5.RFw12.Day1


title: EXP713RNA015

description: Library name: EXP713RNA015


title: Fw12_Day7

description: Library name: SPF5.RFw12.Day7


title: Fw12_Day0

description: Library name: SPF5.RFw12.Day0


title: EXP713RNA013

description: Library name: EXP713RNA013


title: EXP713RNA012

description: Library name: EXP713RNA012


title: EXP713RNA014

description: Library name: EXP713RNA014


title: EXP713RNA016

description: Library name: EXP713RNA016


title: EXP713RNA010

description: Library name: EXP713RNA010


title: Et12_Day7

description: Library name: SPF5.REt12.Day7


title: U2OS SETD2 KO Cell POINTseq rep3

description: Library name: Sample6


title: U2OS SETD2 KO Cell POINTseq rep1

description: Library name: Sample4


title: EXP713RNA008

description: Library name: EXP713RNA008


title: Et12_Day3

description: Library name: SPF5.REt12.Day3


title: EXP713RNA007

description: Library name: EXP713RNA007


title: U2OS SETD2 KO Cell POINTseq rep2

description: Library name: Sample5


title: EXP713RNA006

description: Library name: EXP713RNA006


title: EXP713RNA009

description: Library name: EXP713RNA009


title: U2OS Parental Cell POINTseq rep2

description: Library name: Sample2


title: EXP713RNA011

description: Library name: EXP713RNA011


title: U2OS Parental Cell POINTseq rep3

description: Library name: Sample3


title: EXP713RNA004

description: Library name: EXP713RNA004


title: Et12_Day1

description: Library name: SPF5.REt12.Day1


title: EXP713RNA005

description: Library name: EXP713RNA005


title: U2OS Parental Cell POINTseq rep1

description: Library name: Sample1


title: EXP713RNA003

description: Library name: EXP713RNA003


title: Dj15_Day7

description: Library name: SPF5.RDj15.Day7


title: Et12_Day0

description: Library name: SPF5.REt12.Day0


title: Dj15_Day3

description: Library name: SPF5.RDj15.Day3


title: EXP713RNA002

description: Library name: EXP713RNA002


title: ACHN POINTseq rep1

description: Library name: Sample3

source_name: ACHN

growth_protocol: ACHN and A498 cells were maintained in EMEM supplemeted with 10% FBS and PS in humidified atmosphere with 5% CO2 at 37C

value: ACHN

value: Renal cell carcinoma


title: Direct RNA sequencing,  IVT

city: Beijing

first: Jia-xian

last: Jing

address: Beijing Academy of Agriculture and Forestry Science

description: Library name: DRS_IVT

data_processing:
DRS: The base-calling, adapter trimming, and m6A prediction of DRS raw electric signals were performed using Dorado (https://github.com/nanoporetech/dorado). The trimmed Reads were then aligned to the reference genome by minimap2 (2.26-r1175) with parameters "-ax map-ont --eqx -L --MD --splice -y -Y --secondary y -t 40". We calculated the m6A methylation level of each A site with more than 20 reads as the read number of methylated A divided by the total read number of methylated A plus unmethylated A using three p-value cutoffs including 0.01, 0.05, and 0.1.
Assembly: 97103 v2.5
Supplementary files format and content: bigWig, narowPeak

organism: Citrullus lanatus

source_name: leaves

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Thermo Fisher Scientific, #15596026) following the manufacturer’s instructions followed by removing the residual genomic DNAs with TURBO DNase (Invitrogen, #AM2238). rRNA depletion reaction was carried out with the Plant Ribo-off rRNA depletion Kit (Vazyme, #N409-01) according to the manufacturer’s protocol.
DRS: 200 ng RNAs with poly-A tails were used for the DRS library construction using the Oxford Nanopore DRS protocol (Oxford Nanopore Technologies, #SQK-RNA004). The library was loaded onto a Nanopore R10.4 sequencing microarray and sequenced for 48-72 hours on a PromethION platform (Oxford Nanopore Technologies). The sequencing was performed by Wuhan Benagen Technology.

value: leaves


title: ACHN POINTseq rep2

description: Library name: Sample4


title: EXP713RNA001

last: Zhang

description: Library name: EXP713RNA001


title: Dj15_Day1

description: Library name: SPF5.RDj15.Day1


title: GLORIseq, IVT, rep1

institute: Beijing Academy of Agriculture and Forestry Science

description: Library name: GLORI-IVT-1

data_processing:
GLORIseq: The sequenced reads after adapter and quality trimming using Trim_Galore (https://github.com/FelixKrueger/TrimGalore) were collapsed into non-redundant reads. These non-redundant reads were mapped separately to the A-to-G and T-to-C versions of the 97103 v2.5 watermelon genome using STAR (v.2.7.11.a) with maximal 8 mismatches. We calculated the m6A methylation level of each A site with a read number larger than 20 as the number of reads with unconverted A divided by the total read number of converted A plus and unconverted A
Assembly: 97103 v2.5
Supplementary files format and content: bigWig, narowPeak

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Thermo Fisher Scientific, #15596026) following the manufacturer’s instructions followed by removing the residual genomic DNAs with TURBO DNase (Invitrogen, #AM2238). rRNA depletion reaction was carried out with the Plant Ribo-off rRNA depletion Kit (Vazyme, #N409-01) according to the manufacturer’s protocol.
GLORIseq:200 ng ribo-minus RNAs or IVT RNAs were used for GLORI-seq. RNA protection, deamination, and deprotection were performed as previously described (Liu et al., 2023). The GLORI-treated RNAs were subjected to a two-step ending repair step using Antarctic Phosphatase (NEB, #M0289) and T4 Polynucleotide Kinase (NEB, #M0201S) to obtain RNAs with 5′-P and 3′-OH, which were purified using Monarch® Spin RNA Cleanup Kit (NEB, #T2030L). 100 ng ending-repaired RNAs were used to construct the NGS library with VAHTS Small RNA Library Prep Kit for Illumina (Vazyme, #NR801) according to the manufacturer’s protocols. The libraries were sequenced on the Illumina HiSeq platform in the 150-nt paired-end mode.


title: A498 POINTseq rep2

description: Library name: Sample2


title: Dj15_Day0

description: Library name: SPF5.RDj15.Day0


title: GLORIseq, virus-infected samples, rep2

description: Library name: GLORI-virus-2


title: GLORIseq, virus-infected samples, rep1

description: Library name: GLORI-virus-1


title: GLORIseq, IVT, rep2

description: Library name: GLORI-IVT-2


title: Cg16_Day3

description: Library name: SPF5.RCg16.Day3


title: Cg16_Day7

description: Library name: SPF5.RCg16.Day7


title: virus-infected watermelon leaves(Input), rep2

description: Library name: Virus_INPUT_R2

data_processing:
m6ARIPseq: The sequenced reads after adapter and quality trimming using Trim_Galore (https://github.com/FelixKrueger/TrimGalore) were collapsed into non-redundant reads and mapped to the Watermelon reference genome (97103 v2.5) using STAR (v.2.7.11.a). Candidate m6A peaks were called using three approaches, including using the R package exomePeak2 (https://github.com/ZW-xjtlu/exomePeak2), macs (ref), and IGV manual checking. The enrichment of m6A peaks was calculated as the coverage between the IP-seq and Input-seq using in-house Python codes.
Assembly: 97103 v2.5
Supplementary files format and content: bigWig, narowPeak

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Thermo Fisher Scientific, #15596026) following the manufacturer’s instructions followed by removing the residual genomic DNAs with TURBO DNase (Invitrogen, #AM2238). rRNA depletion reaction was carried out with the Plant Ribo-off rRNA depletion Kit (Vazyme, #N409-01) according to the manufacturer’s protocol.
m6ARIPseq:3 µg ribo-minus RNAs or IVT RNAs were fragmented by NEBNext® Magnesium RNA Fragmentation Module (NEB, #E6150S) at 94°C for 4 minutes and purified by ethanol precipitation. 2 μg m6A antibodies (Synaptic Systems, #202003) and 40ul Dynabeads protein A/G (Thermo Scientific, #10003D) were incubated in IP buffer (10mM Tris-HCl (pH 7.4), 150mM NaCl, 0.1% Igepal CA-630) at room temperature for 1 hours. Fragmented RNAs were subsequently added to the antibody-conjugated beads in reaction buffer (10 mM Tris-HCl, pH 7.4; 150 mM NaCl; 0.1% Igepal CA-630), supplemented with 5 μL RNasin Plus RNase Inhibitor (Promega, #N2615), and incubated at 4°C for 1 hours. The beads were then collected and sequentially washed twice with 1 mL of IP buffer, low salt buffer (10 mM Tris-HCl, pH 7.5; 50 mM NaCl; 0.1% Igepal CA-630), and high salt buffer (10 mM Tris-HCl, pH 7.5; 500 mM NaCl; 0.1% Igepal CA-630) at 4°C for 10 minutes per wash. m6A-enriched RNAs were eluted from the beads using the Monarch® Spin RNA Cleanup Kit (NEB, #T2030L). Approximately 20 ng of immunoprecipitated (IP) RNAs and input RNAs were subjected to perform first-strand cDNA synthesis to construct next-generation sequencing libraries following the manufacturer’s instructions for the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, #NR605). The libraries were sequenced on the Illumina HiSeq platform in the 150-nt paired-end mode.


title: virus-infected watermelon leaves(IP), rep1

description: Library name: Virus_IP_R1


title: A498 POINTseq rep1

description: Library name: Sample1


title: Direct RNA sequencing, virus-infected samples

description: Library name: DRS_Virus


title: U2OS SETD2 KO Cell nuclei 3mRNAseq rep3

description: Library name: Sample12

data_processing:
Raw sequencing data were demultiplexed and converted to FastQ format with bcl2fastq (v2.20.0.422) following Illumina’s protocol. Subsequent processing of the FastQ files was carried out according to Lexogen’s QuantSeq analysis workflow, including alignment and generation of BAM files. Strand-specific separation of aligned reads was performed using SAMtools (v1.10).
Assembly: hg38
Supplementary files format and content: stranded bigwig files include read coverage for each sample

extract_protocol:
Total or nuclei RNA dissolved in TRI reagent was extracted by ethanol precipitation according to the manufacturer’s instructions.
Following the protocol of the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV.


title: virus-infected watermelon leaves(Input), rep1

description: Library name: Virus_INPUT_R1


title: Cg16_Day1

description: Library name: SPF5.RCg16.Day1


title: virus-infected watermelon leaves(IP), rep2

description: Library name: Virus_IP_R2


title: endogenous transcriptome of virus-infected samples without any RNA modifications(IP), rep1

description: Library name: IVT_IP_R1


title: U2OS SETD2 KO Cell nuclei 3mRNAseq rep1

description: Library name: Sample10


title: U2OS SETD2 KO Cell nuclei 3mRNAseq rep2

description: Library name: Sample11


title: U2OS SETD2 KO Cell total 3mRNAseq rep3

description: Library name: Sample9


title: endogenous transcriptome of virus-infected samples without any RNA modifications(Input), rep1

description: Library name: IVT_INPUT_R1


title: Cg16_Day0

description: Library name: SPF5.RCg16.Day0


title: Az15_Day7

description: Library name: SPF5.RAz15.Day7


title: endogenous transcriptome of virus-infected samples without any RNA modifications(Input), rep2

description: Library name: IVT_INPUT_R2


title: Az15_Day3

description: Library name: SPF5.RAz15.Day3


title: endogenous transcriptome of virus-infected samples without any RNA modifications(IP), rep2

description: Library name: IVT_IP_R2


title: U2OS SETD2 KO Cell total 3mRNAseq rep2

description: Library name: Sample8


title: Donor 8 cells perturbed with Non-targeting control 2 by CRISPRi

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Donor8_NTC2
Donor8_bulkRNAseq.csv

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts, normalized counts (CPM)

growth_protocol: Naive human CD4+ T cells were isolated isolated with the EasySep Human Naive CD4+ T Cell Isolation Kit (catalog no. #19555, STEMCELL Technologies) according to the manufacturer’s protocol from PBMC-enriched leukapheresis products (Leukopaks, STEMCELL Technologies, catalog no. 70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). At day 0, primary naive human CD4+ T cells were seeded at 1 x 106 cells/ml in cXVIVO and 200 IU/ml IL-2 at 150µL/well in 96-well flat bottom plates. Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells in each well were transduced with a distinct, individual single gRNA expressing lentivirus at 2% v/v. On day 3, cells were split to ~5 x 105 cells/mL and Blasticidin was added at 10 µg/mL final concentration. At day 5, cells were centrifuged and resuspended with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin at ~5 x 105 cells/mL. At day 7, cells were counted and diluted to 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At day 8, cells were centrifuged and resuspended at 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. On day 10 morning, cells were centrifuged and resuspended at 2 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours.

extract_protocol:
Cells were centrifuged and resuspended in DNA/RNA Shield (Zymo Research) and sent for bulk RNAseq by Plasmidsaurus.
plasmidsaurus library preparation - conversion of mRNA into complementary DNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Donor 8 cells perturbed with Non-targeting control 1 by CRISPRi

description:
Library name: Donor8_NTC1
Donor8_bulkRNAseq.csv

treatment_protocol: 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours

tag: tissue

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

value: Male


title: Donor 7 cells perturbed with Non-targeting control 3 by CRISPRi

description:
Library name: Donor7_NTC3
Donor7_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage


title: Donor 7 cells perturbed with Non-targeting control 2 by CRISPRi

description:
Library name: Donor7_NTC2
Donor7_bulkRNAseq.csv

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi control

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


title: U2OS SETD2 KO Cell total 3mRNAseq rep1

description: Library name: Sample7

tag: cell line

tag: cell type

value: Osteosarcoma

tag: genotype

value: SETD2 CRISPR  KO


title: Donor 6 cells perturbed with Non-targeting control 2 by CRISPRi

description:
Library name: Donor6_NTC2
Donor6_bulkRNAseq.csv

tag: tissue

tag: treatment

tag: experimental perturbation

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: O+

value: ACDA

value: STEMCELL technologies

value: Female

value: Caucasian

tag: enriched cell_types

tag: library protocol


title: Donor 6 cells perturbed with Non-targeting control 1 by CRISPRi

description:
Library name: Donor6_NTC1
Donor6_bulkRNAseq.csv

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO


title: U2OS Parental Cell nuclei 3mRNAseq rep3

description: Library name: Sample6

tag: cell line

tag: cell type

tag: genotype

value: WT


title: Az15_Day0

description: Library name: SPF5.RAz15.Day0

tag: tissue

value: blood

value: PBMCs

tag: treatment

value: Influenza vaccination


title: U2OS Parental Cell nuclei 3mRNAseq rep2

description: Library name: Sample5


title: Az15_Day1

description: Library name: SPF5.RAz15.Day1


title: Donor 5 cells perturbed with Non-targeting control 2 by CRISPRi

description:
Library name: Donor5_NTC2
Donor5_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: No

value: Male

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Ta11_Day7

description: Library name: SPF4.RTa11.Day7


title: C42BmCher_2

city: Tucson

first: Jack

last: Tran

state: AZ

address: 1515 N. Campbell Avenue

department: Cancer Center

institute: University of Arizona

description: Library name: C42BmCher_2

data_processing:
All computational analyses were performed on the Galaxy web platform (https://usegalaxy.org). Raw sequence quality was evaluated using FastQC (Galaxy Version 0.74+galaxy1). Adapter sequences and low-quality bases (Phred score $< 20$) were removed using Trimmomatic (Galaxy Version 0.39+galaxy2). Trimmed reads were aligned to the GRCh38 reference genome using BWA MEM (Galaxy Version 0.7.19). Resulting BAM files were sorted and filtered for blacklisted regions using SortSAM (Galaxy Version 3.1.1.0) and bedtools Intersect intervals (Galaxy Version 2.31.1+galaxy0). Peak Calling and Normalization. Identification of enriched genomic regions was performed using MACS2 callpeak (Galaxy Version 2.2.9.1+galaxy0). For each sample, ChIP reads were compared against the input DNA control (C4-2B mCher). The effective genome size was set to H.sapiens 2.7e9, and a q-value (FDR) threshold of 0.05 was applied. For narrow peaks, the standard shifting model was used. To visualize enrichment, signal tracks were generated using MACS2 to produce bedGraph files, and subsequently signal tracks (bigWig) were generated via bamcov-erage (Galaxy Version 3.5.4+galaxy0), with normalization to Bin Size 10 and RPKM (Reads Per Kilobase per Million mapped reads) to enable quantitative comparison be-tween samples and visualization in the Integrative Genomics Viewer (IGV). Genomic Annotation and Motif Discovery. Peak annotation relative to the nearest Transcription Start Site (TSS) was performed using the R/Bioconductor package ChIPseeker (v.1.26.0). De novo motif enrichment was calculated using MEME-ChIP (Galaxy Ver-sion 4.11.2+galaxy1) using a 100 bp window around peak centers. Statistical signifi-cance for motif enrichment was determined by Fisher’s Exact Test, E < 0.05.
Assembly: GRCH38
Supplementary files format and content: .xls and csv :entries of peak calls and genomic location

extract_protocol:
Cells were then harvested per ChIP-seq kit and protocol per Cell-Signaling-Technologies, for downstream chromatin immunoprecipitation and high throughput sequencing. Snail1-chromatin was then immunoprecipitated with anti-FLAG antibody. Column-purified DNA was then submitted to Novogene for ChIPseq sequencing.
ChIP-seq DNA library preparation using Illumina-compatible adapters (exact kit unknown)

value: Prostate Cancer Epithelial

value: mCherry-control

tag: chip antibody

value: Anti-FLAG CST 14793S


title: Du145_Snail1_AB2

description: Library name: Du145_Snail1_AB2


title: Ta11_Day3

description: Library name: SPF4.RTa11.Day3


title: U2OS Parental Cell total 3mRNAseq rep3

description: Library name: Sample3

value: Osteosarcoma


title: C42B_Snail1_AB1

description: Library name: C42B_Snail1_AB1


title: Du145_Snail1_AB1

description: Library name: Du145_Snail1_AB1


title: Ta11_Day0

description: Library name: SPF4.RTa11.Day0


title: Ta11_Day1

description: Library name: SPF4.RTa11.Day1


title: D6_CD_2

description:
Library name: D6_CD_2
DiffGenes_D6_CD.txt
MyTopHits_D6_CD.txt

data_processing:
Raw sequencing data was first subjected to quality assessment using the FastQC (v0.11.9) tool to evaluate base quality scores, adapter contamination, and sequence duplication levels. Transcript quantification was performed using Kallisto (v0.48.0), a pseudoalignment-based method that estimates transcript abundance [42]. Reads were aligned against the Ensembl GRCh38 transcriptome index. The output transcript-level abundance estimates were imported into R (v4.4.2) using the tximport package (v1.34.0) to summarize counts at the gene level. Normalization and differential expression analysis were conducted using DESeq2 (v1.46.0). Differentially expressed genes were identified by applying Benjamini–Hochberg correction to adjust p-values for multiple comparisons. Genes with an adjusted p-value < 0.1 and an absolute log2 fold change > 0.85 were considered significant. Visualizations such as PCA plots, heatmaps, and volcano plots were generated using ggplot2 (v3.5.2). Gene Set Enrichment Analysis (GSEA) was performed using the Broad Institute’s software [43] on the full list of ranked genes.
Assembly: Ensembl GRCh38
Supplementary files format and content: .txt : differential expressed genes and TopHits

source_name: Prostate Cancer

extract_protocol:
cells were harvested in trizol lysis reagent for downstream total RNA isolation. Total RNA was isolated using standard alcohol precipitation. Isolated total RNA were submitted to NOVOGENE for next generation, selective for mRNA.
Non-Directional: AB Clonal mRNA Seq Library Prep Kit (poly A selection)

value: Prostate Cancer

value: Cumate-Snail1 tetON-shRA

value: Cumate+Dox

tag: batch


title: D6_CD_3

description:
Library name: D6_CD_3
DiffGenes_D6_CD.txt
MyTopHits_D6_CD.txt


title: U2OS Parental Cell total 3mRNAseq rep1

description: Library name: Sample1

value: WT


title: U2OS Parental Cell nuclei 3mRNAseq rep1

description: Library name: Sample4


title: Nn10_Day7

description: Library name: SPF4.RNn10.Day7

value: blood

value: PBMCs


title: Donor 5 cells perturbed with Non-targeting control 1 by CRISPRi

description:
Library name: Donor5_NTC1
Donor5_bulkRNAseq.csv

value: CD4-positive, alpha-beta T cells

tag: donor smoker

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

tag: enriched cell_types

tag: library protocol


title: C42B_Snail1_AB2

description: Library name: C42B_Snail1_AB2

tag: cell line

tag: cell type

value: Prostate Cancer Epithelial

tag: treatment

value: Anti-FLAG CST 14793S


title: Nn10_Day3

description: Library name: SPF4.RNn10.Day3

tag: tissue

value: Influenza vaccination


title: D6_cumate_2

description:
Library name: D6_cumate_2
DiffGenes_D6_CM_lfc_0.85.txt
MyTopHits_D6_CM.txt

value: Prostate Cancer

tag: genotype

value: Cumate-Snail1 tetON-shRA

value: Cumate


title: D6_CD_1

description:
Library name: D6_CD_1
DiffGenes_D6_CD.txt
MyTopHits_D6_CD.txt

value: Cumate+Dox

tag: batch


title: U2OS Parental Cell total 3mRNAseq rep2

description: Library name: Sample2

value: Osteosarcoma

value: WT


title: ACHN 3mRNAseq rep3

description: Library name: Sample6

value: ACHN

value: Renal cell carcinoma


title: C42B_Snail1_AB3

description: Library name: C42B_Snail1_AB3

tag: chip antibody


title: Nn10_Day1

description: Library name: SPF4.RNn10.Day1

value: blood

value: PBMCs


title: D6_cumate_3

description:
Library name: D6_cumate_3
DiffGenes_D6_CM_lfc_0.85.txt
MyTopHits_D6_CM.txt


title: ACHN 3mRNAseq rep1

description: Library name: Sample4


title: D6_cumate_1

description:
Library name: D6_cumate_1
DiffGenes_D6_CM_lfc_0.85.txt
MyTopHits_D6_CM.txt


title: ACHN 3mRNAseq rep2

description: Library name: Sample5


title: D4_CD_3

description:
Library name: D4_CD_3
DiffGenes_D4_CD.txt
MyTopHits_D4_CD.txt


title: D4_CD_2

description:
Library name: D4_CD_2
DiffGenes_D4_CD.txt
MyTopHits_D4_CD.txt


title: Nn10_Day0

description: Library name: SPF4.RNn10.Day0


title: D4_cumate_2

description:
Library name: D4_cumate_2
DiffGenes_D4_CM_lfc_0.85.txt
MyTopHits_D4_CM.txt


title: D4_cumate_3

description:
Library name: D4_cumate_3
DiffGenes_D4_CM_lfc_0.85.txt
MyTopHits_D4_CM.txt


title: Mg12_Day7

description: Library name: SPF4.RMg12.Day7


title: D4_CD_1

description:
Library name: D4_CD_1
DiffGenes_D4_CD.txt
MyTopHits_D4_CD.txt


title: Mg12_Day3

description: Library name: SPF4.RMg12.Day3


title: A498 3mRNAseq rep3

description: Library name: Sample3


title: A498 3mRNAseq rep2

description: Library name: Sample2


title: D4_cumate_1

description:
Library name: D4_cumate_1
DiffGenes_D4_CM_lfc_0.85.txt
MyTopHits_D4_CM.txt


title: Veh_3

description: Library name: Veh_3


title: A498 3mRNAseq rep1

description: Library name: Sample1


title: Mg12_Day1

description: Library name: SPF4.RMg12.Day1


title: Veh_2

description: Library name: Veh_2


title: Veh_1

description: Library name: Veh_1


title: Mg12_Day0

description: Library name: SPF4.RMg12.Day0