title: shTRIM25shAGO2_1_miRNA

city: 上海市

first: Jianxiu

last: Yu

state: 上海市

address: Room 202, Building 7, 280 South Chongqing Road,

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 11
miRNA_Expression.xlsx

data_processing:
For H1299mRNA data, paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
For H1299 miRNA data, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: hg38 for RNA-Seq, miRBase for miRNA-Seq
Supplementary files format and content: Excel files

extract_protocol:
RNA was extracted from total cell lysates.
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols


title: A549_attached_rep1

status: Public on Apr 25 2026

type: RNA

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

department: Department of Pathology

country: Japan

institute: Jichi Medical University

description: Gene expression of A549 in attached conditions.

hyb_protocol: The labeled cRNA was fragmented and hybridized to an array, using Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

molecule: total RNA

organism: Homo sapiens

source_name: Lung adenocarcinoma cell line A549, attached

label_protocol: RNA was reverse-transcribed using an oligo(dT) primer to generate double-stranded cDNA, followed by in vitro transcription to produce Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit, one-color.

growth_protocol: Cells were maintained in RPMI-1640 medium, supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit.

treatment_protocol: Trypsinized cells were plated onto ultra-low attachment culture plate (Corning), and RNA was extracted at indicated time points.

tag: cell type

value: lung adenocarcinoma

tag: cell line

tag: treatment

value: attached


title: MV4-11 DMSO 12h rep2

type: SRA

city: MONROVIA

first: Yahuei

last: Kuo

state: CA

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

country: USA

institute: City of Hope National Medical Center

description:
Library name: COHP_56995_MV4-11_DMSO_rep2
MV4-11 control

library_source: transcriptomic

data_processing:
Quality control of raw FASTQ files using FastQC.
Adapter trimming and low-quality base removal using Trim Galore.
Alignment to the human reference genome (GRCh38) using STAR.
Gene-level quantification using featureCounts to generate count matrices.
Normalization and QC using DESeq2 or edgeR.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: Gene-level raw count matrix in txt format for all samples.

growth_protocol: Cells (MV4-11, Kasumi-1, KG-1) were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the Zymo Research Direct-zol RNA Microprep Kit according to the manufacturer's instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s protocol.

treatment_protocol: Cells were treated with 10 μM HDAC8 inhibitor (compound 22d) or DMSO (control) for 12 hours.

value: Leukemia

value: DMSO 12h


title: LungILC2_Cnot3CKO_2

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v. 0.23.2) (parameters - Quality >= Q15, N base limit = 10)
Trimmed sequence reads were mapped to GRCm39 using STAR aligner (v. 2.7.11a) with default parameters
Read count exxtraction were performed using featureCounts (v. 2.0.3)
Read count normalization were caliculated by R (v. 4.1.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: lung

extract_protocol:
Cells were isolated and directly brought into First-Strand cDNA Synthesis step using SMART-Seq® Stranded Kit (Takara).
Libraries were generated using SMART-Seq® Stranded Kit according to manufacturer's instruction

tag: tissue

value: lung

tag: genotype

value: Cnot3f/f Il7r-Cre


title: anti-PRAME CAR-T cells cocultured with OCI-AML3-2

city: Shanghai

first: Xintong

last: Liu

state: Please select your state

address: Ruijin second road

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample11
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.

data_processing:
Raw reads were filtered using fastp (version 0.18.0) to remove adapters and low-quality reads.
rRNA reads were removed by mapping to rRNA database using Bowtie2 (version 2.2.8).
Clean reads were mapped to the reference genome (GRCh38.p14) using HISAT2 (version 2.1.0) with default parameters.
Mapped reads were assembled using StringTie (version 1.3.1) and gene expression levels were quantified as TPM using RSEM.
Assembly: GRCh38.p14
Supplementary files format and content: files includes TPM values and counts for each samples

source_name: CD3+ T cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: CD3+ T cells


title: A549_detached_7 days_rep1

description: Gene expression of A549 at day 7 in detached condition, i.e., day 7 after replating cells onto ultra-low attachment culture plate.

source_name: Lung adenocarcinoma cell line A549, detached for 7 days

value: detached for 7 days


title: MV4-11 DMSO 12h rep1

description:
Library name: COHP_56994_MV4-11_DMSO_rep1
MV4-11 control


title: LungILC2_control_3


title: LungILC2_control_2


title: Kasumi-1 HDAC8i 10μM 12h rep3

description:
Library name: COHP_56987_Kasumi-1_HDAC8i_10uM_12h_rep3
Kasumi-1 treated

value: HDAC8i 10μM 12h


title: MV4-11 DMSO 12h rep3

description:
Library name: COHP_56996_MV4-11_DMSO_rep3
MV4-11 control


title: FR_0hpa_1: Foot regeneration RNA-seq, 0 hours post amputation, replicate 1, DMSO

city: Davis

first: Sergio

middle: Esteban

last: Campos

address: One Shields Ave

department: Molecular and Cellular Biology

institute: University of California Davis

description: Library name: FR_0hpa_1

data_processing:
Raw reads were trimmed with Trimmomatic v0.39 to remove adapter sequences and low quality reads, with the following parameters: PE -threads 16 -phred33 / ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 \         SLIDINGWINDOW:4:15 MINLEN:32
Resulting reads were mapped to a reference transcriptome using rsem with the following parameters: rsem-calculate-expression --num-threads 16 --no-bam-output \         --bowtie2 --paired-end
Assembly: GCA_004118135.1
Supplementary files format and content: comma delimited text files including raw counts and FPKM

molecule: polyA RNA

organism: Hydra oligactis

source_name: body column

growth_protocol: Hydra oligactis strain innsbruck 12 polyps were cultured according to standard protocol (Lenhoff, 1983) at 18˚C and fed 3 times weekly with Artemia nauplii.

extract_protocol:
30 tissue segments adjacent to the wound site were collected per sample, put in Trizol and homogeneized with a vortex. Trizol:chloroform protocol was used to extract total nucleic acids. After treatment with DNAse I, samples were passed through RNA purification columns (Zymo Research).
mRNA libraries were prepared by Novogene

treatment_protocol: For alsterpaullone treatment, Hydra were incubated in 5 uM alsterpaullone for 3 hours after amputation. Following, this incubation Hydra polyps were washed and put in Hydra media until tissue was collected.

value: body column

value: DMSO

tag: batch


title: shTRIM25shAGO2_2_miRNA

description:
Library name: Sample 12
miRNA_Expression.xlsx


title: A549_detached_1 day_rep1

description: Gene expression of A549 at day 1 in detached condition, i.e., day 1 after replating cells onto ultra-low attachment culture plate.

source_name: Lung adenocarcinoma cell line A549, detached for 1 day

value: detached for 1 day


title: shCtrl_2_miRNA

description:
Library name: Sample 8
miRNA_Expression.xlsx

value: shCtrl


title: anti-PRAME CAR-T cells cocultured with OCI-AML3-3

description:
Library name: Sample12
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: FR_0hpa_2: Foot regeneration RNA-seq, 0 hours post amputation, replicate 2, DMSO

description: Library name: FR_0hpa_2


title: Kasumi-1 HDAC8i 10μM 12h rep2

description:
Library name: COHP_56986_Kasumi-1_HDAC8i_10uM_12h_rep2
Kasumi-1 treated


title: MV4-11 HDAC8i 10μM 12h rep1

description:
Library name: COHP_56997_MV4-11_HDAC8i_10uM_12h_rep1
MV4-11 treated


title: anti-PRAME CAR-T cells cocultured with THP-1-2

description:
Library name: Sample8
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: anti-PRAME CAR-T cells cocultured with THP-1-3

description:
Library name: Sample9
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: shTRIM25_2_miRNA

description:
Library name: Sample 10
miRNA_Expression.xlsx


title: shCtrl_1_miRNA

description:
Library name: Sample 7
miRNA_Expression.xlsx


title: LungILC2_control_1


title: anti-PRAME CAR-T cells cocultured with OCI-AML3-1

description:
Library name: Sample10
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: FR_0hpa_3: Foot regeneration RNA-seq, 0 hours post amputation, replicate 3, DMSO

description: Library name: FR_0hpa_3


title: shTRIM25_1_miRNA

description:
Library name: Sample 9
miRNA_Expression.xlsx


title: anti-PRAME CAR-T cells-3

description:
Library name: Sample6
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.

value: anti-PRAME CAR-T cells


title: LungILC2_Cnot3CKO_1


title: anti-PRAME CAR-T cells cocultured with THP-1-1

description:
Library name: Sample7
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: C57Bl/6J mouse 11; liver specific Marchf6 knockout; 10-weeks-old; male

city: Amsterdam

first: Sebastian

last: Hendrix

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: UMC Amsterdam location AMC

description: Library name: 20180507_S69_LKO5

data_processing:
Reads were subjected to quality control (FastQC v0.11.15, Picard Tools)
reads were trimmed using Trimmomatic v0.36 (PMID: 24695404)
Reads were aligned to the genome (Ensembl v93) using HISAT2 (v2.1.0) (PMID: 25751142) default parameters; -p 2 --dta-cufflinks; genome: Ensembl v93, corresponding to GCA_000001635.8
Counts were obtained using HTSeq (v0.6.1) using the corresponding GTFs. (PMID: 25260700) parameters: --stranded=no; default parameters used: --order=name --minaqual=10 --type=exon --idattr=gene_id --mode=union)
Statistical analyses were performed using the edgeR (PMID: 19910308) and limma/voom (PMID: 25605792) R packages.
Assembly: Ensembl v93, corresponding to GRCm38.p6 ( GCA_000001635.8)
Supplementary files format and content: Tab-delimited text file contains raw counts for all samples.

source_name: liver

growth_protocol: Mice were group housed under SPF conditions with a 12 h light/dark cycle and temperature-controlled environment in individually ventilated cages with ad libitum access to drinking water and food. At an age of 10 weeks, male littermates were randomly assigned to the experimental groups and fasted for 4 h before sacrifice.

extract_protocol:
Total RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research), quantified using a Qubit 3 Fluorimeter (Invitrogen)
KAPA mRNA hyperPrep kit (KAPA Biosystems) was used to create the library; 50 ng input RNA per sample

value: liver

tag: Sex

value: male

value: Marchft liver KO


title: Kasumi-1 DMSO 12h rep2

description:
Library name: COHP_56983_Kasumi-1_DMSO_rep2
Kasumi-1 control


title: NK_control_3

source_name: spleen

value: spleen

value: NK cell


title: Kasumi-1 DMSO 12h rep1

description:
Library name: COHP_56982_Kasumi-1_DMSO_rep1
Kasumi-1 control

value: Leukemia


title: anti-PRAME CAR-T cells-1

description:
Library name: Sample4
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: Kasumi-1 HDAC8i 10μM 12h rep1

description:
Library name: COHP_56985_Kasumi-1_HDAC8i_10uM_12h_rep1
Kasumi-1 treated


title: K562, TAi, H3K27ac_R1, ChIP, rep1

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

description: Library name: TAi_K27ac_R1

library_source: genomic

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) using Trimmomatic.
Filtered reads were aligned to hg19 Canonical genome using Bowtie2.
Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files.
Enriched peaks were identified using MACS2 with input BAM files served as controls.
Bigwig files generated from BAM files using BamCompare to normalize data against histone H3. Bigwig files for ChIP-seq data without spike-in control were generated using BamCoverage and BigwigCompare to normalize data against H3.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: K562 cells were cultured in RPMI mediun containing 10% FBS, 20 mM HEPES, 10% P/S, and 2 mM L-Glutamine.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (5 ng for H3K27ac) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 175 bp size using NEBNext sample purification bead and amplified using the adaptor primers. The fragments are purified using NEBNext sample purification beads.

treatment_protocol: Lentiviral vectors containing a shRNA against GATA1 or TAL1 mRNA were transduced into K562 cells. Empty vector was used as an experimental control.

value: erythroleukemia cells

tag: chip antibody


title: NK_Cnot3CKO_3


title: K562, TAi, H3K27ac_R2, ChIP, rep2

description: Library name: TAi_K27ac_R2


title: untransduced T cells-3

description:
Library name: Sample3
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.

value: CD3+ T cells without transduced with the CAR


title: K562, GAi, H3K27ac_R2,ChIP, rep2

description: Library name: GAi_K27ac_R2


title: C57Bl/6J mouse 9; liver specific Marchf6 knockout; 10-weeks-old; male

description: Library name: 20180505_S67_LKO3


title: untransduced T cells-2

description:
Library name: Sample2
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: C57Bl/6J mouse 12; liver specific Marchf6 knockout; 10-weeks-old; male

description: Library name: 20180508_S70_LKO6


title: anti-PRAME CAR-T cells-2

description:
Library name: Sample5
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.


title: NK_Cnot3CKO_2

value: Cnot3f/f Il7r-Cre


title: K562, GAi, H3K27ac_R1,ChIP, rep1

description: Library name: GAi_K27ac_R1


title: C57Bl/6J mouse 6; Wildtype; 10-weeks-old; male

description: Library name: 20180502_S64_WT6

value: WT


title: C57Bl/6J mouse 10; liver specific Marchf6 knockout; 10-weeks-old; male

description: Library name: 20180506_S68_LKO4


title: NK_control_2


title: SIILC3_Cnot3RIP_2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v. 0.23.2) (parameters - Quality >= Q15, N base limit = 10)
Trimmed sequence reads were mapped to GRCm39 using STAR aligner (v. 2.7.11a) with default parameters
Read count exxtraction were performed using featureCounts (v. 2.0.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Small intestine

extract_protocol:
RNAs were extracted from input or IP fraction of cell lysate using TRIreagent.
libraries were generated using SMART-Seq® Stranded Kit according to manufacturer's instruction

value: Small intestine

value: Rorgt-GFP


title: 80mM_br3

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: 80mM_br3
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 80mM_br3

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads that passed the quality control were mapped to mouse genome (mm10) with hisat2 (version 2.0.4). Stringtie (version 2.1.4) were then used to estimate transcript abundance in fragments per kilobase per million (FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample

extract_protocol:
Total RNA was extracted with a Trizol-based protocol.
Libraries were prepared according to the instructions for the Illumina TruSeq RNA Sample Preparation kit. Sequencing was performed on a MiSeq instrument.

value: embryonic stem cells

value: 80mM sodium lactate


title: 80mM_br2

description:
Library name: 80mM_br2
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 80mM_br2


title: C57Bl/6J mouse 8; liver specific Marchf6 knockout; 10-weeks-old; male

description: Library name: 20180504_S66_LKO2


title: NK_control_1


title: Kasumi-1 DMSO 12h rep3

description:
Library name: COHP_56984_Kasumi-1_DMSO_rep3
Kasumi-1 control

value: DMSO 12h


title: NK_Cnot3CKO_1


title: untransduced T cells-1

description:
Library name: Sample1
CD3+ T cells were enriched from PBMCs using Human T Cell Isolation Kit (STEMCELL Technologies, 17951). After being activated with CD3/CD28 beads (1:1 bead-to-cell ratio, Gibco, 11161D) for 48 h, T cells were transduced with the CAR lentivirus. The CAR-T cells were expanded in vitro with T cell expansion medium (ExcellBio, TE000-N022) supplemented with 300 IU/ml human recombinant IL-2. CAR-T cells were co-cultured with THP-1 or OCI-AML3 cells at a 1:1 E:T ratio for 24 h and then the CD3+ CAR-T cells were isolated by FACS for RNA-Seq.

value: CD3+ T cells


title: SIILC3_Cnot3RIP_1


title: C57Bl/6J mouse 5; Wildtype; 10-weeks-old; male

description: Library name: 20180501_S63_WT5


title: K562, Con, H3K27ac_R1, ChIP, rep1

description: Library name: Con_K27ac_R1

value: empty vector


title: K562, Con, H3K27ac_R2, ChIP, rep2

description: Library name: Con_K27ac_R2


title: 60mM_br3

description:
Library name: 60mM_br3
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 60mM_br3

value: 60mM sodium lactate


title: C57Bl/6J mouse 7; liver specific Marchf6 knockout; 10-weeks-old; male

description: Library name: 20180503_S65_LKO1

value: liver

value: male


title: 80mM_br1

description:
Library name: 80mM_br1
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 80mM_br1


title: SIILC2_Cnot3RIP_2


title: C57Bl/6J mouse 3; Wildtype; 10-weeks-old; male

description: Library name: 20180499_S61_WT3


title: SIILC3_input_2


title: Nail tissue from infant 2

first: SHIHUI

last: LIN

state: Shanghai

address: No. 639 Zao Zhi Ju Road, Huangpu District, Shanghai, China

description:
Library name: Sample2
Infant nail with duplicated thumb, post-surgery

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v6.1.2) was used for demultiplexing, alignment to reference genome (GRCh38), filtering, UMI counting, and gene-barcode matrix generation.
Assembly: GRCh38
Supplementary files format and content: Each sample folder contains barcodes.tsv, features.tsv, and matrix.mtx files, representing the filtered gene-barcode expression matrix output from Cell Ranger.

source_name: nail

extract_protocol:
Nail tissues were enzymatically dissociated to generate single-cell suspensions, combining proximal nail fold, nail matrix, and nail bed in a 2:2:1 ratio. Total input ≥20,000 cells at 700–1000 cells/μL.
Libraries were constructed using the 10x Genomics Chromium Single Cell 3’ v3.1 protocol. GEMs were generated, reverse-transcribed, purified, PCR amplified, fragmented, end-repaired, adapter-ligated, and indexed by PCR.

value: nail

value: mixed nail cells

value: normal


title: Nail tissue from infant 3

description:
Library name: Sample3
Infant nail with duplicated thumb, post-surgery


title: 60mM_br2

description:
Library name: 60mM_br2
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 60mM_br2


title: C57Bl/6J mouse 2; Wildtype; 10-weeks-old; male

description: Library name: 20180498_S60_WT2


title: SIILC3_input_1


title: SIILC2_Cnot3RIP_1


title: Nail tissue from infant 1

description:
Library name: Sample1
Infant nail with duplicated thumb, post-surgery


title: C57Bl/6J mouse 1; Wildtype; 10-weeks-old; male

description: Library name: 20180497_S59_WT1


title: C57Bl/6J mouse 4; Wildtype; 10-weeks-old; male

description: Library name: 20180500_S62_WT4


title: 60mM_br1

description:
Library name: 60mM_br1
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 60mM_br1


title: 0mM_br3

description:
Library name: 0mM_br3
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 0mM_br3


title: shTRIM25shAGO2_2_mRNA

description:
Library name: Sample 6
mRNA Expression Profiling.xlsx


title: SIILC2_input_1


title: shTRIM25shAGO2_1_mRNA

description:
Library name: Sample 5
mRNA Expression Profiling.xlsx


title: SIILC2_input_2


title: 0mM_br2

description:
Library name: 0mM_br2
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 0mM_br2


title: LT rat hippocampus biological replicate 4

city: Калининград

first: Irina

last: Shalaginova

state: Калининградская область

address: Черняховского 36-11

country: Russia

institute: Pavlov Institute of Physiology

description: Library name: LT_4

data_processing:
Reads were aligned to the Rnor_6.0 reference genome using STAR 2.7.9a with outFilterMismatchNmax set to 3. Gene-level counts were generated using the quantMode GeneCounts option in STAR. Differential expression analysis was performed in R using DESeq2 v1.28.1 with Benjamini-Hochberg FDR correction.
Assembly: Rnor_6.0
Supplementary files format and content: Processed data files include a DESeq2 differential expression results table in XLSX format.

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Male rats of two selectively bred strains, HT (high-threshold, low-excitability) and LT (low-threshold, high-excitability), were maintained in the vivarium under controlled conditions (23 ± 2 °C, 12 h light/dark cycle) with ad libitum access to standard chow and water. Animals were group-housed until 5 months of age.

extract_protocol:
The whole hippocampus was rapidly dissected, placed in RNAlater, and homogenized. Total RNA was extracted using TRIzol reagent followed by purification with the PureLink RNA Micro Kit according to the manufacturer’s instructions.
Poly(A)+ RNA was purified using oligo(dT) magnetic beads. cDNA libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit. Library quality was assessed using Agilent BioAnalyzer / High Sensitivity DNA Kit, and sequencing was performed on the Illumina HiSeq1500 platform to generate single-end 50-bp reads.

treatment_protocol: Intact animals without experimental treatment were used.

value: hippocampus

value: low-excitability strain

value: intact

value: single batch


title: LT rat hippocampus biological replicate 3

state: Калининградская область

address: Черняховского 36-11

description: Library name: LT_3


title: shTRIM25_2_mRNA

description:
Library name: Sample 4
mRNA Expression Profiling.xlsx


title: 0mM_br1

description:
Library name: 0mM_br1
FPKM_All_lactate.txt
Column name in FPKM_All_lactate.txt: 0mM_br1

value: WT


title: LungILC2_Cnot3RIP_1

value: lung

value: wt


title: LungILC2_Cnot3RIP_2


title: LT rat hippocampus biological replicate 5

state: Калининградская область

address: Черняховского 36-11

description: Library name: LT_5


title: LT rat hippocampus biological replicate 2

state: Калининградская область

address: Черняховского 36-11

description: Library name: LT_2


title: MEFs_br3

description:
Library name: MEFs_br3
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: MEFs_br3

value: Mouse Embryonic Fibroblast


title: shTRIM25_1_mRNA

description:
Library name: Sample 3
mRNA Expression Profiling.xlsx


title: LungILC2_input_1


title: HT rat hippocampus biological replicate 5

state: Калининградская область

address: Черняховского 36-11

description: Library name: HT_5

value: high-excitability strain


title: LT rat hippocampus biological replicate 1

state: Калининградская область

address: Черняховского 36-11

description: Library name: LT_1


title: MEFs_br2

description:
Library name: MEFs_br2
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: MEFs_br2


title: MEFs_br1

description:
Library name: MEFs_br1
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: MEFs_br1


title: shCtrl_1_mRNA

description:
Library name: Sample 1
mRNA Expression Profiling.xlsx

value: shCtrl


title: LungILC2_input_2


title: shCtrl_2_mRNA

description:
Library name: Sample 2
mRNA Expression Profiling.xlsx


title: NK_Cnot3RIP_3

value: spleen

value: NK cell


title: NK_Cnot3RIP_2


title: EG4-2 (Case t4)

city: Fuzhou

first: Zhiren

state: Fujian

address: 20 Chazhong Road

institute: the First Affiliated Hospital of Fujian Medical University

data_processing:
We utilized FastQC and fastp (https://github.com/OpenGene/fastp) to evaluate the quality of data and filter out low-quality reads, followed by HISAT2 alignment of the remaining high-quality reads to the annotated human genome (GRCh38)
The raw sequencing reads underwent quality control and trimming processes using FastQC and Trimmomatic software.
processed data files format and content: reads counts were inclued in the gene expression level

source_name: MI oocytes with an agar-like ZP

extract_protocol:
RNALib Single cell WTA Kit (Lifeint, China) was used to synthesize and amplify cDNA based on total RNA from individual oocytes.
Lifeint Transpose DNA Library Prep Kit for Illumina and Lifeint Library Prep Index Kit V1 for Illumina (Lifeint, China) were utilized to prepare a cDNA library.

value: MI oocytes with an agar-like ZP


title: HT rat hippocampus biological replicate 3

state: Калининградская область

address: Черняховского 36-11

description: Library name: HT_3


title: HT rat hippocampus biological replicate 4

state: Калининградская область

address: Черняховского 36-11

description: Library name: HT_4


title: EG3-2 (Case t4)

source_name: MI oocytes with a relatively normal ZP

value: MI oocytes with a relatively normal ZP


title: EpiSCs_br2

description:
Library name: EpiSCs_br2
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: EpiSCs_br2

value: epiblast stem cells


title: EpiSCs_br3

description:
Library name: EpiSCs_br3
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: EpiSCs_br3


title: NK_input_3


title: HT rat hippocampus biological replicate 2

state: Калининградская область

address: Черняховского 36-11

description: Library name: HT_2


title: EG2-2 (Case t3)


title: NK_Cnot3RIP_1


title: EG4-1 (Case t4)


title: EG3-1 (Case t4)


title: EpiSCs_br1

description:
Library name: EpiSCs_br1
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: EpiSCs_br1


title: HT rat hippocampus biological replicate 1

state: Калининградская область

address: Черняховского 36-11

description: Library name: HT_1


title: ESCs_br2

description:
Library name: ESCs_br2
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: ESCs_br2

value: embryonic stem cells


title: NK_input_2


title: NK_input_1


title: ESCs_br3

description:
Library name: ESCs_br3
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: ESCs_br3


title: NCI-H2228_control_rep1

hyb_protocol: The biotinylated RNA was cleaned with an RNeasy Mini kit, fragmented to 50 to 200 nt, and then hybridized.

scan_protocol: After being washed, the array was stained with streptavidin±phycoerythrin, amplified by biotinylated anti-streptavidin, and then scanned on an HP Gene array scanner.

data_processing:
The intensity for each feature of the array was captured with Affymetrix GeneChip Software, according to standard Affymetrix procedures.
Signal intensities for each probe cell were calculated using the Affymetrix Microarray Suite or GeneChip Operating Software.

label: Biotin

source_name: Lung adenocarcinoma cell line NCI-H2228

label_protocol: RNA was reverse-transcribed with an oligo(dT) primer to synthesize double-stranded cDNA, followed by in vitro transcription to generate biotin-labeled cRNA.

treatment_protocol: No treatment performed.

value: lung adenocarcinoma


title: EG1-1 (Case t2)


title: Kidney Explants D9, Replicate 1, scRNA-Seq

city: Los Angeles

first: Zhongwei

last: Li

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

description: 10X Genomics Chromium Single Cell 3' Reagent Kits v3

data_processing:
Sequencing reads were aligned to the mouse genome (GRCm39) with the Cell Ranger ARC software (version 2.0.2) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: arc-GRCm39-2024-A-v7.2.0
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression

source_name: Kidney explants

growth_protocol: Kidney explants were cultured with Stage I or II medium, 37C, 5% CO2

extract_protocol:
Kidney explants were dissociated using 10 mg/mL Bacillus licheniformis cold active protease (Sigma P5380) mixed with 2.5 mg/mL collagenase type 2 (Worthington, #LS00417) and 125 U/mL DNase I (Worthington, #LS002058) in DPBS at 12°C for 30 min (1 mL total reaction volume). The digestion mix was mixed twenty times with P-200 pipette tips/5 min. The dissociation reaction was terminated by mixing with 1mL of 20% fetal bovine serum (FBS) in DPBS to a final concentration of 10%FBS. The cells were filtered through a pre-wetted 40-um strainer (Falcon), and 1 mL of DPBS was used to wash cells off the strainer. The 3 mL dissociated cell mix was combined with 3 mL of AutoMACS Running Buffer (Miltenyl Biotec, 130-091-221) and cells were briefly pelleted at 300g for 5 mins at 4°C. The cell pellet was then resuspended in AutoMACS Running Buffer, with 14 μM DAPI and 5 μM DRAQ5 added freshly. Singlet live cells (DAPI- and DRAQ5+) were selected by fluorescence-activated cell sorting (FACS) on a BD SORP FACSAria IIu (ARIA #1) cell sorter. Single cells were pelleted to concentrate at 300G x 5 mins. The targeted number of cells then proceeded to drop-seq separation on the 10X machine (Chip B).
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10 X Genomics).

value: Kidney explants

value: Kidney cells

value: Wildtype

value: Kidney explants were cultured with Stage II medium


title: Kidney Explants D9, Replicate 2, scRNA-Seq


title: Kidney Explants D5, Replicate 2, scRNA-Seq

value: Kidney explants were cultured with Stage I medium


title: EG2-1 (Case t3)


title: 2CLCs_br2

description:
Library name: 2CLCs_br2
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: 2CLCs_br2

value: two cell like cells

value: WT


title: 2CLCs_br3

description:
Library name: 2CLCs_br3
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: 2CLCs_br3


title: NCI-H441_control_rep1

source_name: Lung adenocarcinoma cell line NCI-H441


title: EG1-2 (Case t2)


title: Kidney Explants D5, Replicate 1, scRNA-Seq


title: LC-2/ad_control_rep1

source_name: Lung adenocarcinoma cell line LC-2/ad


title: CG-1 (Case t1)

source_name: MI oocytes with a normal ZP

value: MI oocytes with a normal ZP


title: ESCs_br1

description:
Library name: ESCs_br1
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: ESCs_br1


title: NCI-H2009_control_rep1

source_name: Lung adenocarcinoma cell line NCI-H2009


title: CG-2 (Case t1)


title: RNA from patient HTA3_80030, derived from AAH #11 [HTA3_80030_6010017]

status: Public on Apr 24 2026

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: HTA3_80030_6010017

data_processing:
After sequencing, FASTQ files for each sample were aligned to hg38 using STAR.
After alignment of FASTQ files, RSEM was used to summarize gene and transcript counts.
Quality metrics were generated by STAR and RSeQC to evaluate sample quality.
Somalier was used to confirm relatedness among samples from the same patient.
Assembly: hg38
Supplementary files format and content: Processed data are stored as a count matrix in a TSV (tab-separated values) file.

source_name: Resected lung tissue

extract_protocol:
Formalin-fixed parrafin-embedded (FFPE) tissue was annotated for normal, tumor, and premalignant histology, and then laser capture microdissected. RNA was isolated from LCM FFPE samples using the Qiagen All-Prep FFPE kit.
Sequencing libraries were prepared with the Illumina TruSeq Paired-End Cluster Kit.
Total RNA sequencing was performed on an Illumina NextSeq 500 (generating paired-end 75-nucleotide reads), or on an Illumina NextSeq 2000 (generating paired-end 100-nucleotide reads).

value: Resected lung tissue

tag: htan id

tag: sample histology

value: AAH

tag: flow cells


title: RNA from patient HTA3_80030, derived from AAH #8 [HTA3_80030_6008011]

description: Library name: HTA3_80030_6008011


title: RNA from patient HTA3_80030, derived from AAH #13 [HTA3_80030_6011019]

description: Library name: HTA3_80030_6011019


title: RNA from patient HTA3_80030, derived from AAH #10 [HTA3_80030_6010016]

description: Library name: HTA3_80030_6010016


title: HCC4006_control_rep1

source_name: Lung adenocarcinoma cell line HCC4006


title: RNA from patient HTA3_80030, derived from AAH #9 [HTA3_80030_6010015]

description: Library name: HTA3_80030_6010015


title: 2CLCs_br1

description:
Library name: 2CLCs_br1
FPKM_All_4stages.txt
Column name in FPKM_All_4stages.txt: 2CLCs_br1


title: A549_control_rep1

source_name: Lung adenocarcinoma cell line A549


title: RNA from patient HTA3_80030, derived from AIS/MIA [HTA3_80030_6005006]

description: Library name: HTA3_80030_6005006

value: AIS/MIA


title: RNA from patient HTA3_80030, derived from AAH #12 [HTA3_80030_6011018]

description: Library name: HTA3_80030_6011018


title: RNA from patient HTA3_80030, derived from AAH #7 [HTA3_80030_6007010]

description: Library name: HTA3_80030_6007010


title: RNA from patient HTA3_80030, derived from AAH #3 [HTA3_80030_6004004]

description: Library name: HTA3_80030_6004004


title: RNA from patient HTA3_80030, derived from AAH #4 [HTA3_80030_6004005]

description: Library name: HTA3_80030_6004005


title: RNA from patient HTA3_80028, derived from AAH #1 [HTA3_80028_6001001]

description: Library name: HTA3_80028_6001001


title: RNA from patient HTA3_80027, derived from Normal [HTA3_80027_6004006]

description: Library name: HTA3_80027_6004006

value: N


title: RNA from patient HTA3_80029, derived from Normal [HTA3_80029_6003004]

description: Library name: HTA3_80029_6003004


title: RNA from patient HTA3_80030, derived from MIA (Stage 1A) [HTA3_80030_6001001]

description: Library name: HTA3_80030_6001001


title: RNA from patient HTA3_80030, derived from AAH #1 [HTA3_80030_6003003]

description: Library name: HTA3_80030_6003003


title: RNA from patient HTA3_80028, derived from LUAD (Stage 1B) [HTA3_80028_6005005]

description: Library name: HTA3_80028_6005005

value: ADC


title: RNA from patient HTA3_80028, derived from Normal [HTA3_80028_6002002]

description: Library name: HTA3_80028_6002002


title: RNA from patient HTA3_80028, derived from AAH #3 [HTA3_80028_6004004]

description: Library name: HTA3_80028_6004004


title: RNA from patient HTA3_80027, derived from AAH #3 [HTA3_80027_6003004]

description: Library name: HTA3_80027_6003004


title: RNA from patient HTA3_80027, derived from LUAD (Stage 1A) [HTA3_80027_6002002]

description: Library name: HTA3_80027_6002002


title: RNA from patient HTA3_80026, derived from AAH #5 [HTA3_80026_6009011]

description: Library name: HTA3_80026_6009011


title: RNA from patient HTA3_80026, derived from AIS/MIA [PCGA02_30026_6007008]

description: Library name: PCGA02_30026_6007008


title: RNA from patient HTA3_80027, derived from AAH #2 [HTA3_80027_6003003]

description: Library name: HTA3_80027_6003003


title: RNA from patient HTA3_80026, derived from LUAD (Stage 1A) [PCGA02_30026_6003004]

description: Library name: PCGA02_30026_6003004


title: RNA from patient HTA3_80026, derived from Normal [PCGA02_30026_6005006]

description: Library name: PCGA02_30026_6005006


title: RNA from patient HTA3_80028, derived from AAH #2 [HTA3_80028_6003003]

description: Library name: HTA3_80028_6003003


title: RNA from patient HTA3_80025, derived from Normal [PCGA02_30025_6003004]

description: Library name: PCGA02_30025_6003004


title: intestinal contents,Aged+YF,4

city: Nanjing

first: Feixue

last: Wang

address: Xuanwu District

institute: Nanjing Agricultural University

description: Library name: YA304

library_source: other

data_processing:
The raw subreads were processed to generate Circular Consensus Sequencing (CCS) reads using SMRT Link (version 8.0).
Subsequently, the CCS reads were demultiplexed and identified for different samples based on barcode sequences, and chimeras were removed using lima (v1.7.0) to obtain high-quality CCS reads.
Supplementary files format and content: xlsx，Relative abundance of bacterial taxa at the genus level for each sample

molecule: other

source_name: intestinal contents

extract_protocol:
Use the TGuide S96 Magnetic Universal DNA Kit (Tiangen, DP812) to extract nucleic acids
16S rRNA gene V1-V9 region was amplified using primers 27F and 1492R.

value: intestinal contents


title: RNA from patient HTA3_80025, derived from AAH [PCGA02_30025_6003003]

description: Library name: PCGA02_30025_6003003


title: RNA from patient HTA3_80026, derived from AAH #6 [HTA3_80026_6010012]

description: Library name: HTA3_80026_6010012


title: RNA from patient HTA3_80025, derived from AIS/MIA [PCGA02_30025_6001001]

description: Library name: PCGA02_30025_6001001


title: intestinal contents,Aged+YF,5

description: Library name: YA305


title: RNA from patient HTA3_80025, derived from LUAD (Stage 1A) [PCGA02_30025_6002002]

description: Library name: PCGA02_30025_6002002


title: intestinal contents,Aged+YF,3

description: Library name: YA303


title: RNA from patient HTA3_80027, derived from AAH #1 [HTA3_80027_6001001]

description: Library name: HTA3_80027_6001001


title: intestinal contents,Aged+YF,1

description: Library name: YA301


title: RNA from patient HTA3_80024, derived from Normal [PCGA02_30024_6002003]

description: Library name: PCGA02_30024_6002003


title: intestinal contents,Aged+YF,2

description: Library name: YA302


title: intestinal contents,Aged+AF,5

description: Library name: AA305


title: RNA from patient HTA3_80024, derived from AAH [PCGA02_30024_6002002]

description: Library name: PCGA02_30024_6002002


title: RNA from patient HTA3_80024, derived from AIS/MIA (Stage 0) [PCGA02_30024_6001001]

description: Library name: PCGA02_30024_6001001


title: RNA from patient HTA3_80023, derived from AAH #2 [PCGA02_30023_6005005]

description: Library name: PCGA02_30023_6005005


title: RNA from patient HTA3_80023, derived from LUAD (Stage 1A) [PCGA02_30023_6003003]

description: Library name: PCGA02_30023_6003003


title: intestinal contents,Aged+AF,2

description: Library name: AA302


title: intestinal contents,Aged+AF,4

description: Library name: AA304


title: intestinal contents,Aged+AF,3

description: Library name: AA303


title: intestinal contents,Aged+AF,1

description: Library name: AA301


title: RNA from patient HTA3_80022, derived from AAH [PCGA02_30022_6002002]

description: Library name: PCGA02_30022_6002002


title: RNA from patient HTA3_80023, derived from AIS/MIA [PCGA02_30023_6002002]

description: Library name: PCGA02_30023_6002002


title: RNA from patient HTA3_80023, derived from Normal [PCGA02_30023_6001001]

description: Library name: PCGA02_30023_6001001


title: intestinal contents,Young+YF,5

description: Library name: YY305


title: RNA from patient HTA3_80021, derived from LUAD (Stage 1A) [PCGA02_30021_6003004]

description: Library name: PCGA02_30021_6003004


title: intestinal contents,Young+YF,2

description: Library name: YY302


title: RNA from patient HTA3_80021, derived from Normal [PCGA02_30021_6001002]

description: Library name: PCGA02_30021_6001002


title: intestinal contents,Young+YF,4

description: Library name: YY304


title: RNA from patient HTA3_80020, derived from LUAD Region 2 (Stage 1A) [PCGA02_30020_6009013]

description: Library name: PCGA02_30020_6009013


title: RNA from patient HTA3_80022, derived from Normal [PCGA02_30022_6003003]

description: Library name: PCGA02_30022_6003003


title: MDP H3K4me3 CUTAC WT

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: K4me3_WT_MDP

data_processing:
Raw paired-end FASTQ files were trimmed using Trimmomatic with the following parameters: -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25. Trimmed reads were aligned to mm10 using Bowtie2. Aligned reads were converted to BAM format, sorted, and indexed using SAMtools. Duplicate reads were removed using Picard.
BigWig files were generated from BAM files using bam2bw from the cgpbigwig (v1.6.0) Docker image.
Peak calling was performed using MACS2 (v2.2.9.1) with an IgG control sample, using parameters -g mm -f BAMPE -q 0.1 --keep-dup all.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for control samples)
Library strategy: CUT&Tag

source_name: bone marrow

extract_protocol:
CUTAC was performed using the CUTANA CUT&Tag Kit (EpiCypher, Version 4) following the manufacturer’s protocol with a no-salt tagmentation condition. A total of 1 × 105 cells were used per sample. Primary antibodies used were H3K4me3 and Rabbit IgG (included in the kit), and H3K4me2 (EpiCypher 13-0027). A secondary anti-Rabbit IgG (ABIN 101961) antibody was used.
Libraries were prepared using the CUTANA CUT&Tag Kit (EpiCypher, Version 4) following the manufacturer’s protocol. Indexed libraries were pooled and sequenced as 150-bp paired-end reads on an Illumina NovaSeq X Plus platform.

value: bone marrow

value: MDP


title: RNA from patient HTA3_80020, derived from AAH #9 [PCGA02_30020_6010014]

description: Library name: PCGA02_30020_6010014


title: RNA from patient HTA3_80020, derived from AAH #8 [PCGA02_30020_6008012]

description: Library name: PCGA02_30020_6008012


title: cMoP IgG CUTAC WT

description: Library name: IgG_WT

value: cMoP


title: intestinal contents,Young+YF,3

description: Library name: YY303


title: RNA from patient HTA3_80020, derived from AIS/MIA #2 [PCGA02_30020_6007010]

description: Library name: PCGA02_30020_6007010


title: cMoP H3K4me2 CUTAC DE_2

description: Library name: K4me2_DE_2

value: DE


title: cMoP H3K4me2 CUTAC WT_2

description: Library name: K4me2_WT_2


title: cMoP H3K4me3 CUTAC WT

description: Library name: K4me3_WT


title: RNA from patient HTA3_80020, derived from AAH #6 [PCGA02_30020_6007009]

description: Library name: PCGA02_30020_6007009


title: cMoP H3K4me2 CUTAC DE_1

description: Library name: K4me2_DE_1


title: intestinal contents,Young+YF,1

description: Library name: YY301


title: RNA from patient HTA3_80020, derived from AAH #5 [PCGA02_30020_6006008]

description: Library name: PCGA02_30020_6006008


title: RNA from patient HTA3_80020, derived from AAH #7 [PCGA02_30020_6008011]

description: Library name: PCGA02_30020_6008011


title: RNA from patient HTA3_80020, derived from AAH #4 [PCGA02_30020_6005007]

description: Library name: PCGA02_30020_6005007


title: CEBPa CUT&RUN in DC progenitors (batch 2)

description: Library name: CEBPa_DC_2

data_processing:
Paired-end reads were adapter-trimmed and aligned to the mm10 reference genome using CUT&RUNTools 2.0. Briefly, raw paired-end FASTQ files were trimmed using Trimmomatic with the following parameters: -phred33 ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25. Trimmed reads were aligned to mm10 using Bowtie2 with parameters --dovetail --phred33. Aligned reads were converted to BAM format and filtered using SAMtools to retain properly paired, mapped reads (-f 3 -F 4 -F 8), ensuring that both mates were uniquely aligned.
BigWig files were generated from BAM files using bam2bw from the cgpbigwig (v1.6.0) Docker image.
Peak calling was performed using MACS2 (v2.2.9.1) with matched IgG controls, using parameters -g mm -f BAMPE -q 0.1 --keep-dup all.
For differential binding analysis, peaks were first merged using HOMER (mergePeaks) and subsequently annotated using annotatePeaks.pl (mm10 -size given -raw). Differentially bound regions were identified using getDiffExpression.pl with an FDR threshold of 0.01, incorporating batch as a covariate.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG control samples)
Library strategy: CUT&Run

extract_protocol:
CUT&RUN on sorted BM lin- KIThi-int FLT3+ cells was performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher, Version 5) following the manufacturer’s protocol. A total of 5 × 105 cells were used per sample. Briefly, cells were immobilized on Concanavalin A-coated magnetic beads and incubated with 3 uL anti-C/EBPa antibody (8178S, Cell Signaling Technology) or 1 uL rabbit IgG negative control antibody (EpiCypher) in a total volume of 50 uL. After binding with pAG-MNase, chromatin digestion was initiated by addition of Ca2+ and incubated on ice for 30 minutes. Digested DNA fragments were released into the supernatant, purified using the DNA Clean & Concentrator-5 kit (ZYMO), and used for library preparation.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Briefly, end-repair and A-tailing were performed using the End Prep module at 20°C for 30 minutes followed by 50°C for 60 minutes. Adapters (1.875 pmol) were ligated at 20°C for 15 minutes followed by digestion with USER enzyme. Libraries were cleaned using 1.75× volumes of AMPure XP beads (Beckman Coulter) to retain short ligation products. PCR amplification was carried out for 14 cycles. Final libraries were size-selected using a two-step AMPure XP cleanup (0.8× followed by 1.2×) to enrich for fragments between 150–350 bp. Indexed libraries were pooled and sequenced as 150-bp paired-end reads on an Illumina NovaSeq X Plus platform.

value: Lin- KIThi-int FLT3+ cells

value: DC


title: RNA from patient HTA3_80020, derived from AAH #3 [PCGA02_30020_6003005]

description: Library name: PCGA02_30020_6003005


title: CEBPa CUT&RUN in DE progenitors (batch 2)

description: Library name: CEBPa_DE_2


title: RNA from patient HTA3_80020, derived from LUAD Region 1 (Stage 1A) [PCGA02_30020_6001001]

description: Library name: PCGA02_30020_6001001


title: IgG CUT&RUN in WT progenitors (batch 2)

description: Library name: IgG_WT_2


title: CEBPa CUT&RUN in WT progenitors (batch 2)

description: Library name: CEBPa_WT_2


title: RNA from patient HTA3_80019, derived from LUAD (Stage 0) [PCGA02_30019_6001001]

description: Library name: PCGA02_30019_6001001


title: RNA from patient HTA3_80019, derived from AAH [PCGA02_30019_6002002]

description: Library name: PCGA02_30019_6002002


title: RNA from patient HTA3_80019, derived from Normal [PCGA02_30019_6002003]

description: Library name: PCGA02_30019_6002003


title: CEBPa CUT&RUN in DE progenitors (batch 1)

description: Library name: CEBPa_DE_1


title: RNA from patient HTA3_80019, derived from AIS/MIA [PCGA02_30019_6003004]

description: Library name: PCGA02_30019_6003004


title: CEBPa CUT&RUN in WT progenitors (batch 1)

description: Library name: CEBPa_WT_1


title: Young4_Homo_Non_BT_cell

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GB14496

data_processing:
Sequencing was performed on an Illumina NovaSeq X Plus platform in single-read mode and 151 base reads were obtained.
Illumina RTA v4 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38.p4) reference genome using HISAT2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted with RNeasy micro kit (QIAGEN).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: spleen

tag: developmental stage

value: Young

value: Non-BT cells

value: Psmb8 G201V/G201V

value: No treatment


title: RNA from patient HTA3_80018, derived from LUAD Region 2 (Stage IIIA) [PCGA02_30018_6012011]

description: Library name: PCGA02_30018_6012011

value: Resected lung tissue


title: CEBPa CUT&RUN in DC progenitors (batch 1)

description: Library name: CEBPa_DC_1


title: cMoP H3K4me2 CUTAC WT_1

description: Library name: K4me2_WT_1

value: WT


title: RNA from patient HTA3_80018, derived from LUAD Region 1 (Stage IIIA) [PCGA02_30018_6010007]

description: Library name: PCGA02_30018_6010007


title: RNA from patient HTA3_80018, derived from AAH #2 [PCGA02_30018_6010010]

description: Library name: PCGA02_30018_6010010

value: AAH


title: Young4_WT_Non_BT_cell

description: Library name: GB14494

value: Psmb9 +/+


title: IgG CUT&RUN in WT progenitors (batch 1)

description: Library name: IgG_WT_1


title: RNA from patient HTA3_80018, derived from Normal #4 [PCGA02_30018_6008005]

description: Library name: PCGA02_30018_6008005

value: N


title: RNA from patient HTA3_80020, derived from Normal [PCGA02_30020_6002003]

description: Library name: PCGA02_30020_6002003


title: RNA from patient HTA3_80018, derived from Normal #5 [PCGA02_30018_6009006]

description: Library name: PCGA02_30018_6009006


title: Young3_Homo_Non_BT_cell

description: Library name: GB14495


title: Young4_WT_T_cell

description: Library name: GB14490

value: T cells


title: Young3_WT_Non_BT_cell

description: Library name: GB14493

value: Psmb8 +/+


title: RNA from patient HTA3_80018, derived from Normal #3 [PCGA02_30018_6007004]

description: Library name: PCGA02_30018_6007004


title: Young4_Homo_T_cell

description: Library name: GB14492


title: Young3_Homo_T_cell

description: Library name: GB14491


title: RNA from patient HTA3_80018, derived from Normal #2 [PCGA02_30018_6005003]

description: Library name: PCGA02_30018_6005003


title: RNA from patient HTA3_80018, derived from Normal #6 [PCGA02_30018_6003009]

description: Library name: PCGA02_30018_6003009


title: Young4_Homo_B_cell

description: Library name: GB14488

value: B cells


title: RNA from patient HTA3_80018, derived from AAH #1 [PCGA02_30018_6003001]

description: Library name: PCGA02_30018_6003001


title: Young3_WT_T_cell

description: Library name: GB14489


title: RNA from patient HTA3_80018, derived from Normal #1 [PCGA02_30018_6004002]

description: Library name: PCGA02_30018_6004002


title: Young3_Homo_B_cell

description: Library name: GB14487


title: RNA from patient HTA3_80005, derived from AIS/MIA [PCGA02_30005_6002004]

description: Library name: PCGA02_30005_6002004

value: AIS/MIA


title: Young4_WT_B_cell

description: Library name: GB14486


title: RNA from patient HTA3_80005, derived from AAH [PCGA02_30005_6003002]

description: Library name: PCGA02_30005_6003002


title: RNA from patient HTA3_80005, derived from LUAD (Stage 1A) [PCGA02_30005_6001003]

description: Library name: PCGA02_30005_6001003

value: ADC


title: RNA from patient HTA3_80005, derived from Normal [PCGA02_30005_6004001]

description: Library name: PCGA02_30005_6004001


title: RNA from patient HTA3_80002, derived from Normal [PCGA02_30002_6004001]

description: Library name: PCGA02_30002_6004001


title: Young3_WT_B_cell

description: Library name: GB14485


title: Young1_homo_Non_BT_cell

description: Library name: GB13379


title: RNA from patient HTA3_80002, derived from AAH [PCGA02_30002_6002002]

description: Library name: PCGA02_30002_6002002


title: RNA from patient HTA3_80002, derived from LUAD Region 1 (Stage 1A) [PCGA02_30002_6001003]

description: Library name: PCGA02_30002_6001003


title: Young2_WT_Non_BT_cell

description: Library name: GB13380


title: Young2_homo_T_cell

description: Library name: GB13375


title: Young1_WT_Non_BT_cell

description: Library name: GB13378


title: HEK293, KMT2F, input

city: Hyderabad

first: Shweta

last: Tyagi

state: Telangana

address: Opp. to Metro Rail Pillar No.NUP-9, Inner Ring Road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics (CDFD)

data_processing:
quality of raw sequence data from experimental (IP) and input DNA samples was assessed using FastQC version 0.11.4
Adapter removal from raw sequencing read pairs was performed using TrimGalore (v0.6.7)  or Trimmomatic.
The trimmed sequencing reads were then mapped to the customized human reference genome (hg38-rDNA) using indexed Bowtie2 (version 2.3.2). SAM files obtained after alignment were converted to BAM format using Samtools (version 1.9).
Sorting and indexing of BAM files was done using Samtools (version 1.9)
Visualization tracks were created using DeepTools (BamCoverage). Subsequently, BigWig (BW) files generated for input and experimental data (IP) post-BamCoverage were compared using BW Compare
Assembly: hg38-rDNA
Supplementary files format and content: BW

growth_protocol: DMEM, 10% FBS, 1% (v/v) GlutaMAX, and 100 U/ml penicillin-streptomycin

extract_protocol:
Cells were fixed with 1% formaldhyde for 10 minutes, after quenching with 125 mM  Glycine, cells were lysed and sonicated in Diagenode Bioruptor
Chip seq libariries were prepared using NEB Next Ultra II DNA Library preparation kit, 10ng of Experimental and input DNA was used for making libariries

value: Human embryonic kidney


title: RNA from patient HTA3_80002, derived from LUAD Region 2 (Stage 1A) [PCGA02_30002_6003004]

description: Library name: PCGA02_30002_6003004


title: Old-3_homo_Non_BT_cell

description: Library name: GB13377

value: Old


title: Old-3_WT_Non_BT_cell

description: Library name: GB13376

value: spleen


title: Young2_homo_Non_BT_cell

description: Library name: GB13381

value: Young


title: HEK293, KMT2A, ChIP

value: KMT2A (Bethyl# A300-374A)


title: Young1_WT_T_cell

description: Library name: GB13372


title: Young2_WT_T_cell

description: Library name: GB13374


title: Young1_homo_T_cell

description: Library name: GB13373

value: Psmb8 G201V/G201V


title: HEK293, KMT2A, input


title: Young2_homo_B_cell

description: Library name: GB13369

value: No treatment


title: Omental metastasis, patient 9

city: Nanchang

first: Shaolin

last: Ma

address: No.17 Yongwai Street

institute: The first affilated Hospital of Nanchang University

description:
Library name: MSL26OM
om26

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software and clean data (after removing reads containing adapter, reads containing ploy-N and low quality reads from raw data) were used for furhter analysis.
Assembly: The Hisat2 v2.0.5 were slected as the mapping tool and paired-end clean reads were aligned to the reference genome.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: omental metastasis

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions.
The library was constructed using the Fast RNA-seq Lib Prep Kit V2 (Cat. No. RK20306) according to the manufacturer's instructions.

value: omental metastasis

tag: tissue source

value: high-grade serous ovarain cancer


title: HEK293, KMT2F, ChIP

value: KMT2F (Bethyl # A300-289A)


title: Old-3_WT_T_cell

description: Library name: GB13370


title: Young2_WT_B_cell

description: Library name: GB13368


title: Omental metastasis, patient 7

description:
Library name: MSL13OM
om13


title: Old-3_homo_T_cell

description: Library name: GB13371


title: Omental metastasis, patient 5

description:
Library name: MSL2214OM
MSL2214M


title: Young1_homo_B_cell

description: Library name: GB13367


title: Omental metastasis, patient 6

description:
Library name: MSL2215OM
MSL2215M


title: GlycoRNA from HeLa cells

first: Yunlong

last: Chen

address: No. 163, Xianlin Avenue, Qixia District

department: School of Chemistry

institute: Nanjing University

description:
Library name: Sample1
SURFSeq 5000

data_processing:
Small RNA sequencing reads were annotated using SPORTS1.1 with one mismatch tolerance (-M 1).
Reads were sequentially mapped to non-coding RNA databases: miRBase 21, GtRNAdb, mitotRNAdb, rRNA/YRNA databases, piRBase/piRNABank, and Ensembl/Rfam 12.3.
tsRNAs were annotated based on pre‑tRNA and mature tRNA sequences; mature tRNAs were processed by removing introns, adding CCA to 3′ ends, and adding a 5′ G for histidine tRNAs. tsRNAs were categorized into 5′ tsRNA, 3′ tsRNA, 3′ tsRNA-CCA end, and internal tsRNAs.
rsRNAs were annotated by mapping small RNAs to parent rRNAs in ascending order of rRNA length to ensure unique assignment.
Differential expression analysis of small non‑coding RNAs (sncRNAs) was performed using DESeq2 (R package) with biological/technical replicates.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of SPORTS1.1 annotation results with columns: Length, Reads, Match, Genome, Annotation.

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM. All the media contained 10% FBS (Gibco), penicillin (100 μg/mL) and streptomycin (100 μg/mL), and all the cells were cultured at 37 °C under a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNAs from the Ac4GlcNAz metabolically labelled and then RNase treated HeLa cells were extracted with a traditional procedure using Trizol reagent.
Glycosylated RNA was enriched using the Ac4GlcNAz-based click chemistry and streptavidin magnetic beads as described. Both input and IP RNA were then subjected to PANDORA-seq library preparation using QIAseq miRNA Library Kit.

treatment_protocol: 40 mM of stocks of Ac4GlcNAc was prepared in DMSO. The metabolic labelling experiments were performed by incubating the cells in DMEM containing 40 μM of Ac4GlcNAc at 37 °C under a humidified 5% CO2 atmosphere for 48 h.

value: HeLa cells

value: epithelial cell

value: WT

value: 40uM Ac4GlcNAz, 48h


title: Omental metastasis, patient 4

description:
Library name: MSL2211OM
MSL2211OM


title: Old-3_homo_B_cell

description: Library name: GB13365

value: B cells


title: Old-2_homo_Non_BT_cell

description: Library name: GB13357

value: Non-BT cells


title: Omental metastasis, patient 8

description:
Library name: MSL21OM
om21


title: Omental metastasis, patient 3

description:
Library name: MSL2209OM
MSL2209OM


title: Old-1_homo_Non_BT_cell

description: Library name: GB13355


title: Young1_WT_B_cell

description: Library name: GB13366

value: Psmb8 +/+


title: Old-2_WT_Non_BT_cell

description: Library name: GB13356


title: Old-1_WT_Non_BT_cell

description: Library name: GB13354


title: Primary sites, patient 13

description:
Library name: MSL23OC
oc23

source_name: primary sites

value: primary sites


title: Primary sites, patient 14

description:
Library name: MSL27OC
oc27


title: Primary sites, patient 11

description:
Library name: MSL19OC
oc19


title: Old-3_WT_B_cell

description: Library name: GB13364

value: Old


title: Omental metastasis, patient 1

description:
Library name: MSL25OM
m25


title: Old-2_homo_T_cell

description: Library name: GB13353

value: spleen

value: T cells


title: Primary sites, patient 12

description:
Library name: MSL20OC
oc20


title: Old-1_homo_T_cell

description: Library name: GB13351


title: Primary sites, patient 10

description:
Library name: MSL18OC
oc18


title: Old-1_WT_T_cell

description: Library name: GB13350


title: Omental metastasis, patient 2

description:
Library name: MSL2208OM
MSL2208M


title: Old-2_homo_B_cell

description: Library name: GB13349


title: Primary sites, patient 9

description:
Library name: MSL13OC
oc13


title: Old-2_WT_B_cell

description: Library name: GB13348


title: Old-2_WT_T_cell

description: Library name: GB13352


title: Old-1_WT_B_cell

description: Library name: GB13346


title: Primary sites, patient 8

description:
Library name: MSL12OC
oc12


title: Old-1_homo_B_cell

description: Library name: GB13347


title: Primary sites, patient 5

description: Library name: MSL2214OC


title: Primary sites, patient 7

description: Library name: MSL2217OC


title: Primary sites, patient 4

description: Library name: MSL2211OC


title: Primary sites, patient 3

description: Library name: MSL2208OC


title: Primary sites, patient 6

description: Library name: MSL2215OC


title: Ribo_6072_homo

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

description: Library name: Sample 10

data_processing:
Basecalling with Illumina Casava 1.8 software
Quality filtering and 3' adapter trimming by Fastp 0.21.0
Library sorting based on sample barcode sequence by cutadapt 3.7
UMI extraction by UMI-tools 1.1.2
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Deduplication using UMI by UMI-tools 1.1.2
Read quantitation using custom scripts
Assembly: mm39
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-Seq

source_name: small intestine organoid

growth_protocol: Organoid basal medium with epithelial growth factor, Noggin, and R-spondin-1 for 3 days

extract_protocol:
Matrigel domes containing organoids were pulverized with 300 μl frozen lysis buffer using Multi-beads Shocker.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, ligation of preadenylated linker with T7 promoter, rRNA depeletion by riboPOOL for mouse (siTOOLs), in vitro transcription, ligation of another linker, reverse transcription, and PCR amplification. For RNA-Seq, SEQuoia Express Stranded RNA Library Prep Kit (Bio-Rad).

treatment_protocol: 0.5 μM 4-OHT for 24 hours

value: small intestine organoid


title: Primary sites, patient 2

description: Library name: MSL2207OC


title: Primary sites, patient 1

description: Library name: MSL2203OC


title: Ribo_6136_hetero

description: Library name: Sample 11


title: YTHDC1 (5096) eCLIP in K562 cells, INPUT replicate 2

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description:
Library name: YTHDC1_K562_5096_INPUT_rep2
YTHDC1_K562_5096.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for YTHDC1, biological replicate 2

data_processing:
Supplementary files format and content: Tab-delimited BED-like files containing reproducible enriched windows identified by eCLIP. Columns include: chromosome, start, end, feature type, enrichment odds ratio, p-value, FDR.
eCLIP data processing pipeline (Skipper v1.99.0)
Reads were trimmed, mapped to hg38 using STAR, deduplicated, and binding sites identified using beta-binomial model accounting for GC bias.
Reproducible enriched windows were identified at FDR < 0.2 across biological replicates.
Assembly: hg38
Supplementary files format and content: reproducible_enriched_windows.tsv.gz files contain reproducible enriched windows between two replicates (using uniquely mapped reads).
Supplementary files format and content: .bw files contain reads-per-million scaled read densities.
Library strategy: iCLIP

extract_protocol:
Cells were UV crosslinked at 400 mJ/cm2, lysed, and treated with RNase I. Target RBP was immunoprecipitated with specific antibody. RNA was dephosphorylated, ligated to 3' RNA adaptor, and run on SDS-PAGE. Protein-RNA complexes were transferred to nitrocellulose membrane, excised, and treated with proteinase K.
RNA was reverse transcribed with AffinityScript (Agilent) and size-selected on TBE-Urea gel. 5' Illumina adaptor was ligated, and cDNA was PCR amplified. Libraries were sequenced on Illumina platforms. Detailed protocol in Van Nostrand et al., 2017, DOI: 10.1007/978-1-4939-7204-3_14.

value: YTHDC1 (5096) eCLIP  INPUT


title: Ribo_6026_WT

description: Library name: Sample 7


title: YTHDC1 (5096) eCLIP in K562 cells, IP replicate 2

description:
Library name: YTHDC1_K562_5096_IP_rep2
YTHDC1_K562_5096.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for YTHDC1, biological replicate 2

value: YTHDC1 (5096) eCLIP  IP


title: Ribo_6028_WT

description: Library name: Sample 8


title: Ribo_6139_hetero

description: Library name: Sample 12


title: RNA_6136_hetero

description: Library name: Sample 5

data_processing:
Basecalling with Illumina Casava 1.8 software
Quality filtering and 3' adapter trimming by Fastp 0.21.0
Library sorting based on sample barcode sequence by cutadapt 3.7
UMI extraction by UMI-tools 1.1.2
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Deduplication using UMI by UMI-tools 1.1.2
Read quantitation using custom scripts
Assembly: mm39
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts


title: YTHDC1 (5096) eCLIP in K562 cells, IP replicate 1

description:
Library name: YTHDC1_K562_5096_IP_rep1
YTHDC1_K562_5096.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for YTHDC1, biological replicate 1


title: Ribo_6070_homo

description: Library name: Sample 9


title: RNA_6072_homo

description: Library name: Sample 4


title: YTHDC1 (5096) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: YTHDC1_K562_5096_INPUT_rep1
YTHDC1_K562_5096.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for YTHDC1, biological replicate 1


title: RNA_6139_hetero

description: Library name: Sample 6


title: RNA_6070_homo

description: Library name: Sample 3


title: RNA_6028_WT

description: Library name: Sample 2


title: WDR77 (5076) eCLIP in K562 cells, IP replicate 2

description:
Library name: WDR77_K562_5076_IP_rep2
WDR77_K562_5076.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for WDR77, biological replicate 2

value: WDR77 (5076) eCLIP  IP


title: WDR77 (5076) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: WDR77_K562_5076_INPUT_rep1
WDR77_K562_5076.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for WDR77, biological replicate 1

value: WDR77 (5076) eCLIP  INPUT


title: RNA_6026_WT

description: Library name: Sample 1


title: ovary,Aged+YF,2

description: Library name: RYA2

data_processing:
The raw data was filtered with SOAPnuke by removing readscontaining adapters
Removing reads whose unknown base ratio is more than 5%
Removing reads whose low-quality base ratio  is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format.
Assembly: The clean data were mapped to the assembled unique gene by Bowtie2.The expression level of genes was calculated by RSEM.
Supplementary files format and content: xlsx text file include TPM, FPKM, and Read count values for each sample

source_name: ovary

extract_protocol:
Total RNA extraction from mouse ovary by magnetic bead method
Low-input RNA-Seq library construction uses amplification of cDNA via SMART-SeqII combined with transposase-based library construction technique.

value: ovary

value: Fecal microbiota from young mice to aged mice


title: WDR77 (5076) eCLIP in K562 cells, IP replicate 1

description:
Library name: WDR77_K562_5076_IP_rep1
WDR77_K562_5076.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for WDR77, biological replicate 1


title: ovary,Aged+YF,3

description: Library name: RYA3


title: WDR77 (5076) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: WDR77_K562_5076_INPUT_rep2
WDR77_K562_5076.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for WDR77, biological replicate 2


title: USP10 (5089) eCLIP in K562 cells, IP replicate 2

description:
Library name: USP10_K562_5089_IP_rep2
USP10_K562_5089.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for USP10, biological replicate 2

value: USP10 (5089) eCLIP  IP


title: ovary,Aged+YF,1

description: Library name: RYA1

value: WT


title: ovary,Aged+AF,4

description: Library name: RAA4

value: Fecal microbiota from aged mice to aged mice


title: USP10 (5089) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: USP10_K562_5089_INPUT_rep1
USP10_K562_5089.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for USP10, biological replicate 1

value: USP10 (5089) eCLIP  INPUT


title: ovary,Aged+AF,3

description: Library name: RAA3


title: USP10 (5089) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: USP10_K562_5089_INPUT_rep2
USP10_K562_5089.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for USP10, biological replicate 2


title: ovary,Aged+YF,4

description: Library name: RYA4


title: UBAP2L (5090) eCLIP in K562 cells, IP replicate 2

description:
Library name: UBAP2L_K562_5090_IP_rep2
UBAP2L_K562_5090.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for UBAP2L, biological replicate 2

value: UBAP2L (5090) eCLIP  IP


title: ovary,Aged+AF,2

description: Library name: RAA2


title: UBAP2L (5090) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: UBAP2L_K562_5090_INPUT_rep2
UBAP2L_K562_5090.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for UBAP2L, biological replicate 2

value: UBAP2L (5090) eCLIP  INPUT


title: TIAL1 (5080) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TIAL1_K562_5080_INPUT_rep2
TIAL1_K562_5080.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TIAL1, biological replicate 2

value: TIAL1 (5080) eCLIP  INPUT


title: ovary,Young+YF,4

description: Library name: RYY4

value: Fecal microbiota from young mice to young mice


title: ovary,Young+YF,3

description: Library name: RYY3


title: USP10 (5089) eCLIP in K562 cells, IP replicate 1

description:
Library name: USP10_K562_5089_IP_rep1
USP10_K562_5089.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for USP10, biological replicate 1


title: UBAP2L (5090) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: UBAP2L_K562_5090_INPUT_rep1
UBAP2L_K562_5090.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for UBAP2L, biological replicate 1


title: ovary,Young+YF,2

description: Library name: RYY2


title: TIAL1 (5080) eCLIP in K562 cells, IP replicate 2

description:
Library name: TIAL1_K562_5080_IP_rep2
TIAL1_K562_5080.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TIAL1, biological replicate 2

value: TIAL1 (5080) eCLIP  IP


title: ovary,Aged+AF,1

description: Library name: RAA1


title: UBAP2L (5090) eCLIP in K562 cells, IP replicate 1

description:
Library name: UBAP2L_K562_5090_IP_rep1
UBAP2L_K562_5090.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for UBAP2L, biological replicate 1


title: TIAL1 (5080) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TIAL1_K562_5080_INPUT_rep1
TIAL1_K562_5080.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TIAL1, biological replicate 1


title: ovary,Young+YF,1

description: Library name: RYY1


title: TIAL1 (5080) eCLIP in K562 cells, IP replicate 1

description:
Library name: TIAL1_K562_5080_IP_rep1
TIAL1_K562_5080.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TIAL1, biological replicate 1


title: TIAL1 (5014) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TIAL1_K562_5014_INPUT_rep2
TIAL1_K562_5014.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TIAL1, biological replicate 2

value: TIAL1 (5014) eCLIP  INPUT


title: intestinal contents,Aged+AF,5

description: Library name: MCC5

data_processing:
Raw reads were filtered by SOAPnuke v2.2.1 to remove adapters and low-quality reads.
Clean reads were mapped to the host genome using SOAP2 to eliminate host contamination.
Assembly: De novo assembly was performed using MEGAHIT; contigs <300 bp were discarded.
Supplementary files format and content: An xlsx text file containing the species composition for each sample

extract_protocol:
Total genomic DNA was extracted from mouse intestinal contents using kit
The DNA of all microorganisms is directly extracted from environmental samples to construct a metagenomic WGS library.

value: intestinal contents


title: intestinal contents,Aged+AF,8

description: Library name: MCC8


title: TIAL1 (5014) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TIAL1_K562_5014_INPUT_rep1
TIAL1_K562_5014.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TIAL1, biological replicate 1


title: intestinal contents,Aged+AF,7

description: Library name: MCC7


title: TIAL1 (5014) eCLIP in K562 cells, IP replicate 2

description:
Library name: TIAL1_K562_5014_IP_rep2
TIAL1_K562_5014.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TIAL1, biological replicate 2

value: TIAL1 (5014) eCLIP  IP


title: TFAM (5069) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TFAM_K562_5069_INPUT_rep2
TFAM_K562_5069.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TFAM, biological replicate 2

value: TFAM (5069) eCLIP  INPUT


title: intestinal contents,Aged+AF,6

description: Library name: MCC6


title: TIAL1 (5014) eCLIP in K562 cells, IP replicate 1

description:
Library name: TIAL1_K562_5014_IP_rep1
TIAL1_K562_5014.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TIAL1, biological replicate 1


title: intestinal contents,Aged+AF,3

description: Library name: MCC3


title: TFAM (5069) eCLIP in K562 cells, IP replicate 2

description:
Library name: TFAM_K562_5069_IP_rep2
TFAM_K562_5069.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TFAM, biological replicate 2

value: TFAM (5069) eCLIP  IP


title: intestinal contents,Aged+AF,2

description: Library name: MCC2


title: intestinal contents,Aged+AF,4

description: Library name: MCC4


title: intestinal contents,Aged+AF,1

description: Library name: MCC1


title: intestinal contents,Aged+YF,8

description: Library name: MAA8


title: TFAM (5069) eCLIP in K562 cells, IP replicate 1

description:
Library name: TFAM_K562_5069_IP_rep1
TFAM_K562_5069.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TFAM, biological replicate 1


title: TAF15 (5013) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TAF15_K562_5013_INPUT_rep2
TAF15_K562_5013.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TAF15, biological replicate 2

value: TAF15 (5013) eCLIP  INPUT


title: TFAM (5069) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TFAM_K562_5069_INPUT_rep1
TFAM_K562_5069.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TFAM, biological replicate 1


title: intestinal contents,Aged+YF,7

description: Library name: MAA7


title: intestinal contents,Aged+YF,5

description: Library name: MAA5


title: TAF15 (5013) eCLIP in K562 cells, IP replicate 2

description:
Library name: TAF15_K562_5013_IP_rep2
TAF15_K562_5013.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TAF15, biological replicate 2

value: TAF15 (5013) eCLIP  IP


title: intestinal contents,Aged+YF,4

description: Library name: MAA4


title: TAF15 (5013) eCLIP in K562 cells, IP replicate 1

description:
Library name: TAF15_K562_5013_IP_rep1
TAF15_K562_5013.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for TAF15, biological replicate 1


title: SUZ12 (5033) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SUZ12_K562_5033_INPUT_rep2
SUZ12_K562_5033.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for SUZ12, biological replicate 2

value: SUZ12 (5033) eCLIP  INPUT


title: SUZ12 (5033) eCLIP in K562 cells, IP replicate 2

description:
Library name: SUZ12_K562_5033_IP_rep2
SUZ12_K562_5033.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for SUZ12, biological replicate 2

value: SUZ12 (5033) eCLIP  IP


title: TAF15 (5013) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TAF15_K562_5013_INPUT_rep1
TAF15_K562_5013.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for TAF15, biological replicate 1


title: intestinal contents,Aged+YF,1

description: Library name: MAA1


title: intestinal contents,Aged+YF,6

description: Library name: MAA6


title: SUZ12 (5033) eCLIP in K562 cells, IP replicate 1

description:
Library name: SUZ12_K562_5033_IP_rep1
SUZ12_K562_5033.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for SUZ12, biological replicate 1


title: intestinal contents,Aged+YF,2

description: Library name: MAA2


title: intestinal contents,Aged+YF,3

description: Library name: MAA3


title: intestinal contents,Young+YF,7

description: Library name: MYY7


title: intestinal contents,Young+YF,6

description: Library name: MYY6


title: SUZ12 (5033) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SUZ12_K562_5033_INPUT_rep1
SUZ12_K562_5033.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for SUZ12, biological replicate 1


title: RBM5 (5018) eCLIP in K562 cells, IP replicate 1

description:
Library name: RBM5_K562_5018_IP_rep1
RBM5_K562_5018.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM5, biological replicate 1

value: RBM5 (5018) eCLIP  IP


title: intestinal contents,Young+YF,8

description: Library name: MYY8


title: intestinal contents,Young+YF,5

description: Library name: MYY5


title: RBM15 (5008) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RBM15_K562_5008_INPUT_rep2
RBM15_K562_5008.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM15, biological replicate 2

value: RBM15 (5008) eCLIP  INPUT


title: RBM5 (5018) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RBM5_K562_5018_INPUT_rep1
RBM5_K562_5018.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM5, biological replicate 1

value: RBM5 (5018) eCLIP  INPUT


title: intestinal contents,Young+YF,3

description: Library name: MYY3


title: intestinal contents,Young+YF,2

description: Library name: MYY2


title: RBM5 (5018) eCLIP in K562 cells, IP replicate 2

description:
Library name: RBM5_K562_5018_IP_rep2
RBM5_K562_5018.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM5, biological replicate 2


title: RBM15 (5008) eCLIP in K562 cells, IP replicate 2

description:
Library name: RBM15_K562_5008_IP_rep2
RBM15_K562_5008.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM15, biological replicate 2

value: RBM15 (5008) eCLIP  IP


title: RBM15 (5008) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RBM15_K562_5008_INPUT_rep1
RBM15_K562_5008.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM15, biological replicate 1


title: RBM15 (5008) eCLIP in K562 cells, IP replicate 1

description:
Library name: RBM15_K562_5008_IP_rep1
RBM15_K562_5008.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM15, biological replicate 1


title: RBM5 (5018) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RBM5_K562_5018_INPUT_rep2
RBM5_K562_5018.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM5, biological replicate 2


title: intestinal contents,Young+YF,1

description: Library name: MYY1


title: Neurons_elavl3_6dpf_enucleated_MUT_SQ_rep2

city: Barcelona

first: Tahnee

last: Mackensen

address: Dr. Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: MUT_SQ_10

data_processing:
RNA-seq: Reads were mapped to the Danio rerio transcriptome (GRCz10) using Salmon (v 1.5.1). ATAC-seq: Read quality control and adapter trimming were performed using trimmomatic (v0.39). Reads were aligned to the Danio rerio genome (GRCz10) using bwa (v0.7.18), deduplicated and coordinate-sorted with biobambam2 (v2.0.183) and samtools (v1.21). Nucleosome-free fragments (1–120 bp) were selected and shifted to account for transposase binding sites using alignmentSieve from deeptools (v3.5.5). Consensus peak calling was performed using macs3 (v3.0.2) in narrowPeak mode. scRNA-seq: Sequencing data was processed using cellranger (v 6.1.2, 10X Genomics) and a reference was generated for the Danio rerio (zebrafish) genome assembly version GRCz10.9.
Assembly: Danio rerio (zebrafish) genome assembly version GRCz10
Supplementary files format and content: RNA-seq: comma separated file with raw gene counts. ATAC-seq: comma separated file with raw counts at peaks including all fragment lengths. Count table generation with featureCounts (v 2.0.8) with reads requiring 20% minimum overlap. scRNA-seq: HDF5 format files from cellranger count with filtered count matrix (barcodes passing QC).

organism: Danio rerio

source_name: FACS-sorted neurons from Tg(elavl3:GFP) background

extract_protocol:
For RNA-seq of neurons from non-treated samples RNA was harvested using trizol following the instructions for PhasemakerTM Tubes (Invitrogen, Cat. A33248) and from DMSO/drug-treated samples using PicoPure Mini RNA isolation kit (ThermoFisher, Cat:KIT0204). RIN values were between 7.7-10 and 20-35 ng of total RNA was used for the construction of sequencing libraries. ATAC-seq: Nuclear extraction with extraction buffer and Dounce homogenization, following Fernandez-Albert et al. 2019 (PMID: 31501571). Tn5 tagmentation as described in Buenrostro et al. 2013 (PMID: 24097267), with subsequent purification using a MinElute PCR purification kit (Qiagen). scRNA-seq: FACS-sorting into a 96-well plate to a final concentration of 0.04% BSA in 1 x PBS.
RNA-seq: Library construction was performed using the SMART-Seq v4 Ultra Low Input RNA kit in combination with the NEBNext Ultra II kit. ATAC-seq: Library amplification and barcoding were performed with NEBNext Q5 Hot Start HiFi PCR Master Mix (ref. M0543L, New England Biolabs) using dual index nextera primers, at a final concentration of 1.25 µM. scRNA-seq: Library construction was performed according to the manufacturer's instructions using the Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics).

treatment_protocol: For DMSO/drug-treated samples: zebrafish larvae were exposed to treatment + DMSO or to a matched % of control DMSO (maximum 0.1%) in the afternoon by adding the treatment directly to the media. They were left in the treatment for 16 - 18 h, and, if applicable enucleated (eyes removed with tungsten needle), and dissociated prior to FACS-sorting the following day.


title: intestinal contents,Young+YF,4

description: Library name: MYY4


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep9

description: Library name: WT_DMS_10

value: FACS-sorted neurons from Tg(elavl3:GFP) background

value: WT


title: Neurons_elavl3_6dpf_enucleated_MUT_ROL_rep2

description: Library name: MUT_ROL_9


title: QKI (5007) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: QKI_K562_5007_INPUT_rep2
QKI_K562_5007.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for QKI, biological replicate 2

value: QKI (5007) eCLIP  INPUT


title: PTBP1 (5030) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PTBP1_K562_5030_INPUT_rep2
PTBP1_K562_5030.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PTBP1, biological replicate 2

value: PTBP1 (5030) eCLIP  INPUT


title: QKI (5007) eCLIP in K562 cells, IP replicate 2

description:
Library name: QKI_K562_5007_IP_rep2
QKI_K562_5007.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for QKI, biological replicate 2

value: QKI (5007) eCLIP  IP


title: QKI (5007) eCLIP in K562 cells, IP replicate 1

description:
Library name: QKI_K562_5007_IP_rep1
QKI_K562_5007.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for QKI, biological replicate 1


title: PTBP1 (5030) eCLIP in K562 cells, IP replicate 2

description:
Library name: PTBP1_K562_5030_IP_rep2
PTBP1_K562_5030.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PTBP1, biological replicate 2

value: PTBP1 (5030) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_WT_SQ_rep2

description: Library name: WT_SQ_10


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep8

description: Library name: WT_DMS_9


title: Neurons_elavl3_6dpf_enucleated_MUT_ROL_rep1

description: Library name: MUT_ROL_8


title: Neurons_elavl3_6dpf_enucleated_WT_ROL_rep2

description: Library name: WT_ROL_9


title: Neurons_elavl3_6dpf_enucleated_MUT_SQ_rep1

description: Library name: MUT_SQ_8


title: PTBP1 (5030) eCLIP in K562 cells, IP replicate 1

description:
Library name: PTBP1_K562_5030_IP_rep1
PTBP1_K562_5030.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PTBP1, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep8

description: Library name: MUT_DMS_10


title: PTBP1 (5030) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PTBP1_K562_5030_INPUT_rep1
PTBP1_K562_5030.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PTBP1, biological replicate 1


title: PTBP1 (5015) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PTBP1_K562_5015_INPUT_rep2
PTBP1_K562_5015.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PTBP1, biological replicate 2

value: PTBP1 (5015) eCLIP  INPUT


title: QKI (5007) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: QKI_K562_5007_INPUT_rep1
QKI_K562_5007.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for QKI, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_WT_ROP_rep2

description: Library name: WT_ROP_6


title: PTBP1 (5015) eCLIP in K562 cells, IP replicate 2

description:
Library name: PTBP1_K562_5015_IP_rep2
PTBP1_K562_5015.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PTBP1, biological replicate 2

value: PTBP1 (5015) eCLIP  IP


title: PTBP1 (5015) eCLIP in K562 cells, IP replicate 1

description:
Library name: PTBP1_K562_5015_IP_rep1
PTBP1_K562_5015.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PTBP1, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_MUT_ROP_rep2

description: Library name: MUT_ROP_6


title: PRKRA (5068) eCLIP in K562 cells, IP replicate 1

description:
Library name: PRKRA_K562_5068_IP_rep1
PRKRA_K562_5068.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PRKRA, biological replicate 1

value: PRKRA (5068) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_WT_ROL_rep1

description: Library name: WT_ROL_8


title: PRK2 (5064) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PRK2_K562_5064_INPUT_rep2
PRK2_K562_5064.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PRK2, biological replicate 2

value: PRK2 (5064) eCLIP  INPUT


title: PTBP1 (5015) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PTBP1_K562_5015_INPUT_rep1
PTBP1_K562_5015.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PTBP1, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_MUT_PTZ_rep1

description: Library name: MUT_PTZ_2


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep7

description: Library name: MUT_DMS_8


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep2

description: Library name: MUT_DMS_2


title: PSMD4 (5077) eCLIP in K562 cells, IP replicate 1

description:
Library name: PSMD4_K562_5077_IP_rep1
PSMD4_K562_5077.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PSMD4, biological replicate 1

value: PSMD4 (5077) eCLIP  IP


title: PRK2 (5064) eCLIP in K562 cells, IP replicate 2

description:
Library name: PRK2_K562_5064_IP_rep2
PRK2_K562_5064.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PRK2, biological replicate 2

value: PRK2 (5064) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_MUT_FSK_rep2

description: Library name: MUT_FSK_2


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep7

description: Library name: WT_DMS_8


title: Neurons_elavl3_6dpf_enucleated_WT_SQ_rep1

description: Library name: WT_SQ_8


title: PSMD4 (5077) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PSMD4_K562_5077_INPUT_rep2
PSMD4_K562_5077.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PSMD4, biological replicate 2

value: PSMD4 (5077) eCLIP  INPUT


title: Neurons_elavl3_6dpf_enucleated_WT_CLO_rep2

description: Library name: WT_CLO_6


title: PRKRA (5068) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PRKRA_K562_5068_INPUT_rep1
PRKRA_K562_5068.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PRKRA, biological replicate 1

value: PRKRA (5068) eCLIP  INPUT


title: Neurons_elavl3_6dpf_enucleated_MUT_CLO_rep2

description: Library name: MUT_CLO_6


title: PSMD4 (5077) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PSMD4_K562_5077_INPUT_rep1
PSMD4_K562_5077.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PSMD4, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep6

description: Library name: WT_DMS_6


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep6

description: Library name: MUT_DMS_6


title: PRKRA (5068) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PRKRA_K562_5068_INPUT_rep2
PRKRA_K562_5068.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PRKRA, biological replicate 2


title: PSMD4 (5077) eCLIP in K562 cells, IP replicate 2

description:
Library name: PSMD4_K562_5077_IP_rep2
PSMD4_K562_5077.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PSMD4, biological replicate 2