title: PRK2 (5064) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PRK2_K562_5064_INPUT_rep1
PRK2_K562_5064.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PRK2, biological replicate 1


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

status: Public on Apr 24 2026

type: SRA

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

country: USA

institute: UCSD

description:
Library name: PRKRA_K562_5068_IP_rep2
PRKRA_K562_5068.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PRKRA, biological replicate 2

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

tag: cell line

tag: treatment

value: PRKRA (5068) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_WT_FSK_rep2

city: Barcelona

first: Tahnee

last: Mackensen

address: Dr. Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: WT_FSK_2

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).

molecule: polyA RNA

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.

tag: cell type

tag: genotype

value: WT

tag: developmental stage

tag: batch


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep2

description: Library name: WT_DMS_2

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


title: Neurons_elavl3_6dpf_enucleated_MUT_FSK_rep1

description: Library name: MUT_FSK_1


title: PDCD4 (5075) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PDCD4_K562_5075_INPUT_rep2
PDCD4_K562_5075.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PDCD4, biological replicate 2

value: PDCD4 (5075) eCLIP  INPUT


title: snRNA-seq, MAFB induced

city: Santa Cruz

first: Bradley

last: Colquitt

address: 1156 High St, Sinsheimer Labs 329

institute: University of California, Santa Cruz

description: Library name: MAFBp

library_source: transcriptomic single cell

data_processing:
FASTQ files were mapped using Illumina DRAGEN 4.4.6000 to a custom chicken reference index consisting of a chicken assembly (bGalGal1.mat.broiler.GRCg7b, GCF_016699485.2) combined with either the pPIDNB2-MAFB or pPIDNB2-EMX2 sequence. Using Seurat v5.2.1, nuclei were removed that had greater than 2% mitochondrial reads, greater than 20,000 UMIs, and less than 1000 UMIs. Gene expression was then normalized using SCTransform, transformed via principal components analysis, then reduced using uniform manifold approximate projection (UMAP) and the first 30 PCs.
Assembly: bGalGal1.mat.broiler.GRCg7b, GCF_016699485.2
Supplementary files format and content: DRAGEN output files: filtered.barcodes.tsv.gz, filtered.features.tsv.gz, filtered.matrix.mtx.gz

organism: Gallus gallus

source_name: telencephalon

extract_protocol:
For snRNA-seq, microdissected tissue from chicken embryos was pooled by condition (e.g. tissue from all pPIDNB2-MAFB electroporated, doxycycline treated individuals was combined) before proceeding to nucleus isolation. Nuclei were isolated using a modified version of the Optiprep method.  Several stable buffers were prepared before nuclei isolation and stored a 4C: 1.079x Homogenization Buffer Stable Solution ("HBS", 260 mM sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH pH 7.8), Diluent Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH pH 7.8), 50% iodixanol solution (diluted from 60% Optiprep Density Gradient Medium, Sigma, D1556, using Diluent Buffer), and 5X ATAC-RSB (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 15 mM MgCl2). On the day of nuclei isolation, the following buffers were prepared: 1x Homogenization Buffer Unstable Solution ("HBU", HBS to 1x, 1 mM DTT, 0.5 mM spermidine, 0.15 mM spermine, 0.3\% NP-40, 0.2 U/uL Protector RNase Inhibitor (Sigma 3335402001, 10 mg/mL Kollidon VA-64 (Sigma, 190845)), 1x Complete Protease Inhibitor (prepared from a 25x solution consisting of one tablet (Sigma, 11697498001) dissolved in 2 mL nuclease-free water)), 30\% Iodixanol Solution and 40\% Iodixanol Solution (both diluted from 50\% iodixonal solution using 1x Homogenization Buffer Unstable Solution), and ATAC-RSB-Tween (1x ATAC-RSB, 0.1\% Tween-20, 1% BSA, and 1 U/uL Protector RNase Inhibitor). Samples from different birds were pooled and 1 mL 1x HBU was added. Samples were incubated on ice for 5 minutes, then transferred to a 2 mL glass dounce (Kimble). Samples were homogenized with 15 strokes of the loose pestle, then 15 strokes of the tight pestle. Samples were transferred to 2 mL tubes then centrifuged for 5 minutes at 350xg at 4degreeC using a swing-out rotor. All but 200 uL of supernatant was removed, the total volume was brought up to 400 uL using 1x HBU, then the pellet was gently resuspended by pipetting. 400 uL 50% iodixanol solution was added and mixed well by pipetting. 600 uL 30% iodixanol solution was layered underneath the 25% iodixonal/tissue layer, followed by 600 uL 40% iodixanol solution underneath the 30% layer. In a pre-chilled swing-out rotor, samples were centrifuged for 20 minutes at 10,000xg at 4C with the brake off. Starting at the top of the solution, enough solution was aspirated off to leave 200-300 uL above the interface between the 30% and 40% iodixanol layers, which contains nuclei. 200 uL of the nuclei band was aspirated and transferred to a clean 1.5 mL tube containing 1 mL of ATAC-RSB-Tween. Nuclei were centrifuged for 10 minutes at 500xg at 4C using a swing-out rotor. Following isolation, nuclei were washed in 1 mL of Illumina Nuclei Suspension Buffer (NSB) and pelleted by centrifugation at 500 × g for 5 minutes at 4℃ according to Illumina Single Cell 3′ RNA Prep protocol. Nuclei were resuspended in 20uL of NSB before counting. Nuclei were counted Revvity Cellometer K2 Fluorescent Cell Counter and diluted to 2500 nuclei/uL in NSB for samples at higher concentrations.
snRNA-seq libraries were prepared according to the Illumina Single Cell 3′ RNA Prep, T2 protocol. Reactions were overloaded with 10,000 nuclei for samples whose concentrations supported this. Library concentrations were quantified using NEBNext Library Quant Kit for Illumina (NEB, E7630) before pooling. Libraries were sequenced on an AVITI PE150 flow cell at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center.

tag: tissue

value: telencephalon

tag: age


title: Grp2-7

type: RNA

city: Watertown

first: Borislav

last: Dejanovic

address: 100 Forge Rd

institute: Vigil Neuroscience

description: Gene expression profiles detected using the MERSCOPE™ platform with the customized panel.

hyb_protocol: Probe hybridization follows 'FFPE Tissue Sample Preparation User Guide' Rev D (or fresh frozen?)

scan_protocol: MERFISH images were scanned on MERSCOPE™ platform provided by Vizgen

data_processing:
cell segmentation, cell-by-gene matrix and cell-metadata matrix follow MERSCOPE™ software version 234 provided by Vizgen
Individual transcript count per cell are presented in cell-by-gene matrix. Values in cell-metadata matrix are defined in 'MERSCOPE Instrument User Guide' Rev H

label: MERFISH

organism: Mus musculus

source_name: Brain

growth_protocol: 5xFAD;hTREM2 mice were aged to 7 months at the start of the experiment.

treatment_protocol: Mice were dosed orally with 30mg/kg of VG-3909. 12 hours post-dose, mice were perfused with ice-cold saline and brains were rapidly extracted and frozen, followed by cryostat sectioning.

value: 5xFAD;hTREM2 amyloidosis mouse

tag: dosing

value: Vehicle

value: 7 months

tag: Sex

value: male


title: Grp2-4


title: Grp2-6


title: snRNA-seq, EMX2 induced

description: Library name: EMX2p


title: AdV-iCD47-Fe3O4@PACM_3

city: Nantong

first: Jie

last: Dong

address: Qixiu road 19

country: China

institute: Nantong University

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt: AdV-iCD47-Fe3O4@PACM

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters- mismath cost 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction:0.8)
Supplementary files format and content: csv file include FPKM values for all the Samples:20260413.csv

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tumor

value: TAM

value: Macrophage

value: 24 hours


title: PDCD4 (5075) eCLIP in K562 cells, IP replicate 1

description:
Library name: PDCD4_K562_5075_IP_rep1
PDCD4_K562_5075.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PDCD4, biological replicate 1

value: PDCD4 (5075) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep1

description: Library name: WT_DMS_1


title: PDCD4 (5075) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PDCD4_K562_5075_INPUT_rep1
PDCD4_K562_5075.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PDCD4, biological replicate 1


title: Grp1-2


title: Grp2-5


title: Grp1-1


title: PDCD4 (5075) eCLIP in K562 cells, IP replicate 2

description:
Library name: PDCD4_K562_5075_IP_rep2
PDCD4_K562_5075.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PDCD4, biological replicate 2


title: Neurons_elavl3_6dpf_enucleated_WT_FSK_rep1

description: Library name: WT_FSK_1


title: AdV-iCD47-Fe3O4@PACM_2

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt: AdV-iCD47-Fe3O4@PACM


title: Grp1-3


title: Neurons_elavl3_5dpf_MUT_rep2

description: Library name: Neurons_HuC_5dpf_Srrm3_17_KO_b_quant_25_Dr10


title: AdV-Fe3O4@PACM_3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt: AdV-Fe3O4@PACM


title: NOP2 (5098) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NOP2_K562_5098_INPUT_rep2
NOP2_K562_5098.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NOP2, biological replicate 2

value: NOP2 (5098) eCLIP  INPUT


title: AdV-iCD47-Fe3O4@PACM_1

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt: AdV-iCD47-Fe3O4@PACM


title: Neurons_elavl3_5dpf_MUT_rep1

description: Library name: Neurons_HuC_5dpf_Srrm3_17_KO_a_quant_25_Dr10


title: AdV-Fe3O4@PACM_2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt: AdV-Fe3O4@PACM


title: Neurons_elavl3_6dpf_enucleated_WT_PTZ_rep1

description: Library name: WT_PTZ_2


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep1

description: Library name: MUT_DMS_1


title: snRNA-seq, MAFB uninduced

description: Library name: MAFBn


title: PRK2 (5064) eCLIP in K562 cells, IP replicate 1

description:
Library name: PRK2_K562_5064_IP_rep1
PRK2_K562_5064.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PRK2, biological replicate 1

value: PRK2 (5064) eCLIP  IP


title: NOP2 (5098) eCLIP in K562 cells, IP replicate 2

description:
Library name: NOP2_K562_5098_IP_rep2
NOP2_K562_5098.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NOP2, biological replicate 2

value: NOP2 (5098) eCLIP  IP


title: Neurons_elavl3_5dpf_WT_rep2

description: Library name: Neurons_HuC_5dpf_Srrm3_17_WT_b_quant_25_Dr10


title: NOP2 (5098) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NOP2_K562_5098_INPUT_rep1
NOP2_K562_5098.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NOP2, biological replicate 1


title: Neurons_elavl3_5dpf_WT_rep1

description: Library name: Neurons_HuC_5dpf_Srrm3_17_WT_a_quant_25_Dr10


title: RNA-seq of scramble siRNA PYMT-R221A replicate #2

city: Montreal

first: Shafaat A.

last: Rabbani

state: QC

address: 1001 Bd Décarie

country: Canada

institute: McGill University

description: Library name: siRNA_C_2_RNA

data_processing:
Raw sequencing reads (FASTQ files) were aligned to the reference genome of Mus musculus (mm10/GRCm38.p6) using the DRAGEN RNA v4.1.23 tool.
DESeq2 (v1.44.0) was used for differential expression analysis (50).
Group comparisons (treatment versus control; siMbd2 versus scramble) were performed using generalized linear models, and p-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate method.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Processed data file (Genes.RawCounts.csv) containing raw gene counts for all 12 samples. Rows correspond to genes and columns correspond to samples. Values represent raw read counts obtained from RNA-seq. This file includes samples from wildtype PYMT-R221A cells, KCC-07-treated cells, siMbd2 knockdown cells, and siRNA scramble controls.

extract_protocol:
Total RNA was extracted from control, 40 µM KCC-07-treated, PyMT-R221A, scramble, and siMbd2-treated cells using the RNeasy kit from Qiagen (Catalog # 71404; Hilden, Germany) in accordance with the manufacturer’s protocol.
Their integrity was confirmed with an Agilent 2100 Bioanalyzer and subsequently sequenced on a NovaSeq X platform.

value: biol rep 2


title: AdV-Fe3O4@PACM_1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt: AdV-Fe3O4@PACM

value: WT


title: RNA-seq of scramble siRNA PYMT-R221A replicate #3

description: Library name: siRNA_C_3_RNA

value: biol rep 3


title: Collagen, wounded, 72 hrs

city: Irvine

first: Wendy

middle: F

last: Liu

email: wendy.liu@uci.edu, enriqud2@uci.edu

state: California

address: 419 S. Circle View Drive

department: Biomedical Engineering

institute: University of California Irvine

description:
Library name: Sample 2
Processed data is contained within wounded_filtered_matrix.h5

data_processing:
Raw sequencing reads were processed using Cell Ranger version 3.1.0 (10x Genomics).
Reads were aligned to the mouse reference transcriptome (mm10-3.0.0) and quantified.
Cell Ranger's default cell-calling algorithm was used to distinguish valid cell barcodes from empty droplets to generate the filtered feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Processed data are provided in HDF5 (.h5) format, generated by the Cell Ranger 'count' pipeline (v3.1.0). Each file contains the filtered feature-barcode matrix including gene expression counts (UMI counts), feature (gene) names, and cell barcodes for each sample.

growth_protocol: Monocytes were harvested from the bone marrow of 6–12-week-old C57BL/J6 mice and differentiated into bone marrow-derived macrophages (BMDMs) using DMEM supplemented with 10% of MCSF, 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin for 7 days. NIH/3T3 fibroblasts were cultured below 85% confluency in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin and used between passages 3-12. BMDMs and 3T3s were cocultured at a 1:1 ratio for 48 hours within collagen gels.

extract_protocol:
Collagen gels were digested with collagenase (10 mg/mL, Fisher Scientific) for 10 minutes, and a Dead Cell Removal kit (Miltenyi Biotec) was used according to the manufacturer’s instructions to deplete dead cells. The resulting single-cell suspension was loaded onto the 10x Genomics Chromium Controller for single-cell droplet generation, cell lysis, and RNA barcoding.
Single-cell RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq instrument using 100-cycle paired-end (PE) sequencing.

treatment_protocol: After 48 hours of coculture (BMDMs + NIH/3T3), collagen gels were punctured with a 0.2 mm blunt needle and incubated for additional 72 hours.

value: Bone marrow-derived macrophages, fibroblasts

value: WT, WT

value: 0.2 mm puncture


title: Collagen, unwounded, 72 hrs

description:
Library name: Sample 1
Processed data is contained within unwounded_filtered_matrix.h5


title: RNA-seq of scramble siRNA PYMT-R221A replicate #1

description: Library name: siRNA_C_1_RNA

value: biol rep 1


title: NKRF (5005) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NKRF_K562_5005_INPUT_rep2
NKRF_K562_5005.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NKRF, biological replicate 2

value: NKRF (5005) eCLIP  INPUT


title: RNA-seq of siMBD2-transfected PYMT-R221A replicate #2

description: Library name: siMBD2_2_RNA


title: RNA-seq of siMBD2-transfected PYMT-R221A replicate #3

description: Library name: siMBD2_3_RNA


title: RNA-seq of KCC-treated PYMT-R221A replicate #3

description: Library name: KCC_4_PyMT_RNA


title: NKRF (5005) eCLIP in K562 cells, IP replicate 2

description:
Library name: NKRF_K562_5005_IP_rep2
NKRF_K562_5005.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NKRF, biological replicate 2

value: NKRF (5005) eCLIP  IP


title: Ngn3OE

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: Library name: Ngn3OE

library_source: genomic

data_processing:
Raw reads were filtered and trimmed to remove adapters using Trimmomatic to obtain clean reads. The clean reads were aligned to the mouse reference genome (mm10) using Bowtie2. Duplicated reads were removed using Picard; Mitochondrial reads were removed using samtools; ENCODE blacklist regions were removed using bedtools intersect command; fragments ≤ 120 bp was extracted for downstream accessible peak analyses. Before peak calling, to account for the 9 bp duplication generated during Tn5 transposase fragmentation step, all reads were shifted +4 bp and -5 bp for positive and negative strand respectively using deepTools’ alignmentSieve command. Accessible region read peaks of each sample were called using MACS2 with parameters set as: -f BAMPE -q 0.05.
Assembly: mm10
Supplementary files format and content: peaks called by MACS2 was given in narrowPeak format

molecule: genomic DNA

source_name: retina

extract_protocol:
5x104 FACS sorted cells were used for each ATAC-seq library construction. Cells were lysed using Lysis buffer (10mM Tris-HCl, 10mM NaCl2, 3mM MgCl2, 0.1% Igepal CA-30, 0.1% Tween 20).
After lysis, nuclei were collected by 500g centrifugation for 5 minutes at 4 ℃, and immediately resuspended in Tn5 fragmentation reaction mixture (Vazyme) at 37 ℃ for 30 min. Fragments were then purified using VAHTS DNA clean Beads (Vazyme), and proceeded for library construction by PCR using TruePrep Index Kit V2 for Illumina primers (Vazyme).

value: retina

value: retinal progenitor cells


title: RNA-seq of KCC-treated PYMT-R221A replicate #2

description: Library name: KCC_2_PyMT_RNA


title: RNA-seq of KCC-treated PYMT-R221A replicate #1

description: Library name: KCC_1_PyMT_RNA


title: RNA-seq of siMBD2-transfected PYMT-R221A replicate #1

description: Library name: siMBD2_1_RNA


title: NKRF (5005) eCLIP in K562 cells, IP replicate 1

description:
Library name: NKRF_K562_5005_IP_rep1
NKRF_K562_5005.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NKRF, biological replicate 1


title: NKRF (5005) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NKRF_K562_5005_INPUT_rep1
NKRF_K562_5005.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NKRF, biological replicate 1


title: Ctrl

description: Library name: Ctrl


title: Ngn3-3

description: Library name: Ngn3-3

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: read counts for each genes were given in the processed data files

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol


title: NOP2 (5098) eCLIP in K562 cells, IP replicate 1

description:
Library name: NOP2_K562_5098_IP_rep1
NOP2_K562_5098.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NOP2, biological replicate 1


title: RNA-seq of Control PYMT-R221A replicate #3

description: Library name: C_4_PyMT_RNA

value: control


title: Ngn3-2

description: Library name: Ngn3-2


title: RNA-seq of Control PYMT-R221A replicate #2

description: Library name: C_2_PyMT_RNA


title: NCL (5086) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NCL_K562_5086_INPUT_rep2
NCL_K562_5086.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NCL, biological replicate 2

value: NCL (5086) eCLIP  INPUT


title: Ccl25-flox Foxn1-Cre-Tg mouse thymic stromal cells

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: Library name: Ccl25-flox Foxn1-Cre-Tg

data_processing:
Base calling was performed using RTA 3.4.4
Demultiplexing with fastq generation was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0)
Parsing and handling of cell barcodes, UMI's, and alignment and quantification of reads was performed using v7.1.0 (STAR 2.7.2a). Reference used was 10x Genomics provided annotated mouse reference (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: filtered data matrix in HDF5 format (.h5)

source_name: thymus

extract_protocol:
Enzymatically digested thymic cells were mixed with Anti-CD45 MicroBeads to deplete hematopoietic cells. Single cell suspensions were generated and loaded onto the 10x Genomics Chromium platform following manufacturer recommendations in Chromium Next GEM Single Cell 3’v3.1 (Dual Index) User Guide. Cells were lysed and polyA transcripts from each partitioned cell were reverse transcribed and single cell barcoded.
Library construction of single-cell barcoded cDNA libraries was performed on the 10x Genomics Chromium Connect instrument following manufacturer recommendations. In short, cDNA libraries were fragmented, had adapters ligated, and sample indices and additional Illumina sequencing adapters added on by limited cycle PCR. Libraries were quantified, normalized and loaded on a NovaSeq 6000 instrument using 10x Genomics recommended run parameters.

value: thymus


title: Ngn3-1

description: Library name: Ngn3-1


title: Ccl25-flox Wt mouse thymic stromal cells

description: Library name: Ccl25-flox Wt


title: RNA-seq of Control PYMT-R221A replicate #1

description: Library name: C_1_PyMT_RNA


title: CDI Host Colon

city: Cincinnati

first: Rajat

last: Madan

state: OH

address: 231 Albert Sabin Way

department: Infectious Disease

institute: University of Cincinnati

description:
Library name: Colon_CDI
10X Genomics
Mouse_Neutrophils_Colon_CDI_Seurat.rds

data_processing:
Cell Ranger 7.0.0 (https://www.10xgenomics.com/) was utilized for sequencing read alignment to the mm10 mouse transcriptome, quantification of the expression of cellular transcripts, and to generate a matrix file with expression counts for each sample, with genes as rows and cell Unique Molecular Identifier (UMI) as columns. HDF5 file formats were produced and utilized for analysis in Seurat using the Read10X_h5 function.
Assembly: Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol.
Supplementary files format and content: Processed file formats are in rds format. Mouse_Neutrophils_BM_Blood_CDI_Control_Seurat.rds contains processed bone marrow and blood neutrophils from uninfected and C. difficile-infected hosts.Mouse_Neutrophils_Colon_CDI_Seurat.rds contains processed colon neutrophils from a C. difficile-infected host.

source_name: Colon

extract_protocol:
Bone marrow cells were harvested from naïve and C. difficile-infected mice by flushing cleaned femur and tibia with ice cold phosphate-buffered saline (PBS) containing 2% fetal bovine serum (FBS) and red blood cells were lysed using ACK lysing buffer. Blood was obtained by intra-cardiac puncture from naïve and C. difficile-infected mice and collected in ethylenediaminetetraacetic acid microtainers, followed by an RBC lysis with ACK lysing buffer. For lamina propria leukocyte isolation, approximately 2 cm sections were excised from cecal tissue of C. difficile-infected mice and cleaned by gentle shaking in buffer A (HBSS with 5% FBS and 25mM HEPES) two times. Clean tissue was transferred to Buffer B (HBSS buffer with 2mM EDTA and 25mM HEPES) and vortexed vigorously to remove mucus layer. Samples were then incubated at 37oC shaking water bath in a buffer containing HBSS + 15 mM HEPES + 5 mM EDTA + 10% FBS + 0.015% or 1mM Dithiothreitol. Resulting tissue was mechanically minced and digested enzymatically in Iscove’s media containing liberase TL (Roche; 0.17 mg/ml) and DNase (Sigma; 30 ug/ml) for 30 min in a 37oC shaking water bath. Samples underwent further dissociation using gentleMACS™ Dissociator. Samples were resuspended in Buffer B and then filtered with a 100 µm filter. Final cell suspension was prepared in 1 x PBS with 1U/µl of RNase inhibitor. Neutrophils from each tissue were magnetically sorted using MACS MS columns (Miltenyi Biotech #130-097-658, Germany) according to the manufacturer’s instructions. Neutrophil sorting buffer was supplemented with 1U/µl of RNase inhibitor. For colon samples, in addition to magnetic beads that were part of the kit, mouse CD326 (EpCAM) MicroBeads were also used to select out EpCAM+ cells and thus reduce the amount of intestinal epithelial cells. Cells were then resuspended in 1 x PBS with 1U/µl RNase inhibitor and 10% FBS at room temperature. Cell viability was determined by trypan blue exclusion. All samples sent for sequencing had viability >70%. Sequencing was performed using Chromium X scRNAseq and Illumina platform equipment at CCHMC Single Cell Genomics Core. For cell preparation, NextGEM assay was used and sequencing with 3'v3.1 assay chemistry.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol.

value: Colon

tag: strain

value: Neutrophil-enriched cells

value: Male

value: C. difficile 10^6 M7404 spores

value: 12 weeks


title: NCL (5086) eCLIP in K562 cells, IP replicate 2

description:
Library name: NCL_K562_5086_IP_rep2
NCL_K562_5086.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NCL, biological replicate 2

value: NCL (5086) eCLIP  IP


title: CDI Host Blood

description:
Library name: Blood_CDI
10X Genomics
Mouse_Neutrophils_BM_Blood_CDI_Control_Seurat.rds

source_name: Peripheral Blood

value: Peripheral Blood


title: Ctl-3

description: Library name: Ctl-3


title: NCL (5086) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NCL_K562_5086_INPUT_rep1
NCL_K562_5086.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NCL, biological replicate 1


title: CDI Host Bone Marrow

description:
Library name: BM_CDI
10X Genomics
Mouse_Neutrophils_BM_Blood_CDI_Control_Seurat.rds

source_name: Bone Marrow

value: Bone Marrow


title: Ctl-2

description: Library name: Ctl-2


title: Uninfected Host Blood

description:
Library name: Blood_control
10X Genomics
Mouse_Neutrophils_BM_Blood_CDI_Control_Seurat.rds

value: Untreated

value: 10 weeks


title: NCL (5086) eCLIP in K562 cells, IP replicate 1

description:
Library name: NCL_K562_5086_IP_rep1
NCL_K562_5086.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NCL, biological replicate 1


title: Ctl-1

description: Library name: Ctl-1


title: Uninfected Host Bone Marrow

description:
Library name: BM_control
10X Genomics
Mouse_Neutrophils_BM_Blood_CDI_Control_Seurat.rds


title: LARS (5082) eCLIP in K562 cells, IP replicate 2

description:
Library name: LARS_K562_5082_IP_rep2
LARS_K562_5082.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for LARS, biological replicate 2

value: LARS (5082) eCLIP  IP


title: LARS (5082) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: LARS_K562_5082_INPUT_rep1
LARS_K562_5082.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for LARS, biological replicate 1

value: LARS (5082) eCLIP  INPUT


title: P6.5_45

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description:
Library name: P6_5_45
SMART-Seq2

data_processing:
The RNA-seq data were first subjected to adaptor trimming and low-quality read filtering with flexbar (version 2.5).
The trimmed paired-end reads were then aligned to the human reference genome (mm10) by STAR (version 2.7.10b) under the parameters: -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated.
HTSeq (v0.13.5) was employed for gene expression quantification.
RSEM (v1.3.3) was employed for gene expression normalization as FPKM
Assembly: mm10
Supplementary files format and content: gzipped tsv, FPKM values, gene expression levels
Supplementary files format and content: gzipped tsv, gene expression read counts

source_name: female germ cell

extract_protocol:
Each sample is lysed using a 2 µL lysis buffer with 0.2% TritonX-100 and 40 U/mL Recombinant RNase Inhibitor, which disrupts cell membranes to release RNA and other cellular contents while preventing RNA degradation.
Transcriptome libraries were prepared following the Smart-seq2 protocol. Sequencing libraries were constructed by using KAPA HyperPlus Kit according to the manufacturer’s instructions.  All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 150-bp paired-end mode.

value: female germ cell

tag: Stage


title: P6.5_44

description:
Library name: P6_5_44
SMART-Seq2


title: Top2b_Homo_rep3

city: Tokyo

first: Chiaki

last: Ohtaka-Maruyama

state: Tokyo

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Developmental Neuroscience Project

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: Library name: N22.R1.2.dNdN

data_processing:
Sequencing was performed on the DNBSEQ-T7 platform (MGI Tech) with a paired-end 150 bp (PE150) strategy, generating >20 million read-pairs per sample.
Assembly: Mus musculus (mm39)
Supplementary files format and content: Raw count matrix (text/tab-separated format) containing unnormalized gene-level read counts for all samples generated by RSEM.

source_name: brain

growth_protocol: Mice were housed in an animal facility maintained at 23 °C ± 1 °C and 50 % ± 10 % relative humidity under a 12 h/12 h light/dark cycle (lights on at 8:00 AM, off at 8:00 PM). Food and water were freely available. Mice were grown until 10 weeks of age prior to tissue extraction.

extract_protocol:
Mice were deeply anesthetized with an inhalation anesthetic (isoflurane) prior to euthanasia by cervical dislocation. Total RNA was extracted from the whole left brain of 10-week-old mice using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions. RNA integrity was evaluated using the Agilent Fragment Analyzer.
RNA sequencing libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Polyadenylated mRNA was enriched from 400 ng of total RNA using oligo-dT magnetic beads, fragmented, and reverse-transcribed into first-strand cDNA using random hexamer primers. Following second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and size selection, the libraries were amplified and purified. Libraries were circularized using the MGIEasy Universal Library Conversion Kit (MGI Tech).

treatment_protocol: No specific chemical or drug treatment was applied. Wild-type and Top2b-low expressing homozygous male mice were used. The Top2bL/L mice carry an auxin-inducible degron (AID) tag at the 5′ end of the Top2b coding sequence, generated via CRISPR/Cas9.

value: brain

value: Top2b-L (Homo)


title: P6.5_43

description:
Library name: P6_5_43
SMART-Seq2


title: P6.5_46

description:
Library name: P6_5_46
SMART-Seq2


title: Top2b_Homo_rep2

description: Library name: NT.Homo


title: LARS (5082) eCLIP in K562 cells, IP replicate 1

description:
Library name: LARS_K562_5082_IP_rep1
LARS_K562_5082.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for LARS, biological replicate 1


title: P6.5_42

description:
Library name: P6_5_42
SMART-Seq2


title: P6.5_40

description:
Library name: P6_5_40
SMART-Seq2


title: P6.5_41

description:
Library name: P6_5_41
SMART-Seq2


title: P6.5_38

description:
Library name: P6_5_38
SMART-Seq2


title: P6.5_37

description:
Library name: P6_5_37
SMART-Seq2


title: P6.5_47

description:
Library name: P6_5_47
SMART-Seq2


title: P6.5_39

description:
Library name: P6_5_39
SMART-Seq2


title: Top2b_Homo_rep1

description: Library name: X390.Homo


title: IGF2BP1 (5093) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: IGF2BP1_K562_5093_INPUT_rep2
IGF2BP1_K562_5093.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for IGF2BP1, biological replicate 2

value: IGF2BP1 (5093) eCLIP  INPUT


title: LARS (5082) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: LARS_K562_5082_INPUT_rep2
LARS_K562_5082.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for LARS, biological replicate 2


title: WT_rep2

description: Library name: X385.WT

value: WT


title: P6.5_36

description:
Library name: P6_5_36
SMART-Seq2


title: WT_rep3

description: Library name: N22.L1.1.WT


title: P6.5_34

description:
Library name: P6_5_34
SMART-Seq2


title: IGF2BP1 (5093) eCLIP in K562 cells, IP replicate 2

description:
Library name: IGF2BP1_K562_5093_IP_rep2
IGF2BP1_K562_5093.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for IGF2BP1, biological replicate 2

value: IGF2BP1 (5093) eCLIP  IP


title: P6.5_35

description:
Library name: P6_5_35
SMART-Seq2


title: WT_rep1

description: Library name: X392.WT


title: IGF2BP1 (5093) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: IGF2BP1_K562_5093_INPUT_rep1
IGF2BP1_K562_5093.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for IGF2BP1, biological replicate 1


title: IGF2BP1 (5093) eCLIP in K562 cells, IP replicate 1

description:
Library name: IGF2BP1_K562_5093_IP_rep1
IGF2BP1_K562_5093.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for IGF2BP1, biological replicate 1


title: oocytes,G,4

first: Feixue

address: Xuanwu District

institute: Nanjing Agricultural University

description: Library name: RG4

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: oocytes

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: oocytes


title: P6.5_33

description:
Library name: P6_5_33
SMART-Seq2


title: P6.5_32

description:
Library name: P6_5_32
SMART-Seq2


title: GFPT1 (5078) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: GFPT1_K562_5078_INPUT_rep2
GFPT1_K562_5078.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for GFPT1, biological replicate 2

value: GFPT1 (5078) eCLIP  INPUT


title: P6.5_30

description:
Library name: P6_5_30
SMART-Seq2


title: P6.5_31

description:
Library name: P6_5_31
SMART-Seq2


title: P6.5_29

description:
Library name: P6_5_29
SMART-Seq2


title: GFPT1 (5078) eCLIP in K562 cells, IP replicate 2

description:
Library name: GFPT1_K562_5078_IP_rep2
GFPT1_K562_5078.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for GFPT1, biological replicate 2

value: GFPT1 (5078) eCLIP  IP


title: oocytes,G,3

description: Library name: RG3


title: P6.5_26

description:
Library name: P6_5_26
SMART-Seq2


title: FUS (5012) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FUS_K562_5012_INPUT_rep2
FUS_K562_5012.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for FUS, biological replicate 2

value: FUS (5012) eCLIP  INPUT


title: P6.5_24

description:
Library name: P6_5_24
SMART-Seq2


title: P6.5_25

description:
Library name: P6_5_25
SMART-Seq2


title: FUS (5012) eCLIP in K562 cells, IP replicate 2

description:
Library name: FUS_K562_5012_IP_rep2
FUS_K562_5012.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for FUS, biological replicate 2

value: FUS (5012) eCLIP  IP


title: oocytes,G,1

description: Library name: RG1


title: oocytes,A,4

description: Library name: RA4


title: GFPT1 (5078) eCLIP in K562 cells, IP replicate 1

description:
Library name: GFPT1_K562_5078_IP_rep1
GFPT1_K562_5078.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for GFPT1, biological replicate 1


title: oocytes,G,2

description: Library name: RG2


title: P6.5_28

description:
Library name: P6_5_28
SMART-Seq2


title: P6.5_21

description:
Library name: P6_5_21
SMART-Seq2


title: GFPT1 (5078) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: GFPT1_K562_5078_INPUT_rep1
GFPT1_K562_5078.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for GFPT1, biological replicate 1


title: P6.5_27

description:
Library name: P6_5_27
SMART-Seq2


title: P6.5_20

description:
Library name: P6_5_20
SMART-Seq2


title: oocytes,A,3

description: Library name: RA3


title: P6.5_23

description:
Library name: P6_5_23
SMART-Seq2


title: P6.5_19

description:
Library name: P6_5_19
SMART-Seq2


title: P6.5_22

description:
Library name: P6_5_22
SMART-Seq2


title: FUS (5012) eCLIP in K562 cells, IP replicate 1

description:
Library name: FUS_K562_5012_IP_rep1
FUS_K562_5012.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for FUS, biological replicate 1


title: FUS (5012) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FUS_K562_5012_INPUT_rep1
FUS_K562_5012.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for FUS, biological replicate 1


title: P6.5_18

description:
Library name: P6_5_18
SMART-Seq2


title: oocytes,A,1

description: Library name: RA1


title: P6.5_17

description:
Library name: P6_5_17
SMART-Seq2


title: intestinal contents,Young+B.ca,5

description: Library name: MB5

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

source_name: intestinal contents

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: P6.5_16

description:
Library name: P6_5_16
SMART-Seq2


title: FUBP3 (5040) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FUBP3_K562_5040_INPUT_rep2
FUBP3_K562_5040.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for FUBP3, biological replicate 2

value: FUBP3 (5040) eCLIP  INPUT


title: P6.5_15

description:
Library name: P6_5_15
SMART-Seq2


title: P6.5_14

description:
Library name: P6_5_14
SMART-Seq2


title: oocytes,A,2

description: Library name: RA2


title: intestinal contents,Young+B.ca,4

description: Library name: MB4


title: FUBP3 (5040) eCLIP in K562 cells, IP replicate 2

description:
Library name: FUBP3_K562_5040_IP_rep2
FUBP3_K562_5040.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for FUBP3, biological replicate 2

value: FUBP3 (5040) eCLIP  IP


title: P6.5_13

description:
Library name: P6_5_13
SMART-Seq2


title: intestinal contents,Young+B.ca,2

description: Library name: MB2


title: P6.5_12

description:
Library name: P6_5_12
SMART-Seq2


title: P6.5_9

description:
Library name: P6_5_9
SMART-Seq2


title: intestinal contents,Young+B.ca,3

description: Library name: MB3


title: P6.5_11

description:
Library name: P6_5_11
SMART-Seq2


title: P6.5_7

description:
Library name: P6_5_7
SMART-Seq2


title: P6.5_8

description:
Library name: P6_5_8
SMART-Seq2


title: P6.5_10

description:
Library name: P6_5_10
SMART-Seq2


title: EIF4H (5074) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF4H_K562_5074_INPUT_rep2
EIF4H_K562_5074.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF4H, biological replicate 2

value: EIF4H (5074) eCLIP  INPUT


title: FUBP3 (5040) eCLIP in K562 cells, IP replicate 1

description:
Library name: FUBP3_K562_5040_IP_rep1
FUBP3_K562_5040.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for FUBP3, biological replicate 1


title: P6.5_6

description:
Library name: P6_5_6
SMART-Seq2


title: P6.5.5

description:
Library name: P6_5_5
SMART-Seq2


title: EIF4H (5074) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF4H_K562_5074_IP_rep2
EIF4H_K562_5074.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF4H, biological replicate 2

value: EIF4H (5074) eCLIP  IP


title: intestinal contents,Young,5

description: Library name: MY5


title: EIF4H (5074) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF4H_K562_5074_INPUT_rep1
EIF4H_K562_5074.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF4H, biological replicate 1


title: FUBP3 (5040) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FUBP3_K562_5040_INPUT_rep1
FUBP3_K562_5040.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for FUBP3, biological replicate 1


title: intestinal contents,Young+B.ca,1

description: Library name: MB1


title: intestinal contents,Young,4

description: Library name: MY4


title: P6.5_2

description:
Library name: P6_5_2
SMART-Seq2


title: P2.5_317

description:
Library name: P2_5_317
SMART-Seq2


title: intestinal contents,Young,2

description: Library name: MY2


title: P6.5_4

description:
Library name: P6_5_4
SMART-Seq2


title: P6.5_1

description:
Library name: P6_5_1
SMART-Seq2


title: EIF4H (5074) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF4H_K562_5074_IP_rep1
EIF4H_K562_5074.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF4H, biological replicate 1


title: intestinal contents,Young,3

description: Library name: MY3


title: P6.5_3

description:
Library name: P6_5_3
SMART-Seq2


title: intestinal contents,Young,1

description: Library name: MY1


title: EIF4G2 (5065) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF4G2_K562_5065_INPUT_rep2
EIF4G2_K562_5065.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF4G2, biological replicate 2

value: EIF4G2 (5065) eCLIP  INPUT


title: P2.5_316

description:
Library name: P2_5_316
SMART-Seq2

value: female germ cell


title: P2.5_315

description:
Library name: P2_5_315
SMART-Seq2


title: P2.5_312

description:
Library name: P2_5_312
SMART-Seq2


title: shNumb-ctr-3

city: Xi'an

first: Zhang

last: Siyu

state: ShanXi

address: GaoQiao

institute: Xi'an Jiaotong University

description: Library name: Sample 6

data_processing:
The raw image data files acquired via high-throughput sequencing platforms (DNBSEQ) and undergo base calling analysis using CASAVA software to generate sequencing raw data. The project utilized DESeq2 software for differential expression analysis, with a significance threshold set at P-value < 0.05 and a minimum fold-change requirement of ≥2 (|log2FC| ≥ 1) as the criteria for statistically significant differences.
KEGG database and GO enrichment analysis was conducted using a cutoff of P-value ≤ 0.05. The P values were adjusted using Benjamini–Hochberg multiple-testing correction.
Assembly: NCBI genome build number.
Supplementary files format and content: tab-delimited text file includes raw counts foe each Sample.

extract_protocol: BV-2 cell samples (n = 3) were collected with TRIzol reagent (Vazyme, R401). Ship samples on dry ice to Company (Tsingke) for RNA sequencing.

value: Microglia

value: shNumb-ctr


title: P2.5_311

description:
Library name: P2_5_311
SMART-Seq2


title: P2.5_313

description:
Library name: P2_5_313
SMART-Seq2


title: EIF4G2 (5065) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF4G2_K562_5065_IP_rep2
EIF4G2_K562_5065.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF4G2, biological replicate 2

value: EIF4G2 (5065) eCLIP  IP


title: EIF4G2 (5065) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF4G2_K562_5065_INPUT_rep1
EIF4G2_K562_5065.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF4G2, biological replicate 1


title: shNumb-ctr-2

description: Library name: Sample 5


title: P2.5_310

description:
Library name: P2_5_310
SMART-Seq2


title: P2.5_314

description:
Library name: P2_5_314
SMART-Seq2


title: P2.5_308

description:
Library name: P2_5_308
SMART-Seq2


title: EIF4G2 (5065) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF4G2_K562_5065_IP_rep1
EIF4G2_K562_5065.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF4G2, biological replicate 1


title: P2.5_309

description:
Library name: P2_5_309
SMART-Seq2


title: EIF3E (5025) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF3E_K562_5025_INPUT_rep2
EIF3E_K562_5025.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3E, biological replicate 2

value: EIF3E (5025) eCLIP  INPUT


title: P2.5_307

description:
Library name: P2_5_307
SMART-Seq2


title: shNumb-ctr-1

description: Library name: Sample 4


title: P2.5_306

description:
Library name: P2_5_306
SMART-Seq2


title: shscr-ctr-3

description: Library name: Sample 3

value: shscr-ctr


title: shscr-ctr-2

description: Library name: Sample 2


title: EIF3E (5025) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF3E_K562_5025_IP_rep2
EIF3E_K562_5025.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3E, biological replicate 2

value: EIF3E (5025) eCLIP  IP


title: P2.5_305

description:
Library name: P2_5_305
SMART-Seq2


title: P2.5_304

description:
Library name: P2_5_304
SMART-Seq2


title: shscr-ctr-1

description: Library name: Sample 1


title: EIF3E (5025) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF3E_K562_5025_INPUT_rep1
EIF3E_K562_5025.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3E, biological replicate 1


title: P2.5_302

description:
Library name: P2_5_302
SMART-Seq2


title: EIF3E (5025) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF3E_K562_5025_IP_rep1
EIF3E_K562_5025.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3E, biological replicate 1


title: P2.5_303

description:
Library name: P2_5_303
SMART-Seq2


title: P2.5_301

description:
Library name: P2_5_301
SMART-Seq2


title: EIF3C (5060) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF3C_K562_5060_INPUT_rep2
EIF3C_K562_5060.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3C, biological replicate 2

value: EIF3C (5060) eCLIP  INPUT


title: P2.5_300

description:
Library name: P2_5_300
SMART-Seq2


title: P2.5_298

description:
Library name: P2_5_298
SMART-Seq2


title: P2.5_299

description:
Library name: P2_5_299
SMART-Seq2


title: P2.5_297

description:
Library name: P2_5_297
SMART-Seq2


title: P2.5_296

description:
Library name: P2_5_296
SMART-Seq2


title: EIF3C (5060) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF3C_K562_5060_INPUT_rep1
EIF3C_K562_5060.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3C, biological replicate 1


title: EIF3C (5060) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF3C_K562_5060_IP_rep2
EIF3C_K562_5060.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3C, biological replicate 2

value: EIF3C (5060) eCLIP  IP


title: EIF3B (5061) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF3B_K562_5061_INPUT_rep2
EIF3B_K562_5061.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3B, biological replicate 2

value: EIF3B (5061) eCLIP  INPUT


title: P2.5_293

description:
Library name: P2_5_293
SMART-Seq2


title: P2.5_295

description:
Library name: P2_5_295
SMART-Seq2


title: P2.5_291

description:
Library name: P2_5_291
SMART-Seq2


title: P2.5_294

description:
Library name: P2_5_294
SMART-Seq2


title: EIF3C (5060) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF3C_K562_5060_IP_rep1
EIF3C_K562_5060.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3C, biological replicate 1


title: EIF3B (5061) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF3B_K562_5061_IP_rep2
EIF3B_K562_5061.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3B, biological replicate 2

value: EIF3B (5061) eCLIP  IP


title: P2.5_289

description:
Library name: P2_5_289
SMART-Seq2


title: P2.5_292

description:
Library name: P2_5_292
SMART-Seq2


title: P2.5_288

description:
Library name: P2_5_288
SMART-Seq2


title: P2.5_287

description:
Library name: P2_5_287
SMART-Seq2


title: P2.5_286

description:
Library name: P2_5_286
SMART-Seq2


title: P2.5_290

description:
Library name: P2_5_290
SMART-Seq2


title: EIF3B (5061) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF3B_K562_5061_IP_rep1
EIF3B_K562_5061.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF3B, biological replicate 1


title: P2.5_285

description:
Library name: P2_5_285
SMART-Seq2


title: 4ehp-1 mutant plants, heat stress temperature 45 ºC, biol rep 3

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

description:
Library name: HP45_R3_S47
Column name in 45_Normalized_counts_all.txt: HP45_3
45_Normalized_counts_all.txt

data_processing:
Raw reads were quality-filtered and trimmed using Trim Galore (v0.6.6).
Cleaned reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using HISAT2 (v2.2.1).
Read counts were generated using HTSeq (v0.13.5) with default parameters.
Differential gene expression analysis was performed using the DESeq2 package in Galaxy.
Assembly: Arabidopsis thaliana TAIR10 reference genome
Supplementary files format and content: tab-delimited text file includes normalized counts (generated with the DESeq2 package) for all samples corresponding to each temperature

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana seedlings were grown on Murashige and Skoog medium supplemented with 1% sucrose for seven days under long day conditions (16 h light, 8 h dark) at 22 ºC in an incubator with controlled temperature.

extract_protocol:
Total RNA was isolated with Trizol and purified with RNA Clean and Concentrator columns  (Zymo Research). One microgram of RNA was used for library construction
Libraries were constructed with Illumina-TruSeq DNA and RNA kit

treatment_protocol: Seven-days-old seedlings were subjected to acclimation at 38°C for 90 min in a temperature-controlled incubator, followed by 2 hours recovery period at 22°C. Then seedlings were exposed to a heat stress at 45°C for 2 hours. In parallel control seedlings were kept at 22 ºC. Samples were taken after the incubation at each temperature.

value: seedling

value: mutant 4ehp-1

value: heat stress


title: EIF3B (5061) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF3B_K562_5061_INPUT_rep1
EIF3B_K562_5061.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF3B, biological replicate 1

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


title: 4ehp-1 mutant plants, acclimation temperature 38 ºC, biol rep 3

description:
Library name: HP38_R3_S46
Column name in 38_Normalized_counts_all.txt: HP38_3
38_Normalized_counts_all.txt

value: acclimation


title: P2.5_284

description:
Library name: P2_5_284
SMART-Seq2


title: 4ehp-1 mutant plants, control temperature 22 ºC, biol rep 3

description:
Library name: HP22_R3_S45
Column name in 22_Normalized_counts_all.txt: HP22_3
22_Normalized_counts_all.txt

value: control


title: P2.5_280

description:
Library name: P2_5_280
SMART-Seq2


title: P2.5_283

description:
Library name: P2_5_283
SMART-Seq2


title: EIF2S2 (5023) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF2S2_K562_5023_IP_rep2
EIF2S2_K562_5023.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2S2, biological replicate 2

value: EIF2S2 (5023) eCLIP  IP


title: EIF2S2 (5023) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF2S2_K562_5023_INPUT_rep2
EIF2S2_K562_5023.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2S2, biological replicate 2

value: EIF2S2 (5023) eCLIP  INPUT


title: Model4

city: zhejiang

first: Runrun

last: Zhang

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang

institute: Zhejiang Chinese Medical University

hyb_protocol: ArrayStar protocol

scan_protocol: ArrayStar protocol

data_processing: ArrayStar protocol

organism: Rattus norvegicus

source_name: penile tissues

label_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

extract_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

treatment_protocol: Erectile function was evaluated using the apomorphine (APO, 100 μg/kg) test. APO was injected subcutaneously into the loose skin at the back of the neck. Rats were immediately placed in individual observation cages under quiet, dimly lit conditions and monitored continuously for 30 min. A positive erectile response was defined as penile engorgement and glans swelling with visible penile body protrusion. Rats showing no erectile response during the 30-min observation period were identified as DMED.

value: penile tissues


title: Model2


title: Model3


title: P2.5_279

description:
Library name: P2_5_279
SMART-Seq2

value: female germ cell


title: EIF2S2 (5023) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF2S2_K562_5023_IP_rep1
EIF2S2_K562_5023.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2S2, biological replicate 1

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.


title: Control2


title: Model1


title: 4ehp-1 mutant plants, heat stress temperature 45 ºC, biol rep 2

description:
Library name: HP45_R2_S44
Column name in 45_Normalized_counts_all.txt: HP45_2
45_Normalized_counts_all.txt


title: Control4


title: P2.5_278

description:
Library name: P2_5_278
SMART-Seq2


title: Control1


title: P2.5_277

description:
Library name: P2_5_277
SMART-Seq2


title: EIF2S2 (5023) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF2S2_K562_5023_INPUT_rep1
EIF2S2_K562_5023.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2S2, biological replicate 1


title: 4ehp-1 mutant plants, acclimation temperature 38 ºC, biol rep 2

description:
Library name: HP38_R2_S43
Column name in 38_Normalized_counts_all.txt: HP38_2
38_Normalized_counts_all.txt


title: P2.5_282

description:
Library name: P2_5_282
SMART-Seq2


title: P2.5_281

description:
Library name: P2_5_281
SMART-Seq2


title: EIF2B5 (5020) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF2B5_K562_5020_INPUT_rep2
EIF2B5_K562_5020.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2B5, biological replicate 2

value: EIF2B5 (5020) eCLIP  INPUT


title: P2.5_276

description:
Library name: P2_5_276
SMART-Seq2


title: EIF2B5 (5020) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF2B5_K562_5020_IP_rep2
EIF2B5_K562_5020.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2B5, biological replicate 2

value: EIF2B5 (5020) eCLIP  IP


title: 4ehp-1 mutant plants, control temperature 22 ºC, biol rep 2

description:
Library name: HP22_R2_S42
Column name in 22_Normalized_counts_all.txt: HP22_2
22_Normalized_counts_all.txt


title: Control3


title: 4ehp-1 mutant plants, heat stress temperature 45 ºC, biol rep 1

description:
Library name: HP45_R1_S41
Column name in 45_Normalized_counts_all.txt: HP45_1
45_Normalized_counts_all.txt


title: P2.5_273

description:
Library name: P2_5_273
SMART-Seq2


title: P2.5_274

description:
Library name: P2_5_274
SMART-Seq2


title: P2.5_275

description:
Library name: P2_5_275
SMART-Seq2


title: EIF2B5 (5020) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF2B5_K562_5020_INPUT_rep1
EIF2B5_K562_5020.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2B5, biological replicate 1


title: 4ehp-1 mutant plants, acclimation temperature 38 ºC, biol rep 1

description:
Library name: HP38_R1_S40
Column name in 38_Normalized_counts_all.txt: HP38_1
38_Normalized_counts_all.txt


title: P2.5_271

description:
Library name: P2_5_271
SMART-Seq2


title: P2.5_270

description:
Library name: P2_5_270
SMART-Seq2


title: P2.5_272

description:
Library name: P2_5_272
SMART-Seq2


title: 4ehp-1 mutant plants, control temperature 22 ºC, biol rep 1

description:
Library name: HP22_R1_S39
Column name in 22_Normalized_counts_all.txt: HP22_1
22_Normalized_counts_all.txt


title: EIF2B5 (5020) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF2B5_K562_5020_IP_rep1
EIF2B5_K562_5020.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2B5, biological replicate 1


title: wild type plants, heat stress temperature 45 ºC, biol rep 3

description:
Library name: WT45_R3_S38
Column name in 45_Normalized_counts_all.txt: WT45_3
45_Normalized_counts_all.txt

value: wild type Col-0


title: P2.5_269

description:
Library name: P2_5_269
SMART-Seq2


title: EIF2B4 (5019) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF2B4_K562_5019_INPUT_rep2
EIF2B4_K562_5019.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2B4, biological replicate 2

value: EIF2B4 (5019) eCLIP  INPUT


title: CS52iALS-C9n6- mutant-derived i3 neurons, rep 3

city: Worcester

first: Alberto

last: Brusati

state: MA

address: N Lake Ave 55

department: Neurology

institute: UMass Chan Medical School

description:
Library name: C952_Mutant_Rep3
Quant file provided by salmon for each sample.

data_processing:
Reads were realigned on the reference genome (GRCh38) with the STAR tool using Genecode.v29 as gene annotation file. Post-alignment quality control was performed using Qualimap.
Quantification was performed using Salmon.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files containing raw counts

source_name: i3 Neurons

growth_protocol: iPSCs were maintained under Stemflex media and differentiated  into i3 cortical neurons by doxycycline-inducible NGN2 expression followed by maturation in neurotrophic factor–supplemented media.

extract_protocol:
RNA was extracted using the Rneasy mini  kit (Qiagen). 200ng of total RNA was used for construction of sequencing libraries
RNA libraries for RNA -seq were prepared by Novogene

value: i3 Neurons

value: Mut

value: Untreated


title: EIF2B4 (5019) eCLIP in K562 cells, IP replicate 2

first: Brian

address: 9500 Gilman Dr

institute: UCSD

description:
Library name: EIF2B4_K562_5019_IP_rep2
EIF2B4_K562_5019.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2B4, biological replicate 2

value: EIF2B4 (5019) eCLIP  IP


title: P2.5_268

description:
Library name: P2_5_268
SMART-Seq2


title: wild type plants, acclimation temperature 38 ºC, biol rep 3

description:
Library name: WT38_R3_S37
Column name in 38_Normalized_counts_all.txt: WT38_3
38_Normalized_counts_all.txt

value: seedling


title: wild type plants, heat stress temperature 45 ºC, biol rep 2

description:
Library name: WT45_R2_S35
Column name in 45_Normalized_counts_all.txt: WT45_2
45_Normalized_counts_all.txt


title: wild type plants, control temperature 22 ºC, biol rep 3

description:
Library name: WT22_R3_S36
Column name in 22_Normalized_counts_all.txt: WT22_3
22_Normalized_counts_all.txt


title: P2.5_266

description:
Library name: P2_5_266
SMART-Seq2


title: P2.5_265

description:
Library name: P2_5_265
SMART-Seq2


title: DNAJC2 (5084) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DNAJC2_K562_5084_INPUT_rep2
DNAJC2_K562_5084.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DNAJC2, biological replicate 2

value: DNAJC2 (5084) eCLIP  INPUT


title: P2.5_264

description:
Library name: P2_5_264
SMART-Seq2


title: DNAJC2 (5084) eCLIP in K562 cells, IP replicate 2

description:
Library name: DNAJC2_K562_5084_IP_rep2
DNAJC2_K562_5084.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DNAJC2, biological replicate 2

value: DNAJC2 (5084) eCLIP  IP


title: EIF2B4 (5019) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF2B4_K562_5019_IP_rep1
EIF2B4_K562_5019.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2B4, biological replicate 1


title: Replicate 4, mid cells

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

country: Germany

institute: Helmholtz Insitute

description: Library name: R4_mid_cells

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism: Bacteroides thetaiotaomicron

growth_protocol: Cells were grown in tryptone yeast glucose (TYG) media to mid-exponential phase (OD2), anaerobiaclly at 37 degrees.

extract_protocol:
MATQ-Seq and ribosomal RNA depletion with DASH
100 cells per replcates were sorted in a 96 well plate. Cells were lysed using mechanical sonication. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH, optimized for bacteroides thetaiotaomicron.

treatment_protocol: Cells fixated with 50% RNAlater

value: WT


title: P2.5_267

description:
Library name: P2_5_267
SMART-Seq2


title: Replicate 4, small cells

description: Library name: R4_small_cells


title: EIF2B4 (5019) eCLIP in K562 cells, INPUT replicate 1

city: La Jolla

last: Yee

description:
Library name: EIF2B4_K562_5019_INPUT_rep1
EIF2B4_K562_5019.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2B4, biological replicate 1


title: CS52iALS-C9n6- mutant-derived i3 neurons, rep 2

description:
Library name: C952_Mutant_Rep2
Quant file provided by salmon for each sample.


title: wild type plants, acclimation temperature 38 ºC, biol rep 2

description:
Library name: WT38_R2_S34
Column name in 38_Normalized_counts_all.txt: WT38_2
38_Normalized_counts_all.txt

value: acclimation


title: wild type plants, control temperature 22 ºC, biol rep 2

description:
Library name: WT22_R2_S33
Column name in 22_Normalized_counts_all.txt: WT22_2
22_Normalized_counts_all.txt

value: control


title: P2.5_263

description:
Library name: P2_5_263
SMART-Seq2


title: Replicate 3, small cells

description: Library name: R3_small_cells


title: DNAJC2 (5084) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DNAJC2_K562_5084_INPUT_rep1
DNAJC2_K562_5084.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DNAJC2, biological replicate 1


title: Replicate 4, big cells

description: Library name: R4_big_cells


title: Replicate 3, mid cells

description: Library name: R3_mid_cells


title: wild type plants, heat stress temperature 45 ºC, biol rep 1

description:
Library name: WT45_R1_S32
Column name in 45_Normalized_counts_all.txt: WT45_1
45_Normalized_counts_all.txt

value: heat stress


title: DNAJC2 (5084) eCLIP in K562 cells, IP replicate 1

description:
Library name: DNAJC2_K562_5084_IP_rep1
DNAJC2_K562_5084.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DNAJC2, biological replicate 1


title: Replicate 3, big cells

description: Library name: R3_big_cells


title: wild type plants, acclimation temperature 38 ºC, biol rep 1

description:
Library name: WT38_R1_S31
Column name in 38_Normalized_counts_all.txt: WT38_1
38_Normalized_counts_all.txt


title: P2.5_261

description:
Library name: P2_5_261
SMART-Seq2


title: Replicate 2, small cells

description: Library name: R2_small_cells


title: P2.5_260

description:
Library name: P2_5_260
SMART-Seq2


title: wild type plants, control temperature 22 ºC, biol rep 1

description:
Library name: WT22_R1_S30
Column name in 22_Normalized_counts_all.txt: WT22_1
22_Normalized_counts_all.txt


title: DDX5 (5094) eCLIP in K562 cells, IP replicate 2

description:
Library name: DDX5_K562_5094_IP_rep2
DDX5_K562_5094.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DDX5, biological replicate 2

value: DDX5 (5094) eCLIP  IP


title: P2.5_262

description:
Library name: P2_5_262
SMART-Seq2

value: female germ cell


title: Replicate 2, mid cells

description: Library name: R2_mid_cells


title: P2.5_259

description:
Library name: P2_5_259
SMART-Seq2


title: Replicate 2, big cells

description: Library name: R2_big_cells


title: DDX5 (5094) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DDX5_K562_5094_INPUT_rep1
DDX5_K562_5094.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DDX5, biological replicate 1

value: DDX5 (5094) eCLIP  INPUT


title: DDX5 (5094) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DDX5_K562_5094_INPUT_rep2
DDX5_K562_5094.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DDX5, biological replicate 2


title: P2.5_258

description:
Library name: P2_5_258
SMART-Seq2


title: Replicate 1, small cells

description: Library name: R1_small_cells


title: P2.5_255

description:
Library name: P2_5_255
SMART-Seq2


title: DDX41 (5081) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DDX41_K562_5081_INPUT_rep1
DDX41_K562_5081.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DDX41, biological replicate 1

value: DDX41 (5081) eCLIP  INPUT


title: Replicate 1, big cells

description: Library name: R1_big_cells


title: P2.5_256

description:
Library name: P2_5_256
SMART-Seq2


title: human adult (1350); chimpanzee adult (Frits)

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: Library name: g018

data_processing:
read processing and count matrix generation were performed using cellranger (v6) pipeline.
Assembly: hg38
Supplementary files format and content: tab separated values / matrix files.

molecule: nuclear RNA

source_name: Prefrontal cortex

extract_protocol:
50 mg of tissue was pulverized in liquid nitrogen using a pestle and mortar on cry ice. Powdered tissue was then homogenized in 2 mL EZ buffer (Nuclei isolation kit, Sigma NUC101) in a glass douncer (Kontes Glass Co.), followed by a 5’ incubation on ice. Homogenates were centrifuged for 15’ at 65 x g at 4 oC, resuspended in 2 mL EZ buffer and incubated for 5’ on ice. Samples were centrifuged again for 15’ at 65 x g at 4 oC, resuspended in 4 mL nuclear suspension buffer (NB: 0.01% BSA, 1x ‘complete’ protease inhibitor cocktail (Roche) in MQ) and filtered through a 40 µM cell strainer. Following this, samples were centrifuged for 15’ at 65 x g at 4 oC. to separate the nuclei from other cell organelles after which a density gradient was created with OpitPrep (Sigma D1556). Pellets were resuspended in 30 mL NB after which 10 mL of 30% OptiPrep was carefully added at the bottom with a syringe and needle, followed by another 5 mL layer of 60% OptiPrep underneath. Samples were centrifuged for 15’ at 1,000 x g at 4 oC. Nuclei were retrieved from between the 30% OptiPrep and PBS layers with a syringe and needle and checked for quality under a bright field microscope. Nuclei were stained using Hoechst-33342 (Molecular Probs, 1:1000 dilution) and filtered through a 35 µm strainer (Corning) before sorting. Sorting was performed using a FACS Fusion to sort for DAPI+ positive nuclei and to remove leftover debris and doublets.
After sorting, nuclei were spun for 5 min at 500×g and resuspended in PBS + 1% BSA to be loaded on the 10x microfluidic chip device. To limit the influence of technical variation we combined cells from separate species on a 1:1 cell count basis per sequencing sample for processing using the 10x Chromium V3 single cell RNA Gene Expression kit according to the manufacturer’s protocols. Nuclei were loaded aiming to recover 10,000 nuclei per sample. Single cell RNA-Seq samples were sequenced on an Illumina Hiseq 2500.

value: Prefrontal cortex

value: 24-50 years

value: male


title: rhesus infant (R12121); chimpanzee adult (Ruben)

description: Library name: rbpa

value: 0-18 years


title: human infant (1490); chimpanzee infant (chimp2)

description: Library name: g011

value: 0-4 months


title: P2.5_257

description:
Library name: P2_5_257
SMART-Seq2


title: human infant (1623); chimpanzee infant (chimp3)

description: Library name: g015

value: 4-5 months


title: DDX41 (5081) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DDX41_K562_5081_INPUT_rep2
DDX41_K562_5081.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for DDX41, biological replicate 2


title: human infant (1452); rhesus infant (R17043)

description: Library name: hbrb


title: CS52iALS-C9n6ISO-isogenic control-derived i3 neurons, rep 3

description:
Library name: C952_IsoControl_Rep3
Quant file provided by salmon for each sample.

value: i3 Neurons

value: Untreated


title: human adult (1385); chimpanzee adult (Bart)

description: Library name: g012

value: 35-36 years


title: Neurons_elavl3_6dpf_enucleated_MUT_rep2

city: Barcelona

first: Tahnee

last: Mackensen

address: Dr. Aiguader, 88

institute: Universitat Pompeu Fabra

description: Library name: MUT2_HucGFP_6dpf

data_processing:
RNA-seq: Reads were mapped to the Danio rerio transcriptome (GRCz10) using Salmon (v 1.5.1).
Assembly: Danio rerio (zebrafish) genome assembly version GRCz10
Supplementary files format and content: RNA-seq: comma separated file with raw gene counts.

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

extract_protocol:
For RNA-seq of neurons from enucleated 6dpf WT, srrm3^+/∆eMIC and srrm3^∆eMIC samples RNA was harvested using the PicoPure Mini RNA isolation kit (ThermoFisher, Cat:KIT0204). RIN values were 10 and 30 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq: Library construction was performed using SMARTseq2.

treatment_protocol: Larvae were enucleated at 6dpf prior to dissociation and FACS-sorting.

value: enucleated


title: DDX41 (5081) eCLIP in K562 cells, IP replicate 1

description:
Library name: DDX41_K562_5081_IP_rep1
DDX41_K562_5081.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DDX41, biological replicate 1

value: DDX41 (5081) eCLIP  IP


title: DDX41 (5081) eCLIP in K562 cells, IP replicate 2

description:
Library name: DDX41_K562_5081_IP_rep2
DDX41_K562_5081.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DDX41, biological replicate 2


title: CS52iALS-C9n6- mutant-derived i3 neurons, rep 1

description:
Library name: C952_Mutant_Rep1
Quant file provided by salmon for each sample.

value: Mut


title: P2.5_254

description:
Library name: P2_5_254
SMART-Seq2


title: CELF1 (5041) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: CELF1_K562_5041_INPUT_rep2
CELF1_K562_5041.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CELF1, biological replicate 2

value: CELF1 (5041) eCLIP  INPUT


title: Replicate 1, mid cells

description: Library name: R1_mid_cells

value: WT


title: CS52iALS-C9n6ISO-isogenic control-derived i3 neurons, rep 2

description:
Library name: C952_IsoControl_Rep2
Quant file provided by salmon for each sample.


title: P2.5_253

description:
Library name: P2_5_253
SMART-Seq2

value: female germ cell


title: Neurons_elavl3_6dpf_enucleated_HET_rep2

description: Library name: HET2_HucGFP_6dpf

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


title: Neurons_elavl3_6dpf_enucleated_WT_rep2

description: Library name: WT2_HucGFP_6dpf


title: CELF1 (5041) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: CELF1_K562_5041_INPUT_rep1
CELF1_K562_5041.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CELF1, biological replicate 1


title: DDX5 (5094) eCLIP in K562 cells, IP replicate 1

description:
Library name: DDX5_K562_5094_IP_rep1
DDX5_K562_5094.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for DDX5, biological replicate 1

value: DDX5 (5094) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_MUT_rep1

description: Library name: MUT1_HucGFP_6dpf


title: CS29iALS-C9n1- mutant-derived i3 neurons, rep 3

description:
Library name: C929_Mutant_Rep3
Quant file provided by salmon for each sample.


title: CELF1 (5041) eCLIP in K562 cells, IP replicate 1

description:
Library name: CELF1_K562_5041_IP_rep1
CELF1_K562_5041.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CELF1, biological replicate 1

value: CELF1 (5041) eCLIP  IP


title: CS52iALS-C9n6ISO-isogenic control-derived i3 neurons, rep 1

description:
Library name: C952_IsoControl_Rep1
Quant file provided by salmon for each sample.


title: P2.5_251

description:
Library name: P2_5_251
SMART-Seq2


title: CELF1 (5041) eCLIP in K562 cells, IP replicate 2

description:
Library name: CELF1_K562_5041_IP_rep2
CELF1_K562_5041.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CELF1, biological replicate 2


title: CS29iALS-C9n1- mutant-derived i3 neurons, rep 2

description:
Library name: C929_Mutant_Rep2
Quant file provided by salmon for each sample.


title: Neurons_elavl3_6dpf_enucleated_HET_rep1

description: Library name: HET1_HucGFP_6dpf


title: CS29iALS-C9n1- mutant-derived i3 neurons, rep 1

description:
Library name: C929_Mutant_Rep1
Quant file provided by salmon for each sample.


title: P2.5_249

description:
Library name: P2_5_249
SMART-Seq2


title: P2.5_252

description:
Library name: P2_5_252
SMART-Seq2


title: P2.5_247

description:
Library name: P2_5_247
SMART-Seq2


title: CDC40 (5006) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: CDC40_K562_5006_INPUT_rep2
CDC40_K562_5006.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CDC40, biological replicate 2

value: CDC40 (5006) eCLIP  INPUT


title: CDC40 (5006) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: CDC40_K562_5006_INPUT_rep1
CDC40_K562_5006.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CDC40, biological replicate 1


title: P2.5_250

description:
Library name: P2_5_250
SMART-Seq2


title: P2.5_248

description:
Library name: P2_5_248
SMART-Seq2


title: Neurons_elavl3_6dpf_enucleated_WT_rep1

description: Library name: WT1_HucGFP_6dpf


title: Neurons_elavl3_6dpf_ATAC_MUT_rep2

description: Library name: AT_KO2_HuC_6dpf_enucleated

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).

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).


title: CS29iALS-C9n1ISO- isogenic control-derived i3 neurons, rep 2

description:
Library name: C929_IsoControl_Rep2
Quant file provided by salmon for each sample.


title: P2.5_246

description:
Library name: P2_5_246
SMART-Seq2


title: CDC40 (5006) eCLIP in K562 cells, IP replicate 1

description:
Library name: CDC40_K562_5006_IP_rep1
CDC40_K562_5006.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CDC40, biological replicate 1

value: CDC40 (5006) eCLIP  IP


title: Neurons_elavl3_6dpf_ATAC_MUT_rep1

description: Library name: AT_KO1_HuC_6dpf_enucleated


title: P2.5_245

description:
Library name: P2_5_245
SMART-Seq2


title: Neurons_elavl3_6dpf_ATAC_WT_rep2

description: Library name: AT_WT2_HuC_6dpf_enucleated


title: CS29iALS-C9n1ISO- isogenic control-derived i3 neurons, rep 1

description:
Library name: C929_IsoControl_Rep1
Quant file provided by salmon for each sample.


title: CS29iALS-C9n1ISO- isogenic control-derived i3 neurons, rep 3

description:
Library name: C929_IsoControl_Rep3
Quant file provided by salmon for each sample.


title: Neurons_elavl3_6dpf_ATAC_WT_rep1

description: Library name: AT_WT1_HuC_6dpf_enucleated


title: E_3

city: Guiyang

first: jinbiao

last: lu

address: East Zhongshan Road

department: Department of Ophthalmology

institute: Guizhou Provincial People’s Hospital

description:
Library name: sample6
25years+female+with acute macular neuroretinopathy(AMN)

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: Peripheral blood samples of human

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Peripheral blood samples of human

tag: group

value: AMN

value: female


title: BRD4 (5079) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: BRD4_K562_5079_INPUT_rep2
BRD4_K562_5079.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for BRD4, biological replicate 2

value: BRD4 (5079) eCLIP  INPUT


title: P2.5_244

description:
Library name: P2_5_244
SMART-Seq2


title: CDC40 (5006) eCLIP in K562 cells, IP replicate 2

description:
Library name: CDC40_K562_5006_IP_rep2
CDC40_K562_5006.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CDC40, biological replicate 2


title: Neurons_elavl3_6dpf_enucleated_MUT_PTZ_rep2

description: Library name: MUT_PTZ_5


title: P2.5_242

description:
Library name: P2_5_242
SMART-Seq2


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep5

description: Library name: MUT_DMS_5


title: E_1

description:
Library name: sample4
28years+female+with acute macular neuroretinopathy(AMN)


title: P2.5_243

description:
Library name: P2_5_243
SMART-Seq2


title: C_3

description:
Library name: sample3
34years+female+control patients

value: control


title: BRD4 (5079) eCLIP in K562 cells, IP replicate 1

description:
Library name: BRD4_K562_5079_IP_rep1
BRD4_K562_5079.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for BRD4, biological replicate 1

value: BRD4 (5079) eCLIP  IP


title: C_1

description:
Library name: sample1
26years+female+control patients


title: KARS (5104) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: KARS_K562_5104_INPUT_rep2
KARS_K562_5104.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for KARS, biological replicate 2

value: KARS (5104) eCLIP  INPUT


title: E_2

description:
Library name: sample5
27years+female+with acute macular neuroretinopathy(AMN)


title: Neurons_elavl3_6dpf_enucleated_WT_PTZ_rep2

description: Library name: WT_PTZ_5


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep5

description: Library name: WT_DMS_5


title: P2.5_240

description:
Library name: P2_5_240
SMART-Seq2


title: C_2

description:
Library name: sample2
26years+female+control patients


title: BRD4 (5079) eCLIP in K562 cells, IP replicate 2

description:
Library name: BRD4_K562_5079_IP_rep2
BRD4_K562_5079.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for BRD4, biological replicate 2


title: KARS (5104) eCLIP in K562 cells, IP replicate 2

description:
Library name: KARS_K562_5104_IP_rep2
KARS_K562_5104.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for KARS, biological replicate 2

value: KARS (5104) eCLIP  IP


title: P2.5_238

description:
Library name: P2_5_238
SMART-Seq2


title: KARS (5104) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: KARS_K562_5104_INPUT_rep1
KARS_K562_5104.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for KARS, biological replicate 1


title: P2.5_241

description:
Library name: P2_5_241
SMART-Seq2


title: P2.5_239

description:
Library name: P2_5_239
SMART-Seq2


title: BRD4 (5079) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: BRD4_K562_5079_INPUT_rep1
BRD4_K562_5079.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for BRD4, biological replicate 1


title: KARS (5104) eCLIP in K562 cells, IP replicate 1

description:
Library name: KARS_K562_5104_IP_rep1
KARS_K562_5104.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for KARS, biological replicate 1


title: UPF1 (5002) eCLIP in K562 cells, IP replicate 2

description:
Library name: UPF1_K562_5002_IP_rep2
UPF1_K562_5002.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for UPF1, biological replicate 2

value: UPF1 (5002) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_MUT_CLO_rep1

description: Library name: MUT_CLO_4


title: UPF1 (5002) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: UPF1_K562_5002_INPUT_rep2
UPF1_K562_5002.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for UPF1, biological replicate 2

value: UPF1 (5002) eCLIP  INPUT


title: Neurons_elavl3_6dpf_enucleated_WT_CLO_rep1

description: Library name: WT_CLO_4

value: WT


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep4

description: Library name: MUT_DMS_4


title: P2.5_237

description:
Library name: P2_5_237
SMART-Seq2

value: female germ cell


title: RBM10 (5113) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RBM10_K562_5113_INPUT_rep2
RBM10_K562_5113.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM10, biological replicate 2

value: RBM10 (5113) eCLIP  INPUT


title: UPF1 (5002) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: UPF1_K562_5002_INPUT_rep1
UPF1_K562_5002.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for UPF1, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep4

description: Library name: WT_DMS_4

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


title: P2.5_236

description:
Library name: P2_5_236
SMART-Seq2


title: P2.5_235

description:
Library name: P2_5_235
SMART-Seq2


title: Neurons_elavl3_6dpf_enucleated_MUT_ROP_rep1

description: Library name: MUT_ROP_3


title: UPF1 (5002) eCLIP in K562 cells, IP replicate 1

description:
Library name: UPF1_K562_5002_IP_rep1
UPF1_K562_5002.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for UPF1, biological replicate 1


title: RBM10 (5113) eCLIP in K562 cells, IP replicate 2

description:
Library name: RBM10_K562_5113_IP_rep2
RBM10_K562_5113.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM10, biological replicate 2

value: RBM10 (5113) eCLIP  IP


title: Neurons_elavl3_6dpf_enucleated_MUT_DMSO_rep3

description: Library name: MUT_DMS_3


title: KHSRP (5001) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: KHSRP_K562_5001_INPUT_rep2
KHSRP_K562_5001.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for KHSRP, biological replicate 2

value: KHSRP (5001) eCLIP  INPUT


title: RBM10 (5113) eCLIP in K562 cells, IP replicate 1

description:
Library name: RBM10_K562_5113_IP_rep1
RBM10_K562_5113.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for RBM10, biological replicate 1


title: P2.5_233

description:
Library name: P2_5_233
SMART-Seq2


title: P2.5_234

description:
Library name: P2_5_234
SMART-Seq2


title: KHSRP (5001) eCLIP in K562 cells, IP replicate 2

description:
Library name: KHSRP_K562_5001_IP_rep2
KHSRP_K562_5001.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for KHSRP, biological replicate 2

value: KHSRP (5001) eCLIP  IP


title: KHSRP (5001) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: KHSRP_K562_5001_INPUT_rep1
KHSRP_K562_5001.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for KHSRP, biological replicate 1


title: RBM10 (5113) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RBM10_K562_5113_INPUT_rep1
RBM10_K562_5113.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for RBM10, biological replicate 1


title: Neurons_elavl3_6dpf_enucleated_WT_DMSO_rep3

description: Library name: WT_DMS_3


title: Neurons_elavl3_6dpf_enucleated_WT_ROP_rep1

description: Library name: WT_ROP_3


title: LARP1 (5110) eCLIP in K562 cells, IP replicate 2

description:
Library name: LARP1_K562_5110_IP_rep2
LARP1_K562_5110.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for LARP1, biological replicate 2

value: LARP1 (5110) eCLIP  IP