title: P2.5_106

description:
Library name: P2_5_106
SMART-Seq2


title: RPS10 (4104) eCLIP in K562 cells, INPUT replicate 1

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: RPS10_K562_4104_INPUT_rep1
eCLIP size-matched input control for RPS10, biological replicate 1

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


title: RNA from patient HTA2_90013, derived from LUAD Region 2 (Stage 1A) [HTA2_90013_6000102]

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: HTA2_90013_6000102

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

source_name: Resected lung tissue

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

tag: tissue

value: Resected lung tissue

tag: htan id

tag: sample histology

value: ADC

tag: flow cells


title: Control gRNA untreated 4

city: Bethesda

first: Claire

middle: E

last: LE PICHON

state: MD

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

description: Library name: Sample 36

data_processing:
Sequenced reads from all genotypes were trimmed to remove adaptor sequences using cutadapt v3.4 with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 --minimum-length 25
Trimmed reads were aligned to GRCh38 human reference GENCODE release 28 using STAR 1-pass v2.7.8.a with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate.
Quantitation of aligned reads was performed using the featureCounts of the subread package v2.0.1 with annotation sourced from GRCh38 human reference GENCODE release 28 and the following parameters: -s2  -p
Assembly: GRCh38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: "cortical", NGN2

extract_protocol:
For RNA extraction, 2.5 million neurons were pleated in 6 well plates (Thomas Scientific, #1198D71) and differentiated for 10-14 days. Neurons were treated with DMSO or 5 nM vincristine for 16 hours before RNA extraction. Neurons were washed once with PBS and harvested in 700 µL Qiazol (Qiagen, #79306) and immediately placed on ice. RNA extraction was performed using RNeasy Mini Kit (Qiagen, #74104) following the manufacturer’s instructions. Columns were treated with RNase-Free DNase (Qiagen, #79254), and RNA was eluted in 25 µL of RNAse free water. Eluted RNA was separated into two tubes, one containing 2 µL, subsequently used for quality control and the other used for RNAseq.
For RNA sequencing, 1-4 µg of total RNA samples were purified with PolyA extraction, and then purified mRNAs were constructed to RNA-Seq libraries with specific barcodes using Illumina TruSeq Stranded mRNA Library Prep Kit. All the RNA-Seq libraries were pooled together and sequenced using Illumina NovaSeq 6000 to generate approximately ~40 million 2x100 paired-end reads for each sample. The raw data were demultiplexed and analyzed further.

value: "cortical", NGN2

tag: cell type

value: neuron

tag: genotype

value: Control gRNA

tag: treatment

value: untreated


title: Control gRNA untreated 3

description: Library name: Sample 35


title: RNA from patient HTA2_90012, derived from LUAD Region 3 (Stage 1A) [HTA2_90012_6000104]

description: Library name: HTA2_90012_6000104


title: P2.5_105

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

description:
Library name: P2_5_105
SMART-Seq2

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Mus musculus

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: Control gRNA untreated 2

description: Library name: Sample 34


title: CXXC1 (4088) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: CXXC1_K562_4088_INPUT_rep1
eCLIP size-matched input control for CXXC1, biological replicate 1


title: CXXC1 (4088) eCLIP in K562 cells, IP replicate 1

description:
Library name: CXXC1_K562_4088_IP_rep1
eCLIP immunoprecipitation sample for CXXC1, biological replicate 1


title: RNA from patient HTA2_90012, derived from LUAD Region 1 (Stage 1A) [HTA2_90012_6000101]

description: Library name: HTA2_90012_6000101


title: RNA from patient HTA2_90012, derived from Normal [HTA2_90012_6000103]

description: Library name: HTA2_90012_6000103

value: N


title: P2.5_103

description:
Library name: P2_5_103
SMART-Seq2


title: RNA from patient HTA2_90012, derived from LUAD Region 2 (Stage 1A) [HTA2_90012_6000102]

description: Library name: HTA2_90012_6000102


title: P2.5_104

description:
Library name: P2_5_104
SMART-Seq2


title: DLK LZK double KO vincristine 4

description: Library name: Sample 32

value: DLK LZK double KO

value: vincristine


title: DLK LZK double KO vincristine 3

description: Library name: Sample 31


title: PRPF39 (4068) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PRPF39_K562_4068_INPUT_rep1
eCLIP size-matched input control for PRPF39, biological replicate 1


title: P2.5_102

description:
Library name: P2_5_102
SMART-Seq2


title: PRPF39 (4068) eCLIP in K562 cells, IP replicate 1

description:
Library name: PRPF39_K562_4068_IP_rep1
eCLIP immunoprecipitation sample for PRPF39, biological replicate 1


title: Control gRNA untreated 1

description: Library name: Sample 33


title: CXXC1 (4088) eCLIP in K562 cells, IP replicate 2

description:
Library name: CXXC1_K562_4088_IP_rep2
eCLIP immunoprecipitation sample for CXXC1, biological replicate 2


title: P2.5_101

description:
Library name: P2_5_101
SMART-Seq2


title: RNA from patient HTA2_90011, derived from LUAD Region 3 (Stage 1B) [HTA2_90011_6000108]

description: Library name: HTA2_90011_6000108


title: RNA from patient HTA2_90011, derived from LUAD Region 2 (Stage 1B) [HTA2_90011_6000106]

description: Library name: HTA2_90011_6000106


title: RNA from patient HTA2_90011, derived from LUAD Region 1 (Stage 1B) [HTA2_90011_6000105]

description: Library name: HTA2_90011_6000105

value: HFMTWBGXL


title: RECQ1 (4049) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RECQ1_K562_4049_INPUT_rep2
eCLIP size-matched input control for RECQ1, biological replicate 2


title: PRPF39 (4068) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PRPF39_K562_4068_INPUT_rep2
eCLIP size-matched input control for PRPF39, biological replicate 2


title: RNA from patient HTA2_90010, derived from LUAD Region 3 (Stage 1B) [HTA2_90010_6000106]

description: Library name: HTA2_90010_6000106


title: RECQ1 (4049) eCLIP in K562 cells, IP replicate 2

description:
Library name: RECQ1_K562_4049_IP_rep2
eCLIP immunoprecipitation sample for RECQ1, biological replicate 2


title: DLK LZK double KO vincristine 2

description: Library name: Sample 30


title: P2.5_98

description:
Library name: P2_5_98
SMART-Seq2


title: RNA from patient HTA2_90011, derived from Normal [HTA2_90011_6000107]

description: Library name: HTA2_90011_6000107


title: DLK LZK double KO vincristine 1

description: Library name: Sample 29


title: P2.5_99

description:
Library name: P2_5_99
SMART-Seq2


title: DLK LZK double KO untreated 3

description: Library name: Sample 27


title: RNA from patient HTA2_90010, derived from LUAD Region 2 (Stage 1B) [HTA2_90010_6000105]

description: Library name: HTA2_90010_6000105


title: DLK LZK double KO untreated 2

description: Library name: Sample 26


title: P2.5_100

description:
Library name: P2_5_100
SMART-Seq2


title: PRPF39 (4068) eCLIP in K562 cells, IP replicate 2

description:
Library name: PRPF39_K562_4068_IP_rep2
eCLIP immunoprecipitation sample for PRPF39, biological replicate 2


title: DLK LZK double KO untreated 4

description: Library name: Sample 28


title: RECQ1 (4049) eCLIP in K562 cells, IP replicate 1

description:
Library name: RECQ1_K562_4049_IP_rep1
eCLIP immunoprecipitation sample for RECQ1, biological replicate 1


title: P2.5_97

description:
Library name: P2_5_97
SMART-Seq2


title: RECQ1 (4049) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RECQ1_K562_4049_INPUT_rep1
eCLIP size-matched input control for RECQ1, biological replicate 1


title: P2.5_96

description:
Library name: P2_5_96
SMART-Seq2


title: P2.5_94

description:
Library name: P2_5_94
SMART-Seq2


title: P2.5_95

description:
Library name: P2_5_95
SMART-Seq2


title: RNA from patient HTA2_90009, derived from Normal [HTA2_90009_6000108]

description: Library name: HTA2_90009_6000108


title: RNA from patient HTA2_90010, derived from LUAD Region 1 (Stage 1B) [HTA2_90010_6000104]

description: Library name: HTA2_90010_6000104


title: RNA from patient HTA2_90009, derived from LUAD Region 2 (Stage Unknown) [HTA2_90009_6000103]

description: Library name: HTA2_90009_6000103


title: LZK KO vincristine 4

description: Library name: Sample 24

value: LZK KO


title: SF3A1 (4048) eCLIP in K562 cells, IP replicate 1

description:
Library name: SF3A1_K562_4048_IP_rep1
eCLIP immunoprecipitation sample for SF3A1, biological replicate 1


title: DLK LZK double KO untreated 1

description: Library name: Sample 25


title: RNA from patient HTA2_90009, derived from Normal [HTA2_90009_6000102]

description: Library name: HTA2_90009_6000102


title: LZK KO vincristine 2

description: Library name: Sample 22


title: SF3A1 (4048) eCLIP in K562 cells, IP replicate 2

description:
Library name: SF3A1_K562_4048_IP_rep2
eCLIP immunoprecipitation sample for SF3A1, biological replicate 2


title: P2.5_93

description:
Library name: P2_5_93
SMART-Seq2


title: RNA from patient HTA2_90009, derived from LUAD Region 1 (Stage Unknown) [HTA2_90009_6000101]

description: Library name: HTA2_90009_6000101


title: SF3A1 (4048) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SF3A1_K562_4048_INPUT_rep2
eCLIP size-matched input control for SF3A1, biological replicate 2


title: RNA from patient HTA2_90009, derived from LUAD Region 3 (Stage Unknown) [HTA2_90009_6000107]

description: Library name: HTA2_90009_6000107


title: LZK KO vincristine 3

description: Library name: Sample 23


title: P2.5_92

description:
Library name: P2_5_92
SMART-Seq2


title: P2.5_91

description:
Library name: P2_5_91
SMART-Seq2


title: MBNL1 (4056) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: MBNL1_K562_4056_INPUT_rep2
eCLIP size-matched input control for MBNL1, biological replicate 2


title: SF3A1 (4048) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SF3A1_K562_4048_INPUT_rep1
eCLIP size-matched input control for SF3A1, biological replicate 1


title: MBNL1 (4056) eCLIP in K562 cells, IP replicate 2

description:
Library name: MBNL1_K562_4056_IP_rep2
eCLIP immunoprecipitation sample for MBNL1, biological replicate 2


title: LZK KO vincristine 1

description: Library name: Sample 21


title: RNA from patient HTA2_90008, derived from LUAD Region 3 (Stage 1A) [HTA2_90008_6000104]

description: Library name: HTA2_90008_6000104


title: LZK KO untreated 4

description: Library name: Sample 20


title: P2.5_90

description:
Library name: P2_5_90
SMART-Seq2


title: LZK KO untreated 3

description: Library name: Sample 19


title: P2.5_89

description:
Library name: P2_5_89
SMART-Seq2


title: RNA from patient HTA2_90008, derived from Normal [HTA2_90008_6000103]

description: Library name: HTA2_90008_6000103


title: P2.5_88

description:
Library name: P2_5_88
SMART-Seq2


title: MBNL1 (4056) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: MBNL1_K562_4056_INPUT_rep1
eCLIP size-matched input control for MBNL1, biological replicate 1


title: RNA from patient HTA2_90008, derived from LUAD Region 2 (Stage 1A) [HTA2_90008_6000102]

description: Library name: HTA2_90008_6000102


title: LZK KO untreated 1

description: Library name: Sample 17


title: P2.5_87

description:
Library name: P2_5_87
SMART-Seq2


title: LZK KO untreated 2

description: Library name: Sample 18


title: MBNL1 (4056) eCLIP in K562 cells, IP replicate 1

description:
Library name: MBNL1_K562_4056_IP_rep1
eCLIP immunoprecipitation sample for MBNL1, biological replicate 1


title: RNA from patient HTA2_90008, derived from LUAD Region 1 (Stage 1A) [HTA2_90008_6000101]

description: Library name: HTA2_90008_6000101


title: DLK KO vincristine 4

description: Library name: Sample 16

value: DLK KO


title: SRSF5 (4058) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SRSF5_K562_4058_INPUT_rep2
eCLIP size-matched input control for SRSF5, biological replicate 2


title: RNA from patient HTA2_27117, derived from Normal #3 [HTA2_27117_6000105]

description: Library name: HTA2_27117_6000105

value: HJMCCBGXL


title: RNA from patient HTA2_27117, derived from AAH  [HTA2_27117_6000104]

description: Library name: HTA2_27117_6000104

value: AAH


title: RNA from patient HTA2_27117, derived from Normal #2 [HTA2_27117_6000103]

description: Library name: HTA2_27117_6000103


title: P2.5_84

description:
Library name: P2_5_84
SMART-Seq2


title: P2.5_85

description:
Library name: P2_5_85
SMART-Seq2


title: SRSF5 (4058) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SRSF5_K562_4058_INPUT_rep1
eCLIP size-matched input control for SRSF5, biological replicate 1


title: DLK KO vincristine 2

description: Library name: Sample 14


title: DLK KO vincristine 3

description: Library name: Sample 15


title: DLK KO untreated 4

description: Library name: Sample 12


title: DLK KO vincristine 1

description: Library name: Sample 13


title: FUBP1 (4055) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FUBP1_K562_4055_INPUT_rep2
eCLIP size-matched input control for FUBP1, biological replicate 2


title: P2.5_86

description:
Library name: P2_5_86
SMART-Seq2


title: P2.5_82

description:
Library name: P2_5_82
SMART-Seq2


title: RNA from patient HTA2_27097, derived from Normal #3 [HTA2_27097_6000105]

description: Library name: HTA2_27097_6000105


title: DLK KO untreated 3

description: Library name: Sample 11


title: FUBP1 (4055) eCLIP in K562 cells, IP replicate 2

description:
Library name: FUBP1_K562_4055_IP_rep2
eCLIP immunoprecipitation sample for FUBP1, biological replicate 2


title: SRSF5 (4058) eCLIP in K562 cells, IP replicate 2

description:
Library name: SRSF5_K562_4058_IP_rep2
eCLIP immunoprecipitation sample for SRSF5, biological replicate 2


title: RNA from patient HTA2_27117, derived from LUAD (Stage 1A) [HTA2_27117_6000101]

description: Library name: HTA2_27117_6000101

value: HJLGNBGXL


title: RNA from patient HTA2_27097, derived from Normal #2 [HTA2_27097_6000103]

description: Library name: HTA2_27097_6000103


title: P2.5_83

description:
Library name: P2_5_83
SMART-Seq2


title: P2.5_81

description:
Library name: P2_5_81
SMART-Seq2


title: SRSF5 (4058) eCLIP in K562 cells, IP replicate 1

description:
Library name: SRSF5_K562_4058_IP_rep1
eCLIP immunoprecipitation sample for SRSF5, biological replicate 1


title: RNA from patient HTA2_27097, derived from LUAD (Stage 1A) [HTA2_27097_6000101]

description: Library name: HTA2_27097_6000101


title: FUBP1 (4055) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FUBP1_K562_4055_INPUT_rep1
eCLIP size-matched input control for FUBP1, biological replicate 1


title: P2.5_79

description:
Library name: P2_5_79
SMART-Seq2


title: P2.5_80

description:
Library name: P2_5_80
SMART-Seq2


title: SRSF1 (4045) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SRSF1_K562_4045_INPUT_rep2
eCLIP size-matched input control for SRSF1, biological replicate 2


title: FUBP1 (4055) eCLIP in K562 cells, IP replicate 1

description:
Library name: FUBP1_K562_4055_IP_rep1
eCLIP immunoprecipitation sample for FUBP1, biological replicate 1


title: DLK KO untreated 1

description: Library name: Sample 9


title: DLK KO untreated 2

description: Library name: Sample 10


title: P2.5_78

description:
Library name: P2_5_78
SMART-Seq2


title: WT vincristine 4

description: Library name: Sample 8

value: WT


title: WT vincristine 3

description: Library name: Sample 7


title: SRSF1 (4045) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SRSF1_K562_4045_INPUT_rep1
eCLIP size-matched input control for SRSF1, biological replicate 1


title: RNA from patient HTA2_26866, derived from AAH #3 [HTA2_26866_6000110]

description: Library name: HTA2_26866_6000110

value: Resected lung tissue


title: SRSF1 (4045) eCLIP in K562 cells, IP replicate 2

description:
Library name: SRSF1_K562_4045_IP_rep2
eCLIP immunoprecipitation sample for SRSF1, biological replicate 2


title: P2.5_77

description:
Library name: P2_5_77
SMART-Seq2


title: WT vincristine 2

description: Library name: Sample 6


title: RNA from patient HTA2_26866, derived from Normal #2 [HTA2_26866_6000109]

description: Library name: HTA2_26866_6000109


title: P2.5_76

description:
Library name: P2_5_76
SMART-Seq2


title: P2.5_75

description:
Library name: P2_5_75
SMART-Seq2


title: RNA from patient HTA2_26866, derived from LUAD Region 2 (Stage 1B) [HTA2_26866_6000103]

description: Library name: HTA2_26866_6000103

value: ADC


title: DDX47 (4050) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DDX47_K562_4050_INPUT_rep2
eCLIP size-matched input control for DDX47, biological replicate 2


title: WT untreated 4

description: Library name: Sample 4

value: "cortical", NGN2


title: DDX47 (4050) eCLIP in K562 cells, IP replicate 2

description:
Library name: DDX47_K562_4050_IP_rep2
eCLIP immunoprecipitation sample for DDX47, biological replicate 2


title: RNA from patient HTA2_24958, derived from Normal #2 [HTA2_24958_6000105]

description: Library name: HTA2_24958_6000105


title: RNA from patient HTA2_26866, derived from LUAD Region 1 (Stage 1B) [HTA2_26866_6000101]

description: Library name: HTA2_26866_6000101


title: P2.5_74

description:
Library name: P2_5_74
SMART-Seq2


title: WT vincristine 1

description: Library name: Sample 5

value: neuron


title: RNA from patient HTA2_26866, derived from AAH #2 [HTA2_26866_6000108]

description: Library name: HTA2_26866_6000108


title: SRSF1 (4045) eCLIP in K562 cells, IP replicate 1

description:
Library name: SRSF1_K562_4045_IP_rep1
eCLIP immunoprecipitation sample for SRSF1, biological replicate 1


title: RNA from patient HTA2_26866, derived from AAH #1 [HTA2_26866_6000106]

description: Library name: HTA2_26866_6000106


title: WT untreated 3

description: Library name: Sample 3


title: DDX47 (4050) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DDX47_K562_4050_INPUT_rep1
eCLIP size-matched input control for DDX47, biological replicate 1


title: P2.5_73

description:
Library name: P2_5_73
SMART-Seq2


title: DDX47 (4050) eCLIP in K562 cells, IP replicate 1

description:
Library name: DDX47_K562_4050_IP_rep1
eCLIP immunoprecipitation sample for DDX47, biological replicate 1


title: P2.5_72

description:
Library name: P2_5_72
SMART-Seq2


title: NSUN4 (4047) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NSUN4_K562_4047_INPUT_rep2
eCLIP size-matched input control for NSUN4, biological replicate 2


title: P2.5_71

description:
Library name: P2_5_71
SMART-Seq2


title: WT untreated 2

description: Library name: Sample 2


title: P2.5_70

description:
Library name: P2_5_70
SMART-Seq2


title: C5002; combo 1; Input; ChIP

city: Houston

first: Hey Min

last: Lee

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

institute: University of Texas MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC and human tumor-derived sequence reads were classified from PDX sample using Xenome package. Filtered reads are aligned to the hg38 reference genome using Bowtie, and  sorted and indexed using samtools
Model based analysis of ChIP-seq (MACS) used for  peak calling
Assembly: hg38
Supplementary files format and content: bigwig file

molecule: genomic DNA

growth_protocol: PDX tumors were implanted into 4-6 week-old female immunodeficient nu/nu mice subcutaneously.

extract_protocol:
Snap-frozen tumor tissues were harvested, crosslinked for 10 minutes with formaldehyde, and quenched for 5 minutes with 125 mM glycine. After lysis and sonication with Bioruptor (Diagenode), immunoprecipitation with antibodies was performed.
ChIP-seq libraries were prepared using NEB Ultra II DNA library prep kit.

treatment_protocol: BRAFV600E-mutated CRC PDX (C5002) model treated by either vehicle control, ZEN3694, encorafenib + cetuximab, or combination of ZEN3694 + encorafenib + cetuximab.

value: Patient-derived xenograft

value: combo


title: RNA from patient HTA2_24958, derived from AAH  [HTA2_24958_6000104]

description: Library name: HTA2_24958_6000104


title: WT untreated 1

description: Library name: Sample 1

value: untreated


title: NSUN4 (4047) eCLIP in K562 cells, IP replicate 2

description:
Library name: NSUN4_K562_4047_IP_rep2
eCLIP immunoprecipitation sample for NSUN4, biological replicate 2


title: RNA from patient HTA2_24648, derived from Normal #3 [HTA2_24648_6000105]

description: Library name: HTA2_24648_6000105

value: N


title: C5002; combo 1; BRD4; ChIP

tag: chip antibody

value: BRD4 (Bethyl)


title: RNA from patient HTA2_24958, derived from Normal #1 [HTA2_24958_6000103]

description: Library name: HTA2_24958_6000103


title: P2.5_69

description:
Library name: P2_5_69
SMART-Seq2

value: female germ cell


title: NSUN4 (4047) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NSUN4_K562_4047_INPUT_rep1
eCLIP size-matched input control for NSUN4, biological replicate 1


title: RNA from patient HTA2_24648, derived from AAH [HTA2_24648_6000104]

description: Library name: HTA2_24648_6000104


title: RNA from patient HTA2_24568, derived from Normal #2 [HTA2_24568_6000105]

description: Library name: HTA2_24568_6000105


title: C5002; zen3694 3; Input; ChIP


title: P2.5_68

description:
Library name: P2_5_68
SMART-Seq2


title: ELAVL1 (4044) eCLIP in K562 cells, IP replicate 2

description:
Library name: ELAVL1_K562_4044_IP_rep2
eCLIP immunoprecipitation sample for ELAVL1, biological replicate 2


title: ELAVL1 (4044) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: ELAVL1_K562_4044_INPUT_rep2
eCLIP size-matched input control for ELAVL1, biological replicate 2


title: P2.5_67

description:
Library name: P2_5_67
SMART-Seq2


title: P2.5_66

description:
Library name: P2_5_66
SMART-Seq2


title: C5002; combo 1; BRD2; ChIP

value: BRD2 (Bethyl)


title: NSUN4 (4047) eCLIP in K562 cells, IP replicate 1

description:
Library name: NSUN4_K562_4047_IP_rep1
eCLIP immunoprecipitation sample for NSUN4, biological replicate 1


title: RNA from patient HTA2_24648, derived from Normal #2 [HTA2_24648_6000103]

description: Library name: HTA2_24648_6000103


title: RNA from patient HTA2_24568, derived from AAH  [HTA2_24568_6000104]

description: Library name: HTA2_24568_6000104

value: HFMTWBGXL


title: C5002; zen3694 3; BRD4; ChIP


title: P2.5_65

description:
Library name: P2_5_65
SMART-Seq2


title: C5002; zen3694 2; Input; ChIP


title: ELAVL1 (4044) eCLIP in K562 cells, IP replicate 1

description:
Library name: ELAVL1_K562_4044_IP_rep1
eCLIP immunoprecipitation sample for ELAVL1, biological replicate 1


title: C5002; zen3694 3; BRD2; ChIP


title: P2.5_64

description:
Library name: P2_5_64
SMART-Seq2


title: ELAVL1 (4044) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: ELAVL1_K562_4044_INPUT_rep1
eCLIP size-matched input control for ELAVL1, biological replicate 1


title: RNA from patient HTA2_23998, derived from Normal [HTA2_23998_6000106]

description: Library name: HTA2_23998_6000106


title: RNA from patient HTA2_23998, derived from Normal [HTA2_23998_6000104]

description: Library name: HTA2_23998_6000104


title: GARS (4040) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: GARS_K562_4040_INPUT_rep2
eCLIP size-matched input control for GARS, biological replicate 2


title: RNA from patient HTA2_21522, derived from Normal [HTA2_21522_6000105]

description: Library name: HTA2_21522_6000105


title: C5002; zen3694 2; BRD4; ChIP


title: C5002; zen3694 2; BRD2; ChIP


title: GARS (4040) eCLIP in K562 cells, IP replicate 2

description:
Library name: GARS_K562_4040_IP_rep2
eCLIP immunoprecipitation sample for GARS, biological replicate 2


title: RNA from patient HTA2_21522, derived from AAH [HTA2_21522_6000104]

description: Library name: HTA2_21522_6000104

value: HJMJGBGXL


title: P2.5_63

description:
Library name: P2_5_63
SMART-Seq2


title: P2.5_62

description:
Library name: P2_5_62
SMART-Seq2


title: P2.5_61

description:
Library name: P2_5_61
SMART-Seq2


title: RNA from patient HTA2_21522, derived from Normal [HTA2_21522_6000103]

description: Library name: HTA2_21522_6000103


title: C5002; zen3694 1; Input; ChIP


title: GARS (4040) eCLIP in K562 cells, IP replicate 1

description:
Library name: GARS_K562_4040_IP_rep1
eCLIP immunoprecipitation sample for GARS, biological replicate 1


title: GARS (4040) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: GARS_K562_4040_INPUT_rep1
eCLIP size-matched input control for GARS, biological replicate 1


title: C5002; zen3694 1; BRD4; ChIP


title: RNA from patient HTA2_21522, derived from LUAD (Stage 1B) [HTA2_21522_6000101]

description: Library name: HTA2_21522_6000101

value: HJMCCBGXL


title: P2.5_60

description:
Library name: P2_5_60
SMART-Seq2


title: C5002; zen3694 1; BRD2; ChIP


title: EEF2 (4037) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EEF2_K562_4037_INPUT_rep2
eCLIP size-matched input control for EEF2, biological replicate 2


title: C5002; encorafenib+cetuximab 5; Input; ChIP

value: encorafenib+cetuximab


title: RNA from patient HTA2_20457, derived from Normal #3 [HTA2_20457_6000107]

description: Library name: HTA2_20457_6000107


title: P2.5.59

description:
Library name: P2_5_59
SMART-Seq2


title: EEF2 (4037) eCLIP in K562 cells, IP replicate 2

description:
Library name: EEF2_K562_4037_IP_rep2
eCLIP immunoprecipitation sample for EEF2, biological replicate 2


title: P2.5.58

description:
Library name: P2_5_58
SMART-Seq2


title: EEF2 (4037) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EEF2_K562_4037_INPUT_rep1
eCLIP size-matched input control for EEF2, biological replicate 1


title: RNA from patient HTA2_20457, derived from AAH #2 [HTA2_20457_6000106]

description: Library name: HTA2_20457_6000106

value: AAH


title: C5002; encorafenib+cetuximab 4; BRD4; ChIP


title: P2.5.57

description:
Library name: P2_5_57
SMART-Seq2


title: NCL (4035) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NCL_K562_4035_INPUT_rep2
eCLIP size-matched input control for NCL, biological replicate 2


title: Tumor-12 tsRNA

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
The raw data (Raw sequencing data) was in FASTQ format and firstly, the raw data was quality controlled using FastQC (v 0.11.7) and the corresponding quality scores were generated.
The quality-checked and standardized data were then processed by Cutadapt (v 1.17), which included removing splice sequences and filtering out fragments less than 14 nts or more than 40 nts in length to obtain trimmed data, and the length distributions of reads were counted.
Trimmed data were in FASTA format and were aligned to mature tRNA sequences using Bowtie (v 1.2.2), with the maximum number of mismatched bases allowed to be set to 1.
For Reads that failed to match mature tRNA sequences, they were aligned to the tRNA precursor reference sequences using Bowtie and again, the number of mismatched bases allowed was set to 1. number of bases was set to 1. The abundance of tRNAs was assessed by Counts (number of sequenced Reads matched to the genome) and normalized by Counts Per Million (CPM).
If the CPM values of all samples were lower than 20, the corresponding tsRNAs were filtered and the expression profiles of tsRNAs were finally obtained. The edgeR software was used to analyze the differential expression of tsRNAs, and the tsRNAs with significant differences in expression levels between the two groups of samples were screened out based on the statistical criteria of Fold Change (FC) greater than 1.5 and P-value less than 0.05.
Assembly: hg19
Supplementary files format and content: Expression_tRF.xlsx file include raw counts data for each Sample
Supplementary files format and content: ALL_Differentially_Expressed_tRF.xlsx file include differential expression data of genes between samples

source_name: colorectal

extract_protocol:
Deparaffinization of paraffin-embedded FFPE tissue samples and total RNA was extracted with TRIzol reagent (#15596026, Invitrogen). Sample integrity and concentration were examined by agarose gel electrophoresis and NanoDrop One (Thermo Fisher Scientific, MA, USA). Using the rtStar™ tRF&tiRNA Pretreatment Kit (#AS-FS-005, Arraystar) to remove the 3'-carbamoyl and 3'-cP termini, phosphorylation of the 5'-OH terminus, and demethylation of m1A, m1G, and m3C demethylation to prepare RNA samples suitable for tsRNAs sequencing library construction [29]. The extracted total RNA samples were ligated one by one with small RNA junctions at the 3' and 5' ends, and the cDNA was synthesized and amplified using proprietary reverse transcription primers and amplification primers (Illumina, CA, USA).
Approximately 134-160 bp of PCR amplified fragments were extracted and purified from PAGE gels to ensure the purity and quality of the final PCR amplified fragments obtained. The concentration and purity of the tsRNAs library was determined using an Agilent 2100 Bioanalyzer (Agilent, CA, USA). The library was denatured and diluted to a volume of 1.3 mL at a concentration of 1.8 pM.

treatment_protocol: Clinical samples for this study were obtained from the Department of Gastroenterology, Panyu Central Hospital, Guangzhou Medical University, and were approved by the Ethics Committee. Formalin-fixed paraffin-embedded mass tissues and corresponding paracancerous tissues from 12 colorectal cancer patients were included for tsRNAs sequencing.

value: colorectal

value: colorectal cancer


title: P2.5.56

description:
Library name: P2_5_56
SMART-Seq2


title: C5002; encorafenib+cetuximab 3; BRD2; ChIP


title: Tumor-11 tsRNA


title: P2.5.55

description:
Library name: P2_5_55
SMART-Seq2


title: EEF2 (4037) eCLIP in K562 cells, IP replicate 1

description:
Library name: EEF2_K562_4037_IP_rep1
eCLIP immunoprecipitation sample for EEF2, biological replicate 1


title: C5002; encorafenib+cetuximab 2; BRD4; ChIP


title: RNA from patient HTA2_20457, derived from Normal #2 [HTA2_20457_6000103]

description: Library name: HTA2_20457_6000103

value: Resected lung tissue


title: C5002; encorafenib+cetuximab 2; Input; ChIP


title: C5002; encorafenib+cetuximab 2; BRD2; ChIP


title: NCL (4035) eCLIP in K562 cells, IP replicate 2

description:
Library name: NCL_K562_4035_IP_rep2
eCLIP immunoprecipitation sample for NCL, biological replicate 2


title: P2.5.54

description:
Library name: P2_5_54
SMART-Seq2


title: P2.5.53

description:
Library name: P2_5_53
SMART-Seq2


title: C5002; encorafenib+cetuximab 1; Input; ChIP


title: Tumor-10 tsRNA


title: NCL (4035) eCLIP in K562 cells, IP replicate 1

description:
Library name: NCL_K562_4035_IP_rep1
eCLIP immunoprecipitation sample for NCL, biological replicate 1


title: Tumor-9 tsRNA


title: NCL (4035) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NCL_K562_4035_INPUT_rep1
eCLIP size-matched input control for NCL, biological replicate 1


title: P2.5.52

description:
Library name: P2_5_52
SMART-Seq2


title: Tumor-8 tsRNA


title: EIF4E (4018) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF4E_K562_4018_INPUT_rep2
eCLIP size-matched input control for EIF4E, biological replicate 2


title: C5002; encorafenib+cetuximab 1; BRD4; ChIP


title: P2.5.51

description:
Library name: P2_5_51
SMART-Seq2


title: EIF4E (4018) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF4E_K562_4018_IP_rep2
eCLIP immunoprecipitation sample for EIF4E, biological replicate 2


title: P2.5.50

description:
Library name: P2_5_50
SMART-Seq2


title: C5002; control 3; BRD4; ChIP

value: control


title: Tumor-7 tsRNA


title: P2.5_49

description:
Library name: P2_5_49
SMART-Seq2


title: Tumor-5 tsRNA


title: EIF4E (4018) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF4E_K562_4018_INPUT_rep1
eCLIP size-matched input control for EIF4E, biological replicate 1


title: Tumor-4 tsRNA


title: C5002; control 3; Input; ChIP


title: C5002; control 3; BRD2; ChIP


title: P2.5_48

description:
Library name: P2_5_48
SMART-Seq2


title: C5002; encorafenib+cetuximab 1; BRD2; ChIP


title: EIF4E (4018) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF4E_K562_4018_IP_rep1
eCLIP immunoprecipitation sample for EIF4E, biological replicate 1


title: Tumor-6 tsRNA


title: TDP43 (4014) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TDP43_K562_4014_INPUT_rep2
eCLIP size-matched input control for TDP43, biological replicate 2


title: P2.5_46

description:
Library name: P2_5_46
SMART-Seq2


title: Tumor-3 tsRNA


title: TDP43 (4014) eCLIP in K562 cells, IP replicate 2

description:
Library name: TDP43_K562_4014_IP_rep2
eCLIP immunoprecipitation sample for TDP43, biological replicate 2


title: Tumor-2 tsRNA


title: P2.5_47

description:
Library name: P2_5_47
SMART-Seq2


title: P2.5_45

description:
Library name: P2_5_45
SMART-Seq2


title: C5002; control 2; BRD2; ChIP


title: C5002; control 2; Input; ChIP


title: C5002; control 1; Input; ChIP


title: TDP43 (4014) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TDP43_K562_4014_INPUT_rep1
eCLIP size-matched input control for TDP43, biological replicate 1


title: Normal-12 tsRNA

value: Normal


title: Tumor-1 tsRNA


title: P2.5_43

description:
Library name: P2_5_43
SMART-Seq2


title: TDP43 (4014) eCLIP in K562 cells, IP replicate 1

description:
Library name: TDP43_K562_4014_IP_rep1
eCLIP immunoprecipitation sample for TDP43, biological replicate 1


title: P2.5_44

description:
Library name: P2_5_44
SMART-Seq2


title: C5002; control 1; BRD4; ChIP

value: Patient-derived xenograft


title: Normal-11 tsRNA


title: Normal-10 tsRNA


title: C5002; control 2; BRD4; ChIP


title: C5002; control 1; BRD2; ChIP


title: RPS6 (4012) eCLIP in K562 cells, IP replicate 1

description:
Library name: RPS6_K562_4012_IP_rep1
eCLIP immunoprecipitation sample for RPS6, biological replicate 1


title: RPS6 (4012) eCLIP in K562 cells, IP replicate 2

description:
Library name: RPS6_K562_4012_IP_rep2
eCLIP immunoprecipitation sample for RPS6, biological replicate 2


title: P2.5_41

description:
Library name: P2_5_41
SMART-Seq2


title: RPS6 (4012) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RPS6_K562_4012_INPUT_rep1
eCLIP size-matched input control for RPS6, biological replicate 1


title: P2.5_40

description:
Library name: P2_5_40
SMART-Seq2


title: Normal-9 tsRNA


title: RPS6 (4012) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RPS6_K562_4012_INPUT_rep2
eCLIP size-matched input control for RPS6, biological replicate 2


title: C5002; combo 3; Input; ChIP

value: combo


title: P2.5_42

description:
Library name: P2_5_42
SMART-Seq2


title: NPM1 (4010) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NPM1_K562_4010_INPUT_rep2
eCLIP size-matched input control for NPM1, biological replicate 2


title: C5002; combo 3; BRD4; ChIP


title: Normal-8 tsRNA


title: P2.5_39

description:
Library name: P2_5_39
SMART-Seq2


title: C5002; combo 3; BRD2; ChIP


title: NPM1 (4010) eCLIP in K562 cells, IP replicate 2

description:
Library name: NPM1_K562_4010_IP_rep2
eCLIP immunoprecipitation sample for NPM1, biological replicate 2


title: Normal-7 tsRNA


title: P2.5_38

description:
Library name: P2_5_38
SMART-Seq2


title: Normal-6 tsRNA


title: C5002; combo 2; Input; ChIP


title: NPM1 (4010) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NPM1_K562_4010_INPUT_rep1
eCLIP size-matched input control for NPM1, biological replicate 1


title: C5002; combo 2; BRD4; ChIP


title: P2.5_37

description:
Library name: P2_5_37
SMART-Seq2


title: Normal-5 tsRNA


title: NPM1 (4010) eCLIP in K562 cells, IP replicate 1

description:
Library name: NPM1_K562_4010_IP_rep1
eCLIP immunoprecipitation sample for NPM1, biological replicate 1


title: P2.5_36

description:
Library name: P2_5_36
SMART-Seq2


title: Normal-4 tsRNA


title: C5002; combo 2; BRD2; ChIP


title: P2.5_35

description:
Library name: P2_5_35
SMART-Seq2


title: Normal-2 tsRNA


title: B8120 BET3

data_processing:
Biobambam was used for indexing and duplicate marking, and human tumor-derived sequence reads from PDX model samples were classified using Xenome pakcage. STAR alignment was used for mapping to the human genome (GRCh38) and read counts were extracted using HTSeq.
DESeq2 package has been used for differential expression analysis
Assembly: hg38
Supplementary files format and content: text file includes raw Human genome aligned counts of each Sample

extract_protocol:
Snap-frozen tumor tissue (~40mg) was used for RNA extraction by NORGEN Total RNA Purification Kit (Cat. 37500) (NORGEN BIOTEK CORP) treated with DNase I and cleaned up using AMPure XP beads (Beckman Coulter Life Sciences). The purified RNA was quantified using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher SCIENTIFIC) and the RNA quality was accessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies). The cDNA was prepared from the extracted total RNA using Ovation® RNA-Seq System V2 (NuGEN). The prepared cDNA was quantified using Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher SCIENTIFIC) and quality was accessed using Genomic DNA ScreenTape and Reagents on the Tapestation 4200 (Agilent Technologies)
cDNA was proceeded to library preparation using SureSelect XT Low Input Reagent Kit with indexes 1-96 (Agilent Technologies) as automated method on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.).

treatment_protocol: PDXs were treated with the vehicle vehicle control, binimetinib, iBET-151, or combo (binimetinib + iBET-151).


title: Normal-3 tsRNA


title: HNRNPK (4006) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: HNRNPK_K562_4006_INPUT_rep1
eCLIP size-matched input control for HNRNPK, biological replicate 1


title: Normal-1 tsRNA


title: HNRNPK (4006) eCLIP in K562 cells, IP replicate 2

description:
Library name: HNRNPK_K562_4006_IP_rep2
eCLIP immunoprecipitation sample for HNRNPK, biological replicate 2


title: B8120 BET2


title: P2.5_33

description:
Library name: P2_5_33
SMART-Seq2


title: P2.5_32

description:
Library name: P2_5_32
SMART-Seq2


title: P2.5_31

description:
Library name: P2_5_31
SMART-Seq2


title: B8120 Veh2

value: vehicle


title: HNRNPK (4006) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: HNRNPK_K562_4006_INPUT_rep2
eCLIP size-matched input control for HNRNPK, biological replicate 2


title: B8120BET1


title: DEK (4004) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DEK_K562_4004_INPUT_rep2
eCLIP size-matched input control for DEK, biological replicate 2


title: HNRNPK (4006) eCLIP in K562 cells, IP replicate 1

description:
Library name: HNRNPK_K562_4006_IP_rep1
eCLIP immunoprecipitation sample for HNRNPK, biological replicate 1


title: Sample_2719205

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description: Library name: Sample_2719205

data_processing:
Reads were aligned using STAR aligner
UMIs were extracted and demultiplexed using UMItools
count matrix was built using featureCounts
normalization and differential expressiona analysis was carried out using DESeq2
Assembly: GRCh38
Supplementary files format and content: raw count matrix tsv format
Supplementary files format and content: metadata tsv format

source_name: Bladder tumor

extract_protocol:
RNA was extracted using the Covaris truXTRAC® FFPE total NA kit; RNA quality was assessed using bioanalyzer.
Total RNA samples were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, whereby random primers featured a 6 nt long Unique Molecular Identifier 5' tag to be addressed at data analysis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.  {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

value: Bladder tumor


title: DEK (4004) eCLIP in K562 cells, IP replicate 2

description:
Library name: DEK_K562_4004_IP_rep2
eCLIP immunoprecipitation sample for DEK, biological replicate 2


title: B8120 Veh3


title: P2.5_29

description:
Library name: P2_5_29
SMART-Seq2


title: Sample_2719206

description: Library name: Sample_2719206


title: P2.5_34

description:
Library name: P2_5_34
SMART-Seq2


title: Sample_2719204

description: Library name: Sample_2719204


title: P2.5_30

description:
Library name: P2_5_30
SMART-Seq2


title: Sample_2719203

description: Library name: Sample_2719203


title: C1138 combo3


title: DEK (4004) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DEK_K562_4004_INPUT_rep1
eCLIP size-matched input control for DEK, biological replicate 1


title: DEK (4004) eCLIP in K562 cells, IP replicate 1

description:
Library name: DEK_K562_4004_IP_rep1
eCLIP immunoprecipitation sample for DEK, biological replicate 1


title: P2.5_28

description:
Library name: P2_5_28
SMART-Seq2


title: B8120 Veh1


title: C1138 combo2


title: FXR2 (4002) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FXR2_K562_4002_INPUT_rep2
eCLIP size-matched input control for FXR2, biological replicate 2


title: Sample_2719202

description: Library name: Sample_2719202


title: P2.5_27

description:
Library name: P2_5_27
SMART-Seq2


title: C1138 combo1


title: Sample_2719201

description: Library name: Sample_2719201


title: P2.5_26

description:
Library name: P2_5_26
SMART-Seq2


title: FXR2 (4002) eCLIP in K562 cells, IP replicate 2

description:
Library name: FXR2_K562_4002_IP_rep2
eCLIP immunoprecipitation sample for FXR2, biological replicate 2


title: Sample_2718207

description: Library name: Sample_2718207


title: P2.5_25

description:
Library name: P2_5_25
SMART-Seq2


title: Sample_2718206

description: Library name: Sample_2718206


title: FXR2 (4002) eCLIP in K562 cells, IP replicate 1

description:
Library name: FXR2_K562_4002_IP_rep1
eCLIP immunoprecipitation sample for FXR2, biological replicate 1


title: C1138 BIN2

value: binimetinib


title: Sample_2718204

description: Library name: Sample_2718204


title: FXR2 (4002) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FXR2_K562_4002_INPUT_rep1
eCLIP size-matched input control for FXR2, biological replicate 1


title: C1138 BIN1


title: P2.5_22

description:
Library name: P2_5_22
SMART-Seq2

value: female germ cell


title: C1138 BET2


title: P2.5_21

description:
Library name: P2_5_21
SMART-Seq2


title: P2.5_24

description:
Library name: P2_5_24
SMART-Seq2


title: NONO (4001) eCLIP in K562 cells, IP replicate 1

description:
Library name: NONO_K562_4001_IP_rep1
eCLIP immunoprecipitation sample for NONO, biological replicate 1


title: P2.5_23

description:
Library name: P2_5_23
SMART-Seq2


title: C1138 BIN3


title: NONO (4001) eCLIP in K562 cells, IP replicate 2

description:
Library name: NONO_K562_4001_IP_rep2
eCLIP immunoprecipitation sample for NONO, biological replicate 2


title: Sample_2718205

description: Library name: Sample_2718205


title: Sample_2718201

description: Library name: Sample_2718201


title: P2.5_20

description:
Library name: P2_5_20
SMART-Seq2


title: NONO (4001) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NONO_K562_4001_INPUT_rep2
eCLIP size-matched input control for NONO, biological replicate 2


title: C1138 BET1


title: Sample_2718203

description: Library name: Sample_2718203


title: NONO (4001) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NONO_K562_4001_INPUT_rep1
eCLIP size-matched input control for NONO, biological replicate 1


title: C1138 Veh3


title: Sample_2718202

description: Library name: Sample_2718202


title: C1138 Veh2


title: Sample_2718102

description: Library name: Sample_2718102


title: NSUN2 (4215) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: NSUN2_HepG2_4215_INPUT_rep2
eCLIP size-matched input control for NSUN2, biological replicate 2


title: C1138 BET3


title: NSUN2 (4215) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: NSUN2_HepG2_4215_IP_rep2
eCLIP immunoprecipitation sample for NSUN2, biological replicate 2


title: Sample_2718101

description: Library name: Sample_2718101


title: P2.5_19

description:
Library name: P2_5_19
SMART-Seq2


title: NSUN2 (4215) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: NSUN2_HepG2_4215_INPUT_rep1
eCLIP size-matched input control for NSUN2, biological replicate 1


title: C1138 Veh1


title: Sample_2717102

description: Library name: Sample_2717102


title: P2.5_17

description:
Library name: P2_5_17
SMART-Seq2


title: P2.5_18

description:
Library name: P2_5_18
SMART-Seq2


title: P2.5_16

description:
Library name: P2_5_16
SMART-Seq2


title: B8131 combo3


title: Sample_2717101

description: Library name: Sample_2717101


title: P2.5_15

description:
Library name: P2_5_15
SMART-Seq2


title: B8131 combo2


title: PARP (4214) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: PARP_HepG2_4214_IP_rep2
eCLIP immunoprecipitation sample for PARP, biological replicate 2


title: P2.5_14

description:
Library name: P2_5_14
SMART-Seq2


title: Sample_2716205

description: Library name: Sample_2716205


title: Sample_2716206

description: Library name: Sample_2716206


title: B8131 combo1


title: PARP (4214) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: PARP_HepG2_4214_INPUT_rep2
eCLIP size-matched input control for PARP, biological replicate 2


title: P2.5_13

description:
Library name: P2_5_13
SMART-Seq2


title: Sample_2716202

description: Library name: Sample_2716202


title: PARP (4214) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: PARP_HepG2_4214_IP_rep1
eCLIP immunoprecipitation sample for PARP, biological replicate 1


title: Sample_2716203

description: Library name: Sample_2716203


title: NSUN2 (4215) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: NSUN2_HepG2_4215_IP_rep1
eCLIP immunoprecipitation sample for NSUN2, biological replicate 1


title: DHX38 (4202) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: DHX38_HepG2_4202_INPUT_rep2
eCLIP size-matched input control for DHX38, biological replicate 2


title: B8131 BIN2


title: B8131 BIN3


title: P2.5_11

description:
Library name: P2_5_11
SMART-Seq2


title: Sample_2716201

description: Library name: Sample_2716201


title: P2.5_12

description:
Library name: P2_5_12
SMART-Seq2


title: B8131 BIN1


title: P2.5_10

description:
Library name: P2_5_10
SMART-Seq2


title: P2.5_9

description:
Library name: P2_5_9
SMART-Seq2


title: Sample_2715211

description: Library name: Sample_2715211


title: DHX38 (4202) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: DHX38_HepG2_4202_INPUT_rep1
eCLIP size-matched input control for DHX38, biological replicate 1


title: DHX38 (4202) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: DHX38_HepG2_4202_IP_rep2
eCLIP immunoprecipitation sample for DHX38, biological replicate 2


title: PARP (4214) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: PARP_HepG2_4214_INPUT_rep1
eCLIP size-matched input control for PARP, biological replicate 1


title: B8131 BET3


title: Sample_2715210

description: Library name: Sample_2715210


title: B8131 BET1


title: Sample_2715208

description: Library name: Sample_2715208


title: B8131 Veh3


title: P2.5_7

description:
Library name: P2_5_7
SMART-Seq2


title: P2.5_8

description:
Library name: P2_5_8
SMART-Seq2


title: B8131 BET2


title: DHX38 (4202) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: DHX38_HepG2_4202_IP_rep1
eCLIP immunoprecipitation sample for DHX38, biological replicate 1


title: SNRNP200 (4212) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: SNRNP200_HepG2_4212_IP_rep2
eCLIP immunoprecipitation sample for SNRNP200, biological replicate 2


title: P2.5.5

description:
Library name: P2_5_5
SMART-Seq2


title: Sample_2715206

description: Library name: Sample_2715206


title: B8131 Veh1


title: P2.5_6

description:
Library name: P2_5_6
SMART-Seq2


title: SNRNP200 (4212) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: SNRNP200_HepG2_4212_INPUT_rep2
eCLIP size-matched input control for SNRNP200, biological replicate 2


title: Sample_2715207

description: Library name: Sample_2715207


title: SNRNP200 (4212) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: SNRNP200_HepG2_4212_INPUT_rep1
eCLIP size-matched input control for SNRNP200, biological replicate 1


title: B8131 Veh2


title: SNRNP200 (4212) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: SNRNP200_HepG2_4212_IP_rep1
eCLIP immunoprecipitation sample for SNRNP200, biological replicate 1


title: Sample_2715205

description: Library name: Sample_2715205


title: C0999 combo3


title: Sample_2715204

description: Library name: Sample_2715204


title: P2.5_4

description:
Library name: P2_5_4
SMART-Seq2


title: CNOT2 (4191) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: CNOT2_HepG2_4191_INPUT_rep2
eCLIP size-matched input control for CNOT2, biological replicate 2


title: C0999 combo2


title: C0999 combo1


title: P2.5_3

description:
Library name: P2_5_3
SMART-Seq2


title: CNOT2 (4191) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: CNOT2_HepG2_4191_IP_rep2
eCLIP immunoprecipitation sample for CNOT2, biological replicate 2


title: Sample_2715202

description: Library name: Sample_2715202


title: Sample_2715201

description: Library name: Sample_2715201


title: P2.5_2

description:
Library name: P2_5_2
SMART-Seq2


title: C0999 BIN2


title: P2.5_1

description:
Library name: P2_5_1
SMART-Seq2


title: CNOT2 (4191) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: CNOT2_HepG2_4191_INPUT_rep1
eCLIP size-matched input control for CNOT2, biological replicate 1


title: C0999 BIN3


title: Sample_2715203

description: Library name: Sample_2715203


title: Sample_2715103

description: Library name: Sample_2715103


title: CNOT2 (4191) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: CNOT2_HepG2_4191_IP_rep1
eCLIP immunoprecipitation sample for CNOT2, biological replicate 1


title: E17.5_22

description:
Library name: E17_5_22
SMART-Seq2


title: E17.5_21

description:
Library name: E17_5_21
SMART-Seq2


title: CACTIN (4190) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: CACTIN_HepG2_4190_INPUT_rep2
eCLIP size-matched input control for CACTIN, biological replicate 2


title: CACTIN (4190) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: CACTIN_HepG2_4190_IP_rep2
eCLIP immunoprecipitation sample for CACTIN, biological replicate 2


title: C0999 BET3


title: E17.5_20

description:
Library name: E17_5_20
SMART-Seq2


title: C0999 BET2


title: CACTIN (4190) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: CACTIN_HepG2_4190_INPUT_rep1
eCLIP size-matched input control for CACTIN, biological replicate 1


title: Sample_2715101

description: Library name: Sample_2715101


title: Sample_2714207

description: Library name: Sample_2714207


title: E17.5_19

description:
Library name: E17_5_19
SMART-Seq2


title: CACTIN (4190) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: CACTIN_HepG2_4190_IP_rep1
eCLIP immunoprecipitation sample for CACTIN, biological replicate 1


title: C0999 BIN1


title: E17.5_17

description:
Library name: E17_5_17
SMART-Seq2


title: Sample_2715102

description: Library name: Sample_2715102


title: E17.5_18

description:
Library name: E17_5_18
SMART-Seq2


title: PRPF39 (4149) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: PRPF39_HepG2_4149_INPUT_rep2
eCLIP size-matched input control for PRPF39, biological replicate 2


title: PRPF39 (4149) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: PRPF39_HepG2_4149_INPUT_rep1
eCLIP size-matched input control for PRPF39, biological replicate 1


title: Sample_2714202

description: Library name: Sample_2714202


title: PRPF39 (4149) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: PRPF39_HepG2_4149_IP_rep2
eCLIP immunoprecipitation sample for PRPF39, biological replicate 2


title: C0999 Veh2


title: E17.5_15

description:
Library name: E17_5_15
SMART-Seq2


title: Sample_2714206

description: Library name: Sample_2714206


title: C0999 Veh1


title: E17.5_16

description:
Library name: E17_5_16
SMART-Seq2


title: C0999 BET1


title: Sample_2714204

description: Library name: Sample_2714204


title: E17.5_14

description:
Library name: E17_5_14
SMART-Seq2


title: B8120 combo2


title: PPP1R10 (4148) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: PPP1R10_HepG2_4148_INPUT_rep2
eCLIP size-matched input control for PPP1R10, biological replicate 2


title: PRPF39 (4149) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: PRPF39_HepG2_4149_IP_rep1
eCLIP immunoprecipitation sample for PRPF39, biological replicate 1


title: C0999 Veh3


title: E17.5_13

description:
Library name: E17_5_13
SMART-Seq2


title: Sample_2713207

description: Library name: Sample_2713207


title: E17.5_12

description:
Library name: E17_5_12
SMART-Seq2


title: B8120 BIN3


title: PPP1R10 (4148) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: PPP1R10_HepG2_4148_IP_rep2
eCLIP immunoprecipitation sample for PPP1R10, biological replicate 2


title: Sample_2713206

description: Library name: Sample_2713206


title: B8120 combo3


title: Sample_2713205

description: Library name: Sample_2713205


title: PPP1R10 (4148) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: PPP1R10_HepG2_4148_INPUT_rep1
eCLIP size-matched input control for PPP1R10, biological replicate 1


title: Sample_2714201

description: Library name: Sample_2714201


title: B8120 BIN2


title: PPP1R10 (4148) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: PPP1R10_HepG2_4148_IP_rep1
eCLIP immunoprecipitation sample for PPP1R10, biological replicate 1


title: Sample_2713204

description: Library name: Sample_2713204


title: B8120 BIN1


title: B8120 combo1


title: Sample_2713203

description: Library name: Sample_2713203


title: Sample_2713202

description: Library name: Sample_2713202


title: DEK (4146) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: DEK_HepG2_4146_INPUT_rep2
eCLIP size-matched input control for DEK, biological replicate 2


title: E17.5_9

description:
Library name: E17_5_9
SMART-Seq2


title: DEK (4146) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: DEK_HepG2_4146_IP_rep2
eCLIP immunoprecipitation sample for DEK, biological replicate 2


title: E17.5_10

description:
Library name: E17_5_10
SMART-Seq2


title: Sample_2713201

description: Library name: Sample_2713201


title: E17.5_8

description:
Library name: E17_5_8
SMART-Seq2


title: IP_Con_3

city: Fuzhou

first: Mengting

last: Chen

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: hg19
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: placenta

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: placenta

value: trophoblast cell line

value: trophoblast

value: Wild type

value: Control

tag: rip antibody


title: Sample_2713102

description: Library name: Sample_2713102


title: IP_Con_2


title: DEK (4146) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: DEK_HepG2_4146_INPUT_rep1
eCLIP size-matched input control for DEK, biological replicate 1


title: E17.5_7

description:
Library name: E17_5_7
SMART-Seq2


title: E17.5_11

description:
Library name: E17_5_11
SMART-Seq2


title: DEK (4146) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: DEK_HepG2_4146_IP_rep1
eCLIP immunoprecipitation sample for DEK, biological replicate 1


title: IP_Con_1


title: E17.5.5

description:
Library name: E17_5_5
SMART-Seq2


title: E17.5_6

description:
Library name: E17_5_6
SMART-Seq2


title: Sample_2713101

description: Library name: Sample_2713101


title: IP_ORI_2

value: treat with oridonin


title: Sample_2711101

description: Library name: Sample_2711101


title: SNRPC (4187) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: SNRPC_HepG2_4187_IP_rep2
eCLIP immunoprecipitation sample for SNRPC, biological replicate 2


title: IP_ORI_3


title: Sample_2709207

description: Library name: Sample_2709207


title: E17.5_4

description:
Library name: E17_5_4
SMART-Seq2


title: IP_ORI_1


title: SNRPC (4187) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: SNRPC_HepG2_4187_INPUT_rep2
eCLIP size-matched input control for SNRPC, biological replicate 2


title: E17.5_3

description:
Library name: E17_5_3
SMART-Seq2


title: SNRPC (4187) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: SNRPC_HepG2_4187_INPUT_rep1
eCLIP size-matched input control for SNRPC, biological replicate 1


title: Sample_2709205

description: Library name: Sample_2709205


title: Input_Con_3

value: none (input)


title: Sample_2709206

description: Library name: Sample_2709206


title: SNRPC (4187) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: SNRPC_HepG2_4187_IP_rep1
eCLIP immunoprecipitation sample for SNRPC, biological replicate 1


title: E17.5_2

description:
Library name: E17_5_2
SMART-Seq2


title: Input_Con_2


title: E17.5_1

description:
Library name: E17_5_1
SMART-Seq2


title: Sample_2709204

description: Library name: Sample_2709204


title: Input_Con_1


title: SNRPD3 (4204) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: SNRPD3_HepG2_4204_INPUT_rep2
eCLIP size-matched input control for SNRPD3, biological replicate 2


title: SNRPD3 (4204) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: SNRPD3_HepG2_4204_IP_rep2
eCLIP immunoprecipitation sample for SNRPD3, biological replicate 2


title: Mouse_Ctrl_3

first: Jiatong

last: Ji

address: 639 Longmian Avenue

institute: China Pharmaceutical University

description:
10X Genomics
transcriptomic single nucleus

data_processing:
Raw sequencing data were processed using Cell Ranger (v. 6.0.3). Gene expression counts were generated following the standard Cell Ranger pipeline.
Assembly: mm10
Supplementary files format and content: Processed snRNA-seq matrices in tab-separated values format (counts) corresponding to each sample.

molecule: nuclear RNA

source_name: brain cortex

extract_protocol:
Each fresh brain tissue was kept frozen in liquid nitrogen until nucleus isolation. Frozen tissue was homogenized in NLB buffer containing 250 mM sucrose, 10 mM Tris-HCl, 3 mM MgAc₂, 0.1% Triton X-100 (Sigma Aldrich, USA), 0.1 mM EDTA, and 0.2 U/μL RNase inhibitor (Takara, Japan). Nuclei were purified using sucrose gradient centrifugation and adjusted to ~1000 nuclei/μL for snRNA-seq. Single-nucleus libraries were generated using the 10X Genomics Chromium Controller and Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics, Pleasanton, CA). Nuclei were loaded to generate Gel Bead-In-Emulsions (GEMs), reverse transcribed, and barcoded cDNA was purified and amplified. cDNA was fragmented, A-tailed, ligated with adaptors, and PCR amplified. Final libraries were quantified using Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and library size distribution was assessed with a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by Illumina NovaSeq 6000 (Illumina, San Diego, CA) on a 150 bp paired-end run.
The libraries mice TBI were respectively generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA). Briefly, nucleus were concentrated to approximately 1000 nucleus/uL and loaded into each channel to generate single-nucleus Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent).

value: brain cortex

tag: time after tbi

tag: group

tag: age

value: 8 weeks


title: Sample_2709202

description: Library name: Sample_2709202


title: SNRPD3 (4204) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: SNRPD3_HepG2_4204_INPUT_rep1
eCLIP size-matched input control for SNRPD3, biological replicate 1


title: Input_ORI_3


title: Sample_2709203

description: Library name: Sample_2709203


title: Mouse_Ctrl_2


title: Mouse_Ctrl_1


title: SNRPD3 (4204) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: SNRPD3_HepG2_4204_IP_rep1
eCLIP immunoprecipitation sample for SNRPD3, biological replicate 1


title: Input_ORI_2


title: Input_ORI_1


title: Mouse_STBI_group3_2

value: 4 days

value: STBI


title: Interdigit tissue isolate from Del-/-;ExLox, E12.25_bio rep3

city: Frederick

first: Susan

last: Mackem

address: 1050 Boyles St. Building 560, Room 21-08

institute: NCI-Frederick

description:
Library name: Del_Hom_ExLox_3
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_ExLox_3

data_processing:
All reads for each samples were trimmed adapters and low quality bases using Trimmomatic software.
Trimmed reads were aligned with mouse reference mm9 genome with TopHat Software (2.1.0) with the following parameters: @PG ID:TopHat -r 10 --mate-std-dev 200 --library-type fr-firststrand.
Assembly: mm9
Supplementary files format and content: xlsx files include normalized counts, fold change, FDR for each sample

source_name: E12.25 limb intergital tissue

extract_protocol:
The interdigit tissues were surgically removed and dissociated. The cells were sorted with tdTomato-positive and RNA were collected with RNAqueous Mini kit (Invitrogen). At least 100ng of total RNA was used with low throughput mRNA library protocol for the construction of sequencing libraries.
RNA libraries for RNAseq were prepared with Illumina TruSeq RNA library prep kit, following manufacturer's Protocol RS-930-2001

treatment_protocol: 3mg of Tamoxifen was given to pregnant females at E11.25 and the embryos were collected at E12.25

value: E12.25 limb intergital tissue

value: embryonic mesemchymal cells

value: Tamoxifen injection at E11.25


title: Sample_2709101

description: Library name: Sample_2709101

value: Bladder tumor


title: SNRPA1 (4203) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: SNRPA1_HepG2_4203_INPUT_rep2
eCLIP size-matched input control for SNRPA1, biological replicate 2


title: Sample_2708208

description: Library name: Sample_2708208


title: Mouse_STBI_group3_3


title: Interdigit tissue isolate from Del-/-;ExLox, E12.25_bio rep2

description:
Library name: Del_Hom_ExLox_2_2
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_ExLox_2_2


title: Sample_2708207

description: Library name: Sample_2708207


title: SNRPA1 (4203) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: SNRPA1_HepG2_4203_IP_rep2
eCLIP immunoprecipitation sample for SNRPA1, biological replicate 2


title: Interdigit tissue isolate from Del-/-;ExLox, E12.25_bio rep1

description:
Library name: Del_Hom_ExLox_1
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_ExLox_1


title: SNRPA1 (4203) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: SNRPA1_HepG2_4203_INPUT_rep1
eCLIP size-matched input control for SNRPA1, biological replicate 1


title: SNRPA1 (4203) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: SNRPA1_HepG2_4203_IP_rep1
eCLIP immunoprecipitation sample for SNRPA1, biological replicate 1


title: Sample_2708209

description: Library name: Sample_2708209


title: Sample_2708206

description: Library name: Sample_2708206


title: Mouse_STBI_group2_3

value: 2 days


title: Mouse_STBI_group3_1


title: Interdigit tissue isolate from Del-/-, E12.25_bio rep3

description:
Library name: Del_Hom_3
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_3


title: Interdigit tissue isolate from Del-/-, E12.25_bio rep2

description:
Library name: Del_Hom_2
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_2.1


title: Mouse_STBI_group2_2


title: NONO (4084) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: NONO_HepG2_4084_IP_rep2
eCLIP immunoprecipitation sample for NONO, biological replicate 2


title: Mouse_STBI_group2_1


title: Interdigit tissue isolate from Del-/-, E12.25_bio rep1

description:
Library name: Del_Hom_1
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Hom_1


title: Interdigit tissue isolate from Del+/-, E12.25_bio rep3

description:
Library name: Del_Het_3
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Het_3


title: Mouse_STBI_group1_3

value: 6 hours


title: NONO (4084) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: NONO_HepG2_4084_INPUT_rep2
eCLIP size-matched input control for NONO, biological replicate 2


title: NONO (4084) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: NONO_HepG2_4084_IP_rep1
eCLIP immunoprecipitation sample for NONO, biological replicate 1


title: Sample_2708205

description: Library name: Sample_2708205


title: Sample_2708201

description: Library name: Sample_2708201


title: NONO (4084) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: NONO_HepG2_4084_INPUT_rep1
eCLIP size-matched input control for NONO, biological replicate 1


title: Mouse_STBI_group1_2

description:
10X Genomics
transcriptomic single nucleus


title: Sample_2702202

description: Library name: Sample_2702202


title: Interdigit tissue isolate from Del+/-, E12.25_bio rep2

description:
Library name: Del_Het_2
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Het_2.1


title: Sample_2702201

description: Library name: Sample_2702201


title: Interdigit tissue isolate from Del+/-, E12.25_bio rep1

description:
Library name: Del_Het_1
Column_name_in_complete_normalized_count_and_DE_analysis_data_set.xlsx: Del_Het_1


title: Sample_2708202

description: Library name: Sample_2708202


title: TARDBP (4110) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: TARDBP_HepG2_4110_INPUT_rep2
eCLIP size-matched input control for TARDBP, biological replicate 2


title: TARDBP (4110) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: TARDBP_HepG2_4110_IP_rep2
eCLIP immunoprecipitation sample for TARDBP, biological replicate 2


title: Mouse_STBI_group1_1


title: P126BK TCRseq

city: Hamburg

first: Cedric

last: Ly

address: Falkenried 94

country: Germany

institute: UKE

description:
Library name: P126BK_TCR
Multiplexed: Blood: Hash1 : GTCAACTCTTTAGCG Kidney: Hash2: TGATGGCCTATTGGG

data_processing:
The Cell Ranger software (Cellranger v2.1.0 and v2.2.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome hg19.
Assembly: hg19
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : h5 files output from CellRanger
Library strategy: TCR-Seq

source_name: Blood + kidney

extract_protocol:
Total RNA was extracted from facs sorted CD45+ or CD3+ cells from human kidney (and blood) .
Single‑cell TCR sequencing libraries were generated using the Chromium Single Cell 5ʹ Library & Gel Bead Kit, 10x Genomics and the Chromium Single Cell V(D)J Reagent Kits humanT cell ccording to the manufacturer’s instructions. Briefly, single T cells were captured into droplets, reverse‑transcribed, amplified, and then TCR‑specific cDNA was enriched by targeted PCR using V(D)J enrichment primers. The resulting TCR‑enriched libraries were normalized, pooled, and sequenced on an Illumina  using a paired‑end [bp] run configuration.

value: Blood + kidney


title: Neurons_elavl3_6dpf_sc_MUT_rep1

city: Barcelona

first: Tahnee

last: Mackensen

address: Dr. Aiguader, 88

institute: Universitat Pompeu Fabra

description:
Library name: Neurons_elavl3_6dpf_sc_MUT_rep1
10x Genomics 3' (v 3.1)

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

organism: Danio rerio

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

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

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

tag: developmental stage

value: enucleated

tag: batch


title: TARDBP (4110) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: TARDBP_HepG2_4110_IP_rep1
eCLIP immunoprecipitation sample for TARDBP, biological replicate 1


title: RAW_H3K27ac_NC

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description: anno_merged_RAW_H3K27_TB_ChIPseq_normalize_to_e107_counts.txt

data_processing:
ChIP-seq raw files (fastq, paired-end) were aligned to the mm9 version of the mouse reference genome using Bowtie2 with default parameters. Peaks were called using HOMER. HOMER was then used to construct tag directories from the SAM files, remove duplicate reads, call peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
The raw ATAC-seq files (fastq, paired-end) were aligned to the mouse reference genome version mm9 using Bowtie2 with default parameters. Peak calling was then performed using MACS2. HOMER was then used to create tag directories from the SAM files, eliminate duplicate reads, identify peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks meeting the criteria of fold enrichment over input tag count and local tag count > 4 with a false discovery rate (FDR) < 0.001 (using default settings -F -L -C -fdr) were retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut&Tag raw files (fastq, paired-end) were aligned to the mouse reference genome (mm9) using Bowtie2 with default settings. Peak calling was performed using MACS2. HOMER was then used to construct tag directories from the SAM files, eliminate duplicate reads, call peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks that met the criteria of fold enrichment over input tag count, local tag count > 4, and false discovery rate (fdr) < 0.001 (using default parameters -F -L -C -fdr) were retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.

source_name: Ascites

growth_protocol: RAW264.7 cells were maintained normal 10% FBS DMEM medium

extract_protocol:
Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
The ChIP-seq Library preparation was performed through the manufacturer's introduction.

treatment_protocol: RAW264.7 cells were treated  with or without Mtb H37Ra treatment (24 hours)

value: Ascites

value: Macrophages

tag: strain

value: BALB/c


title: RAW_PPARg_H37Ra

description: anno_merged_RAW_PPARG_TB_ChIPseq_normalize_to_e107_counts.txt

tag: cell line

value: Mycobacterium tuberculosis H37Ra infected  treatment


title: Neurons_elavl3_6dpf_sc_WT_rep2

description:
Library name: Neurons_elavl3_6dpf_sc_WT_rep2
10x Genomics 3' (v 3.1)

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

value: WT


title: RAW_H3K27ac_H37Ra

tag: tissue


title: P144K TCRseq

description: Library name: P144K_TCRseq

source_name: kidney

value: kidney


title: TARDBP (4110) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: TARDBP_HepG2_4110_INPUT_rep1
eCLIP size-matched input control for TARDBP, biological replicate 1


title: P144K ADT

description: Library name: P144K_ADT

library_source: other

data_processing:
The Cell Ranger software (Cellranger v2.1.0 and v2.2.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome hg19.
Assembly: hg19
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : h5 files output from CellRanger
Library strategy: CITE-seq

molecule: protein


title: Neurons_elavl3_6dpf_sc_MUT_rep2

description:
Library name: Neurons_elavl3_6dpf_sc_MUT_rep2
10x Genomics 3' (v 3.1)


title: FXR2 (4098) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: FXR2_HepG2_4098_INPUT_rep2
eCLIP size-matched input control for FXR2, biological replicate 2


title: RAW_PPARg_NC

value: Control


title: Neurons_elavl3_6dpf_sc_WT_rep1

description:
Library name: Neurons_elavl3_6dpf_sc_WT_rep1
10x Genomics 3' (v 3.1)


title: P144K RNAseq

description: Library name: P144K_RNA

data_processing:
The Cell Ranger software (Cellranger v2.1.0 and v2.2.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome hg19.
Assembly: hg19
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : h5 files output from CellRanger


title: RAW_H37Ra_ATACseq_rp3

description: diffanno_anno_RAW_H37Ra_ATAC_seq_norm_raw_counts.txt

extract_protocol:
RAW264.7 cells were plated in triplicate in 12-well plates at a seeding density of 2×10^5 cells per well one day before the experiment. After 24 hours of Mtb infection, cells were harvested, washed with PBS, and resuspended in lysis buffer. Nuclei were pelleted by centrifugation and transferred to transposition reaction buffer, followed by incubation at 37°C for 30 minutes. Genomic DNA was extracted using the Qiagen MinElute PCR Purification Kit. ATAC-seq library preparation was performed according to the protocol described by Buenrostro et al. (2015). The purified ATAC-seq DNA library mix was sequenced on an Illumina NovaSeq 6000 platform.
The ATAC-seq Library preparation was performed through the manufacturer's introduction.


title: FXR2 (4098) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: FXR2_HepG2_4098_INPUT_rep1
eCLIP size-matched input control for FXR2, biological replicate 1


title: P143K TCRseq

description: Library name: P143K_TCRseq


title: WT_LPS_rep3

city: Montréal

first: Lilia

last: Rodriguez

state: Québec

address: 2900, boul. Édouard-Montpetit

country: Canada

institute: University of Montreal

description: Library name: WT_LPS_rep3

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version M24 (based on Ensembl 99)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: RAW

growth_protocol: RAW 264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin (100 U/mL penicillin and 100 µg/mL streptomycin), and 1% GlutaMAX.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (QIAGEN,80224)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: On the day of the experiment, cells were treated with LPS (1.5 µg/mL) for 6 h or left untreated as controls. Cells were then washed once with cold PBS, immediately pelleted, and stored at −80 °C until further processing

value: RAW

value: 6 hrs/LPS


title: P143K RNAseq

description: Library name: P143K RNAseq


title: FXR2 (4098) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: FXR2_HepG2_4098_IP_rep2
eCLIP immunoprecipitation sample for FXR2, biological replicate 2

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


title: WT_LPS_rep1

description: Library name: WT_LPS_rep1


title: RAW_H37Ra_ATACseq_rp1


title: WT_LPS_rep2

description: Library name: WT_LPS_rep2


title: RAW_H37Ra_ATACseq_rp2


title: P140K TCRseq

description: Library name: P140K_TCRseq


title: DEK (4020) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: DEK_HepG2_4020_INPUT_rep2
eCLIP size-matched input control for DEK, biological replicate 2


title: WT_control_rep3

description: Library name: WT_control_rep3

value: 0 hr/NT


title: FXR2 (4098) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: FXR2_HepG2_4098_IP_rep1
eCLIP immunoprecipitation sample for FXR2, biological replicate 1


title: P139K TCRseq

description: Library name: P139K_TCRseq


title: DEK (4020) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: DEK_HepG2_4020_IP_rep2
eCLIP immunoprecipitation sample for DEK, biological replicate 2


title: WT_control_rep2

description: Library name: WT_control_rep2


title: P138K TCRseq

description: Library name: P138K_TCRseq


title: RAW_NC_ATACseq_rp1


title: RAW_NC_ATACseq_rp3


title: DEK (4020) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: DEK_HepG2_4020_INPUT_rep1
eCLIP size-matched input control for DEK, biological replicate 1


title: P137K TCRseq

description: Library name: P137K_TCRseq


title: RAW_NC_ATACseq_rp2


title: WT_control_rep1

description: Library name: WT_control_rep1


title: L. japonicus MYB36 line2  UV control conditions, shoots, biological replicate 3

status: Public on Apr 23 2026

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

institute: Universidad de Sevilla

description:
Library name: MYB36_2_C3
column name in gene_fpkm.txt: MYB36_2_C3

data_processing:
Libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Lotus japonicus Gifu V 1_3
Supplementary files format and content: excel file contains the FPKM values for all the samples

organism: Lotus japonicus

source_name: shoot

growth_protocol: plants grown without UV-B irradiation (control) or 16h UV-B irradiation (UV-B treatment)

extract_protocol:
Tissue was flash-freezed in liquid N2, ground with mortar and pestle and RNA extracted with a modified CTAB protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP.

value: shoot

value: 0h UV-B irradiation


title: L. japonicus MYB36 line2  UV control conditions, shoots, biological replicate 2

description:
Library name: MYB36_2_C2
column name in gene_fpkm.txt: MYB36_2_C2


title: L. japonicus MYB36 line2  UV stress conditions, shoots, biological replicate 2

description:
Library name: MYB36_2_UV2
column name in gene_fpkm.txt: MYB36_2_UV2

value: 16h UV-B irradiation


title: L. japonicus MYB36 line2  UV control conditions, shoots, biological replicate 1

description:
Library name: MYB36_2_C1
column name in gene_fpkm.txt: MYB36_2_C1


title: L. japonicus MYB36 line1  UV stress conditions, shoots, biological replicate 2

description:
Library name: MYB36_1_UV2
column name in gene_fpkm.txt: MYB36_1_UV2


title: L. japonicus MYB36 line1  UV control conditions, shoots, biological replicate 3

description:
Library name: MYB36_1_C3
column name in gene_fpkm.txt: MYB36_1_C3


title: L. japonicus MYB36 line2  UV stress conditions, shoots, biological replicate 3

description:
Library name: MYB36_2_UV3
column name in gene_fpkm.txt: MYB36_2_UV3


title: DEK (4020) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: DEK_HepG2_4020_IP_rep1
eCLIP immunoprecipitation sample for DEK, 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: L. japonicus MYB36 line2  UV stress conditions, shoots, biological replicate 1

description:
Library name: MYB36_2_UV1
column name in gene_fpkm.txt: MYB36_2_UV1


title: L. japonicus MYB36 line1  UV stress conditions, shoots, biological replicate 1

description:
Library name: MYB36_1_UV1
column name in gene_fpkm.txt: MYB36_1_UV1


title: L. japonicus WT  UV control conditions, shoots, biological replicate 2

description:
Library name: WT_C2
column name in gene_fpkm.txt: WT_C2


title: L. japonicus WT  UV stress conditions, shoots, biological replicate 2

description:
Library name: WT_UV2
column name in gene_fpkm.txt: WT_UV2


title: L. japonicus MYB36 line1  UV stress conditions, shoots, biological replicate 3

description:
Library name: MYB36_1_UV3
column name in gene_fpkm.txt: MYB36_1_UV3


title: L. japonicus MYB36 line1  UV control conditions, shoots, biological replicate 1

description:
Library name: MYB36_1_C1
column name in gene_fpkm.txt: MYB36_1_C1


title: L. japonicus WT  UV stress conditions, shoots, biological replicate 1

description:
Library name: WT_UV1
column name in gene_fpkm.txt: WT_UV1


title: L. japonicus MYB36 line1  UV control conditions, shoots, biological replicate 2

description:
Library name: MYB36_1_C2
column name in gene_fpkm.txt: MYB36_1_C2


title: L. japonicus WT  UV control conditions, shoots, biological replicate 3

description:
Library name: WT_C3
column name in gene_fpkm.txt: WT_C3


title: L. japonicus WT  UV stress conditions, shoots, biological replicate 3

description:
Library name: WT_UV3
column name in gene_fpkm.txt: WT_UV3


title: L. japonicus MYB36 line2  stress conditions, shoots, biological replicate 3

description:
Library name: M36_2_100mM3
column name in gene_fpkm.xls: M36_2_100mM3

growth_protocol: plants grown in the presence of ‘Hornum’ nutrient solution (control) or ‘Hornum’ nutrient solution + 100mM NaCl (salt stress treatment)

value: ‘Hornum’ nutrient solution+100mM NaCl


title: L. japonicus WT  UV control conditions, shoots, biological replicate 1

description:
Library name: WT_C1
column name in gene_fpkm.txt: WT_C1


title: L. japonicus MYB36 line2  stress conditions, shoots, biological replicate 2

description:
Library name: M36_2_100mM2
column name in gene_fpkm.xls: M36_2_100mM2


title: L. japonicus MYB36 line1  stress conditions, shoots, biological replicate 3

description:
Library name: M36_1_100mM3
column name in gene_fpkm.xls: M36_1_100mM3


title: L. japonicus MYB36 line2  control conditions, shoots, biological replicate 2

description:
Library name: M36_2_0mM2
column name in gene_fpkm.xls: M36_2_0mM2

value: ‘Hornum’ nutrient solution


title: L. japonicus MYB36 line2  control conditions, shoots, biological replicate 1

description:
Library name: M36_2_0mM1
column name in gene_fpkm.xls: M36_2_0mM1


title: L. japonicus MYB36 line2  control conditions, shoots, biological replicate 3

description:
Library name: M36_2_0mM3
column name in gene_fpkm.xls: M36_2_0mM3


title: L. japonicus MYB36 line2  stress conditions, shoots, biological replicate 1

description:
Library name: M36_2_100mM1
column name in gene_fpkm.xls: M36_2_100mM1


title: L. japonicus MYB36 line1  stress conditions, shoots, biological replicate 2

description:
Library name: M36_1_100mM2
column name in gene_fpkm.xls: M36_1_100mM2


title: L. japonicus MYB36 line1  stress conditions, shoots, biological replicate 1

description:
Library name: M36_1_100mM1
column name in gene_fpkm.xls: M36_1_100mM1


title: L. japonicus WT  stress conditions, shoots, biological replicate 2

description:
Library name: WT_100mM2
column name in gene_fpkm.xls: WT_100mM2


title: L. japonicus MYB36 line1  control conditions, shoots, biological replicate 1

description:
Library name: M36_1_0mM1
column name in gene_fpkm.xls: M36_1_0mM1


title: L. japonicus MYB36 line1  control conditions, shoots, biological replicate 3

description:
Library name: M36_1_0mM3
column name in gene_fpkm.xls: M36_1_0mM3


title: L. japonicus WT  control conditions, shoots, biological replicate 2

description:
Library name: WT_0mM2
column name in gene_fpkm.xls: WT_0mM2


title: L. japonicus WT  stress conditions, shoots, biological replicate 1

description:
Library name: WT_100mM1
column name in gene_fpkm.xls: WT_100mM1


title: L. japonicus WT  stress conditions, shoots, biological replicate 3

description:
Library name: WT_100mM3
column name in gene_fpkm.xls: WT_100mM3


title: L. japonicus MYB36 line1  control conditions, shoots, biological replicate 2

description:
Library name: M36_1_0mM2
column name in gene_fpkm.xls: M36_1_0mM2


title: Colonic eosinophils isolated from water (control)-treated C57Bl/6 WT mice,2,D6

first: Yang

last: Yang

address: 6432 Fannin St, MSB 6.261

department: Department of Anesthesiology, Critical Care and Pain Medicine

institute: University of Texas Health Science Center at Houston

description: Library name: A2

data_processing:
1.Clean reads were mapped to the reference genome using [STAR / Hisat2] (v2.2.1);2.The number of reads mapped to each gene was counted using [featureCounts / HTSeq-count].3.FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.4.Differential expression analysis was performed using the [DESeq2] R package.
Assembly: mm10 (GRCm38)
Supplementary files format and content: The processed data file is a tab-delimited text file containing raw read counts

source_name: Primary colonic eosinophils

extract_protocol:
Total RNA was isolated using the RNA extraction kit (GenDopt) according to the manufacturer’s instructions.
RNA-seq libraries were prepared by Novogene Co., Ltd. (Beijing, China). Briefy, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final library was obtained after adapter ligation and PCR enrichment, and sequenced on the [Illumina NovaSeq X Plus] platform.

value: Primary colonic eosinophils