title: RBM47_IP

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

data_processing: genome-wide de novo peak calling was carried out to test the binding preference of proteins on RNA. Reads ≥ 10 was defined as valid sequence and motif analysis was carried out to predict preference binding sites.

source_name: HCCLM3 cell, RBM47_IP

extract_protocol:
After RBM47Flag fusion protein transfection in HCCLM3 cells, the binding between RBM47 and UPF1 mRNA was explored by employing the RNA-Binding Protein Immunoprecipitation Kit (EMD Millipore, USA) according to the instructions of the manufacturer.
library construction was performed by DNA/cDNA repair, including loading Base A and sequencing connector. Qubit 2.0 (Invitrogen) was used for quality inspection before sequencing on an Illumina sequencer.


title: stage 2, inactive meristem, pair E

status: Public on Apr 28 2025

type: SRA

city: Vienna

first: Chloe

last: Casey

address: Zimmermannplatz 10

country: Austria

institute: St Anna Children's Cancer Research Institute

description: Library name: sample_41

library_source: transcriptomic

data_processing:
Trimmomatic v0.38
Raw reads were trimmed to remove Illumina adaptors and low-quality reads using Trimmomatic v0.38. Parameters -  ILLUMINACLIP:all_adaptors.fasta:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:5:15 MINLEN:25
Salmon v1.5.2
Read counts were quantified using Salmon v1.5.2 in quasi-mapping-based mode against a salmon transcriptome index built from the MpTak_v6.1 transcriptome. Parameters for indexing -k 21; Parameters for read count quantification - --threads 12 --validateMappings
R v4.2.0; tximport v1.26.1
Transcript-level Salmon quantification files were imported and gene-level summarization was performed using tximport v1.26.1. Gene-level TPM values (transcripts per million) were extracted with tximport using a transcript to gene (tx2gene) mapping file constructed from the MpTak_v6.1 transcriptome.
R v4.2.0; DESeq2 v1.38.3
To identify genes that were differentially expressed between inactive and active meristems at each of the three stages, differential gene expression analysis was carried out using DESeq2 v1.38.3. The design formula “ ~ pair + activity ” was used to identify genes differentially expressed between inactive and active meristems while controlling for variability between sample pairs. Significantly differentially expressed genes were defined to have a Log2 Fold Change < -2 or > 2, and a padj < 0.05.
Assembly: MpTak_v6.1
Supplementary files format and content: Transcript-level Salmon quantification files (quant.sf) for each sample

molecule: total RNA

organism: Marchantia polymorpha

source_name: inactive meristem

extract_protocol:
The RNeasy® Plant Mini Kit was used to extract RNA from homogenised samples. 500 ng of total RNA was used for the construction of sequencing libraries.
Poly-A mRNA was isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). Enriched poly-A mRNA sequencing libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the kit instructions. The fragment size of the libraries was assessed using the NGS HS analysis kit on an Agilent fragment analyzer system. The library concentrations were quantified with a Roche KAPA Kit by qPCR.

tag: tissue

value: inactive meristem

tag: genotype

value: WT; Tak-1


title: JS3C1_PS_iPSC_47XYY

city: Thuwal

first: Antonio

last: Adamo

state: Makkah

address: Thuwal 23955-6900 KAUST

department: iological, Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

library_source: genomic

data_processing:
After FastQC quality control,sequence adapters were trimmedwith trimGalore v.0.06.
High quality reads were mapped against the reference genome (GRCh38/Ensembl release 101) using Bismark v.0.23.1
The CpG  extraction was done with MethylDackel v 0.6.1
Assembly: Ensembl GRCh38 v. 101
Supplementary files format and content: One BedGraph for each sample, containing information about methylation levels. Column 1: chromosome, Column 2: start position of CpG site (0-based),  Column 3: ending position of the CpG site (exclusive), Column 4: methylation percentage observed at the CpG site. Percentage is calculated as the proportion of methylated cytosines relative to the total number of cytosines sequenced at that position  (C/C+T *100), Column 5: Total number of reads covering CpG site, Column 6: Counts of methylated cytosines detected at each site.

molecule: genomic DNA

organism: Homo sapiens

source_name: iPSC

growth_protocol: Fibroblasts were cultured and expanded in high glucose DMEM supplemented with 15% FBS, 1% non-essential amino acids and 1% penicillin-streptomycin. The established hiPSC lines were cultured on hESC-qualified Matrigel (Corning) coated 6-well-plates in E8 medium and passaged with Versene in E8 medium supplemented with 5 uM Rock Inhibitor (Y-27632). Human iPSC lines were incubated at 37°C in the presence of 5% CO2 and 5% O2. NSCs have been further expanded in Neural Expansion Media and collected at P2 for RNA extraction and immunostaining.

extract_protocol:
The gDNA was extracted using the DNeasy Blood & Tissue genomic DNA  Extraction Kit From Qiagen.
DNA libraries were generated  by Beijing Novogene Bioinformatics Technology, Co., Ltd. (Beijing, China). Target enrichment was performed to construct the exome library using the Agilent SureSelect Human All Exon V6 kit (Agilent Technologies, Inc., Santa Clara, CA, United States), according to manufacturer’s protocol, then DNA was sequenced using IluminaNovaseq6000/NovaseqX 2 x 150b or Novaseq 6000 as indicated in the table.

treatment_protocol: Fibroblasts were reprogrammed using the the Stemgent® StemRNA-NM Reprogramming Kit. Fibroblasts were transfected daily with synthetic NM-RNAs in presence of Essential 8 Media (E8) for four consecutive days. The differentiation of iPSCs into Neural stem cells was established using the PSC Neural Induction Kit from Thermo Fisher. Briefly, iPSCs were detached when reached 70-80% confluency in small clumps using Versene and seeded at a dilution 1:6-1:8 on Matrigel-coated dishes in the presence of E8 + 10 uM Y-27632. Twenty-four hours after seeding, the Neural Induction Media (Neurobasal Medium + 1X Neural Induction Supplement) was added and used for seven days. On day 7 of neural induction, NSCs that reached P0 were harvested using Accutase, seeded at 1.0*106 cells on Matrigel-coated 6-well plates and cultured in Neural Expansion Media (50% Neurobasal Medium + 50% Advanced DMEM/F12 media + 1X Neural Induction Supplement) for about five days, until they reached 90% confluency.

tag: cell type

value: iPSC

tag: condition

value: JS


title: JS3E1_PS_iPSC_47XYY


title: AML_3_c6_S11

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

country: USA

institute: National Heart Lung and Blood Institute, NIH

description:
Patient 3 end of cycle 6 bulk RNA-seq
S11

data_processing:
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Assembly: GRCh37/hg19 for bulk RNAseq; Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Gene raw count matrix in csv for bulk RNAseq; single-cell processed data contain the gene and protein expression matrices with cell barcodes.

source_name: Bone marrow

growth_protocol: Bone marrow aspirate was collected from enrolled patients at different time points and healthy donors.

extract_protocol:
Bulk RNAseq: RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher. Single-cell: BM mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
Bulk RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA). The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

treatment_protocol: No treatment

value: Bone marrow

tag: age

tag: gender

value: Female


title: AML_3_c4_S10

description:
Patient 3 end of cycle 4 bulk RNA-seq
S10


title: stage 2, inactive meristem, pair D

description: Library name: sample_39


title: RBM47_IP_clean

country: China

data_processing:
Qubit 2.0 (Invitrogen) was used for quality inspection before sequencing on an Illumina sequencer.
Supplementary files format and content: bw files

source_name: HCCLM3 cell, RBM47_IP_clean

extract_protocol:
The DNAzol™ Reagent kit (Thermo Fisher) was implemented for the isolation of DNA from cells in accordance with the instructions of the manufacturer. Cells were lysed through agitating the cultivation plate and slowly pipetting the lysate into an assay tube. Following the precipitation of DNA with 100% ethanol, 75% ethanol was employed for DNA rinses.
library construction was performed by DNA/cDNA repair, including loading Base A and sequencing connector. Qubit 2.0 (Invitrogen) was used for quality inspection before sequencing on an Illumina sequencer.

tag: cell line

value: Hepatocellular Carcinoma


title: KS5P_NS_NSC_46XY

source_name: NSC

value: NSC

value: Healthy


title: JS2E7_PS_iPSC_47XYY


title: AML_3_c2_S9

description:
Patient 3 end of cycle 2 bulk RNA-seq
S9


title: RBM47_input

source_name: HCCLM3 cell, RBM47_input


title: AML_4_c1d8_S13

description:
Patient 4 cycle 1 day 8 bulk RNA-seq
S13

value: Male


title: JS2G12_PS_iPSC_47XYY


title: JS2B2_PS_iPSC_47XYY


title: AML_2_c1d8_S6

description:
Patient 2 cycle 1 day 8 bulk RNA-seq
S6


title: stage 3, active meristem, pair I

description: Library name: sample_36

source_name: active meristem

value: active meristem


title: AML_3_c1d8_S8

description:
Patient 3 cycle 1 day 8 bulk RNA-seq
S8


title: RBM47_input_clean

source_name: HCCLM3 cell, RBM47_input_clean


title: PBMC MN-BMC IL

city: Boston

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

institute: Brigham and Women's Hospital

description: Library name: p0a-PBMC

data_processing:
DNA samples were sequenced on an Illumina NextSeq500 (40 paired end). RNA samples were sequenced on a MiSeq to provide validation of the methodology using a 60nt forward read and were analyzed using the RNAseq NextFLow pipeline.
We calculated the number of reads in 500kb genomic bins throughout the genome. In the case of tumor samples, read counts were normalized based on the read counts from the PBMC sample, followed by GC correction using HMMcopy (108) to get read depth ratio’s R. These values were then logged to get LogR values plotted in the figure. Gains and losses were identified using QDNAseq (109) with a probability cutoff of 0.5. To estimate tumor fraction we calculated the purity that resulted in average purity corrected copy number values of 3 for chromosome 7 and 1 for chromosome 10. Gains on chromosome 7 and losses on chromosome 10 are ubiquitous features in GBM and were assumed clonal. Phylogenetic tree were constructed by generating a binary event matrix where rows were genome segments and columns were samples. Genome segments were defined as continuous regions of the genome that had gains or losses in any sample, we ensured that segment boundaries were identical across samples. Matrix values were 1 if a sample had a copy number alteration in that segment and 0 otherwise. Hamming distances were calculated between all samples and a tree constructed using the neighbor joining algorithm using the distance matrix as input.
Assembly: DNA reads were mapped to the hg19 reference genome using BWA-MEM.
Supplementary files format and content: Bam files

source_name: Peripheral blood

extract_protocol:
Each core was processed for DNA, RNA, and protein extraction using the Nucleospin Tri-kit (Machery-Nagel). Samples were homogenized first in a 1ml pipette and then 10 times through a 26G needle before being prepared per manufacturer's recommendations.
Extracted DNA and RNA were evaluated by Fragment Analyzer (Agilent). Bulk RNAseq libraries were prepared from 10ng of RNA using the Pico-input strand-specific total RNA-seq for mammalian samples v2 kit from Takara.

value: Peripheral blood

value: PBMC


title: thallus, sample K

description: Library name: sample_38

source_name: thallus

value: thallus


title: RBM47_input


title: AML_3_c8_S12

description:
Patient 3 end of cycle 8 bulk RNA-seq
S12


title: thallus, sample J

description: Library name: sample_37


title: AML_1_c8_S4

description:
Patient 1 end of cycle 8 bulk RNA-seq
S4


title: JS1H12_PS_iPSC_47XYY


title: P3-2 MN-BMC IL

description: Library name: p0a-P3-2

source_name: Tumor biopsy

value: Tumor biopsy

value: Bulk Tumor


title: JS1C5_PS_iPSC_47XYY


title: stage 2, active meristem, pair D

description: Library name: sample_40


title: stage 3, inactive meristem, pair I

description: Library name: sample_35


title: RBM47_IP


title: AML_1_c2_S3

description:
Patient 1 end of cycle 2 bulk RNA-seq
S3


title: stage 2, active meristem, pair F

description: Library name: sample_34


title: P3-1 MN-BMC IL

description: Library name: p0a-P3-1


title: AML_1_c1d8_S2

description:
Patient 1 cycle 1 day 8 bulk RNA-seq
S2


title: P2-2 MN-BMC IL

description: Library name: p0a-P2-2


title: JS1E1_PS_iPSC_47XYY


title: 326E1_PS_iPSC_47XYY


title: stage 2, inactive meristem, pair F

description: Library name: sample_33


title: BV2 cells, Tfam-KO, replicate 3

city: Shanghai

first: Erlin

last: Wang

state: Shanghai

address: 748 Zhongshan Middle Road, Songjiang District, Shanghai

department: Songjiang Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
HISAT2 (version 2.1.0)
Samtools (version 1.9)
featureCounts (version 2.0.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated files include raw-count values for each Sample
Supplementary files format and content: Tab-separated files include normalized values for each Sample

molecule: polyA RNA

organism: Mus musculus

growth_protocol: BV2 cells were grown in DMEM high glucose supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin at 37°C in humidified 5% CO2 and 95% air.

extract_protocol:
Total RNAs from BV2 cells were extracted using TRIzol reagent following manufacture's protocols.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: After CRISPR-Cas9-mediated gene knockout, BV2 cells were cultured continuously with puromycin (2 μg/mL).

value: Microglia cells

value: Tfam knockout

tag: treatment


title: stage 1, active meristem, pair C

description: Library name: sample_32

value: WT; Tak-1


title: P2-1 MN-BMC IL

description: Library name: p0a-P2-1


title: BV2 cells, Tfam-KO, replicate 2


title: stage 1, inactive meristem, pair C

description: Library name: sample_31

value: inactive meristem


title: P1-3 MN-BMC IL

description: Library name: p0a-P1-3


title: BV2 cells, Tfam-KO, replicate 1


title: stage 1, active meristem, pair B

description: Library name: sample_30


title: JS3_F_Fibroblast_47XYY

source_name: Fibroblast

value: Fibroblast

value: JS


title: stage 1, inactive meristem, pair B

description: Library name: sample_29


title: P1-2 >4kb IL

description: Library name: p0a-P1-2


title: BV2 cells, WT, replicate 3

value: WT


title: JS2_F_Fibroblast_47XYY


title: P1-1 triprep IL XT RP

description: Library name: p0a-P1-1


title: stage 1, active meristem, pair A

description: Library name: sample_28


title: 230712_16_Gan-HFD-pH4_

type: RNA

city: Sendai

first: Kaname

last: Uno

address: 1-1 Seiryo Aoba-ku

department: Gastroenterology

country: Japan

institute: Tohoku University

description: gene expression data from HFD+ABS-stimulated Gan mice

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse Clariom-S chip at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: Gene chips were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: normalized with SST-RMA (Signal Space Transformation-Robust Multichip Analysis) method implemented in Affymetrix® Power Tools (APT).

label: biotin

source_name: HFD+ABS Diet

label_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol  (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Tumors around the jucntion between forestomach and glandular stomach were observed in Gan mice with/ without high fat diet and acidic bile salts.

extract_protocol: Total RNA was extracted using TRIzol according to manufacturer's protocol

treatment_protocol: Tumor tissues were washed with PBS, and were subjected to RNA extraction.

value: Stimulated Tumor tissue


title: JS1_F_Fibroblast_47XYY


title: KS_F_Fibroblast_46XY


title: BV2 cells, WT, replicate 1


title: 230712_11_Gan-control_

description: gene expression data from control Gan mice

source_name: Control Diet

value: Control Tumor tissue


title: 323_F_Fibroblast_46XY

value: Healthy


title: KS5P_PS_iPSC_46XY

value: iPSC


title: 1L_3L, tri1L_tri3L, replicate1

status: Public on Apr 27 2025

city: Columbia

first: James

last: Birchler

state: MO

address: 310 Tucker Hall

institute: University of Missouri-Columbia

description:
Library name: 42-1-1
rRNA depletion
gene_exp_1L_3L.txt

data_processing:
RNA-seq (rRNA removal): Adaptors or low quality reads weret trimmed or removed using the fastp (Chen, 2023). The remaining reads were aligned to the maize chloroplast and mitochondrial genome using STAR with default parameters and organelle reads were removed. Non-organelle reads were aligned to the maize reference genome W22v2 along with the maize B chromosome using STAT with default parameters.
Assembly: W22v2 along with the maize B chromosome and the maize chloroplast and mitochondrial genome (Springer et al., 2018; Blavet et al., 2021; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary files format and content: Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.

organism: Zea mays

source_name: 45 days leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
RNA extracted by mirVana™ miRNA Isolation Kit
TruSeq library construction

value: 45 days leaf tissue

value: Leaf cell

value: trisom+trisomy


title: 1L_3L, tri1L_mono3L, replicate3

description:
Library name: 42-2-19
rRNA depletion
gene_exp_1L_3L.txt

value: trisomy+monosmy


title: 1L_3L, tri1L_mono3L, replicate2

description:
Library name: 42-2-16
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, tri1L_tri3L, replicate2

description:
Library name: 42-1-2
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, tri1L_mono3L, replicate4

description:
Library name: 42-2-33
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, tri1L_tri3L, replicate4

description:
Library name: 42-1-6
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, diploid, replicate3

description:
Library name: 42-3-10
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, diploid, replicate2

description:
Library name: 42-2-3
rRNA depletion
gene_exp_1L_3L.txt


title: MA9_FLT3ITD_Setd1b_dSET_IL3_rep1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values corrected by Spike-In for each Sample.

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: leukemia

value: Setd4b SET knockout

value: After wash with PBS, the cells were incubated with cytokines for 24 hr.


title: 1L_3L, diploid, replicate1

description:
Library name: 42-2-1
rRNA depletion
gene_exp_1L_3L.txt


title: BV2 cells, WT, replicate 2

value: Microglia cells


title: 6L_9S, mono6L_mono9S, replicate3

description:
Library name: 38-1-79
rRNA depletion
gene_exp_6L_9S.txt

value: monosomy+monosomy


title: 6L_9S, mono6L_mono9S, replicate4

description:
Library name: 38-1-80
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, mono6L_mono9S, replicate2

description:
Library name: 38-1-78
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, mono6L_mono9S, replicate1

description:
Library name: 38-1-74
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_mono9S, replicate5

description:
Library name: 38-2-5
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, mono6L_tri9S, replicate1

description:
Library name: 38-1-14
rRNA depletion
gene_exp_6L_9S.txt

value: monosomy+trisomy


title: 6L_9S, mono6L_tri9S, replicate2

description:
Library name: 38-1-89
rRNA depletion
gene_exp_6L_9S.txt


title: stage 1, inactive meristem, pair A

description: Library name: sample_27

value: inactive meristem

value: WT; Tak-1


title: 6L_9S, tri6L_mono9S, replicate4

description:
Library name: 38-2-7
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_mono9S, replicate3

description:
Library name: 38-2-3
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_tri9S, replicate4

description:
Library name: 38-2-8
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_mono9S, replicate2

description:
Library name: 38-1-5
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_mono9S, replicate1

description:
Library name: 38-1-34
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_tri9S, replicate3

description:
Library name: 38-2-15
rRNA depletion
gene_exp_6L_9S.txt


title: 1L_3L, tri1L_mono3L, replicate1

description:
Library name: 42-2-15
rRNA depletion
gene_exp_1L_3L.txt


title: 1L_3L, tri1L_tri3L, replicate3

description:
Library name: 42-1-3
rRNA depletion
gene_exp_1L_3L.txt


title: 6L_9S, tri6L_tri9S, replicate2

description:
Library name: 38-2-12
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, tri6L_tri9S, replicate1

description:
Library name: 38-2-11
rRNA depletion
gene_exp_6L_9S.txt


title: 6L_9S, diploid, replicate1

description:
Library name: 38-2-23
rRNA depletion
gene_exp_6L_9S.txt

value: WT


title: 4L_6L, mono4L_mono6L, replicate4

description:
Library name: 36-99
rRNA depletion
gene_exp_4L_6L.txt


title: 1L_3L, diploid, replicate4

description:
Library name: 42-3-24
rRNA depletion
gene_exp_1L_3L.txt


title: 4L_6L, mono4L_mono6L, replicate2

description:
Library name: 36-55
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, mono4L_mono6L, replicate1

description:
Library name: 36-105
rRNA depletion
gene_exp_4L_6L.txt


title: 6L_9S, diploid, replicate2

description:
Library name: 38-1-33
rRNA depletion
gene_exp_6L_9S.txt


title: 4L_6L, tri4L_mono6L, replicate4

description:
Library name: 36-64
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, tri4L_mono6L, replicate2

description:
Library name: 36-112
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, tri4L_tetra6L, replicate1

description:
Library name: 36-3
rRNA depletion
gene_exp_4L_6L.txt

value: trisomy+tetrasomy


title: 4L_6L, tri4L_tri6L, replicate3

description:
Library name: 36-68
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, tri4L_mono6L, replicate3

description:
Library name: 36-34
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, mono4L_mono6L, replicate3

description:
Library name: 36-73
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, tri4L_tri6L, replicate1

description:
Library name: 36-12
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, diploid, replicate3

description:
Library name: 36-52
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, diploid, replicate2

description:
Library name: 36-51
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, tri4L_mono6L, replicate1

description:
Library name: 36-111
rRNA depletion
gene_exp_4L_6L.txt


title: 4L_6L, diploid, replicate1

description:
Library name: 36-43
rRNA depletion
gene_exp_4L_6L.txt


title: 3L_5L, tetra3L_tri5L, replicate1

description:
Library name: 33-1
rRNA depletion
gene_exp_3L_5L.txt

value: tetrasomy+trisomy


title: 4L_6L, tri4L_tri6L, replicate2

description:
Library name: 36-22
rRNA depletion
gene_exp_4L_6L.txt


title: 3L_5L, mono3L_mono5L, replicate2

description:
Library name: 32-2-56
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, mono3L_mono5L, replicate1

description:
Library name: 32-2-45
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, mono3L_mono5L, replicate3

description:
Library name: 32-2-80
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_mono5L, replicate4

description:
Library name: 32-2-97
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_mono5L, replicate3

description:
Library name: 32-2-95
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_mono5L, replicate1

description:
Library name: 32-2-76
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_mono5L, replicate2

description:
Library name: 32-2-91
rRNA depletion
gene_exp_3L_5L.txt


title: shRBFOX2_6B [dabg.summary]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization and washing was performed as described in the GeneChip WT PLUS Reagent Kit (Affymetrix).

scan_protocol: Scanning was performed on a 7G scanner and imaged with the AGCC portal.

data_processing: Cel files were analyzed using  Expression Console (build 1.4.1.46, Affymetrix) and data was processed with  Affymetrix  package (Affy Power Tools) apt-probeset-summarize.  Iter-plier algorithm was used to quantify probesets with RMA  normalization and DABG probe-level detection. Only probesets with detection  p-value ≤    0.05 in more than half of the microarray samples were considered for downstream  analysis. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by  SepScore (defined as the normalized change in exclusion minus the normalized  change in inclusion).

source_name: RBFOX2 KnockDown-4

label_protocol: RNA of stably transduced Lenti-X™ HEK 293T cells was submitted to Affymetrix Human Transcriptome Arrays 2.0 to identify alternative splicing events. Microarray sample preparation was performed using Ambion WT Expression Kit (Thermo Fisher Scientific). Labeling was performed using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

growth_protocol: 293T cells were grown in standard media (DMEM + 10% FBS + 1X Penicillin Streptomycin).

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: Knockdowns were performed by transforming shRNA plasmid along with lentivirus packaging plasmids in 293T cells, filtering (.45 micron) supernatant, and infecting a new population of 293T cells. After 48 hours, infected cells were Puromycin selected (1 ug / mL) for 10 days, after which RNA and protein were harvested.


title: shRBFOX2_1C [dabg.summary]

source_name: RBFOX2 KnockDown-3


title: shScramble_2 [dabg.summary]

source_name: RBFOX2 KnockDown-7


title: shRBFOX2_1B [dabg.summary]

source_name: RBFOX2 KnockDown-2


title: shRBFOX2_1A [dabg.summary]

source_name: RBFOX2 KnockDown-1


title: 15252.Yeo.2.sh [dabg.summary]

source_name: DAZAP1 Overexpression-2


title: 15255.Yeo.5.sh [dabg.summary]

source_name: DAZAP1 Overexpression-5


title: 15050.Yeo.19.sh [dabg.summary]


title: 15259.Yeo.9.sh [dabg.summary]

source_name: RBFOX2 Overexpression-2


title: 15260.Yeo.10.sh [dabg.summary]

source_name: RBFOX2 Overexpression-3


title: 3L_5L, tri3L_tri5L, replicate4

description:
Library name: 32-1-9
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_tri5L, replicate3

description:
Library name: 32-1-8
rRNA depletion
gene_exp_3L_5L.txt


title: 3L_5L, tri3L_tri5L, replicate5

description:
Library name: 32-1-12
rRNA depletion
gene_exp_3L_5L.txt


title: 15049.Yeo.18.sh [dabg.summary]

source_name: TIAL1 KnockDown-6


title: 3L_5L, tri3L_tri5L, replicate2

description:
Library name: 32-1-6
rRNA depletion
gene_exp_3L_5L.txt


title: 15263.Yeo.13.sh [dabg.summary]

source_name: RBFOX2 Overexpression-6


title: 15051.Yeo.20.sh [dabg.summary]


title: 3L_5L, tri3L_tri5L, replicate1

description:
Library name: 32-1-5
rRNA depletion
gene_exp_3L_5L.txt


title: 15047.Yeo.16.sh [dabg.summary]

source_name: TIAL1 KnockDown-4


title: 3L_5L, diploid, replicate4

description:
Library name: 32-2-49
rRNA depletion
gene_exp_3L_5L.txt


title: shScramble_3 [dabg.summary]

source_name: RBFOX2 KnockDown-8


title: 15052.Yeo.21.sh [dabg.summary]


title: 15253.Yeo.3.sh [dabg.summary]

source_name: DAZAP1 Overexpression-3


title: 15046.Yeo.15.sh [dabg.summary]

source_name: nonspecific control for CCNL1 KnockDown-6|Knockdown-6|Knock-Downs-3|RBM11 KnockDown-6|TIAL1 KnockDown-3|TRNAU1AP KnockDown-6


title: 3L_5L, diploid, replicate2

description:
Library name: 32-2-20
rRNA depletion
gene_exp_3L_5L.txt


title: 15258.Yeo.8.sh [dabg.summary]

source_name: RBFOX2 Overexpression-1


title: 3L_5L, diploid, replicate1

description:
Library name: 32-2-1
rRNA depletion
gene_exp_3L_5L.txt

source_name: 45 days leaf tissue


title: 15262.Yeo.12.sh_2 [dabg.summary]

source_name: RBFOX2 Overexpression-5


title: 15048.Yeo.17.sh [dabg.summary]

source_name: TIAL1 KnockDown-5


title: 1S_9L, mono1S_tri9L, replicate4

description:
Library name: 27-9-2
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, mono1S_tri9L, replicate3

description:
Library name: 27-4-4
rRNA depletion
gene_exp_1S_9L.txt


title: 15256.Yeo.6.sh [dabg.summary]

source_name: DAZAP1 Overexpression-6


title: 1S_9L, mono1S_tri9L, replicate2

description:
Library name: 27-1-9
rRNA depletion
gene_exp_1S_9L.txt


title: 15257.Yeo.7.sh [dabg.summary]

source_name: DAZAP1 Overexpression-7


title: shRBFOX2_6C [dabg.summary]

source_name: RBFOX2 KnockDown-5


title: 1S_9L, mono1S_tri9L, replicate1

description:
Library name: 27-1-8
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, tri1S_tri9L, replicate4

description:
Library name: 27-5-7
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, tri1S_mono9L, replicate1

description:
Library name: 27-1-10
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, tri1S_tri9L, replicate3

description:
Library name: 27-5-2
rRNA depletion
gene_exp_1S_9L.txt


title: 15045.Yeo.14.sh [dabg.summary]

source_name: nonspecific control for CCNL1 KnockDown-5|Knockdown-5|Knock-Downs-2|RBM11 KnockDown-5|TIAL1 KnockDown-2|TRNAU1AP KnockDown-5


title: 3L_5L, diploid, replicate3

description:
Library name: 32-2-42
rRNA depletion
gene_exp_3L_5L.txt


title: 1S_9L, tri1S_tri9L, replicate1

description:
Library name: 27-5-1
rRNA depletion
gene_exp_1S_9L.txt


title: 15254.Yeo.4.sh [dabg.summary]

source_name: DAZAP1 Overexpression-4


title: 1S_9L, tri1S_tri9L, replicate2

description:
Library name: 27-5-10
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, tri1S_mono9L, replicate2

description:
Library name: 27-1-2
rRNA depletion
gene_exp_1S_9L.txt


title: 15261.Yeo.11.sh [dabg.summary]

source_name: RBFOX2 Overexpression-4


title: 1S_9L, diploid, replicate3

description:
Library name: 27-6-10
rRNA depletion
gene_exp_1S_9L.txt


title: 1S_9L, diploid, replicate2

description:
Library name: 27-4-7
rRNA depletion
gene_exp_1S_9L.txt


title: 15251.Yeo.1.sh [dabg.summary]

source_name: DAZAP1 Overexpression-1


title: shScramble_1 [dabg.summary]

source_name: RBFOX2 KnockDown-6


title: 1S_9L, diploid, replicate1

description:
Library name: 27-4-2
rRNA depletion
gene_exp_1S_9L.txt


title: 4L_5L, mono4L_mono5L, replicate4

description:
Library name: 23-2-94
rRNA depletion
gene_exp_4L_5L.txt


title: 4L_5L, mono4L_mono5L, replicate3

description:
Library name: 23-2-84
rRNA depletion
gene_exp_4L_5L.txt


title: 15039.Yeo.8.sh [dabg.summary]

source_name: RBM11 KnockDown-2


title: 4L_5L, mono4L_mono5L, replicate1

description:
Library name: 23-2-13
rRNA depletion
gene_exp_4L_5L.txt


title: 4L_5L, mono4L_tri5L, replicate2

description:
Library name: 23-2-12
rRNA depletion
gene_exp_4L_5L.txt


title: 4L_5L, mono4L_tri5L, replicate1

description:
Library name: 23-2-10
rRNA depletion
gene_exp_4L_5L.txt


title: 15041.Yeo.10.sh [dabg.summary]


title: 15036.Yeo.5.sh [dabg.summary]

source_name: TRNAU1AP KnockDown-2


title: 4L_5L, tri4L_mono5L, replicate4

description:
Library name: 23-2-43
rRNA depletion
gene_exp_4L_5L.txt


title: 15042.Yeo.11.sh [dabg.summary]


title: 15037.Yeo.6.sh [dabg.summary]

source_name: TRNAU1AP KnockDown-3


title: 15038.Yeo.7.sh [dabg.summary]

source_name: RBM11 KnockDown-1


title: 14863.Yeo.33.sh [dabg.summary]

source_name: DAZAP1 KnockDown-5


title: 15043.Yeo.12.sh [dabg.summary]


title: 15034.Yeo.3.sh [dabg.summary]

source_name: CCNL1 KnockDown-3


title: 4L_5L, tri4L_mono5L, replicate3

description:
Library name: 23-2-41
rRNA depletion
gene_exp_4L_5L.txt

source_name: 45 days leaf tissue


title: 4L_5L, tri4L_mono5L, replicate2

description:
Library name: 23-2-19
rRNA depletion
gene_exp_4L_5L.txt


title: 4L_5L, tri4L_mono5L, replicate1

description:
Library name: 23-2-11
rRNA depletion
gene_exp_4L_5L.txt


title: 15044.Yeo.13.sh [dabg.summary]

source_name: nonspecific control for CCNL1 KnockDown-4|Knockdown-4|Knock-Downs-1|RBM11 KnockDown-4|TIAL1 KnockDown-1|TRNAU1AP KnockDown-4


title: 15032.Yeo.1.sh [dabg.summary]

source_name: CCNL1 KnockDown-1


title: 4L_5L, tri4L_tri5L, replicate1

description:
Library name: 23-1-6
rRNA depletion
gene_exp_4L_5L.txt


title: 14858.Yeo.28.sh [dabg.summary]

source_name: APOBEC4 KnockDown-6


title: 4L_5L, diploid, replicate3

description:
Library name: 23-2-6
rRNA depletion
gene_exp_4L_5L.txt


title: 15033.Yeo.2.sh [dabg.summary]

source_name: CCNL1 KnockDown-2


title: 14860.Yeo.30.sh [dabg.summary]

source_name: CSTF1 KnockDown-5


title: 4L_5L, diploid, replicate2

description:
Library name: 23-2-23
rRNA depletion
gene_exp_4L_5L.txt


title: 4L_5L, diploid, replicate1

description:
Library name: 23-2-16
rRNA depletion
gene_exp_4L_5L.txt


title: 14853.Yeo.23.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 KnockDown-1|CSTF1 KnockDown-1|DAZAP1 KnockDown-1


title: 1L_5S, tri1L_tetra5S, replicate1

description:
Library name: 22-2-83
rRNA depletion
gene_exp_1L_5S.txt


title: 14861.Yeo.31.sh [dabg.summary]

source_name: CSTF1 KnockDown-6


title: 14859.Yeo.29.sh [dabg.summary]

source_name: CSTF1 KnockDown-4


title: 14855.Yeo.25.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 KnockDown-3|CSTF1 KnockDown-3|DAZAP1 KnockDown-3


title: 14856.Yeo.26.sh [dabg.summary]

source_name: APOBEC4 KnockDown-4


title: 1L_5S, mono1L_tri5S, replicate3

description:
Library name: 22-3-40
rRNA depletion
gene_exp_1L_5S.txt


title: 14824.Yeo.27.sh [dabg.summary]

source_name: TRNAU1APv1 Overexpression-6


title: 1L_5S, mono1L_tri5S, replicate4

description:
Library name: 22-3-45
rRNA depletion
gene_exp_1L_5S.txt


title: 4L_5L, mono4L_mono5L, replicate2

description:
Library name: 23-2-24
rRNA depletion
gene_exp_4L_5L.txt


title: 1L_5S, mono1L_tri5S, replicate2

description:
Library name: 22-3-19
rRNA depletion
gene_exp_1L_5S.txt


title: 14823.Yeo..26sh [dabg.summary]

source_name: TRNAU1APv1 Overexpression-5


title: 1L_5S, mono1L_tri5S, replicate1

description:
Library name: 22-3-10
rRNA depletion
gene_exp_1L_5S.txt


title: 14854.Yeo.24.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 KnockDown-2|CSTF1 KnockDown-2|DAZAP1 KnockDown-2


title: 14819.Yeo.22.sh [dabg.summary]

source_name: BOLL Overexpression-4


title: 4L_5L, tri4L_tri5L, replicate2

description:
Library name: 23-1-78
rRNA depletion
gene_exp_4L_5L.txt


title: 14862.Yeo.32.sh [dabg.summary]

source_name: DAZAP1 KnockDown-4


title: 1L_5S, tri1L_mono5S, replicate3

description:
Library name: 22-2-7
rRNA depletion
gene_exp_1L_5S.txt


title: 1L_5S, tri1L_mono5S, replicate2

description:
Library name: 22-2-5
rRNA depletion
gene_exp_1L_5S.txt


title: 1L_5S, tri1L_mono5S, replicate1

description:
Library name: 22-2-4
rRNA depletion
gene_exp_1L_5S.txt


title: 1L_5S, tri1L_mono5S, replicate4

description:
Library name: 22-2-77
rRNA depletion
gene_exp_1L_5S.txt


title: 1L_5S, tri1L_tri5S, replicate4

description:
Library name: 22-1-5
rRNA depletion
gene_exp_1L_5S.txt


title: 14822.Yeo.25.sh [dabg.summary]

source_name: TRNAU1APv1 Overexpression-4


title: 1L_5S, tri1L_tri5S, replicate2

description:
Library name: 22-1-3
rRNA depletion
gene_exp_1L_5S.txt

source_name: 45 days leaf tissue


title: 1L_5S, tri1L_tri5S, replicate1

description:
Library name: 22-1-12
rRNA depletion
gene_exp_1L_5S.txt


title: 14818.Yeo.21.sh [dabg.summary]

source_name: CCNL1 Overexpression-6


title: 14816.Yeo.19.sh [dabg.summary]

source_name: CCNL1 Overexpression-4


title: 14815.Yeo.18.sh [dabg.summary]

source_name: RBM11 Overexpression-6


title: 14820.Yeo.23.sh [dabg.summary]

source_name: BOLL Overexpression-5


title: 1L_5S, diploid, replicate1

description:
Library name: 22-3-2
rRNA depletion
gene_exp_1L_5S.txt


title: 14814.Yeo.17.sh [dabg.summary]

source_name: RBM11 Overexpression-5


title: 14817.Yeo.20.sh [dabg.summary]

source_name: CCNL1 Overexpression-5


title: 14810.Yeo.13.sh [dabg.summary]

source_name: TIAL1 Overexpression-4


title: 3L_4L, mono3L_mono4L, replicate2

description:
Library name: 16-2-64
rRNA depletion
gene_exp_3L_4L.txt


title: 3L_4L, mono3L_mono4L, replicate3

description:
Library name: 16-2-76
rRNA depletion
gene_exp_3L_4L.txt


title: 14811.Yeo.14.sh [dabg.summary]

source_name: TIAL1 Overexpression-5


title: 3L_4L, mono3L_mono4L, replicate1

description:
Library name: 16-2-26
rRNA depletion
gene_exp_3L_4L.txt


title: 3L_4L, mono3L_tri4L, replicate2

description:
Library name: 16-2-80
rRNA depletion
gene_exp_3L_4L.txt


title: 14806.Yeo.9.sh [dabg.summary]

source_name: APOBEC4 Overexpression-6


title: 14813.Yeo.16.sh [dabg.summary]

source_name: RBM11 Overexpression-4


title: 3L_4L, mono3L_tri4L, replicate1

description:
Library name: 16-2-28
rRNA depletion
gene_exp_3L_4L.txt


title: 14808.Yeo.11.sh [dabg.summary]

source_name: TRNAU1APv2 Overexpression-5


title: 14812.Yeo.15.sh [dabg.summary]

source_name: TIAL1 Overexpression-6


title: 14807.Yeo.10.sh_2 [dabg.summary]

source_name: TRNAU1APv2 Overexpression-4


title: 3L_4L, tri3L_mono4L, replicate4

description:
Library name: 16-2-93
rRNA depletion
gene_exp_3L_4L.txt


title: 14857.Yeo.27.sh [dabg.summary]

source_name: APOBEC4 KnockDown-5


title: 3L_4L, tri3L_mono4L, replicate2

description:
Library name: 16-2-44
rRNA depletion
gene_exp_3L_4L.txt


title: 14805.Yeo.8.sh [dabg.summary]

source_name: APOBEC4 Overexpression-5


title: 3L_4L, tri3L_mono4L, replicate3

description:
Library name: 16-2-72
rRNA depletion
gene_exp_3L_4L.txt


title: 3L_4L, tri3L_mono4L, replicate1

description:
Library name: 16-2-43
rRNA depletion
gene_exp_3L_4L.txt


title: 14799.Yeo.2.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 Overexpression-2|BOLL Overexpression-2|CCNL1 Overexpression-2|CSTF1 Overexpression-2|RBM11 Overexpression-2|TIAL1 Overexpression-2|TRNAU1APv1 Overexpression-2|TRNAU1APv2 Overexpression-2


title: 1L_5S, diploid, replicate3

description:
Library name: 22-3-5
rRNA depletion
gene_exp_1L_5S.txt

source_name: 45 days leaf tissue


title: 3L_4L, tri3L_tri4L, replicate4

description:
Library name: 16-1-4
rRNA depletion
gene_exp_3L_4L.txt


title: 1L_5S, tri1L_tri5S, replicate3

description:
Library name: 22-1-4
rRNA depletion
gene_exp_1L_5S.txt


title: 3L_4L, tri3L_tri4L, replicate3

description:
Library name: 16-1-3
rRNA depletion
gene_exp_3L_4L.txt


title: 14802.Yeo.5.sh [dabg.summary]

source_name: CSTF1 Overexpression-5


title: 14607.Yeo.32.sh [dabg.summary]


title: 3L_4L, tri3L_tri4L, replicate2

description:
Library name: 16-1-2
rRNA depletion
gene_exp_3L_4L.txt


title: 14803.Yeo.6.sh [dabg.summary]

source_name: CSTF1 Overexpression-6


title: 14809.Yeo.12.sh [dabg.summary]

source_name: TRNAU1APv2 Overexpression-6


title: 1L_5S, diploid, replicate2

description:
Library name: 22-3-28
rRNA depletion
gene_exp_1L_5S.txt


title: 3L_4L, diploid, replicate3

description:
Library name: 16-2-8
rRNA depletion
gene_exp_3L_4L.txt


title: 14605.Yeo.30.sh [dabg.summary]


title: 14798.Yeo.1.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 Overexpression-1|BOLL Overexpression-1|CCNL1 Overexpression-1|CSTF1 Overexpression-1|RBM11 Overexpression-1|TIAL1 Overexpression-1|TRNAU1APv1 Overexpression-1|TRNAU1APv2 Overexpression-1


title: 3L_4L, diploid, replicate2

description:
Library name: 16-2-74
rRNA depletion
gene_exp_3L_4L.txt


title: 3L_4L, diploid, replicate1

description:
Library name: 16-2-5
rRNA depletion
gene_exp_3L_4L.txt


title: 5L_6L, mono5L_mono6L, replicate3

description:
Library name: 12-2-98
rRNA depletion
gene_exp_5L_6L.txt


title: 14606.Yeo.31.sh [dabg.summary]


title: 14604.Yeo.29.sh [dabg.summary]

source_name: nonspecific control for FUBP1-Overexpression-5|LUC7L2-Overexpression-3


title: 14804.Yeo.7.sh [dabg.summary]

source_name: APOBEC4 Overexpression-4


title: 5L_6L, mono5L_mono6L, replicate1

description:
Library name: 12-2-60
rRNA depletion
gene_exp_5L_6L.txt


title: 14592.Yeo.17.sh [dabg.summary]


title: 14602.Yeo.27.sh [dabg.summary]

source_name: nonspecific control for LUC7L2-Overexpression-3|FUBP1-Overexpression-1


title: 14591.Yeo.16.sh [dabg.summary]


title: 5L_6L, mono5L_tri6L, replicate3

description:
Library name: 12-2-21
rRNA depletion
gene_exp_5L_6L.txt


title: 14800.Yeo.3.sh [dabg.summary]

source_name: nonspecific control for APOBEC4 Overexpression-3|BOLL Overexpression-3|CCNL1 Overexpression-3|CSTF1 Overexpression-3|RBM11 Overexpression-3|TIAL1 Overexpression-3|TRNAU1APv1 Overexpression-3|TRNAU1APv2 Overexpression-3


title: 5L_6L, mono5L_tri6L, replicate2

description:
Library name: 12-2-15
rRNA depletion
gene_exp_5L_6L.txt


title: 14801.Yeo.4.sh [dabg.summary]

source_name: CSTF1 Overexpression-4


title: 5L_6L, mono5L_tri6L, replicate1

description:
Library name: 12-1-1
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, tri5L_mono6L, replicate2

description:
Library name: 12-2-91
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, tri5L_mono6L, replicate1

description:
Library name: 12-2-72
rRNA depletion
gene_exp_5L_6L.txt


title: 3L_4L, tri3L_tri4L, replicate1

description:
Library name: 16-1-1
rRNA depletion
gene_exp_3L_4L.txt


title: 5L_6L, tri5L_tri6L, replicate3

description:
Library name: 12-1-6
rRNA depletion
gene_exp_5L_6L.txt


title: 14603.Yeo.28.sh [dabg.summary]

source_name: nonspecific control for FUBP1-Overexpression-4|LUC7L2-Overexpression-2


title: 5L_6L, tri5L_tri6L, replicate4

description:
Library name: 12-2-23
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, tri5L_tri6L, replicate2

description:
Library name: 12-1-4
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, tri5L_tri6L, replicate1

description:
Library name: 12-1-3
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, diploid, replicate4

description:
Library name: 12-2-52
rRNA depletion
gene_exp_5L_6L.txt


title: 14821.Yeo.24.sh [dabg.summary]

source_name: BOLL Overexpression-6


title: shRBFOX2_6B [quant-norm]

source_name: RBFOX2 KnockDown-4


title: 5L_6L, diploid, replicate3

description:
Library name: 12-2-49
rRNA depletion
gene_exp_5L_6L.txt


title: shScramble_3 [quant-norm]

source_name: RBFOX2 KnockDown-8


title: 5L_6L, mono5L_mono6L, replicate2

description:
Library name: 12-2-94
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, diploid, replicate2

description:
Library name: 12-2-13
rRNA depletion
gene_exp_5L_6L.txt


title: 5L_6L, diploid, replicate1

description:
Library name: 12-2-4
rRNA depletion
gene_exp_5L_6L.txt


title: 15262.Yeo.12.sh_2 [quant-norm]

source_name: RBFOX2 Overexpression-5


title: shRBFOX2_1C [quant-norm]

source_name: RBFOX2 KnockDown-3


title: shRBFOX2_1B [quant-norm]

source_name: RBFOX2 KnockDown-2


title: CD27_low_rep2

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

institute: Institute of Hematology and Blood Disease Hospital

description: Library name: CD27_low_rep2

data_processing:
Quality control of paired-end raw reads was assessed using FastQC (v0.11.7). Low quality bases and adapter sequences were then trimmed by using TrimGalore (v0.5.0). The paired-end clean reads were aligned to the mouse reference genome by using bowtie2 (v4.8.2). Multi-mapped reads, duplicates and reads mapped to mitochondrial DNA were filtered out. By utilizing peak-calling software MACS2 (v2.2.7.1). deepTools (v3.5.5) was used to generate coverage tracks (bigWig files) from bam files.
Assembly: GRCm38
Supplementary files format and content: BigWig and narrow Peak

source_name: Bone marrow

extract_protocol:
Bone marrow (BM) cells were flushed from the tibiae, femora, and pelvis. Cells were then stained with anti-c-Kit microbeads (catalog no. 130-091-224, Miltenyi Biotech) and c-Kit+ cells were enriched by columns. These cells were stained with CD201 (eBio1560), CD150 (TC15-12F12.2), CD48 (HM48-1), Sca-1 (D7), c-Kit(2B8), CD27 (LG.7F9) and with a lineage-marker cocktail of B220 (RA3-6B2), Gr-1 (RB6-8C5), TER-119 (TER-119). Cells were sorted by FACSAria III cell sorter (Becton Dickinson, US) according to surface markers expression under the single-cell sorting mode.
The Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) was used to ATAC-seq library preparation. CD27- or CD27+ ESALAMLSK cells were lysed with a buffer containing RS Buffer, 10% NP40, 10% Tween20, and 1% Digitonin. Chromatin was fragmented using a Tagmentation Mix (TW Buffer, 10% Tween20, 1% Digitonin, nuclease-free ddH2O, 5× TTBL, and TTE Mix V50) by incubated at 37°C for 30 minutes. Reactions were stopped with Stop Buffer, and then the nucleosome-free DNA fragments were extracted using DNA Extract Beads. The extracted DNA fragments were amplified via PCR with 2× CAM and indexed primers (N5XX and N7XX) under the following conditions: 72°C for 3 minutes, 95°C for 3 minutes, followed by 10–21 cycles of 98°C for 10 seconds, 60°C for 5 seconds, and 72°C for 1 minute. Size-selection of PCR products were conducted by using DNA Clean Beads (0.55× and 1.2× ratios) and finally sequenced on an Illumina NovaSeq™ X Plus.

value: Bone marrow

value: Primary cell

value: CD27- ESLAMLSK

tag: time

tag: sorting markers


title: shScramble_1 [quant-norm]

source_name: RBFOX2 KnockDown-6


title: shRBFOX2_6C [quant-norm]

source_name: RBFOX2 KnockDown-5


title: CD27_low_rep1

description: Library name: CD27_low_rep1


title: 15261.Yeo.11.sh [quant-norm]

source_name: RBFOX2 Overexpression-4


title: CD27_low_rep4

description: Library name: CD27_low_rep4


title: 15258.Yeo.8.sh [quant-norm]

source_name: RBFOX2 Overexpression-1


title: CD27_high_rep2

description: Library name: CD27_high_rep2

value: CD27+ ESLAMLSK


title: 15252.Yeo.2.sh [quant-norm]

source_name: DAZAP1 Overexpression-2


title: CD27_low_rep3

description: Library name: CD27_low_rep3


title: 15049.Yeo.18.sh [quant-norm]

source_name: TIAL1 KnockDown-6


title: CD27_high_rep4

description: Library name: CD27_high_rep4


title: CD27_high_rep1

description: Library name: CD27_high_rep1


title: 15263.Yeo.13.sh [quant-norm]

source_name: RBFOX2 Overexpression-6


title: 15255.Yeo.5.sh [quant-norm]

source_name: DAZAP1 Overexpression-5


title: RAW264.7, LPS, input2

city: Suzhou

first: Zhou

last: Yu

address: 100 Chongwen Road

institute: Chinese Academy of Medical Sciences /Suzhou Institute of Systems Medicine

description: Library name: input2

library_source: other

data_processing:
Basecalls were performed using bcl2fastq v2.17 for DNBSEQ-T7 outpuUt.
CLIP-seq reads were trimmed from 3' end until the final base had aquality score > 30,using Fastp v0.20.0, discarding reads left with < 50 bp.
CLIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.1 Only uniquely mapping reads with at most two mismatches were retained.
To create CLIP-seq coverage plots, the locations of the mapped CLIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS2 v2.2.6 with the significance cut-off cvalue <=0.01.
Assembly: bigWig files were generated using the genomicRanges R package. Scorerepresents the normalized coverage of DNA fragments at a given genomic coordinate. naarrowPeak files were generated using MACS2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig

molecule: other

growth_protocol: DMEM containing 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2

extract_protocol:
Ultraviolet-crosslinked (400 mJ/cm²) RAW264.7 macrophages (4 × 10^7) were lysed in lysis buffer and sonicated. Lysates were treated with RNase I to fragment RNA and DNase I to remove DNA.
Linearized DNA was amplified with Phusion High-Fidelity polymerase (12–15 cycles) using indexed primers. Final libraries were size-selected (175–350 bp) on a 3% TBE gel, quantified (Qubit), and validated via Bioanalyzer.

treatment_protocol: treat with LPS (100ng/ml) for 8h

value: macrophage

value: LPS (100ng/ml) for 8 hours

tag: clip antibody


title: 15257.Yeo.7.sh [quant-norm]

source_name: DAZAP1 Overexpression-7


title: 15260.Yeo.10.sh [quant-norm]

source_name: RBFOX2 Overexpression-3


title: 15254.Yeo.4.sh [quant-norm]

source_name: DAZAP1 Overexpression-4


title: CD27_high_rep3

description: Library name: CD27_high_rep3


title: RAW264.7, LPS, input1

description: Library name: input1


title: 15051.Yeo.20.sh [quant-norm]


title: 15052.Yeo.21.sh [quant-norm]


title: 15253.Yeo.3.sh [quant-norm]

source_name: DAZAP1 Overexpression-3


title: 15259.Yeo.9.sh [quant-norm]

source_name: RBFOX2 Overexpression-2


title: 15251.Yeo.1.sh [quant-norm]

source_name: DAZAP1 Overexpression-1


title: 15256.Yeo.6.sh [quant-norm]

source_name: DAZAP1 Overexpression-6


title: shRBFOX2_1A [quant-norm]

source_name: RBFOX2 KnockDown-1


title: RAW264.7, LPS, MKRN2(abcam, ab72055) (rep2)

description: Library name: CLIP_rep2

value: MKRN2(abcam, ab72055)


title: DIPG-XH-01 cells, after radiotherapy5

city: SHANGHAI

first: Ruimin

state: SHANHAI

address: 1954 hUASHAN ROAD

institute: Shanghai Jiao Tong University

description: Library name: Sample18

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads  for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimated text file includes raw counts for each sample

source_name: tumor tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit.
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 21.39-30.61 M raw reads for each sample were generated. Raw reads of FASTQ format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads. Then, about 19.79-26.21 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.

value: tumor tissue

value: DIPG-XH-01 cells

value: human diffuse intrinsic pontine glioma cell line


title: RAW264.7, LPS, MKRN2(abcam, ab72055) (rep1)

description: Library name: CLIP_rep1


title: DIPG-XH-01 cells, after radiotherapy4

description: Library name: Sample17


title: DIPG-XH-01 cells, after radiotherapy3

description: Library name: Sample16


title: 15050.Yeo.19.sh [quant-norm]


title: DIPG-XH-01 cells, after radiotherapy2

description: Library name: Sample15


title: 15045.Yeo.14.sh [quant-norm]

source_name: nonspecific control for CCNL1 KnockDown-5|Knockdown-5|Knock-Downs-2|RBM11 KnockDown-5|TIAL1 KnockDown-2|TRNAU1AP KnockDown-5


title: DIPG-XH-01 cells, before radiotherapy3

description: Library name: Sample10


title: DIPG-XH-01 cells, before radiotherapy6

description: Library name: Sample13


title: DIPG-XH-01 cells, after radiotherapy1

description: Library name: Sample14


title: DIPG-XH-01 cells, before radiotherapy5

description: Library name: Sample12


title: 15048.Yeo.17.sh [quant-norm]

source_name: TIAL1 KnockDown-5


title: DIPG-XH-01 cells, before radiotherapy4

description: Library name: Sample11


title: DIPG-XH-01 cells, before radiotherapy1

description: Library name: Sample8


title: 15041.Yeo.10.sh [quant-norm]


title: 15042.Yeo.11.sh [quant-norm]


title: DIPG-XH-01 cells, before radiotherapy2

description: Library name: Sample9


title: shScramble_2 [quant-norm]

source_name: RBFOX2 KnockDown-7


title: DIPG-XH-01 cells, control3

description: Library name: Sample7

source_name: brainstem normal tissue

value: brainstem normal tissue


title: DIPG-XH-01 cells, control2

description: Library name: Sample6


title: 15046.Yeo.15.sh [quant-norm]

source_name: nonspecific control for CCNL1 KnockDown-6|Knockdown-6|Knock-Downs-3|RBM11 KnockDown-6|TIAL1 KnockDown-3|TRNAU1AP KnockDown-6


title: 15039.Yeo.8.sh [quant-norm]

source_name: RBM11 KnockDown-2


title: DIPG-XH-01 cells, control1

description: Library name: Sample5


title: DIPG-XH-01 cells, tumor4

description: Library name: Sample4

source_name: brainstem tumor tissue

value: brainstem tumor tissue


title: 832/13 cells, Tovar MPRA library, cDNA rep 6

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description: input

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We identified reads with the barcode sequence and trimmed constant sequences using cutadapt v4.3. We used UMI-tools v1.1.2 to identify and cluster UMIs, then used starcode-umi to cluster UMI-barcode and perform deduplication (Zorita et al. 2015; Smith et al. 2017). Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: "tovar_library_counts.txt" is a tab-delimited text file containing the barcode sequences, the RNA counts for the five replicates and DNA counts for the input sample. "tovar_library_barcode_pairing.txt" is a tab-delimited text file containing the oligo IDs and barcode pairing of each element tested in the MPRA library. "tovar_library_annotations.txt" is a tab-delimited text file containing the oligo IDs and hg38 coordinates of each element tested in the MPRA library along with information about overlapping motifs.
Library strategy: MPRA amplicon library

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
We electroporated 30 ug of plasmid into 30 million 832/13 rat insulinoma cells for each biological replicate. We lysed cells 24 hours later with Buffer RLT Plus and isolated total RNA with the Qiagen RNeasy Midi Kit.
We reverse transcribed 30 ug of DNAse I-treated total RNA using SuperScript IV. We performed a cDNA amplification PCR and sample indexing with all cDNA made.

value: synthetic construct


title: DIPG-XH-01 cells, tumor3

description: Library name: Sample3


title: LX2 cells, siPUM1-3

city: Guangzhou

first: Zhiping

last: Wan

state: Guangdong

address: No.600 Tianhe Road, Tianhe District, Guangzhou, China

institute: The Third Affiliated Hospital Of Sun Yat Sen University

description:
Library name: Sample 6
A6_TPM

data_processing:
Fastp v0.23.0
FastQC v0.11.9
Hisat2 2.2.1
Stringtie 2.2.1
HTseq 0.13.5
Assembly: hg38
Supplementary files format and content: TPM values for each Sample
Supplementary files format and content: All_gene_expression_TPM.txt

source_name: LX-2 cells

growth_protocol: LX-2 cells were incubated (5% CO2, 37 °C) in high-glucose Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum.

extract_protocol:
RNA was extracted from LX2 cells using TRIzol reagent. 3 ug of total RNA was used forthe construction ofsequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: For knockdown experiments, 150 nM small interfering RNA (siRNA) targeting PUM1 (si-PUM1) were transfected into cells using a transfection reagent.

value: LX-2 cells

value: Human Hepatic Stellate Cells

value: Knockdown PUM1

value: siRNA PUM1

tag: batch


title: 15036.Yeo.5.sh [quant-norm]

source_name: TRNAU1AP KnockDown-2


title: 15047.Yeo.16.sh [quant-norm]

source_name: TIAL1 KnockDown-4


title: 15043.Yeo.12.sh [quant-norm]


title: LX2 cells, siNC-3

description:
Library name: Sample 3
A3_TPM

value: WT

value: siRNA Control


title: DIPG-XH-01 cells, tumor2

description: Library name: Sample2


title: LX2 cells, siPUM1-2

description:
Library name: Sample 5
A5_TPM


title: DIPG-XH-01 cells, tumor1

description: Library name: Sample1


title: LX2 cells, siPUM1-1

description:
Library name: Sample 4
A4_TPM


title: LX2 cells, siNC-1

description:
Library name: Sample 1
A1_TPM


title: ZT18-2 mouse colonic epithelium

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: time: ZT18

data_processing:
RNA-seq reads were aligned to the reference genome GRCm38 using the STAR software.
Then the differential expression analysis was effectuated employing DESeq2 software.
For functional enrichment analyses, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted, utilizing ClusterProfiler software.
Assembly: mm10
Supplementary files format and content: results.csv

source_name: colonic

extract_protocol:
The RNA purity of RNA-seq samples was detected using NanoPhotometer spectrophotometer (IMPLEN, CA, USA), and then the concentration and integrity of RNA samples were tested using Agilent Technologies 2100 RNA Nano 6000 Assay Kit
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: colonic

value: colonic epithelial cell

tag: circadian clock


title: 15037.Yeo.6.sh [quant-norm]

source_name: TRNAU1AP KnockDown-3


title: LUC7L2_ENDO_IN_02

data_processing:
eCLIP reads were processed as described by Van Nostrand et al., 2016, Nature Methods.
Reads were demultiplexed once per HiSeq standard and once to separate eCLIP inline barcodes.
Reads were then trimmed of adapters (cutadapt v1.9.dev1) and mapped to RepBase (v18.05).
Reads unmapped to repetitive elements were then mapped to hg19 using STAR (2.4.0i).
Unique molecular identifier (UMI) tags for each mapped read were then used to remove duplicates based on its start, end, and UMI. Mapped reads of distinct inline barcodes corresponding to a single sample were merged and used to call peak signals (CLIPper 0.2.0).
Peaks corresponding to each sample were normalized against a size-matched input background, which was processed in the same manner.
Genome_build: hg19
Supplementary_files_format_and_content: bigBed, peaks, bigwig

source_name: Size-matched input

growth_protocol: HEK 293XT cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HEK293 cells were crosslinked with UV (254 nm, 400 mJ/cm2). Cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

tag: antibody

value: none, input

value: HEK 293XT

tag: replicate

tag: rbp

value: LUC7L2 ENDO


title: TIAL1_IN_02


title: LUC7L2_ENDO_IN_01


title: LX2 cells, siNC-2

description:
Library name: Sample 2
A2_TPM


title: 15044.Yeo.13.sh [quant-norm]

source_name: nonspecific control for CCNL1 KnockDown-4|Knockdown-4|Knock-Downs-1|RBM11 KnockDown-4|TIAL1 KnockDown-1|TRNAU1AP KnockDown-4


title: 15038.Yeo.7.sh [quant-norm]

source_name: RBM11 KnockDown-1


title: 15032.Yeo.1.sh [quant-norm]

source_name: CCNL1 KnockDown-1


title: ZT12-2 mouse colonic epithelium

description: time: ZT12


title: ZT18-1 mouse colonic epithelium

description: time: ZT18


title: LUC7L2_IN_02


title: TIAL1_IN_01


title: LUC7L2_IN_01


title: ZT12-1 mouse colonic epithelium

description: time: ZT12


title: APOBEC4_IN_02


title: ZT6-2 mouse colonic epithelium

description: time: ZT6


title: 14860.Yeo.30.sh [quant-norm]

source_name: CSTF1 KnockDown-5


title: ATAC-seq of glioma sample MG22 (Glioblastoma, Grade IV, Primary, IDH1 WT)

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

description: Library name: MG22

data_processing:
ATAC-seq reads in FASTQ format were subjected to quality control using FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1 to assess the need for trimming of adapter sequences or bad quality segments.
Trimmed reads were aligned to the reference human genome version GRCh38/hg38 with the program HISAT2 v2.0.5.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Peaks were called using the program MACS v2.1.2 using the broad peaks mode.
To obtain the consensus set of unique peaks, called peaks from all samples were merged at 50% overlap using BEDtools v2.27.0.
Assembly: GRCh38/hg38
Supplementary files format and content: Consensus peaks were converted to a Gene Transfer Format (GTF) to enable counting of reads under the peaks. Raw read counts were normalized with respect to library size and transformed to log2 scale using rlog() function in R package DESeq2. TPM matrices containing normalized read counts for the most variable peaks (5000 peaks), the 329 peaks selected by cox regression, and the 30 peaks used in the final prediction model.
Supplementary files format and content: Peak-gene correlation matrices listing peaks, their corresponding genes based on topologically associating domain (TAD) regions, and their correlation coefficients (r² > 0.6 and r² > 0.7). Quality control reports and quantification of peak counts above TPM threshold of 10.

source_name: Brain tissue

growth_protocol: Frozen patient tumor tissue (<0.5 cm) was collected from an IRB-approved biorepository.

extract_protocol:
Nuclei were isolated from patient tumor tissue as described by Habib et al., with slight modifications. Frozen tissue samples (<0.5 cm) were incubated on ice in 1 mL of Nuclei EZ Lysis Buffer (Sigma, #Nuc-101). The tissue was homogenized using a glass tissue grinder. Additional EZ Lysis Buffer was added, incubated on ice for 5 min, and filtered through a 70 μm cell strainer. Nuclei were collected by centrifugation and resuspended in ATAC-resuspension buffer.
ATAC-seq library preparation was performed as previously described by Buenrostro et al. Nuclei were filtered through 40 μm and 5 μm cell strainers and resuspended in ATAC-resuspension buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20).

treatment_protocol: All specimens denoted as "Grade II," "Grade III," or "Grade IV primary" were taken from the patient's initial surgery and had not been exposed to any chemotherapy or radiation treatment. Recurrent samples were from patients who underwent standard therapy including temozolomide and radiation after initial surgery.

value: Brain tissue

value: Glioblastoma

value: IDH1 WT


title: 14853.Yeo.23.sh [quant-norm]

source_name: nonspecific control for APOBEC4 KnockDown-1|CSTF1 KnockDown-1|DAZAP1 KnockDown-1


title: 14863.Yeo.33.sh [quant-norm]

source_name: DAZAP1 KnockDown-5


title: 15034.Yeo.3.sh [quant-norm]

source_name: CCNL1 KnockDown-3


title: 14858.Yeo.28.sh [quant-norm]

source_name: APOBEC4 KnockDown-6


title: APOBEC4_IN_01


title: 14862.Yeo.32.sh [quant-norm]

source_name: DAZAP1 KnockDown-4


title: ATAC-seq of glioma sample MG21 (Glioblastoma, Grade IV, Recurrent, IDH1 Mut)

description: Library name: MG21

value: IDH1 Mut

value: temozolomide and radiation


title: 14857.Yeo.27.sh [quant-norm]

source_name: APOBEC4 KnockDown-5


title: 14859.Yeo.29.sh [quant-norm]

source_name: CSTF1 KnockDown-4


title: 15033.Yeo.2.sh [quant-norm]

source_name: CCNL1 KnockDown-2


title: 14856.Yeo.26.sh [quant-norm]

source_name: APOBEC4 KnockDown-4


title: 14861.Yeo.31.sh [quant-norm]

source_name: CSTF1 KnockDown-6


title: ZT6-1 mouse colonic epithelium

description: time: ZT6

source_name: colonic


title: TRNAU1AP_IN_02

source_name: Size-matched input


title: ATAC-seq of glioma sample MG20 (Glioblastoma, Grade IV, Primary, IDH1 Mut)

description: Library name: MG20


title: ZT0-2 mouse colonic epithelium

description: time: ZT0


title: 14855.Yeo.25.sh [quant-norm]

source_name: nonspecific control for APOBEC4 KnockDown-3|CSTF1 KnockDown-3|DAZAP1 KnockDown-3


title: 14854.Yeo.24.sh [quant-norm]

source_name: nonspecific control for APOBEC4 KnockDown-2|CSTF1 KnockDown-2|DAZAP1 KnockDown-2


title: ATAC-seq of glioma sample MG19 (Glioblastoma, Grade IV, Recurrent, IDH1 Unknown)

description: Library name: MG19

value: IDH1 Unknown


title: ZT0-1 mouse colonic epithelium

description: time: ZT0


title: 14824.Yeo.27.sh [quant-norm]

source_name: TRNAU1APv1 Overexpression-6


title: LUC7L_IN_02


title: ATAC-seq of glioma sample MG18 (Anaplastic astrocytoma, Grade III, Primary, IDH1 Unknown)

description: Library name: MG18

value: Anaplastic astrocytoma


title: LUC7L_IN_01


title: Mouse Bmal1 cKO2 colonic epithelium

value: Bmal1 cKO


title: 14823.Yeo..26sh [quant-norm]

source_name: TRNAU1APv1 Overexpression-5


title: Mouse Bmal1 cKO1 colonic epithelium


title: TRNAU1AP_IN_01


title: Mouse WT1 colonic epithelium


title: Mouse WT2 colonic epithelium


title: RBM11_IN_01


title: 832/13 cells, Kyono MPRA library, plasmid input

description: input

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We extracted DNA barcodes from the first 16 bases of the R1 fastq file for the input DNA sample and clustered these at an edit distance of 0. We repeated this process for the cDNA barcode counts and used an added step to remove PCR-duplicated barcodes using the UMI information. The UMI sequence was the reverse complement of the first 6 bp in the R2 file. Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: "kyono_library_counts.txt" is a tab-delimited text file containing the barcode sequences, the RNA counts for the three replicates and DNA counts for the input sample. "kyono_library_barcode_pairing.txt" is a tab-delimited text file containing the oligo IDs and barcode pairing of each element tested in the MPRA library. "kyono_library_annotations.txt" is a tab-delimited text file containing the oligo IDs and hg19 coordinates of each element tested in the MPRA library.
Library strategy: MPRA amplicon library

source_name: synthetic construct

extract_protocol:
We electroporated 50 ug of plasmid into 25 million 832/13 rat insulinoma cells for each biological replicate and lysed cells with TRIzol 24 hours later. After phase separation, we used the Direct-zol RNA Miniprep Kit to isolate total RNA.
We enriched for mature mRNA transcripts with fragment(dT) beads then treated 2 ug of mRNA with DNase I to remove plasmid or genomic DNA contamination. We reverse transcribed 1 ug of mRNA using SuperScript III with a custom primer containing a 6-bp unique molecular identifier (UMI) targeting transcripts derived from the MPRA plasmids (Supplemental Table 3). We treated cDNA samples with DpnI to eliminate any residual plasmid DNA.

value: synthetic construct


title: FUBP1_IN_02


title: RBM11_IN_02


title: Cd27L4

description: Library name: Cd27L4

library_source: transcriptomic single cell

data_processing:
Each Library included paired-end sequencing reads, read 1 contained transcripts sequences while read 2 contained cell-specific barcode sequences and unique molecular identifiers(UMIs). Raw reads of each library were first splitted into individual cells based on the unique barcode sequences, then UMIs sequences were aligned to the head of the corresponding read 1.
Contaminant oligonucleotide sequences such as TSO primer, polyA tail, adaptor, and low-quality sequence (N > 10%) presented in the raw reads were then cut out, and reads whose length were less than 30bp were removed using Trimmomatic (version 0.36). Next, Clean reads were aligned to mouse assembly GRCm38 genome (https://www.gencodegenes.org, release (M15)) using HISAT2 (version 2.1.0). Reads shared the same unique molecular identifiers (UMI) were considered amplified from the same transcripts. Hence, we modified a script from HTSeq (version 0.9.1) to removed duplicated transcripts based on UMI sequences and quantified genes abundance.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each single cells.

source_name: Bone marrow

extract_protocol:
Bone marrow (BM) cells were flushed from the tibiae, femora, and pelvis. Cells were then stained with anti-c-Kit microbeads (catalog no. 130-091-224, Miltenyi Biotech) and c-Kit+ cells were enriched by columns. These cells were stained with CD201 (eBio1560), CD150 (TC15-12F12.2), CD48 (HM48-1), Sca-1 (D7), c-Kit(2B8), CD27 and with a lineage-marker cocktail of B220 (RA3-6B2), Gr-1 (RB6-8C5), TER-119. Cells were sorted by FACSAria III cell sorter (Becton Dickinson, US) according to surface markers expression under the single-cell sorting mode.
The scRNA-seq libraries were prepared based on a modified Smart-seq2(STRT-seq) protocol. Single cells were sorted into individual tubes of a 0.2 mL 8-strip PCR tube containing lysis buffer by FACS. In addition, the single-cell sorting mode was used for cell sorting with the appropriate side scatter pulse width (SSC-W) and side scatter pulse height (SSC-H) settings to avoid doublets. First-strand cDNAs were synthesized using 25-nucleotide oligo-dT barcoding primer and template switch oligo (TSO) primer. Following reverse transcription, the barcoded cDNAs were amplified via 20 cycles of PCR. Next, the cDNAs of each cell were pooled together and purified twice using 0.8 x Agencount AMPure XP beads. Biotin tag and indexing sequences were introduced by additional 4 cycles of PCR amplification using biotinylated primers. Purified once and sonicated (~300 bp by Covaris M220 system), then the 3' ends of the fragmented cDNA were enriched with Dynabeads Myone streptavidin C1 beads (Invitrogen). Finally, the cDNA libraries were generated using a Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced on Illumina Hiseq X Ten (Novogene) using paired-end mode (2×150 bp).

value: Bone marrow

value: Primary cell

value: CD27- ESLAMSK and CD27+ ESLAMSK


title: NCTC_ZT10

city: Fukuoka

first: Satoru

last: Koyanagi

address: 3-1-1 Maidashim Higashi-ku

department: Pharmaceutical Sciences

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: NCTC tumor-bearing mice (ZT10)

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

value: spinal cord

tag: strain


title: 14821.Yeo.24.sh [quant-norm]

source_name: BOLL Overexpression-6


title: FUBP1_IN_01


title: NCTC_ZT22

source_name: NCTC tumor-bearing mice (ZT22)

tag: tissue


title: Cd27L3

description: Library name: Cd27L3


title: Matrigel_ZT22

source_name: Control mice (ZT22)


title: CCNL1_IN_02


title: ATAC-seq of glioma sample MG38 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 WT)

description: Library name: MG38

source_name: Brain tissue

value: Anaplastic oligodendroglioma

tag: genotype


title: Cd27L2

description: Library name: Cd27L2

tag: cell type


title: CCNL1_IN_01

value: none, input


title: Cd27L1

description: Library name: Cd27L1


title: 14822.Yeo.25.sh [quant-norm]

source_name: TRNAU1APv1 Overexpression-4


title: 14816.Yeo.19.sh [quant-norm]

source_name: CCNL1 Overexpression-4


title: Matrigel_ZT10

source_name: Control mice (ZT10)


title: 14814.Yeo.17.sh [quant-norm]

source_name: RBM11 Overexpression-5


title: ATAC-seq of glioma sample MG36 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG36


title: CSTF1_IN_01

value: HEK 293XT


title: ATAC-seq of glioma sample MG37 (Glioblastoma, Grade IV, Recurrent, IDH1 Mut)

description: Library name: MG37


title: ATAC-seq of glioma sample MG35 (Glioblastoma, Grade IV, Recurrent, IDH1 Mut)

description: Library name: MG35


title: CSTF1_IN_02


title: ATAC-seq of glioma sample MG34 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG34


title: BOLL_IN_02

value: BOLL


title: ATAC-seq of glioma sample MG32 (Astrocytoma, Grade II, Primary, IDH1 Mut)

description: Library name: MG32

value: Brain tissue

value: Astrocytoma


title: ATAC-seq of glioma sample MG33 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG33

value: Glioblastoma

value: IDH1 WT


title: 14818.Yeo.21.sh [quant-norm]

source_name: CCNL1 Overexpression-6


title: ATAC-seq of glioma sample MG31 (Oligodendroglioma, Grade II, Primary, IDH1 Mut)

description: Library name: MG31

value: Oligodendroglioma

value: IDH1 Mut


title: LUC7L2_ENDO_IP_02

source_name: RNA Binding Protein

value: LUC7L2 ENDO


title: 14811.Yeo.14.sh [quant-norm]

source_name: TIAL1 Overexpression-5


title: 14808.Yeo.11.sh [quant-norm]

source_name: TRNAU1APv2 Overexpression-5


title: DAZAP1_IN_01

source_name: Size-matched input


title: DAZAP1_IN_02


title: 14820.Yeo.23.sh [quant-norm]

source_name: BOLL Overexpression-5


title: LUC7L2_ENDO_IP_01


title: 14810.Yeo.13.sh [quant-norm]

source_name: TIAL1 Overexpression-4


title: 14817.Yeo.20.sh [quant-norm]

source_name: CCNL1 Overexpression-5


title: ATAC-seq of glioma sample MG29 (Glioblastoma, Grade IV, Recurrent, IDH1 Unknown)

description: Library name: MG29

value: IDH1 Unknown

value: temozolomide and radiation


title: ATAC-seq of glioma sample MG28 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG28


title: TIAL1_IP_01


title: BOLL_IN_01


title: LUC7L2_IP_02


title: 14812.Yeo.15.sh [quant-norm]

source_name: TIAL1 Overexpression-6


title: 14809.Yeo.12.sh [quant-norm]

source_name: TRNAU1APv2 Overexpression-6


title: ATAC-seq of glioma sample MG26 (Anaplastic astrocytoma, Grade III, Primary, IDH1 Mut)

description: Library name: MG26

value: Anaplastic astrocytoma


title: 14819.Yeo.22.sh [quant-norm]

source_name: BOLL Overexpression-4


title: 14813.Yeo.16.sh [quant-norm]

source_name: RBM11 Overexpression-4


title: LUC7L2_IP_01


title: ATAC-seq of glioma sample MG30 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG30

source_name: Brain tissue


title: APOBEC4_IP_02

value: Sigma (Cat#:F1804, Lot#:8LBK1346V)


title: TIAL1_IP_02


title: ATAC-seq of glioma sample MG25 (Astrocytoma, Grade II, Primary, IDH1 Mut)

description: Library name: MG25


title: APOBEC4_IP_01


title: 14805.Yeo.8.sh [quant-norm]

source_name: APOBEC4 Overexpression-5


title: ATAC-seq of glioma sample MG27 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG27


title: 14804.Yeo.7.sh [quant-norm]

source_name: APOBEC4 Overexpression-4


title: TRNAU1AP_IP_02


title: HDFs cells, PBS, 24h, biol rep 3

city: shanghai

first: Fangzhou

last: Xie

state: shanghai

address: 99 Haike Road, Pudong New Area, Shanghai

institute: 上海交通大学第九人民医院

description:
Library name: Sample 6
Control-3

data_processing:
After sample quality assessment, library construction was performed. The specific mRNA capture and library preparation steps are as follows: Since most eukaryotic mRNAs possess a polyadenylated (polyA) tail, magnetic beads with oligo(dT) were used to selectively capture mRNA molecules containing the polyA structure. The captured and fragmented mRNA served as a template for first-strand cDNA synthesis, using random hexamer primers and M-MuLV reverse transcriptase. The RNA strand was then degraded with RNase H, and the second-strand cDNA was synthesized using DNA polymerase I and dNTPs. The resulting double-stranded cDNA was purified, followed by end repair, A-tailing, and ligation of sequencing adapters. AMPure XP beads were used to select cDNA fragments of approximately 200 bp. The selected fragments were PCR-amplified, and the PCR products were purified again with AMPure XP beads to generate the final sequencing libraries.
Assembly: hg38
Supplementary files format and content: Processed data include a single txt file ('allsamples.fpkm') containing FPKM-normalized gene expression values. Rows represent genes, and columns represent individual samples.

source_name: Dermal

extract_protocol:
Total RNA was extracted using Trizol reagent, and RNA integrity was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) was used to construct cDNA libraries following manufacture's protocols.

value: Dermal

value: Fibroblast


title: HDFs cells, PBS, 24h, biol rep 2

institute: 上海交通大学第九人民医院

description:
Library name: Sample 5
Control-2


title: ATAC-seq of glioma sample MG24 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 Mut)

description: Library name: MG24

value: Anaplastic oligodendroglioma


title: ATAC-seq of glioma sample MG23 (Glioblastoma, Grade IV, Recurrent, IDH1 Unknown)

description: Library name: MG23


title: HDFs cells, PBS, 24h, biol rep 1

institute: 上海交通大学第九人民医院

description:
Library name: Sample 4
Control-1


title: ATAC-seq of glioma sample MG16 (Oligodendroglioma, Grade II, Primary, IDH1 Mut)

description: Library name: MG16


title: LUC7L_IP_02


title: ATAC-seq of glioma sample MG15 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG15


title: HDFs cells, 1 U/mL BoNTA, 24h, biol rep 3

institute: 上海交通大学第九人民医院

description:
Library name: Sample 3
CB2201-3


title: LUC7L_IP_01


title: HDFs cells, 1 U/mL BoNTA, 24h, biol rep 2

institute: 上海交通大学第九人民医院

description:
Library name: Sample 2
CB2201-2


title: TRNAU1AP_IP_01


title: RBM11_IP_02


title: 14803.Yeo.6.sh [quant-norm]

source_name: CSTF1 Overexpression-6


title: 14800.Yeo.3.sh [quant-norm]

source_name: nonspecific control for APOBEC4 Overexpression-3|BOLL Overexpression-3|CCNL1 Overexpression-3|CSTF1 Overexpression-3|RBM11 Overexpression-3|TIAL1 Overexpression-3|TRNAU1APv1 Overexpression-3|TRNAU1APv2 Overexpression-3


title: ATAC-seq of glioma sample MG14 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 Mut)

description: Library name: MG14


title: HDFs cells, 1 U/mL BoNTA, 24h, biol rep 1

institute: 上海交通大学第九人民医院

description:
Library name: Sample 1
CB2201-1


title: ATAC-seq of glioma sample MG13 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 Mut)

description: Library name: MG13


title: ATAC-seq of glioma sample MG17 (Oligodendroglioma, Grade II, Primary, IDH1 Mut)

description: Library name: MG17


title: RBM11_IP_01

source_name: RNA Binding Protein


title: CL246563HiC

city: Nantong

first: Tian

last: Xia

address: Xisi Road 20, Nantong, Jiangsu Province

department: Institute of Otolaryngology-Head and Neck Surgery

institute: Affiliated Hospital of Nantong University

description: Library name: sample 1

data_processing:
Capture Hi-C processing FASTQ files (paired-end Illumina data) were processed with the HiC-Pro v2.11.1 using Bowtie2 v2.3.5.1 for mapping short reads to the reference genome mm10/hg19. After the mapping, filtering and deduplication steps of the HiC-Pro pipeline, normalized matrices were generated at 500 kb, 200 kb, 40 kb and 10 kb resolutions.
HiCPlotter was used to map genome-wide or chromosome interactions of interest and furthermore to obtain interactions matrices with a resolution of 5k 10k 20k 40k 500k 1000k.
FitHiC v2.0.7 software was used to screen for significant chromatin interactions. Assigning statistical confidence estimates to mid-range intra-chromosomal contacts by jointly modeling the random polymer looping effect and previously observed technical biases.
Assembly: hg38
Supplementary files format and content: NP69_chrAll.bwt2pairs.FiltPairs.hic

extract_protocol:
Chromatin was isolated from samples using a high-throughput chromatin isolation (HIC) protocol.
Formaldehyde is used to fix cells, followed by DNA digestion with the DpnII enzyme, which recognizes the GATC sequence to create 5'-overhangs. Then, dNTPs and biotin-14-dATP are utilized to fill in the 5'-overhangs, converting them into blunt ends. During this step, blunt ends are ligated, introducing a new restriction enzyme site (ClaI) into the DNA, which can be used to assess the efficiency of the filling-in reaction. After ligation, the cross-links are reversed to remove proteins from the DNA. The DNA is then cut into fragments of 200 to 300 base pairs, suitable for paired-end sequencing. Finally, streptavidin magnetic beads are employed to enrich the ligation products, and sequencing adapters are added in preparation for subsequent sequencing analysis.

value: normal nasopharyngeal epithelial cells


title: ATAC-seq of glioma sample MG12 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG12


title: FUBP1_IP_02

value: HEK 293XT


title: ATAC-seq of glioma sample MG11 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 Mut)

description: Library name: MG11


title: 14815.Yeo.18.sh [quant-norm]

source_name: RBM11 Overexpression-6


title: 14807.Yeo.10.sh_2 [quant-norm]

source_name: TRNAU1APv2 Overexpression-4


title: disulfiram group, replicate3, input RNA

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome.
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m1A peaks with bed format.
HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: m1A-seq

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m1A-specific antibody in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: hepatocellular carcinoma cell

value: hepatocellular carcinoma huh7 cell line under the condition of disulfiram


title: FUBP1_IP_01


title: ATAC-seq of glioma sample MG10 (Oligodendroglioma, Grade II, Primary, IDH1 Mut)

description: Library name: MG10

value: Brain tissue


title: disulfiram group, replicate2, m1A sequencing


title: 14607.Yeo.32.sh [quant-norm]


title: disulfiram group, replicate3, m1A sequencing


title: ATAC-seq of glioma sample MG9 (Anaplastic oligodendroglioma, Grade III, Primary, IDH1 Mut)

description: Library name: MG9


title: CCNL1_IP_01


title: 14801.Yeo.4.sh [quant-norm]

source_name: CSTF1 Overexpression-4


title: 14798.Yeo.1.sh [quant-norm]

source_name: nonspecific control for APOBEC4 Overexpression-1|BOLL Overexpression-1|CCNL1 Overexpression-1|CSTF1 Overexpression-1|RBM11 Overexpression-1|TIAL1 Overexpression-1|TRNAU1APv1 Overexpression-1|TRNAU1APv2 Overexpression-1


title: 14799.Yeo.2.sh [quant-norm]

source_name: nonspecific control for APOBEC4 Overexpression-2|BOLL Overexpression-2|CCNL1 Overexpression-2|CSTF1 Overexpression-2|RBM11 Overexpression-2|TIAL1 Overexpression-2|TRNAU1APv1 Overexpression-2|TRNAU1APv2 Overexpression-2


title: disulfiram group, replicate1, m1A sequencing


title: CCNL1_IP_02


title: disulfiram group, replicate2, input RNA


title: ATAC-seq of glioma sample MG7 (Oligodendroglioma, Grade II, Primary, IDH1 Mut)

description: Library name: MG7


title: CSTF1_IP_02


title: ATAC-seq of glioma sample MG8 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG8

value: Glioblastoma


title: ATAC-seq of glioma sample MG6 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG6

value: IDH1 WT


title: CSTF1_IP_01


title: 14802.Yeo.5.sh [quant-norm]

source_name: CSTF1 Overexpression-5


title: control group, replicate3, m1A sequencing

value: control group


title: DAZAP1_IP_02


title: 14606.Yeo.31.sh [quant-norm]


title: ATAC-seq of glioma sample MG4 (Anaplastic astrocytoma, Grade III, Primary, IDH1 WT)

description: Library name: MG4


title: control group, replicate2, m1A sequencing


title: BOLL_IP_02

value: BOLL


title: 14604.Yeo.29.sh [quant-norm]

source_name: nonspecific control for FUBP1-Overexpression-5|LUC7L2-Overexpression-3


title: ATAC-seq of glioma sample MG3 (Glioblastoma, Grade IV, Primary, IDH1 WT)

description: Library name: MG3


title: 14603.Yeo.28.sh [quant-norm]

source_name: nonspecific control for FUBP1-Overexpression-4|LUC7L2-Overexpression-2


title: DAZAP1_IP_01


title: BOLL_IP_01


title: ATAC-seq of glioma sample MG2 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG2


title: 832/13 cells, Tovar MPRA library, cDNA rep 5

organism: Rattus norvegicus

value: Insulinoma


title: ATAC-seq of glioma sample MG1 (Glioblastoma, Grade IV, Recurrent, IDH1 WT)

description: Library name: MG1


title: control group, replicate1, m1A sequencing


title: disulfiram group, replicate1, input RNA


title: 832/13 cells, Tovar MPRA library, cDNA rep 4


title: 832/13 cells, Tovar MPRA library, plasmid input


title: control group, replicate1, input RNA


title: U2OS cells, starved_Ars_glut: EBSS+VBL+Gln+Ars 3

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the human reference genome sequences  (hg38) using STAR.
The aligned reads were quantitated by Htseq. The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: hg38
Supplementary files format and content: Excel file with all normalized counts for each sample

growth_protocol: U2OS cells  were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested with Zymo RNA extraction commercial kit
Illumina total RNA rRNA depletion library preparation kit (Illumina) was used from 1 ug of starting material. All RNA samples underwent Ribosomal depletion following the manufacturers' protocols. The libraries were amplified 10 PCR cycles in the PCR step.

treatment_protocol: Cells were treated with EBSS+VBL/Gln for 18 hours, Arsenite treatment for 50 minutes.

value: Osteosarcoma cancer cell line

tag: stress

value: EBSS+VBL+Arsenite+Glutamine


title: U2OS cells, noTreat

value: Untreated


title: control group, replicate2, input RNA


title: 14602.Yeo.27.sh [quant-norm]

source_name: nonspecific control for LUC7L2-Overexpression-3|FUBP1-Overexpression-1


title: 832/13 cells, Tovar MPRA library, cDNA rep 2


title: U2OS cells, starved_Ars_glut: EBSS+VBL+Gln+Ars 2


title: 832/13 cells, Tovar MPRA library, cDNA rep 1


title: U2OS cells, starved_Ars_glut: EBSS+VBL+Gln+Ars 1


title: KO monosome RNA rep3

description: Library name: KO monosome RNA rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-guality sequence using fastp(v 0.23.2).
Trimmed seguence reads were mapped to reference genome using Hisat2 (v 2.0.4).
Read count extraction andusing Stringtie(v 1.3.0).
Assembly: tab-delimited text fileincludes raw counts for each sample.
Supplementary files format and content: csv files include FPKM values for each Sample.

source_name: macrophage

growth_protocol: Bone marrow-derived macrophages were obtained by culturing thigh bone-derived bone marrow cells in complete RPMI-1640 medium containing 20ng/ml recombinant macrophage colony-stimulating factor for 6 days

extract_protocol:
the mRNA of whole cell lysate and the mRNA of polysome and monosome fraction after polysome profiling were harvested using Rneasy mini plus kit (Qlagen). mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: macrophage

value: Mkrn2 knockout

value: LPS (100ng/ml) for 8 hours