title: Cepharanthine treatment

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

country: Japan

institute: Kanagawa Institute of Industrial Science and Technology

description: Library name: Sample6

data_processing:
Data processing were conducted using NovaSeq Control Software v1.7.5, Real Time Analysis (RTA) v3.4.4, bcl2fastq2 v2.20, and DRAGEN Bio-IT Platform v3.9.3
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes row counts for each sample

source_name: hair follicle

growth_protocol: Adult human DP cells were obtained from PromoCell (Heidelberg, Germany), passaged up to passage four, and used for 2D culture.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen) from DP cells with/without Oxytocin receptor agonists treatment for 6 days.
RNA library for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit

treatment_protocol: Dermal papilla cells (2 × 104 cells) were suspended in 0.5 mL culture medium supplemented with Oxytocin receptor agonists and seeded into the wells of a 24-well cell culture plate (Corning Inc., Corning, NY, USA). Gene expression in DP cells was assessed  after 6 days of culture.

value: hair follicle

value: dermal papilla cells


title: Berberine treatment

status: Public on Dec 31 2025

type: SRA

description: Library name: Sample4

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: Oxymatrine treatment

description: Library name: Sample3


title: N-Feruloyl serotonin treatment

description: Library name: Sample5


title: FracSHAPE, HeLa, RNA Granule, Untreated, NAIN3, biological replicate 2

city: Singapore

first: Jovi

last: Lim

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description: Library name: FracSHAPE_Untreated_RNAGranule_NAIN3_rep2

library_source: other

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.

molecule: other

source_name: Cervix

extract_protocol:
RNA was harvested using TRIzol/TRIzol LS reagent following manufacturer's instructions. The amount of 500ng and 1,500ng RNA were used for generating icSHAPE and SPLASH libraries, repectively. For SRSF1 eCLIP libraries, cells were fixed with UV (254nm, 400mJ/cm^2) in prior to proceeding to immunoprecipitation and library preparation.
icSHAPE library preparation was carried out according to the protocol described before (Flynn, et al, 2016); SPLASH library preparation was performed according to the protocol described before (Aw, et al, 2016); eCLIP library preparation was performed according to the protocol described before (Blue, et al, 2022).

value: Cervix

tag: cell line

value: HeLa

value: Cervical adenocarcinoma

tag: genotype

value: wt

tag: treatment

tag: group


title: Brain, 3 Months, Rep 7

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

country: Germany

institute: Christian-Albrechts-University Kiel

description:
Library name: sample_3M_N7_B
3M.N7

data_processing:
RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim from both end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Comma separated matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

organism: Mus musculus

source_name: Brain

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.

value: Brain

tag: age

value: 3 Months

tag: strain

tag: batch

value: Prep 1


title: FracSHAPE, HeLa, RNA Granule, Untreated, NAIN3, biological replicate1

description: Library name: FracSHAPE_Untreated_RNAGranule_NAIN3_rep1


title: OXT treatment

description: Library name: Sample2


title: Liver, 3 Months, Rep 7

description:
Library name: sample_3M_N7_L
3M.N7

source_name: Liver

value: Liver


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, DMSO, biological replicate 3

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_DMSO_rep3

molecule: cytoplasmic RNA

value: DMSO


title: MBNL1 KD-1

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Library name: S10

data_processing:
Quality control of raw sequencing reads was performed using FastQC (v0.11.9) and summarized with MultiQC (v1.14). To standardize coverage, sequencing reads were subsampled to 55 million reads per sample using seqtk (v1.3-r106). Alignment to the rattus norvegicus reference genome (build mRatBN7.2) was performed using STAR (STAR_2.7.11b) with default parameters.
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433).
Downstream quality checks and data analysis was performed using the bulkAnalyseR (v1.1.0) shiny app framework (https://doi.org/10.1101/2021.12.23.473982). Density plots, MA plots, Jaccard similarity index heatmaps and PCA were performed as further quality checks. Differential expression analysis was performed using edgeR (v3.40.2) and DESeq2 (1.38.3).
Alternative splicing analysis was performed using the rMATS software (v4.3.0). Splicing events were filtered to retain those with read counts ≥ 50 per group, FDR < 0.05, and |ΔPSI| ≥ 10%, excluding low-confidence junctions (<0.015 junction-to-expression ratio).
Assembly: mRatBN7.2
Supplementary files format and content: Csv file for raw counts. Rows represent features and columns represent samples.
Supplementary files format and content: Csv file for normalised counts (after noise removal). Rows represent features and columns represent samples.

organism: Rattus norvegicus

growth_protocol: Rat PAC-1 cells were cultured in DMEM + Glutamax medium with 10% Foetal Bovine Serum. For the more differentiated state (PAC1-D), the cells were split once per week at a 1:10 dilution. The more proliferative PAC1 cells (PAC1-P) were split at 1:20 dilution twice per week.

extract_protocol:
Cells were lysed with TRI-reagent and total RNA purified by Direct-zol purification column (Zymo Research). The DNase treatment was performed in column during the total RNA purification.
We have used the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (#E7760L) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (#E6440L) in conjunction with NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490L) for these samples.

treatment_protocol: The siRNA knockdown was performed by reverse transfection in a 6-well plate. The 90 pmols of siRNA from Thermo Fisher Scientific and lipofectamine RNAiMAX (Invitrogen) complexes were prepared inside the wells, then 2X10^5 cells/well PAC1 cells were added to the well. After 24 h, the cells were second treated with the same concentration of siRNAs and lipofectamine RNAiMAX. The PAC1 cells were then assessed 48 hr after the second treatment.

value: condition_MBNL1+2-KD in PAC1-D


title: No treatment

description: Library name: Sample1


title: RBPMS KD1-3

description: Library name: S9

value: condition_RBPMS-KD in PAC1-D


title: Brain, 15 Months, Rep 15

description:
Library name: sample_15M_N15_B
15M.N15

value: 15 Months


title: Brain, 28 Months, Rep 18

description:
Library name: sample_28M_N18_B
28M.N18

value: 28 Months


title: Synthetic mitochondrial Leu-CNN m1G modified

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
After sequencing, reads were basecalled using Guppy basecaller v3.6.1 in high-accuracy (hac) mode. All Us were converted to Ts before mapping using BWA, with the following parameters bwa mem -W13 -k6 -xont2d -T20. Reference contained tRNAs with 5‘ and 3‘ RNA adapter sequences included. Differential tRNA modifications were analysed using various basecalling “errors” such as mismatch, insertion and deletion for each position. The basecalling “error” sum was calculated by substracting the frequency of the reference base from 1. The frequency of the reference base equals the number of reads with a basecalled equivalent to the reference base, divided by the depth of coverage for that position. In order to plot differential tRNA modifications, first, get_sum_err.py script was used to calculated the differential sum “errors”, then plot_heatmap.py was used to plot heatmaps. All the scripts were taken from NanotRNA-seq github repo (https://github.com/novoalab/Nano-tRNAseq).
Assembly: hg38
Supplementary files format and content: Each processed data file contains summed basecalling "error" that are used to analyse modification frequency at each tRNA position
Library strategy: NanotRNA-seq (Adapted Nanopore direct RNA sequencing)

molecule: total RNA

organism: synthetic construct

extract_protocol:
Mitochondria were isolated using a MACS antibody based mitochondria extraction kit (Miltenyi Biotech) to obtain high quality and intact mitochondria for subsequent RNA isolation. Subsequently, small and large RNAs were isolated using the miRNeasy Micro Kit (Qiagen).
In order to perform NanotRNA-seq on tRNAs, small RNA fractions isolated from KO and scrambled were deacylated with the following protocol; 10 µL nuclease-free water and deacylated in 95 µL 100 mM Tris-HCl (pH 9.0) at 37°C for 30 min. Deacylated tRNAs were recovered using Zymo RNA Clean and Concentrator-5 kit (Zymo, R1016), following the manufacturer’s instructions. tRNA libraries were prepared using NanotRNA-seq library protocol with some protocol alterations described here. The 5’ and 3’ splint adapters were mix at a 1:1 molar ratio in a solution of 10 mM Tris-HCl (pH 7.5), 50 mM NaCl and 1 µL RNasin® Ribonuclease Inhibitor (Promega, N251A) to a final concentration of 1 uM. The mix was heated to 75°C for 15 s and cooled to 25°C at a rate of 0.1°C/s to anneal splint adapters. 200 ng deacylated tRNAs were ligated to the pre-annealed splint adapters at a molar ratio of 1.2:1 (with median length of 90 nucleotides. Deacylated tRNAs were ligated to the pre-annealed 5’ and 3’ splint adapters at a molar ratio of 1.2:1 (assuming an average tRNA length of 90 nt). The ligation was carried out at room temperature for 2 hours in 25 µL with 20% PEG PEG 8000 (NEB, B10048), 1X T4 RNA Ligase 2 Buffer (NEB, B0239S), 2 µL 6 mg/mL recombinant E. coli T4 RNA 2 Ligase (made in-house) and 0.5 µL RNasin® Ribonuclease Inhibitor. Ligation reaction was then cleaned up with 2X volume of RNAClean XP beads (Beckman, A63987) following manufacturer’s instructions. The RNA concentration was determined using Qubit™ RNA High Sensitivity (HS) assay kit (Thermo, Q32852). At least 50 ng of 5‘ and 3‘ ligated tRNAs were ligated to the RTA adapter (ONT, SQK-RNA002)  at a molar ratio of 1:2 in the presence of 1X Quick Ligation Reaction buffer (NEB, B6058S), 1.5 μL T4 DNA Ligase (NEB, M0202M, 2,000,000 units/mL) and 0.5 µL RNasin® Ribonuclease Inhibitor in 15 µL reaction at room temperature for 10 minutes. Consequently, the reaction mix was added to a reverse transcription mix of 11 µL nuclease-free water, 2 µL 10 mM dNTPs (NEB, N0447S), 8 µL 5X Maxima H Minus Reverse Transcriptase Buffer, and 2 µL Maxima H Minus Reverse Transcriptase (Life Technologies, EP0751). Reverse transcription mix was then mixed well and incubated at 60°C for 1 hour, 85°C for 5 minutes and then brought to 4°C. The linearized tRNAs were cleaned up using 2X RNAClean XP beads following manufacturer’s instructions. Then, 6 ul ONT RMX sequencing adapters (ONT, SQK-RNA002) were ligated at room temperature for 10 minutes in a total reaction volume of 40 µL with 1X Quick Ligation Reaction buffer, 3 μL T4 DNA Ligase. The ligation mix was cleaned up with 2X volume of RNAClean XP beads  following manufacturer’s instructions with a few adjustments. The sample was washed twice with 150 μL WSB (Wash Buffer), in which the pellet was resuspended by flicking the tube. The sample was eluted in 20 μL ELB (Elution Buffer) and incubated for 10 minutes at room temperature on a Hula mixer. The final library was prepared by adding 17.5 μL of nuclease-free water and 37.5 μL of vortexed RRB and kept on ice until loading. The MinION flow cell (FLO-MIN-106) was quality checked, primed, and loaded following the standard ONT SQK-RNA002 protocol.

value: Synthetic

tag: cell compartment


title: WM4404-1_Baseline_1918

city: Philadelphia

first: Haiyin

last: Li

state: PA

address: 3601 Spruce Street

country: USA

institute: The Wistar Institute

description: Library name: WM4404-1_1918

data_processing:
Adapter sequences were trimmed from raw FASTQ files using BBDuk.
Trimmed reads were first aligned to the mouse (mm10) transcriptome using Bowtie, and reads mapping to mouse transcripts were removed.
Remaining reads were aligned to the human transcriptome using Bowtie2 (v2.2.9) and quantified at the gene level using RSEM.
Gene identifiers were converted from Ensembl IDs to gene symbols, and sample identifiers were harmonized across datasets.
Gene expression values were normalized using fragments per kilobase of transcript per million mapped reads (FPKM). Genes with low expression or near-zero variance across samples were excluded from downstream analyses.
Assembly: GRCh38, mm10
Supplementary files format and content: Excel files, expression table

source_name: In-vivo PDX

growth_protocol: Melanoma patient-derived xenograft (PDX) tumors were established in immunodeficient NSG mice. Tumors were monitored for growth and harvested under sterile conditions at indicated experimental time points. Tumor tissues were dissected into small fragments and snap-frozen in liquid nitrogen prior to downstream molecular analyses.

extract_protocol:
Total RNA was extracted from snap-frozen PDX tumor tissues using standard RNA extraction protocols. RNA quantity and quality were assessed prior to library preparation.
RNA sequencing libraries were prepared at the Broad Institute following the Broad Stranded RNA-Seq protocol. Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized prior to library preparation. ERCC spike-in controls were added to each sample. Libraries were constructed using an automated version of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit, which preserves transcript strand orientation. Poly(A)+ mRNA was enriched using oligo-dT beads, followed by fragmentation, cDNA synthesis, adapter ligation, and PCR enrichment. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq platform using paired-end sequencing.

value: In-vivo PDX

value: Melanoma

value: BRAF mutated

value: Treatment naïve


title: RBPMS KD1-2

description: Library name: S8


title: Liver, 28 Months, Rep 18

description:
Library name: sample_28M_N18_L
28M.N18


title: FracSHAPE, HeLa, RNA Granule, Untreated, DMSO, biological replicate 2

description: Library name: FracSHAPE_Untreated_RNAGranule_DMSO_rep2

value: Cervix

value: HeLa


title: WM4404-1_Baseline_1916

description: Library name: WM4404-1_1916


title: RBPMS KD1-1

description: Library name: S7


title: FracSHAPE, HeLa, RNA Granule, Untreated, DMSO, biological replicate 1

description: Library name: FracSHAPE_Untreated_RNAGranule_DMSO_rep1

value: Cervical adenocarcinoma

value: wt


title: P-3

description: Library name: S6

value: condition_Ctrl siRNA in PAC1-P


title: WM4335-1_CPLX_5779

description: Library name: WM4335-1_CPLX_5779

value: Dabrafenib/Trametinib


title: WM4335-1_CPLX_5778

description: Library name: WM4335-1_CPLX_5778


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, NAIN3, biological replicate 3

description: Library name: FracSHAPE_Untreated_SolubleCytosol_NAIN3_rep3


title: Liver, 15 Months, Rep 8

description:
Library name: sample_15M_N8_L
15M.N8

value: Liver

value: Prep 1


title: Brain, 24 Months, Rep 5

description:
Library name: sample_24M_N5_B
24M.N5

value: Brain

value: 24 Months


title: WM4335-1_Baseline_1389

description: Library name: WM4335-1_1389


title: WM4335-1_Baseline_3754

description: Library name: WM4335-1_3754


title: P-2

description: Library name: S5


title: D1-3

description: Library name: S3

value: condition_Ctrl siRNA in PAC1-D


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, NAIN3, biological replicate 2

description: Library name: FracSHAPE_Untreated_SolubleCytosol_NAIN3_rep2


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, NAIN3, biological replicate 1

description: Library name: FracSHAPE_Untreated_SolubleCytosol_NAIN3_rep1


title: D1-2

description: Library name: S2


title: WM4335-1_Baseline_1387

description: Library name: WM4335-1_1387


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, DMSO, biological replicate 3

description: Library name: FracSHAPE_Untreated_SolubleCytosol_DMSO_rep3

value: DMSO


title: Liver, 3 Months, Rep 15

description:
Library name: sample_3M_N15_L
3M.N15

value: 3 Months


title: FracSHAPE, HeLa, RNA Granule, Untreated, DMSO, biological replicate 3

description: Library name: FracSHAPE_Untreated_RNAGranule_DMSO_rep3


title: WM4011-2_Baseline_6125

description: Library name: WM4011-2_6125

value: In-vivo PDX


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, DMSO, biological replicate 2

description: Library name: FracSHAPE_Untreated_SolubleCytosol_DMSO_rep2


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RNASeq, biological replicate 2

description:
Library name: RiboSeq_Recover1h_RNASeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv

value: Input


title: FracSHAPE, HeLa, Soluble Cytosol, Untreated, DMSO, biological replicate 1

description: Library name: FracSHAPE_Untreated_SolubleCytosol_DMSO_rep1


title: D1-1

description: Library name: S1


title: Brain, 9 Months, Rep 16

description:
Library name: sample_9M_N16_B
9M.N16

value: 9 Months


title: Liver, 24 Months, Rep 5

description:
Library name: sample_24M_N5_L
24M.N5


title: Liver, 9 Months, Rep 16

description:
Library name: sample_9M_N16_L
9M.N16


title: P-1

description: Library name: S4


title: Brain, 28 Months, Rep 13

description:
Library name: sample_28M_N13_B
28M.N13

value: 28 Months


title: Brain, 15 Months, Rep 8

description:
Library name: sample_15M_N8_B
15M.N8

value: 15 Months


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover2h, NAIN3, biological replicate 2

description: Library name: Invitro_Recover2h_NAIN3_rep2

value: Cervix

value: HeLa


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover2h, DMSO, biological replicate 2

description: Library name: Invitro_Recover2h_DMSO_rep2

value: Cervical adenocarcinoma

value: wt


title: Brain, 3 Months, Rep 15

description:
Library name: sample_3M_N15_B
3M.N15


title: Right ventricle, 6 week PAB, replicate 2

city: Toronto

first: Michael

middle: Bradley

last: Dewar

state: Ontario

address: 661 University Avenue

department: Physiology

country: Canada

institute: University of Toronto

data_processing:
Trim adapators using the Cutadapt software in paired-end mode
Obtain transcript abundances using Kallisto software. Bootstraps were set to 100
Assembly: rn6
Supplementary files format and content: Abundance.tsv files: Matrix of abundance data in tsv format. Rows are transcript names, columns are transcript length, effective length, estimated counts, and TPM.
Supplementary files format and content: Abundance.h5 files: Matrix of abundance data in HDF5 format. Rows are transcript names, columns are transcript length, effective length, estimated counts, and TPM.

source_name: Heart

growth_protocol: Rats were housed in a pathogen-free environment at the Hospital for Sick Children research institute, and had ad libitum access to water and standard rodent chow.

extract_protocol:
Following excision of the heart, the RV was surgically dissected and weighed. The RV was then divided into 4-transverse sections, snap frozen in liquid nitrogen, and stored at -80°C. Once all samples were collected, RNA was isolated using the RNeasy Micro Kit (Qiagen, Cat.#: 74004) according to manufacturer's instructions and stored at -80°C until library construction.
RNA samples were quantifiedand checked for RNA integrity using the Agilent Bioanalyzer 2100 RNA Pico chip. RNA library preparation was performedusing the Takara SMART-Seq v4 Ultra Low Input kitand the Illumina Nextera XT DNA Library Preparation kit. In brief, 5 ng of RNA was used as the input material for the SMART-Seq v4 Ultra Low Input kit, converting poly-A mRNAto full-length cDNA. cDNA was further amplified using 11 cycles of PCR and amplified cDNA was quantified using the Agilent Bioanalyzer 2100 DNA High Sensitivity chip. 1 ng of amplified cDNA proceeded to Nextera XT library preparation usingtagmentationto fragment the DNA, and dual-index Illumina adapters were added through 12 cycles of PCR. Final libraries were validated on the Agilent Bioanalyzer 2100 DNA High Sensitivity chip to check for size and absence of primer dimers, and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and sequenced on the IlluminaNovaseqplatform following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

treatment_protocol: Rats underwent either pulmonary artery banding surgery, or sham surgery (thoracotomy). Samples were then isolated at either 1-week or 6-weeks post-surgery

value: Heart

tag: tissue region

value: Right ventricle

tag: surgery

value: Pulmonary artery banding

tag: timepoint

value: 6 weeks post-surgery

tag: Sex

value: Male


title: WM4011-2_Baseline_6124

description: Library name: WM4011-2_6124

value: Melanoma

value: BRAF mutated

value: Treatment naïve


title: Liver, 28 Months, Rep 13

description:
Library name: sample_28M_N13_L
28M.N13

value: Liver

value: Prep 1


title: WM4011-2_Baseline_6121

description: Library name: WM4011-2_6121

value: In-vivo PDX


title: WM3942_CPLX_8883

description: Library name: WM3942_CPLX_8883

value: Dabrafenib/Trametinib


title: eCLIP, HeLa, SRSF1 Untreated, Input, biological replicate 1

description: Library name: eCLIP_SRSF1_Untreated_IN_rep1

value: Input

value: eCLIP, HeLa, SRSF1 Untreated, Input


title: Right ventricle, 6 week sham, replicate 3

value: Sham


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover2h, DMSO, biological replicate 1

description: Library name: Invitro_Recover2h_DMSO_rep1

value: Cervix

value: HeLa

value: Cervical adenocarcinoma

value: DMSO


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover2h, NAIN3, biological replicate 1

description: Library name: Invitro_Recover2h_NAIN3_rep1

value: wt


title: Brain, 24 Months, Rep 12

description:
Library name: sample_24M_N12_B
24M.N12

value: Brain

value: 24 Months


title: WM3942_CPLX_8881

description: Library name: WM3942_CPLX_8881

value: Melanoma


title: Right ventricle, 6 week sham, replicate 2

value: Heart

value: Right ventricle

value: 6 weeks post-surgery

value: Male


title: WM3942_Baseline_8752

description: Library name: WM3942_8752

value: In-vivo PDX

value: BRAF mutated

value: Treatment naïve


title: Liver, 24 Months, Rep 12

description:
Library name: sample_24M_N12_L
24M.N12

value: Liver

value: Prep 1


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover1h, DMSO, biological replicate 2

description: Library name: Invitro_Recover1h_DMSO_rep2

value: Cervix


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover1h, NAIN3, biological replicate 2

description: Library name: Invitro_Recover1h_NAIN3_rep2

value: HeLa


title: Right ventricle, 6 week sham, replicate 1

value: Sham


title: Right ventricle, 6 week PAB, replicate 3

value: Pulmonary artery banding


title: Liver, 15 Months, Rep 7

description:
Library name: sample_15M_N7_L
15M.N7

value: 15 Months


title: Right ventricle, 1 week PAB, replicate 4

value: 1 week post-surgery


title: WM3942_CPLX_8884

description: Library name: WM3942_CPLX_8884

value: Dabrafenib/Trametinib


title: C4

city: Beijing

first: Hongyu

last: Zhang

address: No. 30 Shuangqing Road, Haidian District

department: State Key Laboratory of Tribology in Advanced Equipment

country: China

institute: Department of Mechanical Engineering, Tsinghua University

description:
Library name: C4
SL-Gel group, replicate biosample 4, RNAseq

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: HUMSC

value: female


title: C3

description:
Library name: C3
SL-Gel group, replicate biosample 3, RNAseq


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover1h, NAIN3, biological replicate 1

description: Library name: Invitro_Recover1h_NAIN3_rep1

value: Cervical adenocarcinoma

value: wt


title: Right ventricle, 6 week PAB, replicate 1

value: Heart

value: Right ventricle

value: 6 weeks post-surgery

value: Male


title: Brain, 15 Months, Rep 7

description:
Library name: sample_15M_N7_B
15M.N7

value: Brain

value: Prep 1


title: C2

description:
Library name: C2
SL-Gel group, replicate biosample 2, RNAseq


title: Liver, 9 Months, Rep 7

description:
Library name: sample_9M_N7_L
9M.N7

value: Liver

value: 9 Months


title: Right ventricle, 1 week PAB, replicate 2

value: Pulmonary artery banding


title: icSHAPE, In-vitro Refolded, Whole Cell, NaAsO2, NAIN3, biological replicate 2

description: Library name: Invitro_NaAsO2_NAIN3_rep2

value: Cervix

value: HeLa


title: Brain, 9 Months, Rep 7

description:
Library name: sample_9M_N7_B
9M.N7


title: Right ventricle, 1 week PAB, replicate 3

value: 1 week post-surgery


title: Right ventricle, 1 week PAB, replicate 1


title: icSHAPE, In-vitro Refolded, Whole Cell, NaAsO2, DMSO, biological replicate 2

description: Library name: Invitro_NaAsO2_DMSO_rep2

value: DMSO


title: Brain, 3 Months, Rep 4

description:
Library name: sample_3M_N4_B
3M.N4

value: 3 Months


title: B4

description:
Library name: B4
Gel/Friction group, replicate biosample 4, RNAseq

value: cell culture

value: HUMSC

value: female


title: Right ventricle, 1 week sham, replicate 3

value: Heart

value: Sham


title: Liver, 3 Months, Rep 4

description:
Library name: sample_3M_N4_L
3M.N4


title: icSHAPE, In-vitro Refolded, Whole Cell, NaAsO2, NAIN3, biological replicate 1

description: Library name: Invitro_NaAsO2_NAIN3_rep1

value: Cervical adenocarcinoma

value: wt


title: B3

description:
Library name: B3
Gel/Friction group, replicate biosample 3, RNAseq


title: BM_oxa_5

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

description:
Library name: BM_oxa_5
bone marrow oxaliplatin biological replicate 5

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: Ensembl release 101
Supplementary files format and content: Comma Separated CSV file containing the raw gene counts for all samples

source_name: bone marrow

extract_protocol:
For Kidney samples, total RNA was extracted with PureLink RNA mini kit following manufactors' instructions. For bone marrow, RNA was extracted with Trizol followed by column-based purification using PureLink column.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Mice were treated with 5% dextrose or 10 mg/kg oxaliplatin i.p. for 8 weeks

value: bone marrow

value: 10 mg/kg oxaliplatin


title: icSHAPE, In-vitro Refolded, Whole Cell, NaAsO2, DMSO, biological replicate 1

description: Library name: Invitro_NaAsO2_DMSO_rep1


title: Right ventricle, 1 week sham, replicate 2

value: Right ventricle

value: Male


title: B2

description:
Library name: B2
Gel/Friction group, replicate biosample 2, RNAseq


title: Right ventricle, 1 week sham, replicate 1


title: icSHAPE, In-vitro Refolded, Whole Cell, Recover1h, DMSO, biological replicate 1

description: Library name: Invitro_Recover1h_DMSO_rep1


title: BM_oxa_4

description:
Library name: BM_oxa_4
bone marrow oxaliplatin biological replicate 4


title: icSHAPE, In-vitro Refolded, Whole Cell, Untreated, NAIN3, biological replicate 2

description: Library name: Invitro_Untreated_NAIN3_rep2


title: BM_oxa_3

description:
Library name: BM_oxa_3
bone marrow oxaliplatin biological replicate 3


title: icSHAPE, In-vitro Refolded, Whole Cell, Untreated, DMSO, biological replicate 2

description: Library name: Invitro_Untreated_DMSO_rep2


title: lung, COPD, rep5

city: Qiqihar

first: Song

last: Lin

address: Bukui

institute: Qiqihar Medical University

data_processing:
Reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , v1.9).
We aligned reads of all samples to the rat reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , v2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , v1.3.4d) with default parameter.
The gene expression levels were quantified by FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina.

value: Lung

value: WT

value: Tracheal administration with LPS/Smoke


title: BM_oxa_2

description:
Library name: BM_oxa_2
bone marrow oxaliplatin biological replicate 2


title: A4

description:
Library name: A4
control group, replicate biosample 4, RNAseq


title: C1

description:
Library name: C1
SL-Gel group, replicate biosample 1, RNAseq


title: icSHAPE, In-vitro Refolded, Whole Cell, Untreated, NAIN3, biological replicate 1

description: Library name: Invitro_Untreated_NAIN3_rep1

value: Cervix

value: HeLa


title: lung, COPD, rep3


title: lung, COPD, rep4


title: A3

description:
Library name: A3
control group, replicate biosample 3, RNAseq


title: icSHAPE, In-vitro Refolded, Whole Cell, Untreated, DMSO, biological replicate 1

description: Library name: Invitro_Untreated_DMSO_rep1

value: DMSO


title: lung, COPD, rep2


title: A1

description:
Library name: A1
control group, replicate biosample 1, RNAseq

value: cell culture


title: B1

description:
Library name: B1
Gel/Friction group, replicate biosample 1, RNAseq

value: HUMSC


title: BM_oxa_1

description:
Library name: BM_oxa_1
bone marrow oxaliplatin biological replicate 1


title: lung, COPD, rep1


title: icSHAPE, HeLa, Whole Cell, Recover2h, DMSO, biological replicate 2

description: Library name: WholeCell_Recover2h_DMSO_rep2


title: BM_ctrl_5

description:
Library name: BM_ctrl_5
bone marrow control biological replicate 5

value: control (5% dextrose)


title: A2

description:
Library name: A2
control group, replicate biosample 2, RNAseq

value: female


title: lung, WDD, rep5

value: Tracheal administration with LPS/Smoke and intragastric administration with WDD


title: lung, WDD, rep4


title: Untreated CD34+ bone marrow sample 47

city: Houston

first: Ziyi

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

description: Library name: RNA-126

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchmark.
Fastq data were aligned by STAR using reference genome hg38. The raw counts were obtained by counting the overlaps between reads and gene regions using Rsubreads.
hg38
Assembly: comma separated text file (csv) includes raw counts for each sample
Supplementary files format and content: .xlsx file

source_name: Bone marrow

extract_protocol:
RNA was harvested using SMARTer Stranded Total RNA-seq Kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-seq Library Prep Kit following manufacturer's protocols.

value: Bone marrow

value: CD34+ cells

value: Untreated


title: icSHAPE, HeLa, Whole Cell, Recover2h, NAIN3, biological replicate 1

description: Library name: WholeCell_Recover2h_NAIN3_rep1

value: Cervical adenocarcinoma

value: wt


title: Untreated CD34+ bone marrow sample 46

description: Library name: RNA-118

value: NOS


title: icSHAPE, HeLa, Whole Cell, Recover2h, DMSO, biological replicate 1

description: Library name: WholeCell_Recover2h_DMSO_rep1


title: BM_ctrl_2

description:
Library name: BM_ctrl_2
bone marrow control biological replicate 2

value: bone marrow


title: lung, WDD, rep3

value: Lung

value: WT


title: BM_ctrl_3

description:
Library name: BM_ctrl_3
bone marrow control biological replicate 3


title: BM_ctrl_1

description:
Library name: BM_ctrl_1
bone marrow control biological replicate 1


title: icSHAPE, HeLa, Whole Cell, Recover1h, NAIN3, biological replicate 2

description: Library name: WholeCell_Recover1h_NAIN3_rep2

value: Cervix


title: lung, WDD, rep2


title: icSHAPE, HeLa, Whole Cell, Recover1h, DMSO, biological replicate 2

description: Library name: WholeCell_Recover1h_DMSO_rep2

value: HeLa


title: lung, WDD, rep1


title: icSHAPE, HeLa, Whole Cell, Recover2h, NAIN3, biological replicate 2

description: Library name: WholeCell_Recover2h_NAIN3_rep2


title: Sh-2-3

city: Zhengzhou

first: Tongtong

last: Wu

address: 1 Jianshe East Road

institute: Zhengzhou University

description:
Library name: sample 6
Unknown_BY451-001T0010

data_processing:
Use HISAT2 software to perform rapid and precise alignment of the Clean Reads to the reference genome, extracting mapping information of the reads on the reference genome. Subsequently, StringTie is employed to assemble the mapped reads, reconstructing the transcriptome for downstream analysis.
Using StringTie software to assemble the mapped reads, compare the results with existing genome annotation information, and identify previously unannotated transcribed regions. This enables the discovery of novel transcripts and genes for the species, thereby updating and refining the original genome annotation.
Utilize DIAMOND to perform sequence alignment of the novel genes against the NR, Swiss-Prot, COG, KOG, and KEGG databases, obtaining annotation results including KEGG Orthology (KO) assignments. Subsequently, InterProScan analyzes Gene Ontology (GO) terms for novel genes using integrated InterPro databases. Following prediction of the novel genes' amino acid sequences, HMMER is employed to align them against the Pfam database, thereby acquiring comprehensive functional annotation information.
Assembly: Mus_musculus.GRCm38_release95.genome.fa
Supplementary files format and content: fpkm, count

source_name: liver

extract_protocol:
Advanced molecular biology equipment is employed to test the purity, concentration, and integrity of the extracted total RNA:(1) NanoDrop 2000 Spectrophotometer: used to determine/measure the purity and concentration of RNA;(2) Agilent 2100 Bioanalyzer / LabChip GX system: used to accurately assess/measure the integrity of RNA.
After the sample passes the testing phase, library construction is performed according to the following key procedures: (1) Enrich eukaryotic mRNA using magnetic beads coated with Oligo(dT); (2) Add Fragmentation Buffer to randomly fragment the mRNA; (3) Use mRNA as template to synthesize the first cDNA strand and the second strand, followed by cDNA purification; (4) Subject the purified double-stranded cDNA to end repair, A-tailing, and sequencing adapter ligation, then perform size selection using AMPure XP beads; (5) Finally, obtain the cDNA library through PCR amplification.

value: liver


title: Untreated CD34+ bone marrow sample 43

description: Library name: RNA-114


title: icSHAPE, HeLa, Whole Cell, Recover1h, NAIN3, biological replicate 1

description: Library name: WholeCell_Recover1h_NAIN3_rep1


title: BM_ctrl_4

description:
Library name: BM_ctrl_4
bone marrow control biological replicate 4


title: Sh-2-1

description:
Library name: sample 4
Unknown_BY451-001T0008


title: Sh-2-2

description:
Library name: sample 5
Unknown_BY451-001T0009


title: icSHAPE, HeLa, Whole Cell, Recover1h, DMSO, biological replicate 1

description: Library name: WholeCell_Recover1h_DMSO_rep1

value: DMSO


title: lung, control, rep5

value: normal control


title: Untreated CD34+ bone marrow sample 42

description: Library name: RNA-113


title: lung, control, rep4


title: icSHAPE, HeLa, Whole Cell, NaAsO2, NAIN3, biological replicate 2

description: Library name: WholeCell_NaAsO2_NAIN3_rep2


title: AML12-4

description:
Library name: sample 3
Unknown_BY451-001T0004

value: sh-NC


title: Untreated CD34+ bone marrow sample 40

description: Library name: RNA-111


title: AML12-3

description:
Library name: sample 2
Unknown_BY451-001T0003


title: icSHAPE, HeLa, Whole Cell, NaAsO2, DMSO, biological replicate 2

description: Library name: WholeCell_NaAsO2_DMSO_rep2

value: icSHAPE, HeLa, Whole Cell, NaAsO2, DMSO


title: lung, control, rep3


title: Untreated CD34+ bone marrow sample 45

description: Library name: RNA-117


title: Untreated CD34+ bone marrow sample 39

description: Library name: RNA-110


title: Untreated CD34+ bone marrow sample 44

description: Library name: RNA-115


title: lung, control, rep2


title: AML12-2

description:
Library name: sample 1
Unknown_BY451-001T0002


title: Untreated CD34+ bone marrow sample 38

description: Library name: RNA-109


title: icSHAPE, HeLa, Whole Cell, NaAsO2, DMSO, biological replicate 1

description: Library name: WholeCell_NaAsO2_DMSO_rep1


title: lung, control, rep1


title: Untreated CD34+ bone marrow sample 37

description: Library name: RNA-107


title: WT LSK BM 573 (RRBS)

city: New York

first: Alan

last: Shih

state: NY

address: 1 Gustave L Levy Place

institute: Icahn School  of Medicine at Mount Sinai

description: Library name: Sample_BMT1358_573

library_source: genomic

data_processing:
Raw sequence data generated from the sequencer are demultiplexed and converted to FASTQ files using the Illumina bcl2fastq software. Reads were then adapter trimmed, aligned, and post-processed to produce methylation calls at base pair resolution using a previously described in-house pipeline using CUTADAPT instead of FLEXBAR to trim the reads (Garrett-Bakelman F., Sheridan, C. et al. 2015).
Assembly: mm10
Supplementary files format and content: wig files - methylation levels of CpG sites at their location in the genome in a track format

molecule: genomic DNA

growth_protocol: WT and Tet2 P53 mutant bone marrow cells were transplanted into recipient mice.

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012). RRBS starts with MspI DNA digestion, followed by NGS-library preparation and bisulfite conversion of cytosines.

treatment_protocol: After engraftment Lineage- Sca+ cKit+ cells were sorted from these mice and subjected to RRBS.

value: hematopoietic

value: cell sorting


title: EIF2AK2_3rd

city: Changchun

first: Hanqing

last: Cai

institute: Jilin university

data_processing:
The libraries were subjected to 150 nt paired-end sequencing on an Illumina Novaseq 6000 system for high-throughput sequencing.
Short reads of less than 16 nt were omitted.
Following that, tophat2  aligned clear reads to the rat_ensembl_v6 genome while permitting 4 mismatches.
Following that, tophat2  aligned clear reads to the rat_ensembl_v6 genome while permitting 4 mismatches.
The ABLas pipeline was used to define and quantify the alternative splicing events (ASEs) and regulated alternative splicing events (RASEs),
Assembly: rat_ensembl_v6
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated via TRIzol (Invitrogen, Carlsbad, CA, USA), followed by RQ1 DNase (Promega, Madison, WI, USA) treatment to remove DNA. The quantification and quality of the purified RNA were evaluated by using Nanodrop One (Thermo) to measure the absorbance at 260/280 nm (A260/A280).
The libraries were subjected to 150 nt paired-end sequencing on an Illumina Novaseq 6000 system for high-throughput sequencing.

value: EIF2AK2 overexpression in Rat_INS1


title: WT LSK BM 572 (RRBS)

description: Library name: Sample_BMT1358_572


title: icSHAPE, HeLa, Whole Cell, Untreated, DMSO, biological replicate 2

description: Library name: WholeCell_Untreated_DMSO_rep2


title: Untreated CD34+ bone marrow sample 35

description: Library name: RNA-105

value: Bone marrow

value: CD34+ cells

value: Untreated


title: icSHAPE, HeLa, Whole Cell, Untreated, NAIN3, biological replicate 1

description: Library name: WholeCell_Untreated_NAIN3_rep1

value: Cervical adenocarcinoma

value: wt


title: Ctrl_3rd

value: Rat_INS1(control plasmid)


title: Tet2 P53 LSK BM 11846 (RRBS)

description: Library name: Sample_BMT1321_11846

value: bone marrow

value: Tet2 P53


title: WT LSK BM 571 (RRBS)

description: Library name: Sample_BMT1358_571

value: WT


title: Untreated CD34+ bone marrow sample 41

description: Library name: RNA-112


title: Untreated CD34+ bone marrow sample 34

description: Library name: RNA-104


title: icSHAPE, HeLa, Whole Cell, Untreated, DMSO, biological replicate 1

description: Library name: WholeCell_Untreated_DMSO_rep1

value: Cervix

value: HeLa


title: EIF2AK2_1st


title: icSHAPE, HeLa, Whole Cell, Untreated, NAIN3, biological replicate 2

description: Library name: WholeCell_Untreated_NAIN3_rep2


title: Tet2 P53 LSK BM 11847 (RRBS)

description: Library name: Sample_BMT1321_11847


title: Untreated CD34+ bone marrow sample 33

description: Library name: RNA-103

value: NOS


title: Tet2 P53 LSK BM 11844_45 (RRBS)

description: Library name: Sample_BMT1321_11844_45


title: human bone, input

city: Jerusalem

first: Daniel

last: Batyrev

address: Edmond J, Safra Campus (Givat Ram)

department: Department of Genetics, The Institute of Life Sciences, Silberman Building

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
The quality of the sequenced fastq data was checked using FastQC software
Chip-seq reads were aligned to the UCSC hg38 genome using the built-in Bowtie2 tool in Galaxy
Peaks were called using the built-in MACS2 tool in Galaxy with significance cut-off q-value is 0.05
Bigwig files were generated using the built-in bamCoverage tool in Galaxy
HG38 peaks were lifted with the USCS liftover tool to HG19
Assembly: hg38
Supplementary files format and content: bed (peak position), bigwig (bam coverage)

source_name: bone

extract_protocol:
To study the changes of histone acetylome (H3K27ac) in human bone samples, chromatin was isolated from bones obtained from a surgery of hip replacement performed by Dr Liebregall at Hadassah hospital in Jerusalem. Briefly, 300 mgs of bones were thoroughly washed (X3) with cold PBS mixed with 1X protease inhibitor (cOmplete Mini, 11836153001), to clean samples from blood. Bones were crushed using a steel magnet bead in 1 ml of 10% Fetal bovine serum (FBS) using a TissueLyser LT instrument (Qiagen) set at 50 oscillations for 6 min (X2). After thorough disruption, chromatin released from bones was cross-linked by adding 37% formaldehyde (Sigma, F8775) to a final concentration of 1% and incubating in a rotator mixer for 15 min at room temperature. The reaction was stopped by adding 2.5 M glycine to a final concentration of 0.125 M and incubating in a rotator mixer for additional 5 min at room temperature. The fixed samples were washed 2 times using cold PBS mixed with 1X protease inhibitor by centrifuging at 4°C in a speed of 500 rcf for 5 min. To lyse cells, pellets were resuspended in 1 ml of SDS lysis buffer (1% SDS, 10 mM EDTA of pH 8, 50 mM Tris HCl of pH 8.1) and incubated on ice for 25 min. The fragmentation of chromatin DNA was achieved by sonicating the samples for 20 cycles with 30 sec pulse on high and 30 sec pulse off using a water-bath sonicator to the length of 200–600 bp. The sheared chromatin was then centrifuged at 4°C in a speed of 20000 rcf for 15 min. After running electrophoresis on agarose gel to check sonication results, the supernatant containing sheared chromatin was diluted 1:10 in a dilution buffer (1.1% Triton X-100, 1.2 mM EDTA of pH 8, 16.7 mM Tris-HCL of pH 8.1, 167 mM NaCl) containing 1X protease inhibitor. To set up ChIP reactions, the diluted chromatin was mixed with 5 µg of anti-H3K27ac (CMA309, Kimura) and 10 ul of the Magna-ChIP protein A magnetic beads (16-661, Millipore), and the mix was incubated for 14 hours on a rotator mixer at 4°C. Beads were then sequentially washed with rotation for 2 min once with Low Salt Immune Complex Wash Buffer (1% Triton X-100, 2 mM EDTA of pH 8, 20 mM Tris-HCL of pH 8.1, 150 mM NaCl, 0.1% SDS, 1X protease inhibitor), High Salt Immune Complex Wash Buffer (1% Triton X-100, 2 mM EDTA of pH 8, 20 mM Tris-HCL of pH 8.1, 500 mM NaCl, 0.1% SDS, 1X protease inhibitor), LiCl Immune Complex Wash Buffer (1 mM EDTA of pH 8, 10 mM Tris-HCL of pH 8.1, 1% NP-40, 250 mM LiCl, 1% Deoxycholate, 1X protease inhibitor), and once without rotation with TE Buffer (1 mM EDTA of pH 8, 10 mM Tris-HCL of pH 8.1, 1X protease inhibitor). DNA was then eluted from the beads by incubation in 300 μL elution buffer (1 mM EDTA of pH 8, 10 mM Tris-HCL of pH 8.1, 200 mM NaCl, 1% SDS) for 5 min at room temperature. Then, the samples were incubated with 1 μL RNase A (10109142001, Merck) for 30 min at 37°C with 600 rpm shaking. The histone-DNA crosslinks were reversed by the addition of 2 µl of 20 mg/ml Proteinase K (25530049, Thermo Fisher Scientific) and incubation at 65°C for overnight. Finally, DNA was purified using a phenol-chloroform protocol. Briefly, one volume of the lower phase of phenol:chloroform:isoamyl alcohol was added and the samples were vortexed thoroughly for approximately 25 sec. The samples were centrifuged for 10 minutes at 15000 rcf. The upper phase was transferred to a new tube, mixed with 3 M sodium acetate (1:10), 2 µl of 20 mg/ml glycogen and two volumes of 100% cold ethanol. The samples were incubated at -20°C for overnight to precipitate the DNA from the samples. The samples were centrifuged at 4°C in a speed of 15000 rcf for 30 min. The pellets were washed with 70% ethanol and centrifuged at 4°C in a speed of 15000 rcf for 15 min. The pellets were dried in the hood for 15 minutes and resuspended with 10 mM Tris pH 8. The concentration of DNA was quantified using HS Qubit.
ChIP-seq libraries were prepared as previously described in high-throughput ChIP protocol (Blecher-Gonen et. al., 2013) with minor modifications. Briefly, 10 ng of DNA were purified again using SPRI beads and amplified by 14 PCR cycles following end repairing, A-base addition and adapter ligation. The quality of libraries was checked on TapeStation (Agilent) and Qubit (Invitrogen). All ChIP-seq libraries were sequenced in one lane of Illumina® NextSeq® 500 system.

value: bone

tag: chip antibody


title: Untreated CD34+ bone marrow sample 32

description: Library name: RNA-102


title: Ctrl_2nd


title: icSHAPE, HeLa, Whole Cell, NaAsO2, NAIN3, biological replicate 1

description: Library name: WholeCell_NaAsO2_NAIN3_rep1


title: Ctrl_1st


title: Tet2 P53 LSK BM 11843 (RRBS)

description: Library name: Sample_BMT1321_11843_mix


title: Untreated CD34+ bone marrow sample 36

description: Library name: RNA-106


title: human bone, H3K27ac, ChIP

value: antibody H3K27ac CMA309 Kimura


title: hepatocytes from MTDH WT mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep3

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

description: Library name: CM_WT-3

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a.Gene counts were obtained by quantifying against the mm39-Ensembl Transcripts release 108 annotation model. After noise filtering, counts were normalized using the DESeq2 package.
Assembly: mm39-Ensembl Transcripts release 108
Supplementary files format and content: tab-delimited text files with counts normalized as median ratio by DESeq2 in Partek software package

extract_protocol:
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

treatment_protocol: Hepatocytes from age-matched WT and MTDH KO mice were collected. After treatment with TNFa, TGFb, or Kupffer cells conditioned media treated with Py8119-EVPs, total RNA were extracted  and processed to RNA sequencing.

value: liver

value: hepatocytes

tag: condition

value: normal, no tumor


title: AMO-IIIF9-12h-melphalan-20-biol rep 3

city: Helsinki

first: Philipp

last: Sergeev

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11/v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to human genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 110
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 110 for GRCh38.p14) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: GRCh38.p14 (primary assembly and mitochondrion)
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

growth_protocol: Cells were maintained at 37°C/5% CO2 in RPMI medium, supplemented with 10% FBS, pyruvate, glutamine and antibiotics.

extract_protocol:
Accoding to protocol for RNeasy Plus Mini Kit (Qiagen)
DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~300 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 31-46 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina).

treatment_protocol: Drugs or DMSO (solvent control) were added to the culture wells and cells harvested by centrifugation after 2 and 12 hours, respectively

value: plasma cell, myeloma

value: 20 µM melphalan

tag: time point

tag: biological replicate


title: H9C2, LV5-MEF2A-Over, H3K4me3, Input-seq

city: Jining

first: xueying

last: Chen

state: Shandong

address: No.89 Guhuai Road

department: Department of Cardiology

institute: Affiliated Hospital of Jining Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks with qvalue < 0.05.
Peaks were annotated by ChIPseeker package.
Assembly: rn7
Supplementary files format and content: bw

extract_protocol:
Briefly, cells were harvested and crosslinked with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti-H3K4me3. The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (TIANGEN, #DP214).
The ChIP-Seq library was prepared using original Ultra II DNA Library Kits (NEB, #E7645) according to the manufacturer’s instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

tag: cell type

value: Myocardial cells

value: Transfected lentivirus LV5-MEF2A OVER

value: MEF2A overexpression


title: Untreated CD34+ bone marrow sample 30

description: Library name: RNA-100

tag: tissue

value: Bone marrow

value: CD34+ cells

value: Untreated


title: H9C2, LV5-NC, H3K4me3, Input-seq

tag: cell line

value: Transfected lentivirus LV5-NC

tag: genotype

value: control


title: hepatocytes from MTDH WT mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep2

description: Library name: CM_WT-2

value: WT


title: Untreated CD34+ bone marrow sample 29

description: Library name: RNA-98

value: NOS

tag: treatment


title: AMO-IIIF9-12h-melphalan-20-biol rep 2


title: hepatocytes from MTDH WT mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep1

description: Library name: CM_WT-1


title: Untreated CD34+ bone marrow sample 28

description: Library name: RNA-93


title: H9C2, LV5-NC, H3K4me3, ChIP-seq


title: AMO-IIIF9-12h-melphalan-20-biol rep 1


title: hepatocytes from MTDH KO mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep3

description: Library name: CM_KO-3

value: Mtdh KO


title: ALI group rats [SM5]

value: Lung

value: Tracheal administration with LPS


title: AMO-IIIF9-12h-melflufen-0.5-biol rep 3

value: 0.5 µM melflufen


title: Untreated CD34+ bone marrow sample 27

description: Library name: RNA-92


title: hepatocytes from MTDH KO mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep2

description: Library name: CM_KO-2

value: liver

value: hepatocytes

value: normal, no tumor


title: AMO-IIIF9-12h-melflufen-0.5-biol rep 2

value: plasma cell, myeloma


title: Untreated CD34+ bone marrow sample 26

description: Library name: RNA-65


title: Untreated CD34+ bone marrow sample 25

description: Library name: RNA-56


title: ALI group rats [SM3]


title: ALI group rats [SM4]


title: Untreated CD34+ bone marrow sample 31

description: Library name: RNA-101


title: hepatocytes from MTDH WT mice, treatment with TGFb, rep3

description: Library name: TGFb_WT-3


title: AMO-IIIF9-12h-DMSO-biol rep 3

value: DMSO control


title: Untreated CD34+ bone marrow sample 24

description: Library name: RNA-54


title: EIF2AK2_2nd

value: EIF2AK2 overexpression in Rat_INS1


title: hepatocytes from MTDH WT mice, treatment with TGFb, rep2

description: Library name: TGFb_WT-2


title: Untreated CD34+ bone marrow sample 23

description: Library name: RNA-52

value: Bone marrow


title: H9C2, LV5-MEF2A-Over, H3K4me3, ChIP-seq

value: Myocardial cells

value: Transfected lentivirus LV5-MEF2A OVER

value: MEF2A overexpression


title: ALI group rats [SM1]


title: hepatocytes from MTDH WT mice, treatment with TGFb, rep1

description: Library name: TGFb_WT-1


title: AMO-IIIF9-12h-DMSO-biol rep 1


title: Untreated CD34+ bone marrow sample 22

description: Library name: RNA-49

value: CD34+ cells

value: Untreated


title: hepatocytes from MTDH KO mice, treatment with TGFb, rep3

description: Library name: TGFb_KO-3


title: AMO-WT-12h-melphalan-20-biol rep 3

value: WT

value: 20 µM melphalan


title: AMO-IIIF9-12h-melflufen-0.5-biol rep 1


title: hepatocytes from MTDH KO mice, treatment with Kupffer cells conditioned media treated with Py8119-EVPs, rep1

description: Library name: CM_KO-1

value: Mtdh KO


title: Untreated CD34+ bone marrow sample 20

description: Library name: RNA-47

value: NOS


title: hepatocytes from MTDH KO mice, treatment with TGFb, rep2

description: Library name: TGFb_KO-2


title: hepatocytes from MTDH WT mice, treatment with TNFa, rep3

description: Library name: TNFa_WT-3


title: SJY group rats [SD3]

value: Lung

value: Tracheal administration with LPS and intragastric administration with SJY


title: AMO-WT-12h-melflufen-0.5-biol rep 3

value: 0.5 µM melflufen


title: hepatocytes from MTDH KO mice, treatment with TGFb, rep1

description: Library name: TGFb_KO-1

value: liver

value: hepatocytes

value: normal, no tumor


title: SJY group rats [SD4]


title: SJY group rats [SD5]


title: Untreated CD34+ bone marrow sample 18

description: Library name: RNA-39


title: ALI group rats [SM2]

value: Tracheal administration with LPS


title: AMO-WT-12h-melphalan-20-biol rep 2

value: plasma cell, myeloma


title: Untreated CD34+ bone marrow sample 19

description: Library name: RNA-41

value: Bone marrow


title: hepatocytes from MTDH WT mice, treatment with TNFa, rep2

description: Library name: TNFa_WT-2


title: SJY group rats [SD1]


title: AMO-IIIF9-12h-DMSO-biol rep 2

value: DMSO control


title: AMO-WT-12h-melflufen-0.5-biol rep 2


title: control group rats [SB8]

value: normal control


title: Untreated CD34+ bone marrow sample 17

description: Library name: RNA-37

value: CD34+ cells


title: Untreated CD34+ bone marrow sample 16

description: Library name: RNA-34

value: Untreated


title: AMO-WT-12h-melflufen-0.5-biol rep 1

value: WT


title: SJY group rats [SD6]


title: Untreated CD34+ bone marrow sample 21

description: Library name: RNA-48


title: hepatocytes from MTDH KO mice, treatment with TNFa, rep3

description: Library name: TNFa_KO-3


title: AMO-WT-12h-DMSO-biol rep 3


title: control group rats [SB6]


title: hepatocytes from MTDH KO mice, treatment with TNFa, rep2

description: Library name: TNFa_KO-2


title: Untreated CD34+ bone marrow sample 15

description: Library name: RNA-26


title: AMO-WT-12h-melphalan-20-biol rep 1

value: 20 µM melphalan


title: Untreated CD34+ bone marrow sample 14

description: Library name: RNA-25


title: control group rats [SB5]


title: AMO-IIIF9-2h-melphalan-20-biol rep 3

value: 2 h


title: Untreated CD34+ bone marrow sample 11

description: Library name: RNA-22

value: NOS


title: hepatocytes from MTDH KO mice, treatment with TNFa, rep1

description: Library name: TNFa_KO-1

value: Mtdh KO


title: hepatocytes from MTDH WT mice, treatment with TNFa, rep1

description: Library name: TNFa_WT-1


title: AMO-IIIF9-2h-melphalan-20-biol rep 2


title: HFD_2

city: Guangzhou

first: Yizhi

last: Zhan

state: Guangdong

address: 1023 South Shatai Road Baiyun District

department: Department of Pathology

institute: Nanfang Hospital Southern Medical University

description: Library name: sample 6

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9) was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d). The expression levels of all transcripts were estimated and performed as calculating FPKM (FPKM = [total exon fragments / mapped reads (millions) × exon length (kB)] ).
Assembly: Mus musculus Ensembl v101
Supplementary files format and content: tab-delimited text fle includes FPKM for each Sample

source_name: colorectal cancer liver metastasis

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells.
A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

value: colorectal cancer liver metastasis

value: primary cells

value: macrophages

value: high-fat diet


title: Untreated CD34+ bone marrow sample 12

description: Library name: RNA-23


title: AMO-WT-12h-DMSO-biol rep 1


title: Untreated CD34+ bone marrow sample 13

description: Library name: RNA-24


title: HFD_3

description: Library name: sample 7


title: QKI-KD-2

data_processing:
Quality checks were performed using FastQC (v0.11.2), summarised with MultiQC (v1.8). Alignment to the rattus norvegicus reference genome (build mRatBN7.2) was performed using STAR (STAR_2.5.2a) with default parameters.
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433).
Downstream quality checks and data analysis was performed using the bulkAnalyseR (v0.1.1) shiny app framework (https://doi.org/10.1101/2021.12.23.473982). Density plots, MA plots, Jaccard similarity index heatmaps and PCA were performed as further quality checks. Differential expression analysiss was performed using edgeR (v3.28.1) and DESeq2 (1.30.0).
Alternative splicing analysis was performed using the rMATS software (v4.1.2). Splicing results were filtered for p-value < 0.01, absolute IncLevelDifference >= 0.15, total occurances per sample group > 80 and summarised with bar and density plots.
Assembly: mRatBN7.2
Supplementary files format and content: Csv of raw and normalised abundances. Rows represent features and columns represent samples. Values are raw in the first instance, and normalised with noise removed in the second.

growth_protocol: Rat PAC-1 cells were cultured in DMEM + Glutamax medium with 10% Foetal Bovine Serum. For the more differentiated state, the cells were split once per week at a 1:10 dilution.

tag: replicate


title: QKI-KD-1


title: RBPMS-KD-3


title: AMO-IIIF9-2h-melphalan-20-biol rep 1


title: control group rats [SB7]

value: Lung


title: CD_4

description: Library name: sample 4

value: control diet


title: AMO-WT-12h-DMSO-biol rep 2

value: plasma cell, myeloma


title: HFD_1

description: Library name: sample 5


title: AMO-IIIF9-2h-melflufen-2.5-biol rep 3

value: 2.5 µM melflufen


title: Untreated CD34+ bone marrow sample 9

description: Library name: RNA-20

value: Bone marrow


title: Untreated CD34+ bone marrow sample 8

description: Library name: RNA-19


title: Untreated CD34+ bone marrow sample 10

description: Library name: RNA-21


title: AMO-IIIF9-2h-melflufen-2.5-biol rep 2


title: HFD_4

description: Library name: sample 8


title: QKI-KD-3


title: control group rats [SB4]

value: normal control


title: RBPMS-KD-2


title: AMO-IIIF9-2h-melflufen-2.5-biol rep 1


title: CD_3

description: Library name: sample 3


title: Untreated CD34+ bone marrow sample 7

description: Library name: RNA-18

value: CD34+ cells


title: CD_2

description: Library name: sample 2


title: Untreated CD34+ bone marrow sample 6

description: Library name: RNA-17

value: Untreated


title: RBPMS-KD-1


title: AMO-IIIF9-2h-DMSO-biol rep 2

value: DMSO control


title: Untreated CD34+ bone marrow sample 5

description: Library name: RNA-16


title: Untreated CD34+ bone marrow sample 4

description: Library name: RNA-15


title: AMO-IIIF9-2h-DMSO-biol rep 3


title: 6OHDA_7d

city: Shanghai

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

institute: Tongji University

description: Library name: 6OHDA_7d

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed using Cell Ranger software (version 6.1.1) to generate gene expression matrices based on the mm10 genome assembly. The pre-processed mouse reference genome (mm10) was downloaded from the 10x Genomics website. The gene expression matrices were imported into R for downstream analysis using the Read10X function in Seurat (version 4.1.1). Cells with fewer than 200 genes or more than 15% mitochondrial gene content were excluded from further analysis.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: calvarial

extract_protocol:
For calvarial defect creation, anesthesia was performed with 2-3% isoflurane in 100% oxygen at a flow rate of 1 L/min and animals were operated upon on a warm animal surgery station. Firstly, hair overlying the calvaria was clipped, and a 4 mm skin incision was made over the right frontal bone. Next, a 1.8 mm diameter full thickness circular defect was created in the non-suture associated frontal bone using a micro surgical drill and a trephine drill bit (Xemax Surgical, Napa Valley, CA). Meticulous care was taken not to injure the underlying dura mater. Finally, the skin was sutured and the animal was monitored per established postoperative protocols. Post-operative monitoring was performed in accordance with institutional policy. Skulls were harvested up to 7d and 14 d after defect, respectively.
Library preparation and sequencing were conducted by Majorbio Bio-Pharm Technology Co. Single-cell suspensions were loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell gel bead emulsions, following the manufacturer’s guidelines (Chromium Single Cell 3ʹ v3.1). The Chromium Single-Cell 3' Gel Bead and Library V3 Kit was used for cDNA synthesis and amplification, and sequencing was carried out on an Illumina NovaSeq 6000 platform.

value: calvarial

value: tissue

value: 6OHDA 7d


title: AMO-WT-2h-melphalan-20-biol rep 3

value: WT

value: 20 µM melphalan

value: 2 h


title: Untreated CD34+ bone marrow sample 2

description: Library name: RNA-13


title: C2-2

city: Cambridge

first: Irina

institute: University of Cambridge

extract_protocol:
Cells were lysed with TRI-reagent and total RNA purified by Direct-zol purification column (Zymo Research). The DNase treatment was performed in column during the total RNA purification.
We have used the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (#E7760L) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (#E6440L) in conjunction with NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490L) for these samples.


title: C2-1


title: FOX2-KD-3


title: CD_1

description: Library name: sample 1

value: colorectal cancer liver metastasis

value: primary cells

value: macrophages


title: FOX2-KD-2


title: X66: BDE-209 eposure rep4

city: Zunyi

first: Yi-jun

last: Liu

state: Guizhou

address: No.6 Xuefu West Road, Xinpu New District

institute: Zunyi medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Placenta RNA

extract_protocol:
Total RNA was extracted from rat placenta samples using a mirVana miRNA iso-lation kit (Ambion, Austin, TEXAS, USA), according to the manufacturer's instructions.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, Ipswich, MA, USA) was used for cDNA library construction.

tag: strain

value: Sprague-Dawley (SD)

value: placenta

tag: dose

value: 500 mg/ks/day


title: 6OHDA_14d

description: Library name: 6OHDA_14d

value: 6OHDA 14d


title: CD45- cells, Lung, Ctrl

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

description:
Library name: Ctrl
10X Genmoics

data_processing:
The 10X scRNA-seq libraries were sequenced on the Illumina Novaseq-6000 platform, and generated reads were de-multiplexed and mapped to the mouse genome using the Cell Ranger pipeline (v7.0.1) and mm10 reference (refdata-gex-mm10-2020-A, 10x Genomics).
Assembly: mm10
Supplementary files format and content: tab-delimited value files and matrix files

extract_protocol:
Lung lobes were finely minced and enzymatically digested in PBS containing 5 µg/mL Dispase (Corning, 354235), 0.025 mg/mL DNase I (Roche, 10104159001), and 480 µg/mL Collagenase Type I (Thermo Fisher, 17100017) at 37°C for 30 minutes with intermittent agitation. Single-cell suspensions were obtained using a gentleMACS Dissociator (Miltenyi Biotec). The digested samples were washed with FACS buffer (PBS supplemented with 1 mM EDTA, 25 mM HEPES, and 0.5% BSA), passed through a 70-µm cell strainer, and incubated with 1× RBC Lysis Buffer (BioLegend, 420301) on ice for 5 minutes to remove red blood cells. Following lysis, the cells were blocked with anti-mouse CD16/32 (FcR) antibody (BioLegend, 101301) at 4°C for 1 hour. The FcR-blocked suspensions were then labeled with a biotin-conjugated anti-CD45 antibody at 4°C for 1 hour, followed by incubation with anti-biotin microbeads (Miltenyi Biotec, 130-090-485) for 30 minutes. CD45⁻ cells were subsequently isolated using LS columns (Miltenyi Biotec) and washed with FACS buffer prior to downstream processing.
Library was prepared using Chromium Next GEM Single Cell 5' Reagent Kit v2 (10x Genomics) following manufacturer's instruction.

value: Lung

value: Sorted CD45- cells


title: X33: BDE-209 eposure rep3


title: Endothelail Contact Coculture Rep3

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

description: Library name: CC3

data_processing:
The paired-end reads were mapped to the hg38 reference genome using STAR (v2.7.9a).
Gene counts were generated with featureCounts in the Subread package.
DESeq2 (v1.34.0) was used to identify differentially expressed genes  (Padj < 0.05).
Ensemble IDs were converted to gene symbols using the org.Hs.eg.db package.
Assembly: hg38
Supplementary files format and content: counts.csv includes raw count files for each dataset
Supplementary files format and content: NormalizedCounts.csv includeds counts normalized with DESeq2
Supplementary files format and content: NCvEC.csv includes differential expression results of no contact vs monolayer endothelial cells
Supplementary files format and content: CCvEC.csv includes differential expression results of contact vs monolayer endothelial cells
Supplementary files format and content: CCvNC.csv includes differential expression results of contact vs no-contact endothelial cells

source_name: Human coronary artery endothelial cells

extract_protocol:
Quick-RNA MiniPrep (Zymo Research)
PE150 reads were generated with the Illumina NovoSeq 6000 platform

value: Human coronary artery endothelial cells

value: Contact Coculture


title: Endothelail Contact Coculture Rep2

description: Library name: CC2


title: AMO-IIIF9-2h-DMSO-biol rep 1

value: plasma cell, myeloma

value: DMSO control


title: Untreated CD34+ bone marrow sample 3

last: Li

description: Library name: RNA-14

value: Bone marrow

value: CD34+ cells

value: Untreated


title: FOX2-KD-1

last: Mohorianu

address: Puddicombe Way


title: Furmint2

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: Library name: 229-F2-K

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary files format and content: trimmed redundant list, each read with its number of repeats
Assembly: contig were built using CLC assembler

organism: Vitis vinifera

source_name: leaf of the in vitro plantlet

extract_protocol:
CTAB based RNS extraction, based on Gambino et al. doi:https://doi.org/10.1002/pca.1078
modified Illumina Trueseq small RNA kit protocol: doi.org/10.1007/978-1-0716-3515-5_13

value: leaf of the in vitro plantlet


title: X6: BDE-209 eposure rep1


title: C2-3


title: Ctrl_14d

description: Library name: Ctrl_14d

value: calvarial

value: tissue

value: Ctrl 14d


title: AMO-WT-2h-melphalan-20-biol rep 2

value: WT

value: 20 µM melphalan

value: 2 h


title: Ctrl_7d

description: Library name: Ctrl_7d

value: Ctrl 7d


title: AMO-WT-2h-melphalan-20-biol rep 1


title: Furmint1

description: Library name: 227-F1-K


title: Lung CD140b+ cells, FOXF2, Wild Type, rep1

description: Library name: FOXF2_1

data_processing:
FASTQ files were trimmed with Trimgalore to remove adapters and aligned to the mm10 reference genome using bowtie2. MACS2 was used to call peaks. Bigwig files were generated using deepTools
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeak (except for IgG control samples)
Library strategy: CUT&Tag

extract_protocol:
Lung lobes were finely minced and digested with an enzyme solution containing 5 µg/mL Dispase (Corning, 354235), 0.025 mg/mL DNase I (Roche, 10104159001), and 480 µg/mL Collagenase Type I (Thermo Fisher, 17100017) in PBS at 37°C for 30 minutes with periodic agitation. Single-cell suspensions were generated using a gentleMACS Dissociator (Miltenyi Biotec). The digested tissues were washed with FACS buffer (PBS with 1 mM EDTA, 25 mM HEPES, and 0.5% BSA), filtered through a 70-µm cell strainer, and treated with 1× RBC Lysis Buffer (BioLegend, 420301) for 5 minutes on ice to eliminate red blood cells. The samples were then blocked with anti-mouse CD16/32 (FcR) antibody (BioLegend, 101301) at 4°C for 1 hour. The FcR-blocked single-cell suspensions were incubated with biotin-conjugated anti-CD140b (PDGFRβ) antibody at 4°C for 1 hour, followed by anti-biotin microbeads (Miltenyi Biotec, 130-090-485) for 30 minutes. PDGFRβ+ cells bound to microbeads were enriched using LS columns (Miltenyi Biotec) and washed with FACS buffer.
Each reaction was performed with approximately 30,000 cells. To begin, cells were incubated at room temperature for 15 minutes with magnetic beads coated with concanavalin A (Vazyme, N515). Following this, primary antibodies specific to either FOXF2 or H3K4me2 were added, and the mixture was rotated overnight at 4°C. The next day, secondary antibodies were introduced and allowed to incubate for 30 minutes at room temperature. Excess antibodies were removed using a Triton-based wash buffer, after which the pG-Tn5 adapter complex (diluted 1:25) was added, and the samples were incubated for 1 hour at room temperature. For CUT&Tag processing, cells were resuspended in 50 µL of tagmentation buffer consisting of 1 mL Triton-300 wash buffer and 10 µL of 1 M MgCl₂, and incubated at 37°C for 1 hour. In the case of H3K4me2 CUTAC, cells were instead resuspended in 50 µL of a DMF-based tagmentation buffer (10 mM TAPS, 5 mM MgCl₂, 20% DMF, and 0.05% Triton X-100) and incubated at 37°C for 20 minutes. After tagmentation, DNA was extracted using SDS–Proteinase K treatment, and libraries were generated via PCR amplification with the TruePrep CUT&Tag Amplification Mix (Vazyme, TD612), employing Illumina i5 and i7 indexing primers. The amplified products were purified with VAHTS DNA Clean Beads (Vazyme, N411) and sequenced using the Illumina NovaSeq 6000 platform.

value: Lung

value: Sorted CD140b+ cells


title: Untreated CD34+ bone marrow sample 1

description: Library name: RNA-11

value: NOS


title: Endothelial No-contact Coculture Rep1

description: Library name: NC1

value: Human coronary artery endothelial cells

value: No-contact Coculture


title: X13: Control rep3

value: Sprague-Dawley (SD)

value: placenta

value: 0 mg/ks/day


title: AMO-WT-2h-melflufen-0.5-biol rep 3

value: plasma cell, myeloma

value: 0.5 µM melflufen


title: CD45- cells, Lung, KO

description:
Library name: KO
10X Genmoics

value: Sorted CD45- cells


title: Lung CD140b+ cells, H3K4me2, KO, rep2

description: Library name: KO2


title: AMO-WT-2h-melflufen-0.5-biol rep 2


title: Lung CD140b+ cells, IgG, Wild Type, rep2

description: Library name: IgG2


title: AMO-WT-2h-melflufen-0.5-biol rep 1


title: Endothelail Contact Coculture Rep1

description: Library name: CC1

value: Contact Coculture


title: X18: BDE-209 eposure rep2

value: 500 mg/ks/day


title: X53: Control rep1


title: Lung CD140b+ cells, IgG, Wild Type, rep1

description: Library name: IgG1


title: Endothelial No-contact Coculture Rep3

description: Library name: NC3


title: Endothelial Monolayer Rep1

description: Library name: EC1

value: Monolayer


title: Lung CD140b+ cells, FOXF2, Wild Type, rep2

description: Library name: FOXF2_2


title: AMO-WT-2h-DMSO-biol rep 1

value: WT

value: DMSO control


title: Sarfeher1

description: Library name: 226-SF1-K

value: leaf of the in vitro plantlet


title: CPC_QPRT_3

first: Yuning

address: No. 603 Huangpu Avenue, Tianhe District, Guangzhou City, Guangdong Province

department: State Key Laboratory of Bioactive Molecules and Druggability Assessment

institute: Jinan University

description:
Library name: Sample6
All_sample_FPKM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: Colorectal cancer

growth_protocol: Cancer pericyte cells were maintained in PM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1.5 μg of total RNA was used for the construction of sequencing libraries
CLC Genomics Workbench v20.0.4

treatment_protocol: For QPRT overexpression, human cancer pericyte cells were transfected when reaching 70-80% confluency: cells were divided into two groups (control group: empty vector-transfected; experimental group: QPRT-overexpression plasmid-transfected) using Lipofectamine 3000 reagent (Invitrogen) following the manufacturer’s instructions. Transfected cells were cultured for 4 days (logarithmic growth phase) before subsequent experiments (designated as the sampling time point)

value: Colorectal cancer

value: cancer pericyte cell

value: stromal cell

value: QPRT overexpresion

tag: batch


title: Endothelial Monolayer Rep3

description: Library name: EC3

value: Human coronary artery endothelial cells


title: X56: Control rep2

value: Sprague-Dawley (SD)


title: Lung CD140b+ cells, H3K4me2, KO, rep1

description: Library name: KO1

value: Lung

value: Sorted CD140b+ cells


title: Kadarka

description: Library name: 225-KA-K


title: Endothelial Monolayer Rep2

description: Library name: EC2


title: CPC_QPRT_2

description:
Library name: Sample5
All_sample_FPKM.txt


title: Kékfrankos

description: Library name: 228-KF-K


title: GSK1

city: Chengdu, Cihna

first: Xiangmeng

last: Luo

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
Library name: GSK1
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

data_processing:
The RNA-seq reads were aligned to the mouse reference genome (GRCm39) using STAR (v2.7.9a).
Assembly: GRCm39
Supplementary files format and content: csv

source_name: SCLC

value: SCLC


title: Lung CD140b+ cells, H3K4me2, Ctrl, rep2

description: Library name: Ctrl2


title: Endothelial No-contact Coculture Rep2

description: Library name: NC2

value: No-contact Coculture


title: X72: Control rep4

value: placenta

value: 0 mg/ks/day


title: AMO-WT-2h-DMSO-biol rep 3

value: plasma cell, myeloma

value: 2 h


title: 3_Acute_postAC

city: Los Angeles

first: Xiuju

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

description: Library name: 3_Acute_postAC

data_processing:
The demultiplexing and gene counting were performed using Cell Ranger software v7.2.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cells adhering to the acupuncture needles

extract_protocol:
Tissues were placed in tissue collection buffer immediately after collection and snap frozen in dry ice. For nuclei isolation, tissues were thawed in 500 μL homogenization buffer and incubated at room temperature with gentle rotation for 5 minutes. Samples were then transferred to ice to cool rapidly, then were homogenized to harvest the nuclei. Nuclei concentration was determined using the Countess II Automated Cell Counter (Thermo Fisher Scientific) with 0.4% Trypan Blue staining.
snRNA libraries were constructed according to the manufacturer's instructions (Chromium™ Single Cell 3’ Kit v3.1 protocol, 10x Genomics).


title: 2_Chronic_preAC

description: Library name: 2_Chronic_preAC

value: Cells adhering to the acupuncture needles


title: 2-Embryons-KO

city: Laval

first: Kessen

last: Patten

state: Quebec (QC)

address: 531, Boul des Prairies

department: Centre Armand-Frappier Santé Biotechnologie

institute: Institut National de la Recherche Scientifique

description: 10X Genomics

data_processing:
Fastqs were processed by CellRanger count version 6.1.2 using Danio rerio GRCz11 reference genome.
Filtered counts output from CellRanger are provided for each samples.
Assembly: GRCz11
Supplementary files format and content: barcodes.tsv.gz: cell barcodes
Supplementary files format and content: features.tsv.gz: genes detected
Supplementary files format and content: matrix.mtx.gz: cell by gene expression matrix

organism: Danio rerio

source_name: Head + eyes

extract_protocol:
Zebrafish larvae were euthanized with excess tricain. Heads were dissected and gently transferred into NbAct1 (Fisher # NC0319856) in 24 well-plates on ice. Tissues were washed 2 times in 1mL FACSmax (Genlantis #T200100) and incubated for 20min in FACSmax. Tissues were triturated (5 to 10 times) with 1mL tip to help physical dissociation, transferred into Eppendorf tubes and centrifuged at 500g for 5 min at 4°C. Pellet was washed with NbActiv1 medium, then passed through a 40 μm cell strainer (Corning), and centrifuge at 500g for 5 min at 4°C
Library was performed according to the manufacter’s instructions (single cell 3’, 10x Genomics). 10X-based libraries were acquired with the Chromium Single Cell V3.0 reagent kit following the manufacturer’s protocol (10X Genomics # 1000261, Cell Multiplexing Oligo Labeling).

value: Head + eyes

value: med22 knockout

tag: development stage

value: 4dpf (days-post-fertilisation)


title: SCLC2

description:
Library name: SCLC2
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).


title: SCLC1

description:
Library name: SCLC1
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).


title: Lung CD140b+ cells, H3K4me2, Ctrl, rep1

description: Library name: Ctrl1


title: MCF7-2h-2

city: Durham

first: Christopher

middle: R

last: Day

state: NC

address: 111 TW Alexander Dr.

department: ERBL

institute: NIH/NIEHS

data_processing:
Cell barcodes and UMI information was parsed for each read and filtered based on the parameters described in Hoffman et al., Commun Biol., 2020. Reads that were past this filtering step were aligned to hg19 using STAR version 2.5.2b. Unique read counts were assigned to genes using featureCounts v1.5.3.
Assembly: hg38
Supplementary files format and content: Raw counts matrix and meta data.

source_name: Cell Line

growth_protocol: MCF-7 cells (ATCC) were grown in MEM supplemented with 10% FBS (Sigma), 2mM Glutamine and 1X Pen/strep (Gibco).

extract_protocol:
Cells were induced with E2 for 2, 8, or 24h and single-cell suspensions were generated by dissociating cells using 0.25% Trypsin-EDTA (Gibco).
Single-cell emulsions were generated using the BioRad ddSeq Single-Cell Isolator and libraries were generated using the Illumina SureCell WTA 3′ Library Prep kit.

treatment_protocol: MCF7 cells were hormone depleted for 2d prior to treatment. Cells were then treated with 1nM E2 for 2, 8 or 24h.

value: Cell Line

value: ER+ Breast Cancer

value: 2h E2


title: AMO-WT-2h-DMSO-biol rep 2

value: WT

value: DMSO control


title: CPC_Vector_1

last: Lin

description:
Library name: Sample1
All_sample_FPKM.txt

value: Colorectal cancer

value: cancer pericyte cell

value: stromal cell

value: Vector


title: 1_Chronic_preAC

last: Wu

description: Library name: 1_Chronic_preAC


title: 4_Acute_preAC

description: Library name: 4_Acute_preAC


title: 4_Acute_postAC

description: Library name: 4_Acute_postAC


title: 1-Embryons-WT

description: 10X Genomics


title: GSK2

description:
Library name: GSK2
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

value: SCLC


title: MCF7-24h-2


title: 3_Acute_preAC

description: Library name: 3_Acute_preAC


title: MCF7-24h-1


title: CPC_QPRT_1

description:
Library name: Sample4
All_sample_FPKM.txt

value: QPRT overexpresion


title: GSK3

description:
Library name: GSK3
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).


title: human_rpe_mbr_rna_3

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: human_rpe_mbr_rna_3

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts

source_name: RPE

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

value: RPE

tag: lab

value: Skop


title: MCF7-8h-2

value: 8h E2


title: CPC_Vector_3

description:
Library name: Sample3
All_sample_FPKM.txt


title: MCF7-8h-1


title: 2_Chronic_postAC

description: Library name: 2_Chronic_postAC

value: Cells adhering to the acupuncture needles


title: MCF7-0h-1

value: 0h E2