title: RPMI8226, exp1, GFP-KRAS Low, R3

description: Library name: RPMI8226_GFP_KRAS_3L


title: GRKO, 6 months #3

status: Public on Aug 11 2026

type: SRA

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description: Library name: GRKO-6-3

library_source: transcriptomic

data_processing:
Kallisto 0.48.0 pseudo-mapping with k-mer=31, against Danio rerio Ensembl transcriptome
Assembly: GRCz11
Supplementary files format and content: tab-delimited file containing the raw counts for each transcript (Ensembl identifiers)

molecule: total RNA

organism: Danio rerio

source_name: ovary

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit.
NEB UltraExpress RNA Library Prep Kit (pol;y dT capture)

tag: tissue

value: ovary

tag: genotype

value: nr3c1 -/- Female

tag: treatment

value: 6 months post fertilisation


title: PDCs, Ctrl_TOP2B CUT&Tag, rep1

city: Shanghai

first: Chunlong

last: Zhong

state: Shanghai

address: 150 Jimo Road

department: Department of Neurosurgery

country: China

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: Ctrl_TOP2B, rep1

library_source: genomic

data_processing:
Raw sequence reads underwent initial quality control using FastQC (v0.20.0)
Clean reads were obtained by removing adapter sequences, poly-N stretches, and low-quality reads. Quality-filtered reads were then mapped to the reference genome using BWA (v0.7.12)
Peak calling was performed using MACS2 (v2.1.0). Peaks were adjusted to a uniform size (500 bp) centered on peak summits
Motif discovery within these loci was conducted using HOMER (v4.9.1) with the command: findMotifsGenome.pl -len 8,10,12,14 -gc -size given -homer2 -dumpFasta.
Genomic annotation and identification of the nearest genes associated with peaks were performed using ChIPseeker.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: patient-derived glioma cells

growth_protocol: PDCs were maintained in DMEM/F12 medium supplemented with B27 (1:50, Gibco, USA), basic fibroblast growth factor (bFGF, PeproTech, USA) at 25 ng/mL, epidermal growth factor (EGF, PeproTech, USA) at 50 ng/mL, 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin-streptomycin (Thermo, USA).

extract_protocol:
CUT&Tag was performed following previously established protocols using the CUT&Tag assay kit (Vazyme, TD904) (Kaya-Okur et al, 2019).
Approximately 1 × 105 PDCs were bound to ConA beads, followed by overnight incubation at 4°C with either a primary antibody or control IgG on a rotator. The next day, a secondary antibody was added and incubated for 60 minutes at room temperature, followed by pA/G-Tn5 transposome incubation and tagmentation in an activating buffer supplemented with magnesium. Adaptor-ligated DNA fragments were extracted and PCR-amplified using indexing primers (TD202, Vazyme). The amplified products were purified with VAHTS DNA Clean Beads (N411-01, Vazyme), and the DNA library's quantity and quality were assessed using a Qubit™ 4 Fluorometer and Bioanalyzer 2100 (Invitrogen). Libraries were sequenced on the Illumina platform by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), generating 150 bp paired-end reads.

treatment_protocol: 5 μM CX5461 treated for 24 hours

tag: cut&tag antibody

value: TOP2B(20549-1-AP, Proteintech)

tag: cell line

value: patient-derived glioma cells

tag: cell type

value: glioma cells

value: IDH/ATRX WT

value: DMSO


title: 1609 - Male WT

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

country: USA

institute: Indiana University

description: Library name: 1609

library_source: transcriptomic single cell

data_processing:
The sequencing data were processed using the Cell Ranger pipeline (v7.2.0, 10x Genomics) and aligned to the mouse reference genome GRCm38 (gex-mm10-2020-A)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz - cellranger output required for SoupX
Supplementary files format and content: raw_feature_bc_matrix.tar.gz - cellranger output required for SoupX
Supplementary files format and content: analysis.tar.gz - cellranger output required for SoupX

molecule: polyA RNA

organism: Mus musculus

source_name: Anterior cortex

extract_protocol:
Nuclei were isolated using the Singulator 100 system (S2 Genomics) as described before (DOI: 10.1101/2025.03.25.645306), with all steps performed on ice. Briefly, frozen tissue was processed in pre-chilled nucleus isolation cartridges with RNase inhibitor. The resulting nuclear suspension was pelleted by centrifugation, and the pellet was then purified through density gradient centrifugation using a 20% Nuclei Debris Removal Stock Solution in Nuclear Storage Reagent to remove myelin and other debris. Following a final wash and centrifugation step, the purified nuclei were resuspended in resuspension buffer (2% BSA in Nuclear Storage Reagent) for downstream applications.
Purified nuclei were stained with trypan blue and manually counted using a disposable hemocytometer (C-Chip, SKC, Inc., Covington, GA) under a 40x objective on an EVOS XL Core microscope. Each suspension was adjusted to 1,000 nuclei/μL and loaded onto a Chromium Chip G for GEM (gel bead-in-emulsion) generation and barcoding using the Chromium Controller (10x Genomics, Pleasanton, CA). Library preparation followed the manufacturer's protocol using the Chromium Next GEM Single Cell 3′ v3.1 Dual Index kit (10x Genomics) with SPRIselect magnetic bead purification (Beckman Coulter Life Sciences, Indianapolis, IN). cDNA and library integrity were evaluated using an Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA), and concentrations were measured using a Qubit Fluorometer with the dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Waltham, MA). Libraries were sequenced on an Illumina NovaSeq 6000 (v1.5 S2 flow cell) using a 28-10-10-91 read configuration.

value: Anterior cortex

tag: Sex

value: M

value: WT


title: RPMI8226, exp1, GFP-KRAS High, R3

city: Bethesda

first: Ryan

middle: M

last: Young

state: MD

address: 9000 Rockvill Pike, Bld. 10, rm. 6N105

department: LYMB

institute: NIH/NCI

description: Library name: RPMI8226_GFP_KRAS_3H

data_processing:
Demultiplexing was performed with DRAGEN (v3.7.4, Illumina), and sequencing reads were aligned to the reference sgRNA library using Bowtie2 (v2.2.9).
Assembly: hg19
Supplementary files format and content: Normalized readcounts for each sgRNA in the Brunello sgRNA library are found in KRAS-stability-norm-counts.txt
Library strategy: CRISPR Screen

source_name: multiple myeloma cell line

growth_protocol: XG7 and RPMI 8226 cells stably expressing Cas9(26) ectopically expressing mNG-KRASG12D were transduced in triplicate with the Brunello sgRNA library. Following transduction, cells were selected with 1 μg/mL puromycin, and Cas9 expression was induced by 100 ng/mL doxycycline treatment. Cells were expanded for 7 days, after which 5×10⁷ cells were harvested and stored as the baseline (input) sample. The remaining ~8×10⁷ cells were stained with anti-Lyt2 antibody (BioLegend) at a 1:1000 dilution in PBS supplemented with 0.5% FBS for 20 min on ice. Cells were washed, resuspended at ~2×10⁷ cells/mL in PBS with 0.5% FBS, and sorted on a Sony MA900 cell sorter to isolate the top and bottom 5% of mNG–KRAS-expressing populations, yielding ~2×10⁶ cells per fraction.  Each biological replicate was independently sorted in two technical replicates.

extract_protocol:
Genomic DNA from sorted populations was extracted using the QIAamp DNA FFPE Advanced Kit (QIAGEN) according to the manufacturer’s protocol.
Genomic DNA from CRISPR screens was processed using a nested PCR strategy. In the first round, sgRNA sequences were amplified from genomic DNA, followed by a second round of PCR to append Illumina-compatible sequencing adapters. Each PCR reaction was performed with ExTaq DNA polymerase (Takara) for 18–20 cycles per round. Amplified products were size-selected using a 2% E-Gel SizeSelect agarose gel (Invitrogen) and quantified with the Qubit dsDNA High-Sensitivity Assay (Thermo Fisher Scientific).

value: multiple myeloma cell line

value: Cas9 clone


title: PDCs, CX5461_ATRX CUT&Tag, rep3

description: Library name: CX5461_ATRX, rep3

value: ATRX (#14821, Cell Signaling)


title: GRKO, 3 months #13

description: Library name: GRKO-3-13

value: 3 months post fertilisation


title: RPMI8226, exp1, GFP-KRAS High, R2

description: Library name: RPMI8226_GFP_KRAS_2H


title: PDCs, CX5461_ATRX CUT&Tag, rep1

description: Library name: CX5461_ATRX, rep1


title: Neurons_DIV7_CHX_2: In-vitro differentiated neurons at DIV-7, cycloheximide treated, biological replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description:
CONTROL_vs_CHX.diff.ME.microexons.FULL.tab
CONTROL_vs_CHX.diff.ME.microexons.ALT_filter.tab

data_processing:
Alternative splicing analysis of RNA-Seq data from Qk knockdown experiments was performed with vast-tools version 2.5.1 (Tapial et al., 2017). From the primary output, the set of mouse neural-high microexons were filtered for coverage (quality score 1 of VLOW or higher) and junction balance (quality score 4 of OK/B1/B2/Bn). Differential AS was scored using vast-tool’s diff module requiring MV.dPsi._at_0.95 > 0 and a point estimate of |dPSI| > 10. Quantification of microexons in RNA-seq data obtained for CHX experiments was performed using MicroExonator (Parada et al., 2021) and Whippet (Sterne-Weiler et al., 2018), defining microexons with |DeltaPsi|>0.1 and Probability>0.9 as differential AS.
Assembly: mm10
Supplementary files format and content: All files are in tab-delimited or comma-delimited format. For the Qk knockdown experiment, “INCLUSION_LEVELS_FULL-mm10-6.tab” contains the raw vast-tools output showing the percent spliced in (PSI) values for each splicing events across samples. "INCLUSION_QkReg_N2A_226_NeuralMics.csv" contains a list of 226 neural microexons that passed coverage filtering, together with its change in splicing (dPSI) upon Qk knockdown, and a column indicating whether there is a presence of the Qk consensus motif (ACTAAY) within 150nt of its proximal introns. For the Cylcloheximide treatment , CONTROL_vs_CHX.diff.ME.microexons.FULL.tab contains the raw MicroExonator/Whippet output showing mean PSI values for treatment and controls. CONTROL_vs_CHX.diff.ME.microexons.ALT_filter.tab contain a list of 232 microexons that were found to be differentially spliced.

source_name: In-vitro differentiated glutamatergic neurons

growth_protocol: Mouse neuroblastoma (N2A) cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin. In-vitro differentiation of glutamatergic neurons from mouse embryonic stem cells was performed according to Gonatopoulos-Pournatzis et al., 2020 (PMID: 31999954). Neurons at 7 days in vitro (DIV-7) were treated with or without cycloheximide. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on-column DNase digestion, as recommended by the manufacturer.
1000 ng total RNA per sample was used in the library preparation. To obtain larger insert size (540 nt on average after size selection), Illumina’s TruSeq Stranded mRNA sample preparation protocol was modified as follows: 1) fragmentation time and temperature was reduced from 8 minutes at 98°C to 2 minutes at 80°C. Average size distribution prior to library preparation was 232 nt versus 740 nt, respectively; 2) after the final library was generated, the samples were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100 V. The libraries were size selected between 400 and 600 bp. Excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). The rest of the protocol was adapted as described in Illumina’s TruSeq Stranded mRNA sample preparation guide (Part# 15031047 Rev. E, Illumina).

treatment_protocol: For siRNA knockdown and rescue experiments, N2A cells were transfected with 40nM of siGENOME siRNA pools (Dharmacon) targeting mouse Qk, or a non-targeting (siNT) siRNA pool (D-001206-13), using Lipofectamine RNAiMax (Thermo Scientific) as recommended by the manufacturer. Cells were seeded at 100,000 cells per well in 12-well plates, reverse transfected, and total RNA was harvested 72 hours post transfection. In-vitro differentiated mouse glutamatergic neurons at DIV-7 were treated with 100uM cycloheximide (CHX) for 12 hours, after which total RNA was harvested.

value: Cycloheximide treated


title: RPMI8226, exp1, GFP-KRAS LOW, R2

description: Library name: RPMI8226_GFP_KRAS_2L


title: GRKO, 3 months #10

description: Library name: GRKO-3-10


title: 1608 - Male WT

description: Library name: 1608


title: PDCs, CX5461_ATRX CUT&Tag, rep2

description: Library name: CX5461_ATRX, rep2


title: Neurons_DIV7_CHX_1: In-vitro differentiated neurons at DIV-7, cycloheximide treated, biological replicate 1

value: In-vitro differentiated glutamatergic neurons


title: RPMI8226, exp1, GFP-KRAS Low, R1

description: Library name: RPMI8226_GFP_KRAS_1L


title: mousePDAC iKras, mRNAseq, +DOX, rep1

city: Houston

first: Ronald

middle: J

last: Parchem

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files were downloaded from Basespace.
Trimmed, high quality reads were mapped to Mmusculus (GRCm39)  or Hsapien (GRCh38) using STAR (v2.7.9a)
In R (v4.1.1), raw data was corrected for batch effect (if present) using ComBat in sva. Gene count matrices were built with GenomicAlignments tool (v1.28).
Count normalization and differential gene expression was performed using DESeq2 (3.14)
Assembly: GRCm39 or GRCh38
Supplementary files format and content: comma-separated text files include normalized counts for each sample

source_name: mouse PDAC iKRAS

growth_protocol: Cells were seeded in 6 well plates in DMEM/F12 with 10% bovine serum albumin (BSA) in a humidified incubator at 37C at 5% CO2.

extract_protocol:
mRNA: Cells were lysed and RNA was harvested directly into TRIzol and purfied using a RNEasy miniprep spin kit. RNA was eluted into RNAse free water. TSA: cells were fixed, TSA protocol was carried out (see publication). Biotinylated RNA was enriched and isolated in TRIzol.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strandsynthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. 3’ ends of fragments were adenylated and Adaptor with hairpin loop structure were ligated. Library fragments (~370-420 bp) were purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were harvested when at 80% confluency.

value: mouse PDAC iKRAS

value: mouse pancreatic cancer cell line


title: RPMI8226, exp1, GFP-KRAS High, R1

description: Library name: RPMI8226_GFP_KRAS_1H


title: PDCs, Ctrl_ATRX CUT&Tag, rep3

description: Library name: Ctrl_ATRX, rep3

value: ATRX (#14820, Cell Signaling)


title: Neurons_DIV7_CTRL_1: In-vitro differentiated neurons at DIV-7, untreated control, biological replicate 1

value: Untreated control


title: GRKO, 3 months #4

description: Library name: GRKO-3-4

value: ovary

value: WT- Female


title: GRKO, 3 months #7

description: Library name: GRKO-3-7

value: nr3c1 -/- Female


title: XG7, exp2, GFP-KRAS, input 3, match to R5, R6

description: Library name: XG7_exp2_GFP_KRAS_R3


title: PDCs, Ctrl_ATRX CUT&Tag, rep1

description: Library name: Ctrl_ATRX, rep1

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT

value: DMSO


title: N2A_siQk_3: N2A, Qk knockdown, biological replicate 3

description:
INCLUSION_LEVELS_FULL-mm10-6.tab
INCLUSION_QkReg_N2A_226_NeuralMics.csv

source_name: Neuro-2a (N2A)

value: Neuro-2a (N2A)

value: Mouse neuroblastoma

value: Qk knockdown; transfected with siRNA against Qk


title: WT, 6 months #9

description: Library name: WT-6-9-F

value: 6 months post fertilisation


title: XG7, exp2, GFP-KRAS, input 2, match to R3, R4

description: Library name: XG7_exp2_GFP_KRAS_R2

value: multiple myeloma cell line

value: Cas9 clone


title: XG7, exp2, GFP-KRAS, input 1, match to R1, R2

description: Library name: XG7_exp2_GFP_KRAS_R1


title: rABS+shAPE1-3

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

description: Library name: A-3

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality nucleotides using Trimmomatic v0.36. The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome available from Ensembl using STAR v2.5.2b. Unique gene-level read counts were generated using featureCounts from the Subread package v1.5.2. Counts were summarized using the gene_id feature in the annotation file, and only uniquely mapped reads falling within annotated exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: The processed data file, rABS_RNAseq_Genewiz_2025_12samples_count_matrix.tsv.gz, is a gzip-compressed, tab-delimited gene-level raw-count matrix. Rows represent genes identified by Ensembl gene_id identifiers, columns represent the 12 biological samples, and values are unnormalized integer read counts.

source_name: esophageal adenocarcinoma (EAC)

growth_protocol: OE33 cells were cultured RPMI1640 supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Standard RNA-sequencing (mRNA-Seq) in eukaryotic samples: Polyadenylated mRNA is selectively enriched from total RNA using oligo(dT) magnetic beads. High-temperature thermal treatment in divalent cation buffer fragments the mRNA to ~250–300 bp.

treatment_protocol: human EAC cells (OE33) were exposed to an acidified bile salt cocktail (200 µM, pH 5.5) for 20 minutes daily over 15 days (rABS), while untreated parental cells served as baseline controls. Following the 15-day selection protocol, the surviving rABS-adapted OE33 cells were stably transduced with either a non-targeting control shRNA (shCtrl) or an APE1-targeted shRNA (shAPE1).

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: repeated ABS with shAPE1


title: N2A_siQk_2: N2A, Qk knockdown, biological replicate 2


title: WT, 6 months #8

description: Library name: WT-6-8-F


title: XG7, exp2, GFP-KRAS Low, R6

description: Library name: XG7_exp2_GFP_KRAS_6L


title: XG7, exp2, GFP-KRAS High, R6

description: Library name: XG7_exp2_GFP_KRAS_6H


title: rABS+shAPE1-1

description: Library name: A-1


title: WT, 6 months #6

description: Library name: WT-6-6-F


title: WT, 6 months #7

description: Library name: WT-6-7-F


title: rABS+shCtrl-3

description: Library name: Ctrl-3

value: repeated ABS with shCtrl


title: rABS+shCtrl-2

description: Library name: Ctrl-2


title: WT, 6 months #2

description: Library name: WT-6-2-F

value: ovary


title: XG7, exp2, GFP-KRAS High, R5

description: Library name: XG7_exp2_GFP_KRAS_5H


title: XG7, exp2, GFP-KRAS Low, R5

description: Library name: XG7_exp2_GFP_KRAS_5L


title: WT, 6 months #1

description: Library name: WT-6-1-F

value: WT- Female


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H10

status: Public on Aug 12 2026

city: Princeton

first: Bruce

last: Wang

address: Carl Icahn Lab

institute: Princeton University

description:
Library name: delta_del_160_library_3_H10
M3-Seq

data_processing:
The demultiplexing, alignment, data processing, were performed from the raw basecalls using custom scripts here: https://github.com/brwaang55/m3seq_scripts. Raw basecall files were converted into bam files, which were demultiplexed for the data here.
The data files here were then aligned to a combined Pa011 and PaMx41 genome, and processed using M3-Seq scripts
Assembly: Pseu_aeru_BWH011_V1, ASM275751v1
Supplementary files format and content: Single-cell matrices (csv).

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: Cells were grown in LB culture until OD=0.3.

extract_protocol: Libraries were constructed following the M3-Seq protocol.

treatment_protocol: At OD=0.3, cells were infected with PaMx41 Deltaacb2 at an MOI=2.

value: Bacterial cells

value: Pa011 DeltaCBASS

value: Phage infected


title: XG7, exp2, GFP-KRAS Low, R4

description: Library name: XG7_exp2_GFP_KRAS_4L


title: AJ12_S1pr1KO_primary tumors

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Raw data was filtered by CD Genomics.
StringTie software was used to assembly transcript for RNA-Seq
ASprofile was used to compare alternative splicing (AS) events
FPKM was used to estimate gene expression levels. This method considers both sequencing depth and gene length on counting of fragments
The readcount from Gene Expression Analysis was used to determine the differential expression analysis
Assembly: Mus Musculus(GRCm39/mm39)
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes fpkm values for each sample

source_name: Tumors

extract_protocol:
Total RNA was extracted from the primary tumors using QIAzol Lysis Reagent (Qiagen, Cat No./ID: 79306) and processed as per the manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols from CD Genomics

treatment_protocol: After the mice were sacrificed, the primary tumors were collected and immediately placed in RNAlater stabilization solution (ThermoFisher Scientific, cat# AM7021) and placed at 4 degrees Celsius for 24 hours before storing at -80 degrees Celsius.

value: Tumors

tag: strain

value: MMTV-Cre;S1pr1fl/fl; MMTV-PyMT

tag: time

value: 4.5 months

value: Primary Tumors


title: WT, 3 months #2

description: Library name: WT-3-2-F

value: 3 months post fertilisation


title: XG7, exp2, GFP-KRAS High, R4

description: Library name: XG7_exp2_GFP_KRAS_4H


title: rABS-3

description: Library name: R-3

value: repeated ABS


title: AJ11_S1pr1KO_primary tumors


title: rABS-2

description: Library name: R-2


title: XG7, exp2, GFP-KRAS Low, R3

description: Library name: XG7_exp2_GFP_KRAS_3L

value: multiple myeloma cell line


title: AJ10_S1pr1KO_primary tumors


title: WT, 3 months #12

description: Library name: WT-3-12-F


title: rABS-1

description: Library name: R-1


title: XG7, exp2, GFP-KRAS High, R3

description: Library name: XG7_exp2_GFP_KRAS_3H

value: Cas9 clone


title: AJ9_S1pr1KO_primary tumors


title: WT, 3 months #10

description: Library name: WT-3-10-F


title: Parental-3

description: Library name: 7-3

value: esophageal adenocarcinoma (EAC)

value: Parental untreated


title: XG7, exp2, GFP-KRAS LOW, R2

description: Library name: XG7_exp2_GFP_KRAS_2L


title: WT, 3 months #6

description: Library name: WT-3-6-F


title: Parental-2

description: Library name: 7-2

value: Epithelial


title: XG7, exp2, GFP-KRAS High, R2

description: Library name: XG7_exp2_GFP_KRAS_2H


title: AJ7_C3_KO_primary tumors


title: Linf_CCL20_13

type: RNA

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

description: Gene expression data

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Human Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven. Arrays were washed and stained in an Affymetrix Fluidics Station 450 according to Affymettix protocol.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and signal intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher Scientific).

data_processing: Array data quality analysis, normalization (RMA+DAGB) and statistical tests for differential expression (eBayes) were carried out with the Transcriptome Analysis Console software (TAC 4.0.1)

label: Biotin

label_protocol: labelled cRNAwas prepared according to the GeneChip Whole Transcript Expression Arrays protocol (Affymetrix, Thermo Fisher Scientific)

extract_protocol:
PBMC Isolation Method: Ficoll-Paque density gradient
T Lymphocyte Isolation: Magnetic separation (Anti-CD3)
RNeasy® Mini kit

value: Masc

tag: age (years)

tag: health status

value: Healthy

value: Whole Blood - PBMC


title: XG7, exp2, GFP-KRAS Low, R1

description: Library name: XG7_exp2_GFP_KRAS_1L


title: AJ6_C3_KO_primary tumors


title: Linf_IL8_13

description: Gene expression data


title: Old 3,

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

description:
Library name: vc13, N1
FFPE sections
vc13, N1

data_processing:
Samples were processed by Cutadapt (v2.7; --quality-cutoff=15,10 --minimum-length=36), FastQC (v0.11.4), and STAR (v2.5.2b; --quantMode TranscriptomeSAM --outWigType bedGraph --outWigNorm RPM) to do the trimming, QC report and human genome mapping (hg38). Then, human gene expressions in basal ganglia regions was calculated by featureCounts (-p -T 4 -Q 10) based on human GENCODE v27 gene annotation. Removal of unwanted variations (RUV) correction of RNA-seq data was performed by following the manual of the RUVSeq package. Residuals were first calculated using RUVSeq in a general linear regression model, and the removal of unwanted variations by residuals was performed using the RUVr function to produce adjusted gene expression. Differentially expressed genes (DEGs) between young and old were identified by EdgeR with the cutoffs of FoldChange > 1.5 and adjusted p < 0.01.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes CPM for each sample

source_name: cortex

extract_protocol:
Qiagen FFPE Rneasy extraction kit
Sigma Seqplex for FFPE treated samples

tag: disease

value: non-diseased

tag: age

value: 91 yr

value: cortex


title: 1626 - Female 5XFAD

description: Library name: 1626

value: Anterior cortex

value: F


title: XG7, exp2, GFP-KRAS High, R1

description: Library name: XG7_exp2_GFP_KRAS_1H


title: PDCs, CX5461_TOP2B CUT&Tag, rep2

description: Library name: CX5461_TOP2B, rep2

value: TOP2B(20549-2-AP, Proteintech)

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT


title: AJ5_C3_KO_primary tumors

value: Tumors

value: 4.5 months

value: Primary Tumors


title: AJ8_C3_KO_primary tumors


title: Linf_IL32_CCL20_13

description: Gene expression data


title: XG7, exp1, GFP-KRAS, input 3, match to R5, R6

description: Library name: XG7_exp1_GFP_KRAS_R3

value: multiple myeloma cell line

value: Cas9 clone


title: Old 2,

description:
Library name: vc15,  N1
FFPE sections
vc15,  N1

value: 84 yr


title: AJ4_WT_primary tumors

value: MMTV-PyMT

value: WT


title: XG7, exp1, GFP-KRAS, input 2, match to R3, R4

description: Library name: XG7_exp1_GFP_KRAS_R2


title: AJ3_WT_primary tumors


title: Old 1,

description:
Library name: vc6,  N1
FFPE sections
vc6,  N1

value: non-diseased

value: 83 yr


title: Linf_IL32_IL8_13

description: Gene expression data

value: Masc

value: Healthy

value: Whole Blood - PBMC


title: Linf_IL32_13

description: Gene expression data


title: GRKO, 3 months #12

description: Library name: GRKO-3-12

value: ovary

value: nr3c1 -/- Female

value: 3 months post fertilisation


title: GRKO, 3 months #9

description: Library name: GRKO-3-9


title: Parental-1

description: Library name: 7-1

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: Parental untreated


title: Young 3,

description:
Library name: vc2,  N1
FFPE sections
vc2,  N1

value: 19 yr

value: cortex


title: XG7, exp1, GFP-KRAS, input 1, match to R1, R2

description: Library name: XG7_exp1_GFP_KRAS_R1

value: multiple myeloma cell line

value: Cas9 clone


title: AJ2_WT_primary tumors

value: Tumors

value: MMTV-PyMT

value: 4.5 months

value: Primary Tumors


title: Linf_IL15_IL8_13

description: Gene expression data

value: Masc


title: Neurons_DIV7_CTRL_2: In-vitro differentiated neurons at DIV-7, untreated control, biological replicate 2

value: In-vitro differentiated glutamatergic neurons

value: Untreated control


title: XG7, exp1, GFP-KRAS Low, R6

description: Library name: XG7_exp1_GFP_KRAS_6L


title: Young 2,

description:
Library name: vc1,  N1
FFPE sections
vc1,  N1

value: non-diseased

value: 11 yr


title: AJ1_WT_primary tumors

value: WT


title: PDCs, Ctrl_ATRX CUT&Tag, rep2

description: Library name: Ctrl_ATRX, rep2

value: ATRX (#14820, Cell Signaling)

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT

value: DMSO


title: Linf_IL15_CCL20_13

description: Gene expression data

value: Healthy

value: Whole Blood - PBMC


title: Young 1,

description:
Library name: vc3, N1
FFPE sections
vc3, N1

value: 9 yr

value: cortex


title: XG7, exp1, GFP-KRAS High, R6

description: Library name: XG7_exp1_GFP_KRAS_6H

value: multiple myeloma cell line

value: Cas9 clone


title: Control and SNAP single-cell RNA-seq

city: Tainan

first: Li

last: Chung Yen

state: Please Select

address: No.1, University Road, Tainan City 701, Taiwan (R.O.C)

country: Taiwan

institute: NCKU

description:
Sample_Tag 4 = Control
Sample_Tag 6 = SNAP
BD Rhapsody

data_processing:
Platform: Seven Bridges Genomic
Process: BD Rhasody WTA Analysis Pipeline
Assembly: GRCm38, gencode M19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: immune cell

extract_protocol:
Control (Sample tag 4) sequencing: TTAACCGAGGCGTGAGTTTGGAGCGTACCGGCTTTGCGCAGGGCT
SNAP (Sample tag 6) sequencing: GCGGGCACAGCGGCTAGGGTGTTCCGGGTGGACCATGGTTCAGGC
Tumor tissues from LL2 tumor-bearing mice were cut into 2-mm pieces, and tumor tissues were prepared into a single-cell suspension with collagenase A (1 mg/kg) and type I DNase (100 U/ml). Next, red blood cells were removed with red blood cell lysis buffer, and the single-cell suspensions were resuspended in flow staining buffer. Finally, the cells were treated with an Fc blocker to reduce the nonspecific binding of the Fc receptor and antibodies. The cells were labeled with BDTM Abseq Ab-logos (CD4 and CD8; Cat. No: 940108 and Cat. No: 940345), BDTM sample tag (Cat. No: 633793), and rat anti-mouse BV510-CD45 (Cat. No: 563891; BD Pharmingen) and 7-AAD (Cat. No: 51-65875X; BD Pharmingen). A total of 5 x 105 live immune cells (CD45+ 7-AAD-) were sorted and resuspended in sample buffer for single-cell capture. Live CD45+ immune cells were captured using a BD RhapsodyTM system and lysed.
Briefly, cells (10,000 cells/group) were loaded into a cartridge, which had 200,000 wells for cell loading. Then, the cell-capture beads, which carried three different single-stranded DNA fragments to bind the DNA fragments of the sample tag, Abseq Ab-logos, and mRNA, were loaded into the well for cell binding. Nonbinding beads remained on the cartridge after washing with buffer. The cells captured by one bead were lysed, and mRNA was converted into cDNA by a RhapsodyTM cDNA Kit (Cat. No. 633773; BD Pharmingen). Three libraries were established: a sample tag library, an Abseq library, and a whole transcriptome analysis (WTA) library. Briefly, a sample tag library was used to distinguish different samples. The Abseq library could easily identify specific immune cells for transcriptome analysis. The WTA library was used for gene expression analysis.

value: tumor

value: immune cell

value: 8-10 weeks old

value: multiplexed sample:control and SNAP


title: Linf_IL15_13

description: Gene expression data

value: Masc


title: XG7, exp1, GFP-KRAS Low, R5

description: Library name: XG7_exp1_GFP_KRAS_5L


title: RNA-seq in D4_Setd5sh_3rd

city: hefei

first: wenxian

last: wang

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

description:
Library name: Sample28
Column name in allsamples_raw_counts.xls: D4_Setd5sh_3rd

data_processing:
RNA-Seq data were trimmed by Fastp to remove adapters, low-quality bases (Q < 20), and reads shorter than 75 bp.
Trimmed data were aligned to the mm10 reference genome using Hisat2. The aligned reads were sorted and indexed using SAMtools.
HTSeq-count was used to generate count matrices for each sample. We used the DESeq2 in R package to analyze gene expression with count matrices as input.
Assembly: mm10
Supplementary files format and content: raw counts and FPKM values

source_name: Differentiated motor neuron progenitor

growth_protocol: C57BL/6 mouse embryonic stem cells (mESCs) were cultured on a monolayer of Mitomycin-C–treated mouse embryonic fibroblasts in Knockout DMEM medium supplemented with 10% fetal bovine serum, 5% Knockout serum replacement , 100 U/ml penicillin-streptomycin solution, 2 mM L-glutamax, 1X MEM non-essential amino acid solution, 0.1 mM β-mercaptoethanol and 1000 U/ml leukemia inhibitory factor.

extract_protocol:
For RNA-seq, total RNA was extracted in  TRIzol and mRNA was purified for library construction using poly-T oligo-attached magnetic beads.
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Prime and lastly PCR products were purified.

treatment_protocol: mESCs were dissociated with 0.25% trypsin into single cell suspension at 2.5x104 cells/ml in ADFNK medium (Advanced DMEM/F12:Neurobasal (1:1) medium, 10% Knockout Serum Replacement, 100 U/ml penicillin-streptomycin solution, 2 mM L-glutamax, 1X MEM non-essential amino acid solution and 0.1 mM β-mercaptoethanol). Then 20μl of cell mixture (500 cells) was seeded onto the cover of petri dish to initiate formation of embryoid bodies (EBs) (D0: day 0). Two days later (D2: day 2), EBs were harvested and plated into differentiation medium (ADFNK medium supplemented with 1 μM all-trans retinoic acid (RA, Sigma) and 0.5μM Sonic Hedgehog Agonist (SAG, Selleck) for caudalization and ventralization. Culture Medium was then changed at D3 (day 3).   1μg/mL Doxycycline was treated 36 hours earlier and pMNs were harvested at D4 (Day 4).

value: Differentiated motor neuron progenitor

value: WT

tag: differentiation stage_and_treatment


title: BHT101 cells,overexpression,SETDB2

city: Dalian

first: yuesheng

last: lv

address: Lianhe Road

department: Τhe First Affiliated Hospital of Dalian Medical University

institute: Department of General Surgery

description: Library name: sample 2

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 on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Txt file includes raw counts for each Sample
Supplementary files format and content: Txt file includes FPKM values for each Sample

source_name: thyroid

growth_protocol: BHT101 cells were maintained at standard culture conditions (37°C, 5% CO2) in DMEM medium with 20% FBS and sodium pyruvate.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thyroid

value: thyroid cancer cells


title: N2A_siQk_1: N2A, Qk knockdown, biological replicate 1

value: Neuro-2a (N2A)

value: Mouse neuroblastoma

value: Qk knockdown; transfected with siRNA against Qk


title: rABS+shAPE1-2

description: Library name: A-2

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: repeated ABS with shAPE1


title: Linf_Control_13

description: Gene expression data

source_name: Control

value: Healthy

value: Whole Blood - PBMC


title: BHT101 cells,overexpression,Control

description: Library name: sample 1


title: XG7, exp1, GFP-KRAS High, R5

description: Library name: XG7_exp1_GFP_KRAS_5H

value: multiple myeloma cell line

value: Cas9 clone


title: RNA-seq in D4_Setd5sh_2nd

description:
Library name: Sample27
Column name in allsamples_raw_counts.xls: D4_Setd5sh_2nd


title: N2A_siNT_3: N2A, siNT-control, biological replicate 3

value: NT-control; transfected with non-targeting siRNA


title: Linf_CCL20_12

description: Gene expression data

value: Fem


title: XG7, exp1, GFP-KRAS Low, R4

description: Library name: XG7_exp1_GFP_KRAS_4L


title: Sample23

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

description:
Library name: Batch 22
10x Genomics and Singular G4

data_processing:
FASTQ files from all batches were aligned independently using 10x Genomics Cell Ranger v8.0.1 to the reference genome GRCh38-2024-A. For Batch 1, samples were demultiplexed with the following key: anti-humanHashTag7--LNH-94-2M2-TSB = Sample02, anti-humanHashTag9--LNH-94-2M2-TSB = Sample03, and anti-humanHashTag10--LNH-94-2M2-TSB = Sample04.
Assembly: GRCh38-2024-A
Supplementary files format and content: raw and filtered .h5 cellranger outputs

source_name: Tumor

extract_protocol:
FASTQ files from all batches were aligned independently using 10x Genomics Cell Ranger v8.0.1 to the reference genome GRCh38-2024-A. For Batch 1, samples were demultiplexed with the following key: anti-humanHashTag7--LNH-94-2M2-TSB = Sample02, anti-humanHashTag9--LNH-94-2M2-TSB = Sample03, and anti-humanHashTag10--LNH-94-2M2-TSB = Sample04.
All library preparations were performed using 10x Genomics protocols. If cryopreserved, cells were thawed, dead cell removal was performed and cells were counted. Once optimal concentration was achieved, we proceeded with library preparation and sequencing using standard 10x Genomics protocols per chemistry.

value: Tumor

tag: batch

value: Batch 22


title: RNA-seq in D4_Setd5sh_1st

description:
Library name: Sample26
Column name in allsamples_raw_counts.xls: D4_Setd5sh_1st

value: Differentiated motor neuron progenitor

value: WT


title: XG7, exp1, GFP-KRAS High, R4

description: Library name: XG7_exp1_GFP_KRAS_4H


title: RNA-seq in D4_control_3rd

description:
Library name: Sample25
Column name in allsamples_raw_counts.xls: D4_control_3rd


title: Linf_IL8_12

description: Gene expression data


title: Sample22

description:
Library name: Batch 21
10x Genomics and Singular G4

value: Batch 21


title: N2A_siNT_1: N2A, siNT-control, biological replicate 1

value: Neuro-2a (N2A)


title: Sample21

description:
Library name: Batch 19_2
10x Genomics and Singular G4

value: Batch 19_2


title: Linf_IL32_CCL20_12

description: Gene expression data


title: N2A_siNT_2: N2A, siNT-control, biological replicate 2

value: Mouse neuroblastoma


title: Quiescent MuSC H4K20me1 biol rep1

city: Madison

first: Jeonghye

middle: Hannah

last: Hwang

state: Wisconsin

address: 1111 Highland ave.

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: Library name: Q1_H4K20me1

data_processing:
Paired-end raw FASTQ reads were trimmed for adapter sequences and low-quality bases using Trim Galore (v0.6.10) with default parameters.
Trimmed reads were aligned to the mouse reference genome using Bowtie2 (v2.5.4) with the --very-sensitive preset. Alignment parameters were set to --no-mixed --no-discordant -X 1000 for high-confidence paired-end mapping and a maximum fragment length of 1000 bp.
Initial alignments were converted to BAM format and sorted using Samtools (v1.22.1).  Duplicates were identified and removed using Picard Tools (v3.4.0) MarkDuplicates.
Reads overlapping with ENCODE blacklist regions (ENCFF547MET) were removed using bedtools (v2.31.1) intersect. Only propery paired (-f 2) reads with a mapping quiality (MAPQ) score greater than 30 were kept. Reads mapping to the mitochondrial genome were excluded.
The filtered BAM files were converted to bigWig format using deepTools (v3.5.6) bamCoverage. The genome was binned into 10 bp windows, and signal intensity was RPKM normalized. A smoothing window of 30 bp was applied (--smoothLength 30) to reduce local noise.
Assembly: mm10
Supplementary files format and content: bigWig,  RPKM-normalized signal tracks for genome browser visualization
Library strategy: CUT&Tag

source_name: skeletal muscle

extract_protocol:
Freshly isolated MuSCs were bound to Concanavalin A magnetic beads and permeabilized. Cells were incubated overnight at 4 °C with primary antibodies, followed by secondary antibody incubation and binding of protein A–Tn5 transposase preloaded with sequencing adapters. Targeted tagmentation was performed at 37 °C in the presence of MgCl₂. DNA fragments were released by SDS and proteinase K treatment and purified by phenol–chloroform extraction followed by ethanol precipitation.
CUT&Tag DNA fragments were PCR-amplified using indexed i5 and i7 primers and NEBNext HiFi 2× PCR Master Mix. The number of amplification cycles was determined by qPCR to minimize PCR duplicates. Libraries were quantified using the Qubit dsDNA High Sensitivity Assay and fragment size distribution was assessed using an Agilent Bioanalyzer High Sensitivity DNA kit.

treatment_protocol: Muscle stem cells (MuSCs) were isolated from mouse skeletal muscle under quiescent or activated conditions. Quiescent MuSCs were freshly isolated from non-injured muscle, whereas activated MuSCs were isolated 2 days post-injury (2 dpi) following BaCl₂ injection into the tibialis anterior (TA) muscle. For conditional knockout samples, Kmt5a deletion was induced in adult mice using a tamoxifen-inducible Cre recombinase system prior to MuSC isolation. Cells were immediately processed for CUT&Tag.

value: skeletal muscle

value: muscle stem cell


title: RNA-seq in D4_control_2nd

description:
Library name: Sample24
Column name in allsamples_raw_counts.xls: D4_control_2nd


title: XG7, exp1, GFP-KRAS Low, R3

description: Library name: XG7_exp1_GFP_KRAS_3L


title: Linf_IL32_IL8_12

description: Gene expression data


title: XG7, exp1, GFP-KRAS High, R3

description: Library name: XG7_exp1_GFP_KRAS_3H


title: RNA-seq in D4_control_1st

description:
Library name: Sample23
Column name in allsamples_raw_counts.xls: D4_control_1st


title: Sample20

description:
Library name: Batch 20
10x Genomics and Singular G4

value: Batch 20


title: Linf_IL32_12

description: Gene expression data

value: Healthy


title: XG7, exp1, GFP-KRAS LOW, R2

description: Library name: XG7_exp1_GFP_KRAS_2L


title: Sample19

description:
Library name: Batch 19_1
10x Genomics and Singular G4

value: Batch 19_1


title: Young mice, Repeat 5

city: Guangzhou

first: Shixiang

middle: Clover

state: Guangdong

address: Guanzhou street

institute: Guangzhou national labratory

description: Library name: SAMN62238719

data_processing:
Illumina Casava1.7 software was used for basecalling.
Assembly: Reads were aligned against the mm10 mouse reference genome.
Supplementary files format and content: CSV files containing raw read count values (integer counts) for each gene across all samples. Each file includes a header row with sample identifiers and the first column listing gene IDs or gene symbols.

source_name: Small intestine

extract_protocol:
Treated mice instestines were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small intestine


title: Sample18

description:
Library name: Batch 18
10x Genomics and Singular G4

value: Batch 18


title: XG7, exp1, GFP-KRAS High, R2

description: Library name: XG7_exp1_GFP_KRAS_2H

value: multiple myeloma cell line

value: Cas9 clone


title: Young mice, Repeat 4

description: Library name: SAMN62238718


title: Linf_IL15_IL8_12

description: Gene expression data

value: Fem

value: Whole Blood - PBMC


title: E. coli MG1655 hfq-HTF CLASH library 3

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
Library name: hfq_CLASH_3
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.

library_source: other

data_processing:
Data were processed using the Hyb-CRAC-R pipeline described in PMID: 35732665.
Assembly: GCF_000005845.2
Supplementary files format and content: Processed CLASH data files are in table format (TAB). Column descriptions are in the header and more detailed descriptions are given in PMID: 35732665 Suplementary data 3, Table 2.
Supplementary files format and content: Processed CRAC data files are in bedgraph format. This data has been normalised to read per million (RPM).

molecule: other

organism: Escherichia coli str. K-12 substr. MG1655

source_name: whole cell

growth_protocol: Growth with shaking at 27 degress in LB media to OD0.6

extract_protocol:
Bead beating using 0.1mm zirconia beads and FastPrep-5G bead beating (2 cycles for 40seconds)
The library was constructed using the Hfq-CLASH protcol described in PMID: 32356726 with some modifications described in PMID: 35732665

treatment_protocol: Control vs hfq-HTF mutant

value: whole cell

value: hfq-HTF

value: grown in LB media to OD0.6


title: XG7, exp1, GFP-KRAS Low, R1

description: Library name: XG7_exp1_GFP_KRAS_1L


title: Young mice, Repeat 3

description: Library name: SAMN62238717


title: E. coli MG1655 hfq-HTF CLASH library 2

description:
Library name: hfq_CLASH_2
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.


title: Sample17

description:
Library name: Batch 17
10x Genomics and Singular G4

value: Tumor

value: Batch 17


title: XG7, exp1, GFP-KRAS High, R1

description: Library name: XG7_exp1_GFP_KRAS_1H


title: Sample15

description:
Library name: Batch 15
10x Genomics and Singular G4

value: Batch 15


title: Young mice, Repeat 1

description: Library name: SAMN62238715


title: E. coli MG1655 (untagged parent) control CLASH library 3

description:
Library name: control_3
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.

value: WT


title: E. coli MG1655 (untagged parent) control CLASH library 2

description:
Library name: control_2
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.


title: Old mice with evWT treatment, Repeat 4

description: Library name: SAMN62238714


title: C04

description:
Library name: C04
Sequencing was actually performed using the Singular Genomics G4X platform

data_processing:
Onboard Cellpose segmentation was used to initialize Proseg segmentation after nonspecific probes were removed. Data were explored in QuPath 0.5.1 and imported into python using anndata and spatialdata containers. Quality control was performed on each tissue section using a minimum of 20 counts and 5 genes. Cells at the 0.5% and 99.5% extremes for Proseg segmentation area were excluded. Spatial outliers were removed individually for each section by computing a spatial nearest neighbors graph for n neighbors and removing cells with a minimum Euclidean distance of x standard deviations, with n and x customized for each tissue section.
Assembly: Probe-based
Supplementary files format and content: zipped zarr proseg outputs and tiff H&E files per section
Library strategy: Spatial Transcriptomics

extract_protocol:
Samples were prepared from formalin-fixed, paraffin-embedded (FFPE) patient blocks according to the manufacturer’s protocol. Briefly, FFPE blocks were acquired from the Department of Pathology archive and freshly sectioned at a thickness of 5 µm onto custom gel pads. Regions of Interest (ROIs) were selected based on hematoxylin and eosin (H&E) stains previously performed by the Department of Pathology, with areas of high tumor enrichment annotated by a pathologist. ROIs were manually punched out of the gel pad and transferred onto functionalized glass slides.
After deparaffinization, rehydration, and antigen retrieval, hybridization with the Singular G4X breast cancer panel (309 genes) was performed. Ligation of the probes and rolling circle amplification were then performed in situ. The slide was conditioned, framed, and loaded onto the G4X instrument. Fluorescent H&E and spatial sequencing were performed on the G4X instrument.

value: Batch 1


title: B04

description:
Library name: B04
Sequencing was actually performed using the Singular Genomics G4X platform


title: Old mice with evWT treatment, Repeat 2

description: Library name: SAMN62238712


title: ARS1620, 48h, rep3

description: small RNA seq

data_processing:
Reads were trimmed with cutadapt, and aligned to mm10 with STAR
Assembly: mm10, hg38
Supplementary files format and content: Common-separated values of raw read counts of mPDAC
Supplementary files format and content: Common-separated values of raw read counts of MiaPaCa2 cells

source_name: pancreas

growth_protocol: 10% FBS+1xglutamax in DMEM/F12

extract_protocol:
Trizol total RNA extraction
Nextflex small RNA-seq v3

value: pancreas

value: MIA PaCa-2

value: Pancreatic cancer cell

value: ARS-1620 for 48h


title: A04

description:
Library name: A04
Sequencing was actually performed using the Singular Genomics G4X platform


title: ARS1620, 48h, rep2

description: small RNA seq


title: Old mice with evWT treatment, Repeat 1

description: Library name: SAMN62238711

value: Small intestine


title: E. coli MG1655 ∆spot42 pBAD+1::spot42 2

description:
Library name: spot42_pSpot42_2
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pSpot_2

data_processing:
Sequencing reads were processed using the READemption pipeline (PMID: 25123900)(Forstner et al Bioinformatics 2014, 1;30(23)3421-3. https://reademption.readthedocs.io/en/latest/
Assembly: NC_000913.3
Supplementary files format and content: CSV format. The processed data files are the output from READemption DESeq2 analysis biological triplicate samples of sRNA mutant with sRNA expression vector vs the sRNA mutant with an empty vector. The headings describe the data for each column.

growth_protocol: Cultures were grown to mid-exponential phase (OD600 = 0.6), and sRNA expression was induced with 0.2% (w/v) L-arabinose for 30 min.

extract_protocol:
Following induction, cultures were immediately treated with 95:5 (v/v) ethanol:phenol stop solution. Cells were harvested and mechanically lysed with zirconia beads using a FastPrep-24 5G bead-beating system. Total RNA was then isolated using GTC-phenol extraction. Residual genomic DNA was removed by treatment with RQ1-RNase-free DNase (Promega). RNA concentration was determined using a Qubit fluorometer, and RNA integrity was assessed using a TapeStation (Agilent).
Total RNA sequencing with rRNA removal. Library construction was performed at Novogene.

treatment_protocol: sRNA (and control plasmid) expression was induced with 0.2% (w/v) L-arabinose for 30 min.

value: delta_spot42 pBAD::spot42

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: ARS1620, 48h, rep1

description: small RNA seq


title: Old mice, Repeat 4

description: Library name: SAMN62238710


title: E. coli MG1655 ∆spot42 pBAD+1::spot42 1

description:
Library name: spot42_pSpot42_1
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pSpot_1


title: DMSO, 48h, rep3

description: mRNA-seq

extract_protocol:
Trizol total RNA extraction
illumina Truseq stranded mRNA

value: DMSO for 48h


title: Old mice, Repeat 3

description: Library name: SAMN62238709


title: E. coli MG1655 ∆spot42 pBAD+1: replicate 3

description:
Library name: spot42_control_3
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pBAD_3

value: delta_spot42 pBAD


title: F03

description:
Library name: F03
Sequencing was actually performed using the Singular Genomics G4X platform


title: Old mice, Repeat 2

description: Library name: SAMN62238708


title: E. coli MG1655 ∆spot42 pBAD+1: replicate 2

description:
Library name: spot42_control_2
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pBAD_2

value: whole cell


title: E03

description:
Library name: E03
Sequencing was actually performed using the Singular Genomics G4X platform


title: DMSO, 48h, rep1

description: mRNA-seq


title: Old mice, Repeat 1

description: Library name: SAMN62238707


title: E. coli MG1655 ∆spot42 pBAD+1: replicate 1

description:
Library name: spot42_control_1
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pBAD_1


title: D03

description:
Library name: D03
Sequencing was actually performed using the Singular Genomics G4X platform


title: ARS1620, 48h, rep3

description: mRNA-seq


title: C03

description:
Library name: C03
Sequencing was actually performed using the Singular Genomics G4X platform


title: ARS1620, 48h, rep2

description: mRNA-seq


title: DMSO, 48h, rep2

description: mRNA-seq


title: Old mice with evRSPO1 treatment, Repeat 3

description: Library name: SAMN62238705


title: E. coli MG1655 ∆sdsR pBAD+1::sdsR 2

description:
Library name: sdsR_pSdsR_2
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pSdrS_2

value: delta_sdsR pBAD::sdsR


title: B03

description:
Library name: B03
Sequencing was actually performed using the Singular Genomics G4X platform


title: ARS1620, 48h, rep1

description: mRNA-seq


title: Old mice with evRSPO1 treatment, Repeat 4

description: Library name: SAMN62238706


title: Old mice with evRSPO1 treatment, Repeat 2

description: Library name: SAMN62238704


title: E. coli MG1655 ∆sdsR pBAD+1::sdsR 1

description:
Library name: sdsR_pSdsR_1
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pSdrS_1


title: E. coli MG1655 ∆sdsR pBAD+1::sdsR 3

description:
Library name: sdsR_pSdsR_3
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pSdrS_3


title: A03

description:
Library name: A03
Sequencing was actually performed using the Singular Genomics G4X platform


title: MDA-MB-468 cells;FBXW5-2

city: Jinan

first: Tong

last: Chen

address: No.107 Wenhua Xi Road

institute: Qilu Hospital of Shandong University

description:
Library name: Sample 4
Column name in 468_fpkm.csv: F1-2

data_processing:
Raw FASTQ data were processed using fastp v0.20.1 for adapter trimming and quality filtering. Clean reads were aligned to the reference genomes (human: GRCh38.112; mouse: GRCm39.112) using HISAT2 v2.0.4. Transcript assembly and quantification were performed with StringTie v1.3.4d; initial assemblies were merged using gffcompare v0.9.8 to generate a final transcriptome annotation. Expression levels were calculated as FPKM using the ballgown package.
Assembly: human: GRCh38.112; mouse: GRCm39.112
Supplementary files format and content: csv files including FKPM values for each sample

source_name: Cell line

extract_protocol:
RNA was extracted using TRIzol reagent. RNA concentration was quantified by Nanodrop2000, and RNA integrity was assessed using Agilent2100.
Whole transcriptome RNA-seq libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following the manufacturer’s instructions. Library quality was assessed using Qsep-400.Qualified libraries were subjected to paired-end sequencing on the Illumina NovaSeq X Plus platform.

value: Cell line

value: MDA-MB-468 cells

value: Triple-negative breast cancer cells

value: FBXW5 overexpression


title: Old mice with evRSPO1 treatment, Repeat 1

description: Library name: SAMN62238703


title: E. coli MG1655 ∆sdsR pBAD+1 replicate 3

description:
Library name: sdsR_control_3
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pBAD_3

value: delta_sdsR pBAD


title: H02

description:
Library name: H02
Sequencing was actually performed using the Singular Genomics G4X platform

value: Tumor

value: Batch 1


title: MDA-MB-468 cells;FBXW5-1

description:
Library name: Sample 3
Column name in 468_fpkm.csv: F1-1


title: mPDAC, G12D,Ago2Y393A, rep3

description:
Library name: sample18
rawreads.txt
26102FL-01-02-24

data_processing:
Reads were trimmed with cutadapt, and aligned to mm10 with STAR
Assembly: mm10
Supplementary files format and content: Common-separated values of raw read counts of mPDAC

extract_protocol:
Trizol total RNA extraction
Nextflex small RNA-seq v4

value: pancreas

value: mPDAC

value: KrasG12D, Ago2Y393A


title: E. coli MG1655 ∆sdsR pBAD+1 replicate 2

description:
Library name: sdsR_control_2
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pBAD_2


title: Sample16

description:
Library name: Batch 16
10x Genomics and Singular G4

value: Batch 16


title: G02

description:
Library name: G02
Sequencing was actually performed using the Singular Genomics G4X platform


title: MDA-MB-468 cells;control-2

description:
Library name: Sample 2
Column name in 468_fpkm.csv: con1-2

value: WT


title: DMSO, 48h, rep3

description: small RNA seq

value: MIA PaCa-2

value: Pancreatic cancer cell


title: Young mice, Repeat 2

description: Library name: SAMN62238716

value: Small intestine


title: E. coli MG1655 hfq-HTF CLASH library 1

description:
Library name: hfq_CLASH_1
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.

value: whole cell

value: hfq-HTF

value: grown in LB media to OD0.6


title: D04

description:
Library name: D04
Sequencing was actually performed using the Singular Genomics G4X platform


title: DMSO, 48h, rep2

description: small RNA seq

value: DMSO for 48h


title: mPDAC, G12D,Ago2Y393A, rep2

description:
Library name: sample17
rawreads.txt
26102FL-01-02-23


title: E. coli MG1655 ∆sdsR pBAD+1 replicate 1

description:
Library name: sdsR_control_1
deseq_comp_SdsR_vs_control_with_annotation_and_countings.csv
Sdrs_pBAD_1

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: Old mice with evWT treatment, Repeat 3

description: Library name: SAMN62238713


title: DMSO, 48h, rep1

description: small RNA seq


title: MDA-MB-468 cells;control-1

description:
Library name: Sample 1
Column name in 468_fpkm.csv: con1-1

value: Cell line

value: MDA-MB-468 cells

value: Triple-negative breast cancer cells


title: F02

description:
Library name: F02
Sequencing was actually performed using the Singular Genomics G4X platform

value: Tumor

value: Batch 1


title: E. coli MG1655 (untagged parent) control CLASH library 1

description:
Library name: control_1
CLASH libraries use UV-crosslinking and an affinity tagged protein 'bait' to capture RNA-protein and RNA-RNA interactions occuring on the bait protein.


title: mPDAC, G12D,Ago2Y393A, rep1

description:
Library name: sample16
rawreads.txt
26102FL-01-02-22

value: pancreas

value: mPDAC


title: E. coli MG1655 ∆ryhB pBAD+1::ryhB 3

description:
Library name: ryhB_pRyhB_3
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pRhyB_3

value: delta_ryhB pBAD::ryhB


title: E02

description:
Library name: E02
Sequencing was actually performed using the Singular Genomics G4X platform


title: iPSC-derived cortical organoid, LIPUS treated, Day 87, rep 5

city: Suwon

first: Jong-Chan

last: Park

state: Gyeonggi-do

address: 2066, Seobu-ro

department: Department of Biophysics

country: South Korea

institute: Sungkyunkwan University

description:
Library name: US5
US5

data_processing:
Clean reads were aligned to the human reference genome (hg38) using HISAT2, and gene expression levels were quantified with featureCounts. Differentially expressed genes were identified using DESeq2 (|log2FC| ≥ 1, adjusted p ≤ 0.05). GO analysis was performed using ToppGene, and protein–protein interaction (PPI) networks were analyzed using STRING database.
Assembly: HG38
Supplementary files format and content: .txt files include gene count values for each samples
Supplementary files format and content: .txt files include gene count with the fpkm
Supplementary files format and content: .txt files include differential Expression Gene in the group of UsvsControl

source_name: iPSC-derived cortical organoid

growth_protocol: referred to Park et al.,(2021), Nat Comm.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat. No. 74004) according to the manufacturer’s instructions. Briefly, cells were lysed in guanidine-thiocyanate containing buffer, RNA was bound to a silica-gel membrane, washed, and eluted in RNase-free water.
mRNA was enriched using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Strand-specific libraries were generated through end repair, adaptor ligation, PCR amplification, and purification. Libraries were quantified and sequenced on the Illumina platforms, based on the mechanism of SBS (sequencing by synthesis) to produce paired-end reads.

treatment_protocol: The acoustic properties of the ultrasound transducer (V326-SU, Evident) were characterized using pulse-echo testing and hydrophone measurements (Fig. S11). The transducer was positioned over the FOs by adjusting the X and Y axes using a three-axis linear motor stage (L-836, PI). The focal depth along the Z-axis was aligned using a pulser/receiver (DPR 500, JSR). Ultrasound signals were generated by a function generator (33600A, Keysight), amplified with an RF amplifier (325LA, Electronics & Innovation), and delivered to the transducer. A center frequency of 5 MHz and a pulse repetition frequency (PRF) of 1 kHz were used for stimulation.

value: iPSC-derived cortical organoid

value: APOE E3/E4

value: LIPUS-treated


title: E. coli MG1655 ∆spot42 pBAD+1::spot42 3

description:
Library name: spot42_pSpot42_3
deseq_comp_Spot42_vs_control_with_annotation_and_countings.csv
Spot_pSpot_3

value: delta_spot42 pBAD::spot42


title: E. coli MG1655 ∆ryhB pBAD+1::ryhB 2

description:
Library name: ryhB_pRyhB_2
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pRhyB_2

value: whole cell


title: mPDAC, G12D,control, rep3

description:
Library name: sample15
rawreads.txt
26102FL-01-02-21

value: Pancreatic cancer cell

value: KrasG12D, Ago2WT


title: C02

description:
Library name: C02
Sequencing was actually performed using the Singular Genomics G4X platform


title: iPSC-derived cortical organoid, LIPUS treated, Day 87, rep 4

description:
Library name: US4
US4


title: mPDAC, G12D,control, rep2

description:
Library name: sample14
rawreads.txt
26102FL-01-02-20


title: B02

description:
Library name: B02
Sequencing was actually performed using the Singular Genomics G4X platform


title: E. coli MG1655 ∆ryhB pBAD+1::ryhB 1

description:
Library name: ryhB_pRyhB_1
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pRhyB_1


title: iPSC-derived cortical organoid, LIPUS treated, Day 87, rep 3

description:
Library name: US3
US3


title: mPDAC, G12D,control, rep1

description:
Library name: sample13
rawreads.txt
26102FL-01-02-19


title: E. coli MG1655 ∆ryhB pBAD+1 replicate 3

description:
Library name: ryhB_control_3
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pBAD_3

value: delta_ryhB pBAD


title: mPDAC, G12D, MRTX3

description:
Library name: sample12
rawreads.txt
26102FL-02-01-06

value: MRTX1133 for 48h


title: iPSC-derived cortical organoid, LIPUS treated, Day 87, rep 2

description:
Library name: US2
US2


title: H03

description:
Library name: H03
Sequencing was actually performed using the Singular Genomics G4X platform


title: A02

description:
Library name: A02
Sequencing was actually performed using the Singular Genomics G4X platform


title: E. coli MG1655 ∆ryhB pBAD+1 replicate 2

description:
Library name: ryhB_control_2
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pBAD_2

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: H01

description:
Library name: H01
Sequencing was actually performed using the Singular Genomics G4X platform


title: G03

description:
Library name: G03
Sequencing was actually performed using the Singular Genomics G4X platform


title: mPDAC, G12D, MRTX2

description:
Library name: sample11
rawreads.txt
26102FL-02-01-05


title: E. coli MG1655 ∆ryhB pBAD+1 replicate 1

description:
Library name: ryhB_control_1
deseq_comp_RhyB_vs_control_with_annotation_and_countings.csv
RhyB_pBAD_1


title: iPSC-derived cortical organoid, LIPUS treated, Day 87, rep 1

description:
Library name: US1
US1


title: G01

description:
Library name: G01
Sequencing was actually performed using the Singular Genomics G4X platform


title: iPSC-derived cortical organoid, control, Day 87, rep 5

description:
Library name: Con5
Con5

value: non-treated


title: mPDAC, G12D, MRTX1

description:
Library name: sample10
rawreads.txt
26102FL-02-01-04


title: E. coli MG1655 ∆gadY pBAD+1::gadY 3

description:
Library name: gadY_pGadY_3
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pGadY_3

value: delta_gadY pBAD::gadY


title: F01

description:
Library name: F01
Sequencing was actually performed using the Singular Genomics G4X platform

value: Tumor


title: mPDAC, G12D, DMSO3

description:
Library name: sample9
rawreads.txt
26102FL-02-01-03

value: DMSO for 48h


title: iPSC-derived cortical organoid, control, Day 87, rep 4

description:
Library name: Con4
Con4


title: E. coli MG1655 ∆gadY pBAD+1::gadY 2

description:
Library name: gadY_pGadY_2
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pGadY_2


title: E01

description:
Library name: E01
Sequencing was actually performed using the Singular Genomics G4X platform

value: Batch 1


title: iPSC-derived cortical organoid, control, Day 87, rep 3

description:
Library name: Con3
Con3


title: iPSC-derived cortical organoid, control, Day 87, rep 2

description:
Library name: Con2
Con2


title: mPDAC, G12D, DMSO1

description:
Library name: sample7
rawreads.txt
26102FL-02-01-01

value: pancreas

value: mPDAC


title: E. coli MG1655 ∆gadY pBAD+1 replicate 3

description:
Library name: gadY_control_3
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pBAD_3

value: delta_gadY pBAD


title: C01

description:
Library name: C01
Sequencing was actually performed using the Singular Genomics G4X platform


title: iPSC-derived cortical organoid, control, Day 87, rep 1

description:
Library name: Con1
Con1

value: iPSC-derived cortical organoid

value: APOE E3/E4


title: mPDAC, WT, MRTX3

description:
Library name: sample6
rawreads.txt
26102FL-01-02-06

value: KrasWT


title: E. coli MG1655 ∆gadY pBAD+1 replicate 2

description:
Library name: gadY_control_2
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pBAD_2

value: whole cell


title: DST-MNs-treated diabetic wound tissue, biological replicate 3

city: Harbin

first: WenXuan

last: Zhang

address: No. 300 Xuefu Road

institute: The Second Affiliated Hospital of Harbin Medical University

description: Library name: ST3

data_processing:
Raw sequencing reads were subjected to quality control, including removal of adaptor sequences and low-quality reads.
Clean reads were aligned to the rat reference genome using the Rattus norvegicus genome assembly (mRatBN7.2).
Gene expression levels were quantified based on read counts generated from mapped sequencing reads.
Expression normalization and differential expression analysis were performed between Control and DST-MNs-treated groups.
Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, were performed to identify biological processes and signaling pathways associated with DST-MNs-mediated wound regeneration.
Assembly: Rattus norvegicus (NCBI GCF_015227675.2 mRatBN7.2)
Supplementary files format and content: Gene-level expression matrix generated from RNA-seq data, containing gene IDs, gene symbols, FPKM, TPM, raw read counts, and normalized read counts for Control (C1–C3) and DST-MNs-treated (ST1–ST3) samples.

organism: Rattus norvegicus

source_name: Dorsal skin wound tissue

growth_protocol: Male Sprague–Dawley rats were used to establish a diabetic full-thickness dorsal skin wound model. Diabetic rats were generated by feeding a high-fat/high-sucrose diet followed by streptozotocin administration. Full-thickness skin wounds were created on the dorsal region, and animals were maintained under standard laboratory conditions before tissue collection.

extract_protocol:
Total RNA was extracted from diabetic wound tissues using TRIzol reagent according to the manufacturer's instructions. RNA concentration and integrity were evaluated by standard quality control procedures. Qualified RNA samples were used for RNA-sequencing library preparation.
RNA sequencing libraries were prepared using a standard mRNA-seq library construction workflow according to the manufacturer's protocol. Libraries were sequenced on the DNBSEQ-T7 platform using paired-end sequencing.

treatment_protocol: Diabetic wound tissues were collected from untreated diabetic wound animals and animals treated with multifunctional microneedles (DST-MNs) integrating spermidine- and TGF-β3-regulated dental pulp stem cell spheroids. Wound tissues were harvested after treatment for transcriptomic analysis. Three biological replicates were included for each group (Control: C1, C2, and C3; DST-MNs treatment: ST1, ST2, and ST3).

value: Dorsal skin wound tissue

value: DST-MNs-treated diabetic wound


title: E. coli MG1655 ∆gadY pBAD+1 replicate 1

description:
Library name: gadY_control_1
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pBAD_1


title: Sample14

description:
Library name: Batch 14
10x Genomics and Singular G4

tag: library type

value: GEM-X single cell 5'

value: Batch 15


title: DST-MNs-treated diabetic wound tissue, biological replicate 2

description: Library name: ST2


title: E. coli MG1655 ∆chiX pBAD+1::chiX 3

description:
Library name: chiX_pChiX_3
deseq_comp_ChiX_vs_control_with_annotation_and_countings.csv
Chix_pChix_3

value: delta_chiX pBAD::chiX

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: Sample13

description:
Library name: Batch 13
10x Genomics and Singular G4

value: Batch 14


title: DST-MNs-treated diabetic wound tissue, biological replicate 1

description: Library name: ST1


title: E. coli MG1655 ∆chiX pBAD+1::chiX 2

description:
Library name: chiX_pChiX_2
deseq_comp_ChiX_vs_control_with_annotation_and_countings.csv
Chix_pChix_2


title: Sample12

description:
Library name: Batch 12
10x Genomics and Singular G4

value: Tumor

value: Single Cell 3' v3

value: Batch 13


title: mPDAC, WT, DMSO3

description:
Library name: sample3
rawreads.txt
26102FL-01-02-03

value: pancreas

value: Pancreatic cancer cell

value: DMSO for 48h


title: mPDAC, WT, DMSO2

description:
Library name: sample2
rawreads.txt
26102FL-01-02-02

value: mPDAC


title: Control diabetic wound tissue, biological replicate 3

description: Library name: C3

value: untreated diabetic wound


title: Sample11

description:
Library name: Batch 11
10x Genomics and Singular G4

value: Batch 12


title: Control diabetic wound tissue, biological replicate 2

description: Library name: C2


title: E. coli MG1655 ∆chiX pBAD+1 replicate 3

description:
Library name: chiX_control_3
deseq_comp_ChiX_vs_control_with_annotation_and_countings.csv
Chix_pBAD_3

value: whole cell

value: delta_chiX pBAD


title: mPDAC, WT, DMSO1

description:
Library name: sample1
rawreads.txt
26102FL-01-02-01

value: KrasWT


title: Sample10_2

description:
Library name: Batch 10
10x Genomics and Singular G4

value: Batch 10


title: 36_G12D_AGO2Y393A_4sU_3

description:
Library name: 36
SLAM-seq

data_processing:
Reads were trimmed with cutadapt, and aligned to mm10 with STAR
Assembly: mm39
Supplementary files format and content: the fraction (βi) of converted reads within the total read counts after 60 minutes of 4sU labeling

extract_protocol:
Trizol total RNA extraction
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD (192.96, Lexogen)

value: KrasG12D, AGO2Y393A

value: 4sU for 1h


title: Control diabetic wound tissue, biological replicate 1

description: Library name: C1

value: Dorsal skin wound tissue


title: E. coli MG1655 ∆chiX pBAD+1 replicate 2

description:
Library name: chiX_control_2
deseq_comp_ChiX_vs_control_with_annotation_and_countings.csv
Chix_pBAD_2

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: Sample10_1

description:
Library name: Batch 9
10x Genomics and Singular G4

value: Tumor

value: Batch 9


title: 35_G12D_AGO2Y393A_4sU_2

description:
Library name: 35
SLAM-seq


title: E. coli MG1655 ∆chiX pBAD+1 replicate 1

description:
Library name: chiX_control_1
deseq_comp_ChiX_vs_control_with_annotation_and_countings.csv
Chix_pBAD_1


title: 34_G12D_AGO2Y393A_4sU_1

description:
Library name: 34
SLAM-seq


title: Bos taurus, vitrified-warmed (AKG+)2

city: Hefei

first: Wenjie

last: Yu

address: No.130 West Changjiang Road

institute: Anhui Agricultural University

description: Library name: vitrified-warmed (AKG+)2

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)] ). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). And then the GO terms (http://www.geneontology.org/) and KEGG Pathway (http://www.genome.jp/kegg/) of these differentially expressed mRNAs were also annotated.
Assembly: ensembl_v107
Supplementary files format and content: *_fpkm_expression.xlsx

organism: Bos taurus

source_name: embryo

extract_protocol:
According the manufacturer's requirement, RNA sample was extracted with a RNeasy Plus Micro Kit (QIAGEN, Dusseldorf, Germany). Total RNA was reverse transcribed using a reverse transcription kit (Biosharp, Beijing, China).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Japan) was used to prepare the low-input library following the procedures below: 1) Preparing cDNA library; 2) cDNA Purification and size selection (150-300bp); 3) Preparing sequencing ready library (add i5/i7adaptor using PCR method); 4) Library quality control (assess the size and concentration of the library using Agilent 2100 Bioanalyzer ); 5) Library sequencing performed on Illumina platforms using a 2x150bp paired-end sequencing protocol.

value: female

value: embryo

tag: sample group

value: vitrified-warmed (AKG+)


title: Sample08

description:
Library name: Batch 7
10x Genomics and Singular G4

tag: tissue

value: Single Cell 3' v3

value: Batch 7


title: untagged wild type control replicate 3

description:
Library name: WT_3
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)

data_processing:
The raw FASTQ files were demultiplexed using the 5' barcode sequences given in the processed data files names (eg: NNNCACTAGC). pyBarcodeFilter.py from the pyCRAC package was used for demultplexing (https://bitbucket.org/sgrann/pycrac/src/default/).
trimming ->flexbar; Dodt et al Biology (Basel) 2012
alignment ->novoalign; http://www.novocraft.com/products/novoalign/
mapping ->pyReadCounters (pyCRAC package); https://bitbucket.org/sgrann/pycrac/src/default/
The above steps and additional mapping of RNA-RNA interactions is included in the snakemake pipeline Hyb-CRAC-R (https://github.com/IgnatiusPang/Hyb-CRAC-R)
Assembly: Escherichia coli str. K-12 substr. MG1655 NCBI RefSeq assembly GCF_000005845.2
Supplementary files format and content: Supplementary files format and content: CRAC samples: Bedgraph format files containing chromosome, position and read depth. A separate file is provided for each strand - indicated plus or minus in the file name
Supplementary files format and content: Two type of data are presented in the bedgraph files: read count (in reads per million), and deletions (normalised to per million). The file name contains whether it reports reads (*reads.bedgraph) or deletions (*deletions.bedgraph).

growth_protocol: Strains were grown in Lb media to mid-xponential phase (0.8 OD600).

extract_protocol:
RNA-protein complexes were purified using the CRAC protocol described in PMID: 27836995 with updates to the protocol described in PMID: 37925184.
RNA-protein complexes were purified using the CRAC protocol described in PMID: 27836995 with updates to the protocol described in PMID: 37925184.

treatment_protocol: No treatment

tag: genotype

value: E. coli str. MG1655


title: Bos taurus, vitrified-warmed (AKG+)1

description: Library name: vitrified-warmed (AKG+)1


title: 33_G12D_AGO2Y393A_3

city: Houston

first: Ronald

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: 33
SLAM-seq

value: pancreas

value: mPDAC

value: Pancreatic cancer cell

tag: treatment

value: DMSO for 1h


title: untagged wild type control replicate 2

description:
Library name: WT_2
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)

value: whole cell


title: Sample07

description:
Library name: Batch 6
10x Genomics and Singular G4

value: Batch 6


title: Bos taurus, vitrified-warmed (AKG-)3

description: Library name: vitrified-warmed (AKG-)3

value: vitrified-warmed (AKG-)


title: 32_G12D_AGO2Y393A_2

description:
Library name: 32
SLAM-seq

value: KrasG12D, AGO2Y393A


title: untagged wild type control replicate 1

description:
Library name: WT_1
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)


title: Sample06

description:
Library name: Batch 5
10x Genomics and Singular G4

value: Batch 5


title: Bos taurus, vitrified-warmed (AKG-)2

description: Library name: vitrified-warmed (AKG-)2


title: 31_G12D_AGO2Y393A_1

description:
Library name: 31
SLAM-seq


title: D01

description:
Library name: D01
Sequencing was actually performed using the Singular Genomics G4X platform

value: Tumor

value: Batch 1


title: E. coli MG1655 ∆gadY pBAD+1::gadY 1

description:
Library name: gadY_pGadY_1
deseq_comp_GadY_vs_control_with_annotation_and_countings.csv
GadY_pGadY_1

value: delta_gadY pBAD::gadY

value: grown to OD0.6 in LB media and induced with 0.2% L-arabinose for 30 mins


title: mPDAC, G12D, DMSO2

description:
Library name: sample8
rawreads.txt
26102FL-02-01-02

value: DMSO for 48h


title: Sample05

description:
Library name: Batch 4
10x Genomics and Singular G4

value: Single Cell 5' PE

value: Batch 4


title: RNase E full length replicate 3

description:
Library name: FULL_3
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)

value: E. coli str. MG1655


title: Bos taurus, vitrified-warmed (AKG-)1

description: Library name: vitrified-warmed (AKG-)1

value: female

value: embryo


title: 30_G12D_AGO2WT_4sU_3

description:
Library name: 30
SLAM-seq

value: pancreas

value: mPDAC

value: Pancreatic cancer cell

value: KrasG12D, Ago2WT

value: 4sU for 1h


title: B01

description:
Library name: B01
Sequencing was actually performed using the Singular Genomics G4X platform


title: Sample01

description:
Library name: Batch 3
10x Genomics and Singular G4

value: Single Cell 3' v3

value: Batch 3


title: RNase E full length replicate 2

description:
Library name: FULL_2
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)

value: whole cell


title: Bos taurus, Control3

description: Library name: Control3

value: Control


title: 29_G12D_AGO2WT_4sU_2

description:
Library name: 29
SLAM-seq


title: mPDAC, WT, MRTX2

description:
Library name: sample5
rawreads.txt
26102FL-01-02-05

value: KrasWT

value: MRTX1133 for 48h


title: Sample02

description:
Library name: Batch 2
10x Genomics and Singular G4

value: Tumor

value: Batch 2


title: RNase E full length replicate 1

description:
Library name: FULL_1
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)


title: Bos taurus, Control2

description: Library name: Control2


title: mPDAC, WT, MRTX1

description:
Library name: sample4
rawreads.txt
26102FL-01-02-04


title: 28_G12D_AGO2WT_4sU_1

description:
Library name: 28
SLAM-seq


title: RNase E AR2 domain  replicate 3

description:
Library name: AR2_3
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)


title: Sample02, Sample03, Sample04

description:
Library name: Batch 1
10x Genomics and Singular G4

value: Batch 1


title: 27_G12D_AGO2WT_3

description:
Library name: 27
SLAM-seq

value: DMSO for 1h


title: Bos taurus, Control1

description: Library name: Control1

value: female


title: RNase E AR2 domain  replicate 2

description:
Library name: AR2_2
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)

value: E. coli str. MG1655


title: ASQ8B

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

address: 1650 Orleans St - CRB1 Rm 490

department: Oncology

institute: Johns Hopkins University

description: Library name: ASQ8B

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics).
Quality check and filtering with Seurat.
Normalization using SCTransform in Seurat.
Dimensional reduction using PCA in Seurat.
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: spatial barcodes
Supplementary files format and content: features.tsv: genes
Supplementary files format and content: matrix.mtx: sequencing counts
Supplementary files format and content: aligned_fiducials.jpg: capture area fiducial frame
Supplementary files format and content: detected_tissue_image.jpg: image of tissue detected
Supplementary files format and content: scalefactors_json.json; scale factors
Supplementary files format and content: tissue_hires_image.png: high resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: low resolution tissue image
Supplementary files format and content: tissue_positions.csv: coordinates
Supplementary files format and content: <sample>_histologicalannotation.csv: histology annotations for spatial spots
Library strategy: Spatial Transcriptomics

extract_protocol: Visium FFPE Spatial Gene Expression Reagent Kits (10x Genomics).

value: pancreas

tag: tissue type

value: pancreatic adenosquamous tumor


title: mPDAC, Ago2Y393E, rep3

last: Parchem

description: small RNA seq

tag: cell line

value: mPDAC

value: Pancreatic cancer cell

value: KrasWT, Ago2Y393E


title: 26_G12D_AGO2WT_2

description:
Library name: 26
SLAM-seq

tag: cell type

value: KrasG12D, Ago2WT


title: ASQ8A

description: Library name: ASQ8A


title: RNase E AR2 domain  replicate 1

description:
Library name: AR2_1
processed data are bedgraph files of read depth for both reads and deletions (normalised to RPM)


title: mPDAC, Ago2Y393E, rep2

description: small RNA seq


title: 25_G12D_AGO2WT_1

description:
Library name: 25
SLAM-seq


title: ASQ7A

description: Library name: ASQ7A


title: Linf_IL15_CCL20_12

description: Gene expression data

data_processing: Array data quality analysis, normalization (RMA+DAGB) and statistical tests for differential expression (eBayes) were carried out with the Transcriptome Analysis Console software (TAC 4.0.1)

extract_protocol:
PBMC Isolation Method: Ficoll-Paque density gradient
T Lymphocyte Isolation: Magnetic separation (Anti-CD3)
RNeasy® Mini kit

tag: Sex

value: Fem

value: Healthy

value: Whole Blood - PBMC


title: mPDAC, Ago2Y393E, rep1

description: small RNA seq


title: 4T1 cells;Fbxw5-2

description:
Library name: Sample 8
Column name in 4T1_fpkm.csv: F2-2

value: Cell line

value: 4T1 cells

value: Triple-negative breast cancer cells

value: Fbxw5 overexpression


title: ASQ6B

description: Library name: ASQ6B


title: ASQ5B

description: Library name: ASQ5B


title: Linf_IL15_12

description: Gene expression data


title: mPDAC, control, rep3

description: small RNA seq

value: KrasWT, Ago2WT


title: 4T1 cells;Fbxw5-1

description:
Library name: Sample 7
Column name in 4T1_fpkm.csv: F2-1


title: Bos taurus, vitrified-warmed (AKG+)3

description: Library name: vitrified-warmed (AKG+)3

value: embryo

value: vitrified-warmed (AKG+)


title: mPDAC, control, rep2

description: small RNA seq


title: 4T1 cells;control-2

description:
Library name: Sample 6
Column name in 4T1_fpkm.csv: con2-2

value: WT


title: ASQ5A

description: Library name: ASQ5A

value: pancreas


title: Linf_Control_12

description: Gene expression data


title: Sample09

description:
Library name: Batch 8
10x Genomics and Singular G4

extract_protocol:
FASTQ files from all batches were aligned independently using 10x Genomics Cell Ranger v8.0.1 to the reference genome GRCh38-2024-A. For Batch 1, samples were demultiplexed with the following key: anti-humanHashTag7--LNH-94-2M2-TSB = Sample02, anti-humanHashTag9--LNH-94-2M2-TSB = Sample03, and anti-humanHashTag10--LNH-94-2M2-TSB = Sample04.
All library preparations were performed using 10x Genomics protocols. If cryopreserved, cells were thawed, dead cell removal was performed and cells were counted. Once optimal concentration was achieved, we proceeded with library preparation and sequencing using standard 10x Genomics protocols per chemistry.

value: Tumor

value: Single Cell 3' v3

value: Batch 8


title: mPDAC, control, rep1

description: small RNA seq

value: mPDAC

value: Pancreatic cancer cell


title: 4T1 cells;control-1

description:
Library name: Sample 5
Column name in 4T1_fpkm.csv: con2-1


title: Linf_CCL20_11

description: Gene expression data

value: Fem


title: Linf_IL8_11

description: Gene expression data

value: Healthy


title: ASQ4B

description: Library name: ASQ4B

value: pancreatic adenosquamous tumor


title: ASQ4A

description: Library name: ASQ4A


title: mPDAC, Ago2Y393E, rep3

description: mRNA-seq

value: KrasWT, Ago2Y393E


title: mPDAC, Ago2Y393E, rep2

description: mRNA-seq


title: Linf_IL32_CCL20_11

description: Gene expression data

value: Whole Blood - PBMC


title: CLR320

description: Library name: RPS2_KRAS_IP2

data_processing:
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> CLR314.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o CLR314.trim.gz   --report minimal   >>CLR314.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir mus_musculus_repbase_v2     --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix CLR314.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn CLR314.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir /storage/vannostrand/genomes/mm10/star_2_4_0i_gencode15_sjdb --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix CLR314.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn CLR314.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o CLR314.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index CLR314.genome.map.bam umi_tools dedup   --random-seed 1   --stdin CLR314.genome.map.bam   --method unique   --stdout CLR314.bam
Make bigwigs: samtools index CLR314.bam b2bw CLR314.bam  --cpus 1
Get per-gene read counts for each dataset: featureCounts -a gencode.vM20.chr_patch_hapl_scaff.annotation.gtf -s 1 -T 8 -o WT_KRAS.feature.count CLR314.bam CLR316.bam CLR315.bam CLR317.bam
Get the Protein coding only regions of the featurecounts : perl pull_proteincodinggenes.pl WT_KRAS.feature.count.tsv mm10
Quantify translation efficiency with deseq2: deseq WT_KRAS.feature.count.tsv.proteincodingonly.txt  WT_KRAS.experiment.design.tsv WT_KRAS.feature.count.tsv.proteincodingonly.deseq.txt
Assembly: mm10/GRCm38
Supplementary files format and content: *.bw files are standard genome coverage bigwig files containing read density for each genomic position *.feature.count.tsv.proteincodingonly.deseq.txt files contain per-gene read counts
Library strategy: Ribo-Seq

source_name: KRAS mutant mouse pancreatic cancer cells

growth_protocol: 10% FBS +1xglutamax in DMEM/F12

extract_protocol:
Ribosome-associated RNAs were quantified with Ribo-eCLIP (Li. YH, Starner AS, et al. In preparation), a modified variation of the previously described eCLIP protocol (Blue, SM. et al, Nat Protocols 2022) to profile RPS2-associated RNA. Briefly, 20 million mPDAC iKRASG12D cells with constant and no dox were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
Limited RNA fragmentation was performed, 2% of the sample was removed for total RNA isolation, and the remainder was subjected to immunoprecipitation of RPS2-bound RNA with anti-RPS2 antibody (A303-794A, Fortis Life Sciences). Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). After pooling, ribosomal RNA-containing fragments were removed by CRISPR/Cas9 depletion (CRISPRClean Ribodepletion, Jumpcode Genomics). Samples were sequenced on the Illumina Novaseq X Plus platform.

treatment_protocol: Ribo eCLIP

value: IP


title: CLR321

description: Library name: RPS2_KRAS_IN2

data_processing:
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> CLR314.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o CLR314.trim.gz   --report minimal   >>CLR314.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir mus_musculus_repbase_v2     --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix CLR314.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn CLR314.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir /storage/vannostrand/genomes/mm10/star_2_4_0i_gencode15_sjdb --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix CLR314.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn CLR314.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o CLR314.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index CLR314.genome.map.bam umi_tools dedup   --random-seed 1   --stdin CLR314.genome.map.bam   --method unique   --stdout CLR314.bam
Make bigwigs: samtools index CLR314.bam b2bw CLR314.bam  --cpus 1
Get per-gene read counts for each dataset: featureCounts -a gencode.vM20.chr_patch_hapl_scaff.annotation.gtf -s 1 -T 8 -o WT_KRAS.feature.count CLR314.bam CLR316.bam CLR315.bam CLR317.bam
Get the Protein coding only regions of the featurecounts : perl pull_proteincodinggenes.pl WT_KRAS.feature.count.tsv mm10
Quantify translation efficiency with deseq2: deseq WT_KRAS.feature.count.tsv.proteincodingonly.txt  WT_KRAS.experiment.design.tsv WT_KRAS.feature.count.tsv.proteincodingonly.deseq.txt
Assembly: mm10/GRCm38
Supplementary files format and content: *.bw files are standard genome coverage bigwig files containing read density for each genomic position *.feature.count.tsv.proteincodingonly.deseq.txt files contain per-gene read counts

value: KRAS mutant mouse pancreatic cancer cells

value: input


title: ASQ3B

description: Library name: ASQ3B


title: Linf_IL32_IL8_11

description: Gene expression data


title: mPDAC, Ago2Y393E, rep1

description: mRNA-seq


title: ASQ2A

description: Library name: ASQ2A


title: CLR319

description: Library name: RPS2_KRAS_IN1


title: Linf_IL32_11

description: Gene expression data


title: mPDAC, control, rep3

description: mRNA-seq

value: KrasWT, Ago2WT


title: CLR318

description: Library name: RPS2_KRAS_IP1


title: Linf_IL15_IL8_11

description: Gene expression data


title: mPDAC, control, rep2

description: mRNA-seq


title: CLR317

description: Library name: RPS2_WT_IN2

source_name: WT Mouse pancreatic cancer cells

value: WT Mouse pancreatic cancer cells