title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep3

description: Library name: ms3.post

value: M


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep6

status: Public on Dec 12 2025

type: SRA

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

country: USA

institute: Washington University in St. Louis

description: Library name: 3UTR.hek.post6

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: raw files = fastq.gz , processed files = .txt

molecule: total RNA

organism: Homo sapiens

source_name: kidney

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype

value: WT

tag: treatment

value: ISOMPRA Library Transfection

tag: cre status

tag: batch


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep1

description: Library name: ms1.post

organism: Mus musculus

source_name: brain

value: brain

value: ISOMPRA Library AAV Infection

tag: Sex

value: F


title: EPOP-WT EpiLCs, Replicate 2, RNA

city: Dallas

first: Xin

last: Liu

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Pair-end 150 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were aligned to the mm10 reference genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes from gencode (vM4)
Normalized read counts generated using edgeR (v3.18.1)
Assembly: mm10
Supplementary files format and content: xlsx file containing normalized read counts and differential gene expression analysis

source_name: EpiLCs differentiated from E14 mESCs

growth_protocol: mESCs were cultured on 0.2% gelatin-coated plates in 2i/LIF medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with 1 × Pen/Strep, 0.05% BSA, 1 mM GlutaMAX, 100 μM β-mercaptoethanol, 0.5 × N2 supplement, 1 × B27 supplement, 1 μM MEK inhibitor PD0325901, 3 μM GSK3 inhibitor CHIR99021, and home-made LIF).  For the EpiLC differentiation, 1.5 million mESCs were plated on a 10 cm dish coated with human fibronectin (16.7 μg/ml) in N2B27 medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with containing 1 × Pen/Strep, 2 mM GlutaMAX, 50 μM β-mercaptoethanol, 0.5 × N2 supplement, 0.5 × B27 supplement, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR). The medium was replaced every day until 48 hours before cell collection.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. The concentration and purity of RNA were assessed using a NanoDrop device. RNA integrity was checked on a TapeStation system.
The RNA-seq library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of WT EPOP

value: EpiLC differentiation


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep7

description: Library name: 3UTR.hek.post7


title: EPOP-WT EpiLCs, Replicate 3, RNA


title: rnamap.trim.MyoN-514_S2.geneAbundanceHisat2

city: Chicago

first: Ayman

last: Al-Hendy

state: Illinois

address: 5841 S Maryland Ave

department: OBGyN

institute: University of Chicago

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC human reference genome hg38 using STAR.
featureCounts was used to evaluate gene expression level as read counts
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: uterus

extract_protocol:
We used the Qiagen RNeasy kit (74106) to isolate total RNA, with DNAseI treatment (Qiagen 79254).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: MyoF:myometrium adjacent to UF

tag: race

value: black


title: rnamap.trim.MyoN-UI-43_S3.geneAbundanceHisat2


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep17

description: Library name: ms17.pre


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep4

description: Library name: 3UTR.hek.post4


title: rnamap.trim.MyoN-UI-20_S1.geneAbundanceHisat2


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep2

description: Library name: ms2.post


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep3

description: Library name: 3UTR.hek.post3


title: rnamap.trim.MyoF-UI-13_S9.geneAbundanceHisat2

value: MyoN:normal myometrium


title: EPOP-WT mESCs grown in 2i media, Replicate 3, RNA

source_name: E14 mESCs

value: E14 mESCs

value: Embryonic stem cells


title: rnamap.trim.MyoN-432_S4.geneAbundanceHisat2

value: white


title: EPOP-Mutant EpiLCs, Replicate 3, RNA

value: Re-expression of mutant EPOP


title: rnamap.trim.MyoF-UI-10_S7.geneAbundanceHisat2


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep15

description: Library name: ms15.pre


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep5

description: Library name: 3UTR.hek.post5

value: kidney

value: human embryonic kidney cells


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep14

description: Library name: ms14.pre

value: WT


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep16

description: Library name: ms16.pre

value: brain


title: EPOP-WT EpiLCs, Replicate 1, RNA


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep8

description: Library name: 3UTR.hek.pre8

value: ISOMPRA Library Transfection


title: EPOP-WT mESCs grown in 2i media, Replicate 1, RNA


title: rnamap.trim.MyoN-549_S5.geneAbundanceHisat2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep2

description: Library name: 3UTR.hek.post2


title: EPOP-WT mESCs grown in 2i media, Replicate 2, RNA


title: EPOP-Mutant EpiLCs, Replicate 2, RNA


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep1

description: Library name: 3UTR.hek.post1


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep11

description: Library name: ms11.pre

value: ISOMPRA Library AAV Infection

value: M


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep6

description: Library name: 3UTR.hek.pre6


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep10

description: Library name: ms10.pre

value: F


title: rnamap.trim.MyoF-526_S10.geneAbundanceHisat2


title: EPOP-Mutant EpiLCs, Replicate 1, RNA

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells


title: Mesothelioma tumor biposy MOSR10

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Tumoral Biopsy from patient MOSR10

library_source: transcriptomic single cell

data_processing:
Single cell gene-count matrices were obtained with CellRanger
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix in gz

source_name: Mesothelioma

extract_protocol:
The tumoral biopsies and non-tumoral pleura tissues were minced mechanically into small pieces of 1 cm2 using sterile scalpels in sterile conditions. Further tissue dissociation into single-cell suspension was performed using Multi Tissue Dissociation Kit 2 (Cat No. 130-110-203) combining mechanical with enzymatic dissociation, according to the manufacturer´s datasheet. GentleMACS Dissociators were used for the mechanical dissociation steps. After dissociation, each sample was applied to a filter supplied in the kit to remove any remaining larger particles from the single-cell suspension
Cell suspensions were prepared and vitality was assessed for each individual scRNA-seq experiment. Cells were loaded onto a single-cell chip for GEM generation using the 10x Genomics Chromium Controller (10× Genomics, Pleasanton, CA). 3′mRNA-seq gene expression libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s guidelines.

value: Mesothelioma

tag: tissue source


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep5

description: Library name: 3UTR.hek.pre5


title: muscle, WT-Con1-1

city: shanghai

first: Qi

last: Cao

address: NO.325 Guohe Road

country: China

institute: Second Military Medical University

description:
Con vs Mod gene.TPM.matrix.annot
CC_1

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: muscle

extract_protocol:
The tissues were immediately snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using a suitable RNA extraction kit and assessed for quality and quantity. High-quality RNA (RIN > 7) was used for library preparation, including mRNA enrichment or rRNA depletion, cDNA synthesis, and adaptor ligation. The libraries were then sequenced on an Illumina platform with paired-end sequencing. Sequencing data underwent quality control and alignment to the reference genome for further analysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: muscle

tag: time

value: control


title: muscle, WT-Con1-2

description:
Con vs Mod gene.TPM.matrix.annot
CC_2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep2

description: Library name: 3UTR.hek.pre2


title: EPOP-Mutant mESCs grown in 2i media, Replicate 3, RNA

value: E14 mESCs


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep6

description: Library name: ms6.pre


title: EPOP-Mutant mESCs grown in 2i media, Replicate 1, RNA

value: Embryonic stem cells


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep7

description: Library name: 3UTR.hek.pre7


title: HCT116-Cas9 L1 EN/RT MT reporter - Replicate-2

city: Lexington

first: Liyang

last: Diao

state: MA

address: 36 Ledgelawn Ave

institute: Sprout Informatics

description: Library name: ooRT010

data_processing:
Raw RNA-seq reads in FASTQ format were first aligned to the human reference genome (hg38) using STAR (v2.7.11) [55] with default parameters unless otherwise specified. The resulting BAM files were sorted and indexed using Samtools (v1.21) [56]. Gene-level expression quantification was performed using Salmon (v1.10.2) [57] in quasi-mapping mode with transcript-level TPM normalization. Differential expression analysis was conducted using DESeq2 (v1.30.1) [58] in R, where gene expression counts were normalized, and differentially expressed genes (DEGs) were identified based on a threshold of |log2FoldChange| > 1 and adjusted p-value < 0.01 (Benjamini-Hochberg procedure used to calculate the adjusted p-value).
Assembly: GRCh38
Supplementary files format and content: Gene expression tables

molecule: polyA RNA

source_name: Colon

growth_protocol: HCT116 cells stably expressing Cas9 (human colorectal carcinoma) were purchased from Horizon (catalog ID: HD Cas9-002) and maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1 mM L-glutamine at 37°C in a humidified incubator with 5% CO₂. Cells were routinely passaged every 2–3 days at 70–80% confluence to ensure healthy growth. Cells stably expressing Cas9 and dual-reporter constructs were selected with 100 µg/mL hygromycin and expanded for use in downstream experiments.

extract_protocol:
Extraction is performed at Azenta Life Sciences
Library construction is performed at Azenta Life Sciences

value: Colon

value: Colon cancer


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep9

description: Library name: ms9.pre


title: muscle, KO-CTX-Day14-3

description:
WT vs KO gene.TPM.matrix.annot
Day14_km3

value: Gsdme knockdown


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep13

description: Library name: ms13.pre


title: rnamap.trim.MyoF-483_S8.geneAbundanceHisat2

value: MyoN:normal myometrium

value: black


title: HEK293 Cells, eMPRA Library Transfected, Rep6

description: Library name: rep1.6.fastq

value: kidney

value: human embryonic kidney cells

value: WT

value: Empra Library Tranfection


title: rnamap.trim.MyoF-428_S11.geneAbundanceHisat2

value: white


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep12

description: Library name: ms12.pre

value: brain

value: ISOMPRA Library AAV Infection

value: M


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep4

description: Library name: 3UTR.hek.pre4

value: ISOMPRA Library Transfection


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep3

description: Library name: 3UTR.hek.pre3


title: HCT116-Cas9 L1 WT reporter - Replicate-4

description: Library name: ooRT008


title: HCT116-Cas9 L1 EN/RT MT reporter - Replicate-3

description: Library name: ooRT011


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep7

description: Library name: ms7.pre


title: EPOP-Mutant mESCs grown in 2i media, Replicate 2, RNA

value: Re-expression of mutant EPOP


title: muscle, WT-CTX-Day14-3

description:
WT vs KO gene.TPM.matrix.annot
Day14_cm3

value: muscle


title: HEK293 Cells, eMPRA Library Transfected, Rep3

description: Library name: rep1.3.fastq


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep1

description: Library name: 3UTR.hek.pre1


title: HEK293 Cells, eMPRA Library Transfected, Rep2

description: Library name: rep1.2.fastq


title: muscle, WT-Con1-3

description:
Con vs Mod gene.TPM.matrix.annot
CC_3

value: control


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep8

description: Library name: ms8.pre

value: F


title: HCT116-Cas9 L1 EN/RT MT reporter - Replicate-1

description: Library name: ooRT009

value: Colon

value: Colon cancer


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep1

description: Library name: ms1.pre


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep4

description: Library name: ms4.pre


title: rnamap.trim.MyoF-348_S12.geneAbundanceHisat2

value: MyoN:normal myometrium


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep2

description: Library name: ms2.pre


title: HEK293 Cells, eMPRA Library Transfected, Rep1

description: Library name: rep1.1.fastq


title: HEK293 Cells, eMPRA Library Transfected, Rep4

description: Library name: rep1.4.fastq


title: muscle, KO-CTX-Day14-2

description:
WT vs KO gene.TPM.matrix.annot
Day14_km2

value: Gsdme knockdown


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep3

description: Library name: ms3.pre


title: HCT116-Cas9 L1 WT reporter - Replicate-3

description: Library name: ooRT007


title: HCT116-Cas9 L1 EN/RT MT reporter - Replicate-4

description: Library name: ooRT012


title: HEK293 Cells, eMPRA Library Transfected, Rep5

description: Library name: rep1.5.fastq

value: kidney


title: Mouse Brain, ISOMPRA Library AAV Infected Pre-Splice, BiolRep5

description: Library name: ms5.pre


title: muscle, KO-CTX-Day14-1

description:
WT vs KO gene.TPM.matrix.annot
Day14_km1


title: muscle, KO-CTX-Day7-3

description:
WT vs KO gene.TPM.matrix.annot
Day7_km3


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep6

description: Library name: rep1.6.pre

value: human embryonic kidney cells


title: HCT116-Cas9 L1 WT reporter - Replicate-2

description: Library name: ooRT006


title: muscle, KO-CTX-Day7-1

description:
WT vs KO gene.TPM.matrix.annot
Day7_km1


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep6

description: Library name: rep1.6.post

value: WT


title: muscle, WT-CTX-Day7-3

description:
WT vs KO gene.TPM.matrix.annot
Day7_cm3


title: HCT116-Cas9 no reporter - Replicate-1

description: Library name: ooRT001


title: muscle, WT-CTX-Day14-2

description:
WT vs KO gene.TPM.matrix.annot
Day14_cm2


title: HCT116-Cas9 L1 WT reporter - Replicate-1

description: Library name: ooRT005


title: muscle, WT-CTX-Day14-1

description:
WT vs KO gene.TPM.matrix.annot
Day14_cm1


title: Xenium, SSc6, whole skin

type: RNA

city: Lebanon

first: Helen

middle: C

last: Jarnagin

state: NH

address: WTRB 6-84 1 Medical Center Drive

institute: Geisel School of Medicine

hyb_protocol: Xenium protocol

scan_protocol: Xenium protocol

data_processing: Slides were imaged, cells were segmented, and initial QC was completed on the Xenium Analyzer (v3.0.2.0). QC-ed and segmented images were then transferred and converted to anndata objects for downstream Python-based analysis methods.

source_name: Affected skin biopsy

extract_protocol: FFPE histology sections underwent 10X Xenium’s in situ gene expression assay. Proprietary iterative in situ hybridization was conducted using the Xenium Prime 5K Human Pan Tissue and Pathways panel. Tissues were sectioned onto Xenium slides and processed according to the manufacturer’s protocol, including the workflow for cell segmentation staining (CG000760).

value: skin


title: Xenium, SSc7, whole skin


title: muscle, WT-CTX-Day7-2

description:
WT vs KO gene.TPM.matrix.annot
Day7_cm2


title: muscle, KO-CTX-Day7-2

description:
WT vs KO gene.TPM.matrix.annot
Day7_km2


title: HCT116-Cas9 no reporter - Replicate-3

description: Library name: ooRT003


title: T20 replicate 1

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Library name: T20A

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using trimmomatic v.0.33 [PMID: 24695404], replicates were merged and aligned with their reference genome (GRCh38.d1.vd1 human genome build hg38 using subread-align v1.4.6-p4 for human cells).
The BAM files from alignment were processed using STAR with Gencode v.22 gene annotations for human cells to obtain the counts per gene in all samples.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read count  values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Q-RT-PCR was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA).
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subjected to sequencing on Illumina HiSeq3000 platform.

value: Liver

value: helpatocytes

value: TAF2 knockdown


title: Xenium, SSc3, whole skin


title: T20 replicate 3

description: Library name: T20C


title: Xenium, SSc4, whole skin


title: muscle, KO-CTX-Day4-3

description:
WT vs KO gene.TPM.matrix.annot
Day4_km3


title: HCT116-Cas9 no reporter - Replicate-2

description: Library name: ooRT002


title: Xenium, SSc9, whole skin


title: Xenium, SSc8, whole skin


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep5

description: Library name: rep1.5.pre


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep2

description: Library name: rep1.2.pre


title: TAF2-expressing HepG2, replicate 1

description: Library name: TAF2-1

data_processing:
The data was processed using the Nextflow rnaseq v.23.04.3 pipeline using the hg38 genome assembly and star_rsem gene quantification method.
Assembly: hg38
Supplementary files format and content: text, tab-separated

source_name: liver

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Real-time polymerase chain reaction (RT-PCR) was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA)
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subject to two rounds of sequencing on Illumina HiSeq3000 platform.
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.

value: liver

value: HCC


title: HEK293 cells, ISOIMPRA Library Transfected, Post-Splice Rep2

description: Library name: rep1.2.post

value: ISOMPRA Library Transfection


title: Xenium, SSc10, whole skin


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep4

description: Library name: rep1.4.pre


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep1

description: Library name: rep1.1.pre


title: uISOMPRA AAV DNA TechRep 5

description: Library name: 3UTR.AAV.5

organism: Adeno-associated virus 9

value: uISOMPRA Library AAV DNA


title: Xenium, SSc5, whole skin


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep4

description: Library name: rep1.4.post


title: eGFP-expressing HepG2, replicate 1

description: Library name: eGFP-1


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep5

description: Library name: rep1.5.post


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep3

description: Library name: rep1.3.pre


title: HCT116-Cas9 no reporter - Replicate-4

description: Library name: ooRT004


title: T20 replicate 2

description: Library name: T20B


title: muscle, KO-CTX-Day4-1

description:
WT vs KO gene.TPM.matrix.annot
Day4_km1

value: muscle


title: uISOMPRA AAV DNA TechRep 3

description: Library name: 3UTR.AAV.3


title: muscle, WT-CTX-Day7-1

description:
WT vs KO gene.TPM.matrix.annot
Day7_cm1


title: TAF2-expressing HepG2, replicate 3

description: Library name: TAF2-3


title: TAF2-expressing HepG2, replicate 2

description: Library name: TAF2-2


title: uISOMPRA AAV DNA TechRep 2

description: Library name: 3UTR.AAV.2


title: muscle, KO-CTX-Day1-2

description:
WT vs KO gene.TPM.matrix.annot
Day1_km2


title: T7 replicate 2


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep3

description: Library name: rep1.3.post


title: muscle, KO-CTX-Day1-1

description:
WT vs KO gene.TPM.matrix.annot
Day1_km1


title: muscle, WT-CTX-Day1-3

description:
WT vs KO gene.TPM.matrix.annot
Day1_cm3


title: T7 replicate 1


title: Spatial transcriptome sequencing of chicken beaks (HH36)

city: Hangzhou

last: Project

address: YuhangTang

description:
Library name: Chicken_HH36
Fresh frozen Spatial transcriptome sequencing

data_processing:
Data preprocessing through SAW-pipeline (v7.1) and stereopy (v1.6.0) included filtering low-quality spots, normalization, and spatial binning.
Assembly: GRCg6a; IASCAAS_PekinDuck_T2T
Supplementary files format and content: gef: Stores the gene expression matrix along with spatial coordinates of bins/cells, used for spatial visualization.
Supplementary files format and content: h5ad: Stores single-cell level gene expression matrices and associated analysis results (e.g., clustering, dimensionality reduction).
Supplementary files format and content: barcodeToPos.h5: Contains the mapping between sequencing barcodes and their physical spatial coordinates on the chip.
Supplementary files format and content: ipr: Defines polygon regions for manual tissue boundary adjustment and region-specific analysis.
Supplementary files format and content: tiff: High-resolution microscope images of the tissue section
Library strategy: Spatial Transcriptomics

organism: Gallus gallus

source_name: Embryo beak

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptomics was performed on cryosectioned chicken and duck embryonic beaks at stages (HH29 and HH36) using Stereo-seq (BGI). Sections were mounted onto Stereo-seq chips, fixed, and permeabilized to capture poly(A)+ mRNAs on DNA nanoball arrays. cDNA synthesis and library preparation were carried out following manufacturer protocols, and libraries were sequenced on the DNBSEQ platform. Spatial barcodes and unique molecular identifiers (UMIs) were decoded to generate expression matrices with positional information.

value: Embryo beak


title: BY4741_CRISPR_MNase_replicate_2

city: Kansas City

first: Melanie

last: Weilert

institute: Stowers Institute for Medical Research

description: Library name: sc_suppress1_crispr_mutant_fixed_mnase_100U_2

library_source: genomic

data_processing:
Paired-end reads were aligned against the sacCer3 genome using bowtie2 (--very-sensitive -X 1000).
For all paired reads, we created coverage tracks of the 3′ endpoints of each fragment, 5′ endpoints of each fragment, and fragment midpoints (midpoints are provided as supplemental tracks). 3′ and 5′ in this context are with respect to the genome. Fragment midpoints represent the centers of each nucleosomal fragment, thus act as proxy dyad coverage.
Assembly: UCSC sacCer3
Supplementary files format and content: BigWig coverage of MNase-seq fragment midpoints

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S288C-derivative laboratory strain

growth_protocol: BY4741 yeast cultures were grown at 30°C in YPD to OD600 0.8-1.

extract_protocol:
BY4741 yeast cultures were first crosslinked with 1% formaldehyde for 15 minutes at room temperature. 125mM Glycine was added to quench the reaction. Cell pellets were resuspended in spheroplasting buffer (1M Sorbitol, 5 mM fi-mercaptoethanol, 50mM Tris pH 7.5, 2 mg/ml zymolyase (AMS Bio cat no: 120493-1); 1 mL of buffer per 20 mL of cell culture) and incubated for 15 min. at room temperature. The derived spheroplasts were treated with 100U MNase (NEB cat no: M0247S) for 30-40 min at 37°C. The reactions were stopped by the addition of EDTA pH 8.0 (50 mM final conc.) and EGTA pH 8.0 (50 mM final conc.). Samples were then incubated with RNase A (Thermo Scientific, EN0531, final conc. 0.2 mg/ml) at 42°C for 30 min to digest RNA. The crosslinks were reversed by adding SDS and proteinase K (Invitrogen cat no: 25530049, 1mg/ml final concentration) and incubation at 65°C for 45 min.
DNA was extracted using the Monarch PCR & DNA cleanup kit. Samples were resolved on 1% agarose gel to evaluate the digestion. Mononucleosome-sized bands were extracted and libraries were constructed from 10ng purified DNA using the Watchmaker Genomics according to the manufacturer's instructions. Paired-end sequencing was performed on AVITI (2x 75bp cycles).

treatment_protocol: For the CRISPR experiments, derived from BY4741 strains, a mutant strain with three point mutations was created using CRISPR Cas9-based genome editing technique. A 20 bp gRNA close to the mutation site was designed with BsaI overhangs and ordered as oligonucleotides. The gRNA-encoding oligonucleotides were annealed and cloned into the pCASB plasmid (Addgene 190175) using BsaIHF-v2 enzyme and T4 DNA ligase. The cloning reaction was transformed into E. coli and plated on Kanamycin selection plates. The plasmids were then isolated and verified by Sanger sequencing. A 160 bp homology-directed repair (HDR) template was designed to contain the desired mutant sequence, synthesized by Genescript and amplified by PCR.Yeast cells were then co-transformed with the cloned plasmid encoding Cas9 and gRNA, along with the HDR template. Transformants containing pCASB were selected on G418-containing media. Colonies were streaked twice, and isolates were screened for loss of the gRNA plasmid via replica plating to G418. For each isolate, genomic DNA was extracted, and the region of interest was amplified by PCR, purified and validated by Sanger sequencing.

tag: strain

value: S288C-derivative laboratory strain

value: CRISPR Pho5 upstream mutant


title: C2 replicate 3

value: Control


title: Xenium, SSc2, whole skin


title: muscle, WT-CTX-Day4-3

description:
WT vs KO gene.TPM.matrix.annot
Day4_cm3


title: Xenium, SSc1, whole skin


title: BY4741_wildtype_MNase_replicate_2

description: Library name: sc_wt_by4741_fixed_mnase_100U_2


title: AAV DNA, eMPRA

description: Library name: ms.aav.empra

value: eMPRA Library AAV Lysed


title: muscle, WT-CTX-Day4-1

description:
WT vs KO gene.TPM.matrix.annot
Day4_cm1


title: muscle, WT-CTX-Day4-2

description:
WT vs KO gene.TPM.matrix.annot
Day4_cm2


title: eGFP-expressing HepG2, replicate 2

description: Library name: eGFP-2


title: muscle, KO-CTX-Day4-2

description:
WT vs KO gene.TPM.matrix.annot
Day4_km2

value: Gsdme knockdown


title: PD16

status: Public on Dec 11 2025

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.5 μg each) hybridized on Clariom™D array, human (Themofisher Scientific, #902923) for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (ThermoFisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console version 4.0.2.15 (appliedbiosystems) using default settings for backgroud correction, normalization and summarization.

label: biotin

source_name: exosome

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

extract_protocol: Total RNA was isolated from CSF using the exoRNeasy Midi Kit (77144, Qiagen). according to the manufacturer's protocol. 50 ng of total RNA was carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

value: cerebrospinal fluid

value: female

tag: age


title: T7 replicate 3


title: PD12


title: PD13


title: eGFP-expressing HepG2, replicate 3

description: Library name: eGFP-3


title: initial samples

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description:
Library name: A4005_MM_OA
multiplexed single cell libraries

data_processing:
Cellranger count (10X Genomics, v7.1.0) was used to process the raw sequencing reads, which included alignment to the human genome and generation of mRNA count matrices
Demultiplexing was carried out within Seurat using the HTODemux() function
scRNAseq libraries of viral transfectants were further demultiplexed by lentiviral transgene barcodes, as given in the feature_references.csv file
Assembly: GRCh38
Supplementary files format and content: h5 file containing count matrices
Supplementary files format and content: annotated Seurat object (Rdata)

source_name: colorectal cancer cells

growth_protocol: SW480 and DLD1 cells were cultured in Dubecco´s Modified Eagle´s medium (DMEM, Lonza, BE12-707F) supplemented with 10% fetal calf serum

extract_protocol:
For single cell RNA sequencing, cells were harvested using TrypLE, resuspended in PBS, filtered through 30 µm Celltrix filters, resuspended in cell freezing medium and stored at -80°C until further processing. Cryopreserved cells were quickly thawed in a 37°C waterbath, washed in cell culture medium and resuspended in 1xPBS supplemented with 10% fetal calf serum. Cells were counted using an automated cell counter TC20 (BioRad) and equimolar amounts of cells per condition were labelled with 10X Genomics CellPlex barcodes according to the manufacturer’s protocol (CG000391_Rev B).
Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (CG000388_Rev B) and the Chromium Controller iX (10X Genomics) were used according to the manufacturer’s protocol

treatment_protocol: For the generation of RMC-7977-resistant CRC populations, cells were seeded at a density of 10000 cells per 6-well in 1 ml of cell culture medium containing DMSO or RMC-7977 (Revolution Medicines). Logarithmically growing cells were initially treated with GI-30 dosages of the inhibitor in the respective cell line and concentrations were doubled, once cells resumed proliferation similar to the parental line. For short time treatments with ERK inhibitor (SCH772984) or RAS inhibitor (RMC-7977), cells were treated for 72h before harvest.

value: colorectal cancer cells

value: KRAS-mutant


title: C2 replicate 2

value: Liver

value: helpatocytes

value: WT


title: AAV DNA, eMPRA.1

description: Library name: aav.1.empra


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep1

description: Library name: rep1.1.post

value: kidney

value: human embryonic kidney cells


title: PD6

value: male


title: validation and further samples

description:
Library name: A4793_Aust_Revision
multiplexed single cell libraries


title: muscle, KO-CTX-Day1-3

description:
WT vs KO gene.TPM.matrix.annot
Day1_km3

value: muscle


title: PD1


title: PD9


title: MSA-P8


title: muscle, WT-CTX-Day1-2

description:
WT vs KO gene.TPM.matrix.annot
Day1_cm2


title: uISOMPRA AAV DNA TechRep 1

description: Library name: 3UTR.AAV.1

value: uISOMPRA Library AAV DNA


title: uISOMPRA AAV DNA TechRep 4

description: Library name: 3UTR.AAV.4


title: MSA-P4


title: MSA-P2


title: PD14


title: PD8


title: C2 replicate 1


title: PD15


title: AAV DNA, ISOMPRA

description: Library name: ms.aav

value: ISOMPRA Library AAV Lysed


title: BY4741_CRISPR_MNase_replicate_1

description: Library name: sc_suppress1_crispr_mutant_fixed_mnase_100U_1

value: S288C-derivative laboratory strain

value: CRISPR Pho5 upstream mutant


title: ALS13


title: PD11


title: ALS7


title: ALS8


title: ALS4


title: PD7


title: ALS11


title: ALS12


title: BY4741_wildtype_MNase_replicate_1

description: Library name: sc_wt_by4741_fixed_mnase_100U_1


title: PD10


title: MSA-P3


title: muscle, WT-CTX-Day1-1

description:
WT vs KO gene.TPM.matrix.annot
Day1_cm1


title: PD2


title: PD5


title: MSA-P7


title: ALS15


title: PD4


title: PNP, 24h, biol rep 2

city: Cambridge

first: Benjamin

middle: J

last: Steventon

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample 11

data_processing:
Raw reads were processed using the Galaxy web platform (Afgan et al., 2016). Quality control was performed using FastQC (Simon et al., 2010), adaptor trimming was performed with Trim Galore! (Krueger et al., 2023), alignment to the galGal5 reference genome from the Genome Reference Consortium was carried out using HISAT 2 (Kim et al., 2015), PCR duplicates were removed using SAMtools markdup (Li et al., 2009), transcript assembly was performed with StringTie (Pertea et al., 2015), and differential expression analysis was carried out using DESeq2 (Love et al., 2014).
Assembly: galGal5 reference genome (see above)
Supplementary files format and content: Tabular files from Galaxy on gene counts per sample.

source_name: Prospective neural plate from HH4 embryos, 24 hours after being plated on human-fibronectin coated glass

growth_protocol: Migrating explants were prepared as follows (based on methods in Busby et al., 2024). Glass-bottomed dish (MatTek; 35mm Petri dish with 10mm microwell; No. 1.5 coverglass 0.16-0.19mm) microwells were coated with human fibronectin in PBS+/+ for at least 1h at 37C. After removing the ECM protein in PBS+/+ with a pipette, the glass-bottom dishes were left to thoroughly dry at 37C. All ECM-coated dishes were briefly washed with PBS+/+ twice prior to using. When embryos were finished being dissected, the periphery of the glass-bottom dish wells were covered with silicone grease. 200uL of warm chick culture media, composed of 10% KnockOut Serum Replacement (Thermo Fisher Scientific) + 1% Penicillin-Streptomycin (Thermo Fisher Scientific) + GMEM (Gibco), was added directly to the wells. Embryonic regions of interest were dissected using a microlance needle (BD) and transferred to the wells using a pipette. Explanted chick tissues were oriented ventral side down and gently flattened using an eyelash knife. Glass coverslips were placed on top to cover the well. Dishes were flooded with PBS+/+ or chick culture media and wrapped with parafilm to prevent dehydration. Explants were either incubated in a tissue culture incubator or for 24 hours or collected immediately.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following phase separation and isopropanol precipitation. Samples stored in 1mL TRIzol at -80C were thawed on ice and homogenized using a cell pestle. Chloroform (200uL per 1mL TRIzol was added, and samples were mixed and incubated at RT for 3min. Following centrifugation at 12,000×g for 15min at 4C, the clear aqueous phase was carefully collected, avoiding the interphase, and transferred to a fresh tube. To precipitate RNA, 0.5uL GlycoBlue (Thermo Fisher Scientific) and 500uL isopropanol were added to each sample. After 10min at RT, samples were centrifuged at 12,000×g for 10min at 4C. The resulting RNA pellet was washed with 1mL of 75% ethanol, vortexed briefly, and centrifuged at 7,500×g for 5min. Ethanol was removed, and pellets were air-dried for 10min before being resuspended in 20uL RNase-free water and incubated at 55C for 10min. RNA integrity was assessed by agarose gel electrophoresis. Approximately 300-500ng of each sample was mixed with loading dye and resolved on a 1% agarose gel in 1× TAE containing GelRed® Nucleic Acid Gel Stain (Biotium). Electrophoresis was carried out at 100V for 1h. Integrity was verified by the presence of distinct 28S and 18S rRNA bands with minimal smearing. Total RNA concentration was measured using the QuBit RNA High Sensitivity kit (ThermoFisher Scientific), and samples were stored at -80C until further processing.
Polyadenylated mRNA was enriched from 1ug of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), following the manufacturer’s guidelines. Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Dual indexing was performed with NEBNext Multiplex Oligos for Illumina Sets 1 and 2 (New England Biolabs). Cleanup steps throughout library preparation were carried out using SPRIselect magnetic beads (Beckman Coulter). Library quality and fragment size distribution were assessed using an Agilent 2100 Bioanalyzer with High Sensitivity DNA Chips and Reagents (Agilent Technologies). Sequencing was conducted on an Illumina NextSeq 2000 platform (P3 flow cell, single-end 50bp reads, roughly 90 million reads per sample) by Cambridge Genomic Services.

treatment_protocol: Embryonic and explant tissues (N, biological replicate = 3) from 3-4 dozen embryos each were collected in ice cold PBS+/+.

value: Ectoderm

value: Explanted and migrating


title: ALS5

value: cerebrospinal fluid


title: PNP, 24h, biol rep 3

description: Library name: Sample 12

value: Prospective neural plate from HH4 embryos, 24 hours after being plated on human-fibronectin coated glass


title: PNP, 24h, biol rep 1

description: Library name: Sample 10


title: MSA-P5


title: MSA-P6

value: female


title: ALS16


title: MSA-P1


title: PD3


title: ALS14


title: APS, 0h, biol rep 3

description: Library name: Sample 3

source_name: Anterior primitive streak from HH4 embryos

value: Mesoderm

value: Explanted


title: Cytomix_Secretome, Pool 7, GEX

city: South San Francisco

first: Michelle

last: Chen

state: CA

address: 1 DNA Way

department: Cell & Tissue Genomics

institute: Genentech, Inc.

description: Library name: LIB6229839

data_processing:
Libraries were sequenced on a NextSeq2000 or NovaSeq6000 (for HT libraries) targeting 30,000 reads/cell for GEX libraries and 2,000 reads/cell for HTO libraries. Sequenced reads were aligned using the human reference genome GRCh38-2020-A using the CellRanger pipeline (10x Genomics). scRNA-seq data was processed using CellRanger and resulting count matrices were analyzed using Seurat in R. For experiments involving hashing, cells were demultiplexed using the HTODemux function in R. For experiments involving genetic demultiplexing as in the perturbation dataset, the souporcell algorithm was used to distinguish between organoids from unique donors. Doublets were removed from data using the DoubletFinder algorithm. When combining experiments from multiple donors or timepoints, data was batch-corrected using the Harmony algorithm.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed Seurat objects (.Robj)

source_name: colon organoid

extract_protocol:
Organoids were dissociated using the Neural Dissociation-P kit (Miltenyi). Organoids were pipetted out of their microwell plates and into a deep-well 96 well plate (ThermoFisher) for dissociation. Enzyme mix 1 was prepared according to manufacturer protocols with the addition of Y-27632 for a final volume of 1.5mL per well. Organoids in mix 1 were then placed at 10C for 10 minutes, after which enzyme mix 2 was added. Organoids were kept at 10C throughout dissociation for up to 60 minutes, and were removed every 10 minutes to be pipette mixed with a P1000 pipette to aid in dissociation. Once dissociation was complete, organoids were centrifuged for 3 minutes, 500g, 4C and washed twice with PBS. For pooled experiments involving hashing (perturbation experiment, pooled injury experiments), organoids were resuspended in 100µL cell staining buffer (2% BSA, 0.01% Tween in PBS) and then blocked with 5uL human TruStain FCX blocking buffer (BioLegend) for 10 minutes on ice. 1µL of a unique cell hashing antibody (TotalSeqA: BioLegend) was added per condition for 20 minutes on ice, and cells were pipette mixed after 10 minutes. Organoids were then washed three times with cell staining buffer on ice. After the final wash, organoids were resuspended in 0.04% BSA in PBS, filtered through a 70µm Flowmi cell strainer (Sigma Aldrich) and loaded onto a 10X Chromium X according to manufacturer instructions. For organoid and tissue characterization and pooled injury experiments, the standard 10x 3’ v3.1 kit was used. For some injury experiments, the 10x 3’ low throughput kit was used to compare multiple injuries from the same experiment. For the perturbation dataset, the 10x 3’ high throughput kit was used.
Library preparation was prepared according to published 10x Genomics protocols.

value: colon organoid


title: Cytomix_Secretome, Pool 6, HTO

description: Library name: LIB6229842


title: Cytomix_Secretome, Pool 4, HTO

description: Library name: LIB6228903


title: ALS9


title: ALS3


title: ALS1


title: APS, 24h, biol rep 3

description: Library name: Sample 6

source_name: Anterior primitive streak from HH4 embryos, 24 hours after being plated on human-fibronectin coated glass

value: WT


title: Cytomix_Secretome, Pool 1, GEX

description: Library name: LIB6228896


title: Cytomix_Secretome, Pool 8, HTO

description: Library name: LIB6229844


title: APS, 24h, biol rep 2

description: Library name: Sample 5

value: Anterior primitive streak from HH4 embryos, 24 hours after being plated on human-fibronectin coated glass


title: APS, 0h, biol rep 1

description: Library name: Sample 1

value: Anterior primitive streak from HH4 embryos


title: PNP, 0h, biol rep 2

description: Library name: Sample 8

source_name: Prospective neural plate from HH4 embryos


title: PNP, 0h, biol rep 3

description: Library name: Sample 9

value: Prospective neural plate from HH4 embryos


title: Cytomix_Secretome, Pool 8, GEX

description: Library name: LIB6229840


title: ALS2

value: male


title: APS, 24h, biol rep 1

description: Library name: Sample 4


title: Cytomix_Secretome, Pool 6, GEX

description: Library name: LIB6229838


title: ALS6


title: PNP, 0h, biol rep 1

description: Library name: Sample 7


title: Cytomix_Secretome, Pool 4, GEX

description: Library name: LIB6228899


title: APS, 0h, biol rep 2

description: Library name: Sample 2


title: forebrain, ED5, rep3

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

description: Library name: 3LP7_S11

data_processing:
Adapters and low quality bases were trimmed using fastp version 0.23.2 with following specific parameters "-l 17 --detect_adapter_for_pe -g -p "
Reads were mapped to the Passer domesticus isolate 8887266 reference genome (MBAE00000000.1) using hisat2 version 2.2.1
Reads mapped to the annotated genes using featureCounts version 2.0.3 with the following parameters: -Q 20 -O -M --primary -p --countReadPairs --largestOverlap -B -s 2
Assembly: GenBank: MBAE00000000.1
Supplementary files format and content: Tab delimited raw mapped read counts

organism: Passer domesticus

source_name: forebrain

extract_protocol:
Quick-RNA Microprep Kit (Zymo Research)
xGen RNA Library kit (Integrated DNA Technologies, USA)

value: forebrain


title: midbrain, ED5, rep3

description: Library name: 3LP4_S55


title: Cytomix_Secretome, Pool 3, HTO

description: Library name: LIB6228902


title: extraembyronic tissue, ED3, rep5

description: Library name: 3AV40_S17

source_name: extraembryonic tissue

value: extraembryonic tissue


title: Cytomix_Secretome, Pool 5, GEX

description: Library name: LIB6229837


title: Cytomix_Secretome, Pool 2, GEX

description: Library name: LIB6228897


title: extraembyronic tissue, ED5, rep3

description: Library name: 3AV10_S10


title: ALS10


title: forebrain, ED3, rep2

description: Library name: 5LP2_S3


title: Cytomix_Secretome, Pool 3, GEX

description: Library name: LIB6228898


title: extraembyronic tissue, ED3, rep7

description: Library name: 5LP7_S54


title: extraembyronic tissue, ED5, rep4

description: Library name: 3LP7_S12


title: extraembyronic tissue, ED3, rep6

description: Library name: 5LP2_S4


title: forebrain, ED5, rep1

description: Library name: 1LP2_S5


title: Cytomix_Secretome, Pool 7, HTO

description: Library name: LIB6229843


title: Cytomix_Secretome, Pool 5, HTO

description: Library name: LIB6229841


title: Cytomix_Secretome, Pool 1, HTO

description: Library name: LIB6228900


title: Cytomix_Secretome, Pool 2, HTO

description: Library name: LIB6228901


title: extraembyronic tissue, ED3, rep4

description: Library name: 2LP4_S2


title: extraembyronic tissue, ED5, rep1

description: Library name: 1LP2_S6


title: extraembyronic tissue, ED3, rep2

description: Library name: 1AV7_S15


title: midbrain, ED5, rep1

description: Library name: 1LP2_S56

source_name: midbrain

value: midbrain


title: forebrain, ED3, rep1

description: Library name: 1AV6_S13


title: midbrain, ED5, rep2

description: Library name: 3AV10_S58


title: 5 days mock-inoculated soybean roots, rep2, snRNA

city: ATHENS

first: Robert

middle: J.

last: Schmitz

state: GA

address: B416 Davison Life Sciences Department of Genetics University of Georgia 120 East Green Street

institute: University of Georgia

description: Library name: Gm_mock-rep2_rna

library_source: genomic single cell

data_processing:
Briefly, raw BCL files were demultiplexed and converted into FASTQ format using the 10X Genomics tool Cell Ranger ATAC (cellranger-atac makefastq, v1.2.0) with default parameters. Primary read processing, including adapter and quality trimming, alignment, and barcode attachment/correction, was performed using cellranger-atac count (v1.2.0). Reads were mapped to a composite reference consisting of the soybean Williams 82 v4 genome, the Glycine max organelle genomes (NCBI Reference Sequences: NC_007942.1 and NC_020455.1), and the soybean cyst nematode (Heterodera glycines) genome (SCNBase, TN10 strain). Properly paired, uniquely mapped reads with mapping quality scores greater than 30 were retained using samtools view (v1.6; parameters: -f 3 -q 30)[44]. Reads containing alternative alignments (XA tags) were also retained to minimize bias from the ancient whole-genome duplication events in soybean. PCR duplicates were removed on a per-nucleus basis using Picard (http://broadinstitute.github.io/picard) MarkDuplicates (v2.16; BARCODE_TAG=CB REMOVE_DUPLICATES=TRUE). Reads aligning to mitochondrial, chloroplast were quantified per barcode and excluded from downstream analyses. Due to their low abundance, reads mapping to the nematode genome were also excluded from all downstream analyses.
Assembly: soybean Williams 82 v4 genome
Supplementary files format and content: Gm_root_Crude_root_1e+05_feature.soc.processed.rds is the socrates project with clustering for ATAC
Supplementary files format and content: Gm_root_crude_soybeanOnly_metav1_gene_sparse.rds is the gene by cell tn5 count matrix
Supplementary files format and content: Gm_root_integrated_cpm4_ACR_sparse.rds is the ACR by cell tn5 count matrix
Supplementary files format and content: Gm_root_crude_soybeanOnly_metav1_gene_sparse.rds is the gene by cell tn5 count matrix
Supplementary files format and content: Gm_root_integrated_ACR_4cpm_TissueCelltypeRep_counts.txt is the ACR by samples tn5 count matrix
Supplementary files format and content: root.MergedSeuratObjs.cluster.RDS is the Seurat project with clustering for RNA
Supplementary files format and content: Gm_All_root_procambium_integrated_ATACandRNA.uiNMF_liger_obj.rds contains the integrated procambium cell for ATAC and RNA

organism: Glycine max

source_name: root

growth_protocol: The soybean cultivar Williams 82, which is susceptible to SCN (Heterodera glycines Ichinohe) inbred population PA3 (HG type 0) was used for infection assay. The SCN HG type 0 population used in this study was maintained on Williams 82 in the greenhouse at the University of Georgia.

extract_protocol:
Briefly, root tissues were finely chopped   with single edge razor blades on ice for approximately 2 minutes in 600 μL of pre-chilled Nuclei Isolation Buffer (NIB; 10 mM MES-KOH, pH 5.4; 10 mM NaCl; 250 mM sucrose; 0.1 mM spermine; 0.5 mM spermidine; 1 mM DTT; 1% BSA; and 0.5% Triton X-100). The homogenate was passed through a 40-μm cell strainer and centrifuged at 500 × g for 5 minutes at 4 °C. The supernatant was discarded, and the pellet was gently resuspended in 500 μL of NIB wash buffer (10 mM MES-KOH, pH 5.4; 10 mM NaCl; 250 mM sucrose; 0.1 mM spermine; 0.5 mM spermidine; 1 mM DTT; and 1% BSA). The suspension was filtered through a 40-μm cell strainer and carefully layered onto 1 mL of 35% Percoll (prepared by mixing 35% Percoll with 65% NIB wash buffer) in a 1.5-mL centrifuge tube. Nuclei were enriched by centrifugation at 500 × g for 10 minutes at 4 °C. Following centrifugation, the supernatant was removed, and the nuclei pellet was resuspended in 10 μL of diluted nuclei buffer (DNB; 10x Genomics, Cat# 2000207). For quality control, 5 μL of the nuclei suspension were diluted tenfold, stained with DAPI (Sigma, Cat# D9542), and examined under a fluorescence microscope using a hemocytometer to assess integrity and concentration. The nuclei concentration was then adjusted to 3,200 nuclei/μL using DNB buffer, and 5 μL (approximately 16,000 nuclei) were used as input for single-cell ATAC-seq library construction.
Single-cell ATAC-seq libraries were generated using the Chromium Next GEM Single Cell ATAC v1.1 kit (10x Genomics, Cat# 1000175) according to the manufacturer’s protocol (Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 User Guide, CG000209 Rev E). The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform using dual-index mode with 8 cycles for the i7 index and 16 cycles for the i5 index.

treatment_protocol: Briefly, soybean seeds were germinated in ragdolls for three days at 28°C in the dark. Seedlings with uniform radicles were selected for SCN inoculation. Approximately 300 second-stage juveniles (J2) suspended in 0.08% agarose were applied 1 cm above the root tip of each soybean root. Mock-inoculated seedlings were treated with 0.08% agarose without nematodes. The infection was synchronized by washing roots 24 hours after inoculation with running tap water to remove J2s outside the root. Mock-inoculated seedlings were treated the same way. Washed seedlings were rolled into ragdolls, placed in Hoagland’s nutrient solution with constant aeration, and grown in a plant growth chamber at 26°C with a photoperiod of 16 h of light and 8 h of dark for four more days. Five days post-inoculation, root pieces of approximately 1-1.5 cm flanking the inoculation point were excised from both SCN-infected and mock-inoculated samples. Two biological replicates, each consisting of 20 root pieces, were used for nuclei extraction.

value: root

value: William 82


title: 5 days SCN-infected soybean roots, rep2, scatac

description: Library name: Gm_infected-rep2_atac


title: 5 days mock-inoculated soybean roots, rep1, scatac

description: Library name: Gm_mock-rep1_atac


title: Cytomix vs. DSS, DSS, HTO

description: Library name: LIB6231780


title: Cultrex Experiment 1

description: Library name: LIB6227823


title: Cultrex Experiment 2

description: Library name: LIB6220201


title: 5 days SCN-infected soybean roots, rep2, snRNA

description: Library name: Gm_infected-rep2_rna


title: extraembyronic tissue, ED3, rep3

description: Library name: 1LP7_S1


title: Cytomix vs. DSS, Cytomix, HTO

description: Library name: LIB6231781


title: Cytomix vs DSS, Cytomix, GEX

description: Library name: LIB6231779


title: 5 days mock-inoculated soybean roots, rep2, scatac

description: Library name: Gm_mock-rep2_atac


title: Microwell Experiment 1

description: Library name: LIB6227826


title: Injury Atlas,Disociation 8hr

description: Library name: LIB6220791


title: extraembyronic tissue, ED5, rep2

description: Library name: 2AV40_S53


title: Cultrex Experiment 3

description: Library name: LIB6220102


title: Injury Atlas, Cytomix HTO

description: Library name: LIB6227832


title: forebrain, ED5, rep2

description: Library name: 2AV40_S52


title: 5 days SCN-infected soybean roots, rep1, snRNA

description: Library name: Gm_infected-rep1_rna


title: 5 days mock-inoculated soybean roots, rep1, snRNA

description: Library name: Gm_mock-rep1_rna


title: Injury Atlas, Disociation t0

description: Library name: LIB6220707


title: Ci20018_Plate_3_C_B57_CD3_low

city: Birmingham

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

institute: University of Alabama at Birmingham

description:
Library name: Ci20018_Plate_3_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.

data_processing:
Post quality-filtering, reads were passed through a proprietary demultiplexing tool to assign them to individual wells. MixCR software was used to assign TCR α and β loci and clonotypes to individual wells. Assembled count and TCR matrices by well were then used to perform downstream analysis in Seurat.
Assembly: GRCh38
Supplementary files format and content: The processed data files included represent the demultiplexed normalized values for all wells of all plates and wells post preprocessing and Seurat object formation

extract_protocol:
Cells were then stained with Aqua LIVE/DEAD stain (Thermo Fisher Scientific), anti-CD3-PacBlue, -CD4-AlexaFluor780, -CD8-AlexaFluor700, -CD14/16/19/56-PerCP-Cy5.5 (dump channel, all separate antibodies), -CD69-APC, -CD137-PE, -CD94-PE-Cy7, and -CD107a-FITC. As per gating strategy shown in Figure S1A, single cell lymphocytes were gated on, followed by live cells (Aqua -), CD4/dump -/-, CD8+ CD3-dim, CD69/137+.. Cells which fit this gating strategy and met the criteria of having a CD3-dim activated response to the given HLA pulsed with KF11 significantly (and 3X) higher than 41A3.CD4 also pulsed with KF11 were then sorted into a 96-well plate containing the lysis buffer previously described using the Aria II FACS sorter. scTCR and scRNA-seq was performed as previously described.
Library construction was performed at the Institute for Immunology and Infectious Diseases in Perth, Australia. As in the previous publication, uniquely tagged primers were used for reverse transcription and template switching with a preamplification step to increase yield and transcript length of the single-cell cDNA library. Libraries were then run on separate lanes of an Illumina MiSeq instrument utilizing a 2 x 300 bp paired-end chemistry kit (Illumina Inc.).

value: CD8+ T cells

value: KF11-loaded APC cell line


title: Ci20018_Plate_2_C_B57_CD3_low

description:
Library name: Ci20018_Plate_2_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: extraembyronic tissue, ED3, rep1

description: Library name: 1AV6_S14


title: Injury Atlas, Cytomix GEX

description: Library name: LIB6227829


title: Injury Atlas, Control 2

description: Library name: LIB6220794


title: 5 days SCN-infected soybean roots, rep1, scatac

description: Library name: Gm_infected-rep1_atac


title: Injury Atlas, Irradiation Low

description: Library name: LIB6220633


title: Injury Atlas, DSS High

description: Library name: LIB6220632


title: Ci10067_Plate_7_C_E01_CD3_low

description:
Library name: Ci10067_Plate_7_C_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Cytomix vs. DSS, DSS, GEX

description: Library name: LIB6231778


title: Pb4A_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
For data analysis, adapters were trimmed using Cutadapt with parameter “--minimum-length 50”, and trimmed reads were mapped to the reference genome using BSMAP. The reference genome for pear is Pbr_v1.0; ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/295/GCF_000315295.1_Pbr_ v1.0). All scaffold sequences were sorted by length and concatenated to one pseudo chromosome.
Genome_build: Pbr_v1.0
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs(three contexts) with depth >= 4 in all the samples. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Pyrus x bretschneideri

source_name: fruit

extract_protocol: Fruits of "Suli" (Pyrus bretschneideri Rehd.) were collected from the Dangshan Germplasm Resources Center (Dangshan County, Anhui Province, China). Pear fruit samples were stored after picking immediately in liquid nitrogen and then at −80°C until DNA extraction. Genomic DNA was extracted from fruits using a DNeasy Plant Maxi Kit (Qiagen) and then was used for library construction using Illumina’s standard DNA methylation analysis protocol and the NEB Ultra II DNA Library Prep Kit. The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina HiSeq2500.

tag: cultivar

value: Suli

value: fruit

tag: days after bloom


title: Injury Atlas, Dissociation 24hr

description: Library name: LIB6220792


title: Injury Atlas, Dissociation 4hr

description: Library name: LIB6220790


title: Ci10067_Plate_3_C_B57_CD3_low

description:
Library name: Ci10067_Plate_3_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10067_Plate_6_C_E01_CD3_low

description:
Library name: Ci10067_Plate_6_C_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10074_Plate_12_EC_E03_CD3_low

description:
Library name: Ci10074_Plate_12_EC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10074_Plate_13_EC_E03_CD3_low

description:
Library name: Ci10074_Plate_13_EC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10067_Plate_12_C_E03_CD3_low

description:
Library name: Ci10067_Plate_12_C_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci20018_Plate_1_C_B57_CD3_low

description:
Library name: Ci20018_Plate_1_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10071_Plate_3_EC_B57_CD3_low

description:
Library name: Ci10071_Plate_3_EC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10074_Plate_11_EC_E03_CD3_low

description:
Library name: Ci10074_Plate_11_EC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10074_Plate_10_EC_E03_CD3_low

description:
Library name: Ci10074_Plate_10_EC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: methyl-seq_ESC-3

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description: Library name: methyl-seq_ESC-3

data_processing:
Methyl-seq data were processed with the Bismark  pipeline using bowtie2 with default parameters. Biological triplicates were merged for downstream analyses. Methylated and unmethylated CG sites were counted
Assembly: mm10
Supplementary files format and content: gzipped text file (Bismarck output). Columns are : Chromosome, Position, Strand, Count methylated, Count unmethylated, C-context, Trinucleotide context.

growth_protocol: Cells were maintained in Serum+Lif (S/L) medium (KnockOut DMEM supplemented with 15% ES cell qualified FBS, 1% GlutaMAX, 1% MEM non-essential amino acids, 1% penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 10 ng/mL Lif (Miltenyi Biotec, Cat #130-099-895) on gelatine-coated plates in a humidified incubator (37°C, 5% CO2). ES R1 cell line was maintained under the same conditions. To sort MERVL Tomato-positive and Tomato-negative cells, mouse ESCs were seeded in 150mm culture dishes at 5 million cells per plate. In case of treatments, the compounds were supplemented in the media while seeding. After 48h (or 24h post siRNA transfection), cells were trypsinized and resuspended in PBS.  Prior to sorting using The BD FACSAria™ III Cell Sorter, cells were incubated with DRAQ7 (Invitrogen, Cat#D15106) for 10 mins in the dark at room temperature to exclude non-viable cells.

extract_protocol:
DNA was extracted and purified from 100,000 FACS-sorted cells for each condition with the Monarch Genomic DNA Purification Kit (NEB Cat# T3010S) following manufacturer’s instructions. DNA was quantified with Qubit. The NEBNext Enzymatic Methyl-seq Kit (New England Biolabs #E7120S) was used to prepare the libraries.
200 ng of DNA was used as input and sheared to 275 bp fragments using Covaris with the following parameters: Duty Factor = 10%, Peak Incident Power = 175 W, Cycles per burst = 200, Duration = 100 s. Fragment size was assessed by a BioAnalyzer system (Agilent Technologies).  Manufacturer’s instructions were followed for the subsequent steps. Libraries were quantified using Qubit and size determined by BioAnalyzer. The libraries were sequenced on an Illumina HiSeq4000 sequencer as paired-end 100 base reads following Illumina’s instructions.

value: ESC (Mervl -)


title: Ci10067_Plate_11_C_E03_CD3_low

description:
Library name: Ci10067_Plate_11_C_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: methyl-seq_ESC-2

description: Library name: methyl-seq_ESC-2


title: Ci10074_Plate_6_EC_E01_CD3_low

description:
Library name: Ci10074_Plate_6_EC_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Injury Atlas, Irradiation High

description: Library name: LIB6220706


title: Pb4B_MethylC-Seq


title: Injury Atlas, DSS Low

description: Library name: LIB6220795


title: Pb2B_MethylC-Seq


title: Ci10027_Plate_3_NC_E03_CD3_low

description:
Library name: Ci10027_Plate_3_NC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10076_Plate_5_NC_B57_CD3_low

description:
Library name: Ci10076_Plate_5_NC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: mESC-rep2

description: Library name: mESC-rep2

data_processing:
Raw read aligned with STAR on mm10
Alignments were filtered with Samtools on MAPQ30.
Count matrixes for genes or for bins were generated using featuresCount program from the subread suite.
For genes we used the vM23 annotation from gencode. Then DESeq2 was used for computing log2 fold change of genes or bins.
Assembly: mm10
Supplementary files format and content: bigwig files of normalized counts (Counts per Million)
Supplementary files format and content: text file (tabulated table) of counts.

extract_protocol:
100,000 cells were sorted for both 2CLCs and mouse ESCs for each condition and the RNA was extracted using the TRIzol method. RNA was quantified using Qubit and assessed for quality using BioAnalyzer system (Agilent).
The library preparation was done using Library prep stranded total RNA Ribozero Plus Ligation (Illumina) and were sequenced using NextSeq 2000: 10M-50 cyc (SE50) to generate 40 million reads per sample.

treatment_protocol: All the drug treatments were carried out for 48hrs in S/L media unless mentioned otherwise. Curaxin (CBl0137) treatment: 0.5mM; Polyamine inhibition: 0.25mM of DFMO and 15mM of AMXT-1501. Mouse ESCs were plated in Serum/Lif medium in 6-well plates or in 150mm culture plates at 0.2 x 10^6 cells per well or 4 x 10^6 cells per plate. On the following day, the cells were transfected with a combination of two siRNAs against Zscan4; Ambion: Cat#4390771, ID: s233512 and Horizon discovery: J-162176-02-0050) or ON-TARGETplus Non-targeting Control siRNAs using Lipofectamine RNAiMAX at 50pM each per well for a 6-well plate and 1nM for 150mm culture plates. The transfection was repeated the following day and cells were harvested 24h post-transfection.


title: Ci10004_Plate_9_C_E01_CD3_low

description:
Library name: Ci10004_Plate_9_C_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Pb3A_MethylC-Seq


title: Pb2A_MethylC-Seq


title: Pb1B_MethylC-Seq


title: mESC-DFMO-AMXT-48-rep2

description: Library name: mESC-DFMO-AMXT-48-rep2

value: DFMO AMXT 48h


title: mESC-rep1

description: Library name: mESC-rep1


title: Ci10004_Plate_7_C_E01_CD3_low

description:
Library name: Ci10004_Plate_7_C_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10076_Plate_6_NC_B57_CD3_low

description:
Library name: Ci10076_Plate_6_NC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Pb3B_MethylC-Seq


title: Ci10067_Plate_2_C_B57_CD3_low

description:
Library name: Ci10067_Plate_2_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10004_Plate_2_C_B57_CD3_low

description:
Library name: Ci10004_Plate_2_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10074_Plate_9_EC_E03_CD3_low

description:
Library name: Ci10074_Plate_9_EC_E03_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Pb1A_MethylC-Seq


title: methyl-seq_2C-2

description: Library name: methyl-seq_2C-2

value: 2CLC (Mervl +)


title: methyl-seq_2C-3

description: Library name: methyl-seq_2C-3


title: mESC-DFMO-AMXT-24-rep1

description: Library name: mESC-DFMO-AMXT-24-rep1

value: DFMO AMXT 24h


title: biol rep 2, SW48 KRAS WT, Gln 4 mM, E2 10 uM

city: New Haven

first: Lingeng

last: Lu

state: CT

address: 60 College Street

department: Chronic Disease Epidemiology

institute: Yale School of Public Health

description: Library name: Sample_WT2_G4E10

data_processing:
STAR
STAR
Assembly: GRCh38
Supplementary files format and content: D3CRC_normgene.csv
Supplementary files format and content: csv file

source_name: colon

growth_protocol: SW48 MT and WT cells were maintained in DMEM supplemented with 10% fetal bovin serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy min plus kit (Qiagen).
RNA library for RNA-seq were prepared using NEBNext UltraTM RNA library Prep kit for Illumina following manufaturer's protocols

treatment_protocol: hanging-drop 3D model, in the presence or absence of glutamine (4 mM, 0 mM) and E2 (0, 10 uM) for 5 days

value: colon

value: SW48 KRAS WT

value: CRC

value: KRAS WT


title: Ci10074_Plate_2_EC_B57_CD3_low

description:
Library name: Ci10074_Plate_2_EC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: 2CLC-siZscan4-rep2

description: Library name: 2CLC-siZscan4-rep2

value: siRNA Zscan4


title: methyl-seq_2C-1

description: Library name: methyl-seq_2C-1


title: Ci10074_Plate_1_EC_B57_CD3_low

description:
Library name: Ci10074_Plate_1_EC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: Ci10027_Plate_1_NC_B57_CD3_low

description:
Library name: Ci10027_Plate_1_NC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: biol rep 1, SW48 KRAS WT, Gln 4 mM, E2 10 uM

description: Library name: Sample_WT1_G4E10


title: methyl-seq_ESC-1

description: Library name: methyl-seq_ESC-1


title: Injury Atlas, Control 1

description: Library name: LIB6220631

value: colon organoid


title: Ci10074_Plate_4_EC_B57_CD3_low

description:
Library name: Ci10074_Plate_4_EC_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: mESC-siZscan4-rep1

description: Library name: mESC-siZscan4-rep1


title: mESC-siZscan4-rep2

description: Library name: mESC-siZscan4-rep2


title: Ci10004_Plate_8_C_E01_CD3_low

description:
Library name: Ci10004_Plate_8_C_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: biol rep 2, SW48 KRAS WT, Gln 0, E2 10 uM

description: Library name: Sample_WT2_G0E10


title: biol rep 3, SW48 KRAS WT, Gln 0, E2 0

description: Library name: Sample_WT3_G0E0

value: Gln 0, E2 0


title: 2CLC-DFMO-AMXT-48-rep2

description: Library name: 2CLC-DFMO-AMXT-48-rep2


title: Ci10004_Plate_3_C_B57_CD3_low

description:
Library name: Ci10004_Plate_3_C_B57_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: biol rep 2, SW48 KRAS WT, Gln 0, E2 0

description: Library name: Sample_WT2_G0E0


title: 2CLC-DFMO-AMXT-48-rep1

description: Library name: 2CLC-DFMO-AMXT-48-rep1


title: Ci10027_Plate_2_NC_E01_CD3_low

description:
Library name: Ci10027_Plate_2_NC_E01_CD3_low
Activated CD3-low CD8s responding to HLA-transduced KF11-loaded 41A3 cell line at a significantly and 3X higher level than KF11-loaded parental (HLA-null) 41A3 cell line, sorted into individual wells of a plate, run on 2 different lanes and subjected to paired-end RNA-seq at a single well/cell level.


title: 2CLC-DFMO-AMXT-24-rep1

description: Library name: 2CLC-DFMO-AMXT-24-rep1


title: mESC-DFMO-AMXT-48-rep1

description: Library name: mESC-DFMO-AMXT-48-rep1


title: biol rep 2, SW48 KRAS MT, Gln 4 mM, E2 10 uM

description: Library name: Sample_MT2_G4E10

value: SW48 KRAS G12A

value: KRAS G12A


title: biol rep 3, SW48 KRAS WT, Gln 4 mM, E2 0

description: Library name: Sample_WT3_G4E0

value: Gln 4, E2 0


title: biol rep 1, SW48 KRAS MT, Gln 4 mM, E2 10 uM

description: Library name: Sample_MT1_G4E10


title: 2CLC-siZscan4-rep1

description: Library name: 2CLC-siZscan4-rep1


title: biol rep 3, SW48 KRAS WT, Gln 4 mM, E2 10 uM

description: Library name: Sample_WT3_G4E10


title: biol rep 1, SW48 KRAS WT, Gln 4 mM, E2 0

description: Library name: Sample_WT1_G4E0


title: biol rep 3, SW48 KRAS MT, Gln 4 mM, E2 10 uM

description: Library name: Sample_MT3_G4E10


title: biol rep 2, SW48 KRAS MT, Gln 4 mM, E2 0

description: Library name: Sample_MT2_G4E0


title: mESC-DFMO-AMXT-24-rep2

description: Library name: mESC-DFMO-AMXT-24-rep2


title: biol rep 1, SW48 KRAS WT, Gln 0, E2 10 uM

description: Library name: Sample_WT1_G0E10


title: ApoE-deficient (ApoE-/-/C57BL/6) background mice under Western diet (WD)

city: Boston

first: Kulandaisamy

last: Arulsamy

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

description:
Library name: WT-ApoE-aorta-WD
10X Genomics

data_processing:
Cell Ranger (version 7.1.0) to map the raw reads of ScRNA sequencing data to the mouse genome (version mm10) and to count UMI for each gene.
Assembly: mm10
Supplementary files format and content: tsv file; These TSV files contain the raw gene count matrix.

source_name: Aorta

extract_protocol:
Mouse aortas were cut into fine pieces and placed in 5 mL of enzyme solution at 37° C. (Collected the supernatant every 10 min until all the fine pieces were digested). (Enzyme solution: 5 mL of DMEM, Collagenase type I: 5mg/mL (Gibco), Collagenase type IV: 5mg/mL (Gibco), Liberase:5mg/mL (Roche). This solution was then filtered with a 40-µm strainer, centrifuged (400g for 5 minutes), and the cell pellet was suspended in 90 µL of buffer containing 0.5% BSA and 2 mmol/L EDTA in PBS. Then, 20 µL of CD31 microbeads (Miltenyi Biotec) was added to the suspension at 4° C for 15 minutes. Microbeads were passed through an MS column (Miltenyi Biotec).
single-cell RNA-seq library construction following the protocol provided by 10X Genomics.

value: Aorta


title: scTCR-seq_Donor CD4+T, liver, No_GVHD, D60

city: Monrovia

first: Xiwei

last: Wu

address: 655 HUNTINGTON DR.

institute: City of Hope

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Comma-seperated contig annotations and barcode information
Library strategy: scTCR-seq

source_name: Liver

extract_protocol:
number of thymic lymphocytes from non-GVHD and GVHD group were taken and centrifuged.
Single-cell RNA-seq libraries were were constrcted using Single Cell Enrichment kit.

value: Liver

value: Donor CD4+ T cells

value: No GVHD/D60


title: 2CLC-rep1

description: Library name: 2CLC-rep1


title: 2CLC-siCtrl-rep1

description: Library name: 2CLC-siCtrl-rep1

value: siRNA control


title: biol rep 2, SW48 KRAS WT, Gln 4 mM, E2 0

description: Library name: Sample_WT2_G4E0


title: mESC-curaxin-rep1

description: Library name: mESC-curaxin-rep1

value: ESC (Mervl -)

value: curaxin


title: biol rep 1, SW48 KRAS MT, Gln 0, E2 10 uM

description: Library name: Sample_MT1_G0E10

value: colon


title: scRNA-seq_Donor CD4+T, liver, No_GVHD, D60

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Immunocytes were released by dispase/collagenase II solution followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). Cells were then purified by fluorescence-activated cell sorting.
Library preparation for single cell RNA-seq and TCR-seq was done with the Chromium Single Cell 5' Reagent Kits from 10× Genomics according to manufacturer's protocol. Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-in-emulsions (GEMs). GEM-reverse transcriptions (GEM-RTs) were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific). After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing single cell RNA-seq libraries were constructed using the Chromium Single-Cell 5′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. The purity and library size were validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies). The quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen. Sequencing libraries were loaded on a NovaSeq 6000 (Illumina).


title: biol rep 3, SW48 KRAS MT, Gln 0, E2 0

description: Library name: Sample_MT3_G0E0


title: 2CLC-siCtrl-rep3

description: Library name: 2CLC-siCtrl-rep3

value: 2CLC (Mervl +)


title: Hu_iPSCs

description: Library name: Hu_iPSCs

data_processing:
The ParseBioscience processing pipeline (v1.1.2) was used with default settings to align sequencing reads to the mm10 mouse genome and hg38 human genome
The count matrixes were analyzed with the Seurat R package in order to cluster the data and generate UMAPs.
for Hu_iPSCs dataset Hu_iPSCs_ctrl A1-A4, Lib_not_used A5-A8, Hu_iPSCs_Curaxin A9-A12
for Mu_Mervl_to not_used A1-A9, Mu_Mervl_to_Curaxin A12, Mu_Mervl_to_ctrl A10-A11
Assembly: mm10 or hg38
Supplementary files format and content: csv file and matrix files that are output of the ParseBioscience pipeline

source_name: Human iPSCs

growth_protocol: Mouse : Cells were maintained in Serum+Lif (S/L) medium (KnockOut DMEM supplemented with 15% ES cell qualified FBS, 1% GlutaMAX, 1% MEM non-essential amino acids, 1% penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 10 ng/mL Lif (Miltenyi Biotec, Cat #130-099-895) on gelatine-coated plates in a humidified incubator (37°C, 5% CO2). ES R1 cell line was maintained under the same conditions. Human : HuIPSCs were maintained on feeders in PXGL culture medium: N2B27 (1:1 DMEM/F12:Neurobasal, 0.5X N2 supplement, 0.5X B27 supplement, 1X nonessential amino acids, 2mM L-Glutamine, 1X penicillin-streptomycin, 0.1mM 2-mercaptoethanol, supplemented with 1mM PD0325901 (Stemcell Technologies, #72184), 2mM Gö6983 (Stemcell Technologies, #72462), 2mM XAV939 (Stemcell Technologies, #72674) and 10ng/ml human LIF (Stemcell Technologies, #78055). Medium was refreshed every day for all the cell lines.

extract_protocol:
Mouse ESCs and human iPSCs (untreated and treated with curaxin) were subjected to a split-pool combinatorial barcoding method of scRNA-sequencing using single-cell whole-transcriptome kits (Evercode WT Mini v2) from Parse Biosciences according to the manufacturer’s instructions.
(Evercode WT Mini v2) from Parse Biosciences according to the manufacturer’s instructions.

treatment_protocol: Curaxin (CBl0137) treatment: 0.5mM for 48h

value: Human iPSCs

value: none/Curaxin


title: biol rep 3, SW48 KRAS WT, Gln 0, E2 10 uM

description: Library name: Sample_WT3_G0E10

value: SW48 KRAS WT

value: CRC

value: KRAS WT


title: 2CLC-curaxin-rep2

description: Library name: 2CLC-curaxin-rep2


title: 2CLC-rep2

description: Library name: 2CLC-rep2


title: biol rep 1, SW48 KRAS MT, Gln 0, E2 0

description: Library name: Sample_MT1_G0E0

value: SW48 KRAS G12A

value: Gln 0, E2 0


title: biol rep 1, SW48 KRAS WT, Gln 0, E2 0

description: Library name: Sample_WT1_G0E0


title: Ribo_sh-ABCE1_2

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

library_source: other

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.
Supplementary files format and content: comma-delimited text files including normalized read density around stop codons for each sample.

molecule: other

extract_protocol:
For MRPA, fractions of 500 μl corresponding to monosome or polysome were collected for RNA extraction using TRIzol LS. RNA was purified using RNA Clean & Concentrator and eluted with 11 μl of nuclease-free water.  For Ribo-seq, RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
For  Ribo-seq, 14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). For MPRA, The purified RNA was reverse transcribed using SuperScript III and gene-specific primers. In brief, RNA samples were mixed with 1 μl of 10 mM dNTP, 2 pmol reverse primer and incubated at 65 °C for 5 min, then immediately placed on ice for 1 min. The reverse transcription was carried out by incubating with the 7 μl reaction mixture (5 × first strand buffer, 0.1 M DTT, RNaseOUT and SuperScript III) at 50 °C for 60 min followed by heating at 70 °C for 15 minutes. The products were then amplified with Illumina-based sequencing primers with barcode. PCR were performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. The PCR was initiated at 98 °C, 30 s; then (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. The PCR products with the expected size 190 bp were excised from a 8% polyacrylamide TBE gel. The DNA products were recovered from DNA elution buffer.

value: WT


title: 2CLC-DFMO-AMXT-24-rep2

description: Library name: 2CLC-DFMO-AMXT-24-rep2

value: DFMO AMXT 24h


title: mESC-curaxin-rep2

description: Library name: mESC-curaxin-rep2


title: 2CLC-curaxin-rep1

description: Library name: 2CLC-curaxin-rep1


title: RNA_9N_heavy


title: RNA_9N_light


title: OCILY19 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 1

city: Stanford

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

description: Library name: _OCILY19_1nM4hTCIP3_1

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed from adapters using cutadapt using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1.
Transcripts were quantified using kallisto against the human Gencode v33 indexed transcriptome and annotations.
Assembly: human Gencode v33
Supplementary files format and content: tab-delimited files include raw counts for each sample. TPM values should be ignored for 3' end counting-based data.

extract_protocol:
Cells were plated at 1M/mL. For KP422 cells, cells were harvested in TRIsure (Bioline 38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo R2062) treated with DNAseI. For RL, SUDHL4, and OCILY19 cells, cells were harvested in Zymo DNA/RNA Shield (R1100).
For sequencing library preparation for KP422 cells, polyA-tailed mRNA was enriched (NEB E7490) and prepared into paired-end libraries (NEB E7765) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. For sequencing library preparation for RL, SUDHL4, and OCILY19 cells, 3' end counting was used (Plasmidsaurus): polyA mRNA was captured, reverse transcribed, and barcoded with a unique molecular identifier; then, double-stranded cDNA was generated and tagmented; finally, libraries were amplified using Illumina index primers for sequencing.

treatment_protocol: Treated at 1million cells/mL density at indicated timepoints and doses with final DMSO concentration of 0.1%

value: DLBCL

value: 1 nM TCIP3

value: 4 hours


title: OCILY19 cells, DMSO treatment, 4 hours, bio rep 3

description: Library name: _OCILY19_DMSO_3


title: 2CLC-siCtrl-rep2

description: Library name: 2CLC-siCtrl-rep2

value: siRNA control


title: RNA_9N-TAGT_mono


title: OCILY19 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 3

description: Library name: _OCILY19_1nM4hTCIP3_3


title: RNA_9N-TAGT_light


title: SUDHL4 cells, 1 nM TCIP3 treatment,4 hours, bio rep 2

description: Library name: _SUDHL4_1nM4hTCIP3_2


title: Ribo_eRF1IP_+CHX


title: SUDHL4 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 1

description: Library name: _SUDHL4_1nM4hTCIP3_1


title: biol rep 3, SW48 KRAS MT, Gln 4 mM, E2 0

description: Library name: Sample_MT3_G4E0

value: KRAS G12A

value: Gln 4, E2 0


title: EC-specific CD45-deficient mouse strain  on an ApoE-deficient (ApoE-/-/C57BL/6) background mice under WD

description:
Library name: EC-iCD45KO-ApoE-aorta-WD
10X Genomics

value: Aorta


title: SUDHL4 cells, DMSO treatment, 4 hours, bio rep 2

description: Library name: _SUDHL4_DMSO_2


title: SUDHL4 cells, DMSO treatment, 4 hours, bio rep 1

description: Library name: _SUDHL4_DMSO_1


title: Ribo_input_-CHX


title: Ribo_Rps26-OE2

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.

extract_protocol:
RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).


title: OCILY19 cells, DMSO treatment, 4 hours, bio rep 1

description: Library name: _OCILY19_DMSO_1


title: biol rep 1, SW48 KRAS MT, Gln 4 mM, E2 0

description: Library name: Sample_MT1_G4E0

value: colon


title: biol rep 3, SW48 KRAS MT, Gln 0, E2 10 uM

description: Library name: Sample_MT3_G0E10


title: biol rep 2, SW48 KRAS MT, Gln 0, E2 0

description: Library name: Sample_MT2_G0E0


title: scTCR-seq_Donor CD4+T, liver, cGVHD, D60

value: Liver

value: Donor CD4+ T cells


title: scRNA-seq_Donor CD4+T, liver, cGVHD, D60


title: Ribo_Rps26-OE1


title: RL cells, 1 nM TCIP3 treatment, 4 hours, bio rep 1

description: Library name: _RL_1nMTCIP3_4h_1

source_name: RL

value: RL


title: Ribo_vector2