title: UV2_03

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description:
UV♀2
Sample 6

data_processing:
The fastq files were trimmed to remove the adapter sequence and low-quality ends using Trim Galore!.
The resulting reads were aligned to the UCSC mm10 using STAR.
TPM values were obtained using RSEM.
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text file includes count values for all samples

extract_protocol:
Cells were harvested using 0.05% trypsin-EDTA and then total RNA was isolated using the RNeasy Micro Kit (Qiagen).
Library DNAs were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: cell line

value: endothelial cells

value: (BALB/c x C57BL/6)F1


title: IBD_336603, colon

status: Public on Oct 16 2024

type: SRA

city: Chapel Hill

first: Terrence

last: Furey

state: NC

address: 120 Mason Farm Rd

country: USA

institute: University of North Carolina at Chapel Hill

description: IBD tissue

library_source: transcriptomic

data_processing:
STAR v2.7.9a using --WaspOutputMode
Read counts quantified using QTLtools v1.3.1
Read counts were normalized using edgeR TMM and rank inverse normal transformed using R v4.1.3
Assembly: hg38, GENCODE v39
Supplementary files format and content: tab-delimited text file includes normalized count data for each sample
Supplementary files format and content: tab-delimited text file includes eQTL covariates for each sample

molecule: total RNA

organism: Homo sapiens

source_name: colon

extract_protocol:
Tissue was digested with TRIzol and RNA was extracted using chloroform. RNA was isolated using Norgen Biotek Total RNA Isolation Plus Kit (cat#48400).
Libraries were constructed using the Kapa Total RNA Stranded with Ribo Erase.

tag: tissue

value: colon

tag: disease

value: IBD

tag: gender

value: Male

tag: batch

value: I


title: IBD_383068, colon

description: IBD tissue


title: UV2_02

country: Japan

description:
UV♀2
Sample 5

organism: Mus musculus

tag: cell type

tag: strain


title: UV2_01

description:
UV♀2
Sample 4


title: HEC1A C2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: HEC-1-A cells incubated with McCoy's 5A media

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using HISAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName

source_name: Endometrial cancer cell line-HEC-1-A

growth_protocol: HEC-1-A cells were cultured in McCoy's 5A media supplemented with 10% FBS

extract_protocol:
Total RNA from HEC-1-A control and SMIP34-treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide

treatment_protocol: HEC-1-A cells were incubated in 10% FBS McCoy's 5A medium with or without SMIP34 for 24 hrs.

tag: cell-line

tag: treatment

value: Control


title: IBD_105888, colon

description: IBD tissue

value: Female


title: IBD_771279, colon

description: IBD tissue

value: H


title: bEnd.3_03

description: Sample 3

value: BALB/c


title: IBD_268860, colon

description: IBD tissue


title: bEnd.3_02

description: Sample 2


title: scRNA-seq for control mouse, GEX

city: New York

first: Erik

last: Sulman

state: NY

address: 522 1st Ave, Smilow Bldg, Rm 801C

institute: NYU Grossman School of Medicine

description:
barcodes-ctrl.tsv.gz
features-ctrl.tsv.gz
matrix-ctrl.mtx.gz

data_processing:
CellRanger 6.0.1 count and aggr functions were used to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files for each of tumor and control mice.
Cell barcodes from CellRanger output were used as whitelist to quantify ADTs using CITE-seq-Count (v1.4.5)
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes-ctrl.tsv.gz and barcodes-tumor.tsv.gz; features-ctrl.tsv.gz and features-tumor.tsv.gz; matrix-ctrl.mtx.gz and matrix-tumor.mtx.gz
Library strategy: CITE-seq

source_name: peripheral blood

growth_protocol: The DSVD lung adenocarcinoma mouse model was intranasally induced with Ad-CMV-Cre (5 × 107 plaque-forming units).

extract_protocol:
Approximately 1 ml of blood was collected from each mouse by cardiac puncture using an 18 g needle, three weeks after tumor implantation. The samples were stained with a panel of 13 barcoded CITE-seq-compatible antibodies.
The CITE-seq and hashing protocol described by Stoeckius et al (Nat Methods 2017) was used to generate an antibody-derived tag sequencing library and 3' gene expression library.

value: peripheral blood

tag: genotype

value: WT

tag: library type

value: mRNA


title: bEnd.3_01

description: Sample 1


title: IBD_150644, colon

description: IBD tissue


title: 20690, Mouse ONH 12mo C57BL/6J control

city: Madison

first: Emma

middle: K

last: Geiduschek

state: WI

address: 1300 University Ave

institute: University of Wisconsin - Madison

data_processing:
Gene Set Enrichment Analysis (GSEA) was performed by ranked enrichment analysis with MolSigDB (https://www.gsea-msigdb.org/gsea/msigdb, version v7.5.1). The subsequent ONH RNAseq data set was analyzed using recommendations from the GSEA tutorial for RNAseq data (https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html).
Assembly: GRCm39
Supplementary files format and content: GSEA-based analyses using the MolSigDB gene sets for mRNA-Seq datasets including Hallmark (H), RECTOME and KEGG pathway (C2). The version of MolSigDB used was v7.5.1 (released January 2022).

source_name: Optic nerve head

extract_protocol:
ONH sections were harvested via laser capture microdissection. RNA was extracted using Qiagen Rneasy microkit (REF#74034). RNA was verified for purity and integrity using the NanoDropOne Spectrophotometer and Agilent 2100 Bioanalyzer, respectively.
Ultra-low RNA input libraries were generated using the Takara “SMART-Seq v4 Low Input RNA Kit for Sequencing” (Takara, Mountain View, CA, USA) for cDNA synthesis and the Illumina NexteraXT DNA Library Preparation (Illumina, San Diego, CA, USA) kit for cDNA dual indexing. Full length cDNA fragments are generated from 1-10ng total RNA by the Takara SMART technology. cDNA fragments are fragmented and dual indexed in a single step by taking advantage of the Nextera kit’s simultaneous transposon and tagmentation step. Libraries were standardized to 2nM. Paired-end 2x150bp with 30M reads/sample sequencing was performed using standard SBS chemistry on an Illumina NovaSeq6000 sequencer. Generated raw reads were qualitied controlled, aligned, and mapped to Mus musculus using Spliced Transcripts Alignment to a Reference (STAR),58 followed by estimation of mapped pair-end reads using RNA-Seq by Expectation Maximization (RSEM).

value: Optic nerve head


title: IBD_555519, colon

description: IBD tissue


title: intervertebral disc degeneration3

city: WuHan

first: Xiao-Jun

last: Yu

address: Jiefang Blvd

department: Department of Orthopedics, Tongji Hospital, Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: intervertebral disc

extract_protocol:
Take the intervertebral disc of mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: intervertebral disc degeneration


title: IBD_124014, colon

description: IBD tissue


title: IBD_571968, colon

description: IBD tissue


title: IBD_664409, colon

description: IBD tissue


title: 20687, Mouse ONH 12mo C57BL/6J control


title: intervertebral disc degeneration2


title: IBD_900592, colon

description: IBD tissue


title: wild type3

value: wild type


title: 20688, Mouse ONH 12mo C57BL/6J control


title: intervertebral disc degeneration1


title: scRNA-seq for tumor-implanted mouse, ADT

description:
barcodes-tumor.tsv.gz
features-tumor.tsv.gz
matrix-tumor.mtx.gz

library_source: other

molecule: protein

value: EGFRex20ins SVD

value: intranasal induction with adeno-Cre

value: ADT


title: IBD_296868, colon

description: IBD tissue

value: colon


title: wild type2


title: 20404, Mouse ONH 12mo B6.EDA+/+


title: scRNA-seq for control mouse, ADT


title: scRNA-seq for tumor-implanted mouse, GEX


title: 20685, Mouse ONH 12mo C57BL/6J control


title: IBD_271984, colon

description: IBD tissue

value: IBD


title: 20403, Mouse ONH 12mo B6.EDA+/+


title: 20396, Mouse ONH 12mo B6.EDA+/+


title: 20397, Mouse ONH 12mo B6.EDA+/+


title: 20689, Mouse ONH 12mo C57BL/6J control


title: IBD_154488, colon

description: IBD tissue


title: 20395, Mouse ONH 12mo B6.EDA+/+


title: Tumor biopsy, S71wt

city: Bethesda

first: Jayakumar

middle: R

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing
TPM files generated by sequencing each sample from either of the two BRCA status cohorts (n=15 for BRCAmut and n=20 for BRCAwt), obtained from the sequencing core facility, was combined into single files for each cohort and processed to remove low counts, quartile normalized and log2 transformed prior to analysis on graphpad prism software.  The raw TPM data is attached as processed data files for each cohort in excel format.
Assembly: HG38
Supplementary files format and content: The TPM sequence files are provided as excel files.  The unprocessed raw files are provided as gzipped FASTQ files.

source_name: Ovarian

growth_protocol: Tumor needle biopsies were frozen in OCT compound at -80 Celsius.  Sections were used for total RNA isolation

extract_protocol:
Qiagen micro RNA isolation kit
RNA sequencing (RNAseq) data were obtained from total RNA from fresh frozen tumor biopsy samples from 115 BRCAmut HGSOC patients and 20 BRCAwt HGSOC patients  HGSOC patients enrolled in the clinical trial at the National Cancer Institute (ClinicalTrials.gov, NCT02203513). RNAseq was performed using a HiSeq4000 sequencing system (Illumina) at the CCR Sequencing Facility/NCI on pre-treatment biopsy samples.s.  Paired-end sequencing was done.  Quartile normalization and log-transformation prior to analysis were performed on datasets.

value: Ovarian

value: Tumor

value: Homo sapiens

value: Prexasertib

tag: mutation status

value: BRCAwt


title: Tumor biopsy, S73wt


title: 20167, Mouse ONH 22mo C57BL/6J control


title: Tumor biopsy, S68wt


title: IBD_974304, colon

description: IBD tissue

value: Female

value: I


title: IBD_838579, colon

description: IBD tissue

value: Male


title: Tumor biopsy, S55wt


title: Tumor biopsy, S59wt


title: 20166, Mouse ONH 22mo C57BL/6J control


title: IBD_671530, colon

description: IBD tissue


title: Tumor biopsy, S64wt


title: wild type1


title: 20165, Mouse ONH 22mo C57BL/6J control


title: IBD_696153, colon

description: IBD tissue


title: ZR-75-1 enobosarm resistant enobosarm + ruxolitinib-4

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were normalized using CPM
Assembly: hg38
Supplementary files format and content: raw counts

molecule: polyA RNA

source_name: breast

extract_protocol:
RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.
Illumina Stranded RNA

value: breast

value: breast cancer


title: 20139, Mouse ONH 22mo C57BL/6J control

value: Optic nerve head


title: ZR-75-1 enobosarm resistant enobosarm + ruxolitinib-3


title: ZR-75-1 enobosarm resistant enobosarm + ruxolitinib-2


title: flu_D30_tdTomato_neg_rep1

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

library_source: transcriptomic single cell

data_processing:
Read alignment and cell calling using STAR-solo (velocyto output)
Ambient-RNA correction using scvi-tools scAR
h5ad file creation using anndata
h5ad file creation using anndata
Assembly: GRCm39
Supplementary files format and content: .h5ad

source_name: lung

extract_protocol:
Primary mouse lung tissue was dissociated into single-cell suspensions and subjected to FACS.
10X Genomics 3’-biased gene expression library construction (v3.1)

value: lung

tag: time post_treatment

tag: lineage sort

value: influenza


title: 19852, Mouse ONH 22mo B6.EDA+/+


title: Tumor biopsy, S62wt


title: Tumor biopsy, S45wt


title: Tumor biopsy, S39wt


title: IBD_841565, colon

description: IBD tissue


title: Tumor biopsy, S52wt


title: 19851, Mouse ONH 22mo B6.EDA+/+


title: ZR-75-1 enobosarm resistant enobosarm + ruxolitinib-1


title: Tumor biopsy, S44wt


title: 19848, Mouse ONH 22mo B6.EDA+/+


title: ZR-75-1 enobosarm resistant enobosarm-4


title: 3T3-L1, igf2bp2_IP_1

city: Yangling

first: Mingkun

last: Chao

address: No. 22 Xinong Road, Yangling, Shaanxi Province 712100, China

institute: NWAFU

data_processing:
For RNA-seq: The sequencing process involves quality control, alignment, assembly, filtering, and quantification.
For RIP-seq: The sequencing process involves Trimming (fastp), QC (fastqc), mapping (BWA), peak calling (MACS2), and motif identification (homer, findMotifsGenome.pl).
Assembly: https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
For RNA-seq: Total RNA was extracted from the white adipose tissue of both the control and experimental (20mg/kg) groups of mice. Pair-end sequencing of the RNA was conducted using the Illumina platform (Illumina, CA, USA). For IGF2BP2 RIP-seq: Magna RIP RNA-Binding Protein Immunoprecipitation Kit(Merck sigma, USA) was used for IGF2BP2 RNA Immunoprecipitation (RIP). 3T3-L1 cells were lysed by RIP Lysis Buffer. Magnetic beads were co-incubated with IGF2BP2 antibody (Thermo Fisher Scientific, USA). Nucleic acid-protein immune complexes were collected by immunoprecipitation of lysates with incubated magnetic beads overnight at 4 °C. RNA on the protein A/G magnetic beads was collected and purified using proteinase K Buffer, etc., and then subjected to RNA high-throughput sequencing and biosignature analysis studies.
RNA is extracted using the Trizol method and is quality checked before sequencing and before the RIP assay.

value: adipocytes

value: WT

value: adipogenic differentiation


title: 20138, Mouse ONH 22mo C57BL/6J control


title: Tumor biopsy, S72wt


title: ZR-75-1 enobosarm resistant enobosarm-3


title: Tumor biopsy, S69wt


title: WAT, HF_3

source_name: WAT

value: WAT

value: HF solution prepared with DMSO used for intraperitoneal injection.


title: ZR-75-1 enobosarm resistant enobosarm-1


title: WAT, HF_1


title: WAT, Ctrl_3

value: DMSO solution prepared in saline used for intraperitoneal injection.


title: ZR-75-1 enobosarm resistant enobosarm-2


title: WAT, HF_2


title: WAT, Ctrl_2


title: ZR-75-1 parental enobosarm-3


title: Tumor biopsy, S61wt

value: Ovarian

value: Tumor

value: Homo sapiens


title: ZR-75-1 parental enobosarm-4


title: ZR-75-1 parental enobosarm-2


title: Tumor biopsy, S50wt

value: Prexasertib

value: BRCAwt


title: ZR-75-1 parental enobosarm-1


title: Tumor biopsy, S40wt


title: PD-L1 positive D11

city: Tours

first: Guy

last: Ilango

address: 10, boulevard Tonnellé

country: France

institute: University of Tours

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing , genes counting  were made using Cellranger 7.1.0
Assembly: mm10
Supplementary files format and content: tab-separated values and matrix files

extract_protocol:
Freshly collected lungs were harvested and single cell suspension of immune cells was performed. Cell suspensions were labelled with antibodies and neutrophils were purified using a flow cytometry-based sorting (FACS Melody, BD Biosciences) as live CD45+ SiglecF- CD11b+ Ly6G+ PD-L1+/-. Cells were collected in low binding tubes containing PBS pH 7.2 supplemented with 0.04% BSA (Mg2+/Ca2+ EDTA free).
Libraries were performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 Dual Index). Briefly, Gel Beads-in-emulsion (GEM) were generated by combining barcoded gel beads, partitioning oil and the Master Mix containing neutrophils onto a Chromium NextGEM Chip G. After GEM generation, gel beads were dissolved and partitioned cells were lysed before reverse transcription (RT) to obtain barcoded, full-length cDNA from poly-adenylated mRNA (primers contained an Illumina TruSeq Read 1, a 10x Barcode, a Unique Molecular Identifier UMI and poly(dT) sequence). The pooled barcoded cDNA was then cleaned up with Silane magnetic beads to purify the first-strand cDNA and amplified via PCR to generate sufficient mass for library construction. SPRIselect reagent was used to optimize the cDNA fragment size. During the library construction, Illumina TruSeq Read 2 primer, i7 and i5 sample indexes and paired-end constructs with P5 and P7 sequences were added via End Repair, A-tailing, Adaptor Ligation and PCR. The final step was sequencing using an Illumina NovaSeq 6000.

treatment_protocol: C57Bl/6j mice were intranasally infected with 150pfu of a virulent strain of influenza A virus (H3N2/A/Scotland/74)

value: Neutrophils

value: C57Bl/6 WT

value: IAV infected


title: WAT, Ctrl_1


title: Retina_Uninfected S5

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 10X genomics

data_processing:
Demultiplexing, barcode processing, counts and aggregation were performed using cellranger v. 5.0.1.
Assembly: mm10
Supplementary files format and content: tsv.gz
Supplementary files format and content: tsv.gz

source_name: retina

extract_protocol:
Retinas were gently peeled away and transferred to ice cold PBS. A Nuclei PURE Prep Nuclei Isolation Kit (Sigma – Cat. # NUC-201) was used and Nuclei were counted in a hemacytometer and used for 10x Genomics RNAseq analysis
8,000 nuclei per retina pool were loaded on a 10X Genomics Next GEM chip and single-nuclei GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate cDNA and sequencing libraries were performed following 10X Genomics' protocol using the Chromium Next GEM Single Cell 3? Reagent Kits v3.1

value: retina

value: untreated


title: Tumor biopsy, S37wt


title: PD-L1 negative D11

description: 10X genomics

value: lung


title: Tumor biopsy, S57wt


title: Retina_Uninfected S7

description: 10X genomics


title: Tumor biopsy, P10mut

value: BRCAmut


title: Tumor biopsy, P35mut


title: Tumor biopsy, S48wt


title: Tumor biopsy, P11mut


title: BF10D

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

description: primary cells

data_processing:
The raw data was analyzed by Cell Ranger v3.0 using default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Bone callus

extract_protocol:
To isolate the periosteal cells, the muscle was removed from the femur. The callus was separated and thoroughly cleaned to remove bone marrow. The callus was then crushed and digested in type I collagenase (3 mg/mL, Sigma) at 37℃ for 1 hour. The digested cells were then transferred to PBS, centrifuged, and resuspended in PBS plus 2% serum. A single-cell suspension was produced by filtration through a 40-mm mesh. Samples were then stained for flow cytometry using a combination of the select antibodies: anti-CD31 (1:200), anti-CD45 (1:200), anti-TER119 (1:200). All staining was performed on ice for 0.5 hours. Identification and screening of dead cells were achieved by the 7-AAD staining. The lin- live cells were selected for scRNA-seq.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Bone callus

value: bone callus mesenchymal cells

tag: condition

value: femoral fracture

tag: time point

value: Day 10 after fracture


title: BF7D

description: primary cells

value: Day 7 after fracture


title: Tumor biopsy, P33mut

value: Ovarian

tag: cell line


title: Tumor biopsy, P15mut

tag: tissue

value: Tumor


title: Tumor biopsy, P37mut

value: Homo sapiens


title: Tumor biopsy, S53wt

value: Prexasertib


title: BF14D

description: primary cells

value: Day 14 after fracture


title: Tumor biopsy, P6mut


title: REX-1 RFP cells, ND

city: Detroit

middle: A

last: Rappolee

state: MI

address: 275 E Hancock St

department: OBGYN

institute: Wayne State University

data_processing:
Using CellRanger 6.0.1 from 10x Genomics
Raw Chromium scRNA-seq output was processed to align reads, generate feature–barcode matrices.
The mm10 mouse reference genome was used to align the single-cell sequence reads.
Specify the estimated number of cells to be 10,000 for each sample using the ‘force-cell’ option, to reflect the input cells during cell extraction.
The median number of genes detected per cell for 5 samples (NS, ND, S200, S250, S300) are 1,102, 547, 582, 625 and 561, respectively.
The fraction reads in cells are 28.2%, 24.1%, 22.6%, 27.1% and 20.4%, respectively.
The median unique molecular identifier (UMI) counts per cell for each sample (NS, ND, S200, S250, S300) are 2,135, 818, 887, 939 and 800, respectively.
In the quality control process, samples will be filtered based on the genes expressing at least 10 cells and cells expressing at least 200 genes.
Cells with more than 20% of mitochondrial sequencing reads were filtered out.
After quality control, data normalization and scaling were performed in downstream analysis with Seurat 4.1.1 packages in R version 4.1.2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Embryonic Stem Cell

growth_protocol: ESC passaged and grown with LIF+ media for ~18hr until ~24% confluence. They were then grown under their corresponding condition.

extract_protocol:
Cells were then washed and lysed using Trizol.
Lexogen 3' Quant-seq protocol

treatment_protocol: Cells were grown under stimulation for 72hr.

value: REX-1 RFP

tag: lif presence

value: negative

value: ND

tag: treatment time


title: REX-1 RFP cells, NS

value: positive

value: NS


title: REX-1 RFP cells, Sorbitol 250mM

value: Sorbitol 250mM


title: REX-1 RFP cells, Sorbitol 200mM

value: Sorbitol 200mM


title: Tumor biopsy, P4mut

value: BRCAmut


title: REX-1 RFP cells, Sorbitol 300mM

value: Sorbitol 300mM


title: Tumor biopsy, P3mut


title: Tumor biopsy, P2mut


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 3

city: Houston

first: FEI

last: YUAN

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v.0.23.2 (Chen et al. 2018) with default parameters and duplicated reads with the --dup option enabled.
The trimmed reads were aligned to the reference genome mm10 using STAR aligner v.2.7.3a (Dobin et al. 2013) and gene-specific read counts (on reverse strand) were obtained with the --quantMode GeneCounts option enabled
The Transposable Elements (TE) annotation, including their classification in classes and families, was based on GTF file curated by the Hammell Lab: (http://labshare.cshl.edu/shares/mhammelllab/wwwdata/TEtranscripts/TE_GTF/mm10_rmsk_TE.gtf.gz). The reads mapped to TE classes were quantified using featureCounts v.2.0.3 (Liao et al. 2014) with option "-p -M -s 2".
Assembly: mm10
Supplementary files format and content: CSV (comma-separated values) gzip text file include gene level feature counts for each Sample
Supplementary files format and content: CSV (comma-separated values) gzip text file include Transposible Elements class level feature counts for each Sample

source_name: 2153L GEMM TNBC tumor

growth_protocol: Fresh tumor fragments were transplanted into the cleared mammary fat pads of 6- to 8-week-old female BALB/c mice.

extract_protocol:
Input and dsRIP RNAs were extracted using Direct-zol RNA Microprep Kit (ZYMO Research, R2060). The antibodies used in the study were manufactured by Exalpha Biologicals, Inc. with catalog number 10010500.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Kit (Illumina, 20040525) following Illumina’s recommended protocol. First stranded cDNA synthesis was performed using SuperScript III (ThermoFisher, 18080044) with the following modifications: RNA was heated to 70°C for 3 minutes to reduce secondary structure, followed by reverse transcription for 10 minutes at 25°C, 50 minutes at 50°C, and 15 minutes at 70°C. Amplified libraries were purified and quantified using the KAPA quantification kit (Roche).

treatment_protocol: When tumors reached a volume of approximately 100 mm3, mice were randomized and treated with drugs. Tumor volume was monitored using calipers and calculated as length × width2 / 2. The IRE1α RNase inhibitor ORIN1001 formulated in 1% microcrystalline cellulose and 50% sucrose solution was administered by daily oral gavage (150 mg/kg). Docetaxel (MilliporeSigma) was dissolved in 25% Tween 80 and 12% ethanol and administered through weekly i.p. injections at 10 mg/kg dose. Mice undergoing mono-therapy also received vehicle as in the combination treatment study.

value: 2153L GEMM TNBC tumor

value: Bulk Tumor cells

value: p53 knocckout

tag: rip antibody

value: anti double-stranded RNA (J2) [Exalpha, catalog number 10010500)

value: ORIN1001 plus Docetasel


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 2

tag: cell type


title: Tumor biopsy, P34mut

value: Ovarian

value: Tumor

value: Homo sapiens


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 1


title: Tumor biopsy, P38mut

value: Prexasertib


title: Tumor biopsy, P13mut


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 3

value: Docetaxel


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 2


title: Tumor biopsy, P5mut


title: Tumor biopsy, P8mut


title: Ovcar8, Serum starved, rep 3

city: Pittsburgh

first: Katherine

last: Aird

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: Ovcar8 cells were cultured in RPMI-1640 + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)
Next generation sequencing was performed at Novogene using a NovaSeq 6000 Sequencing System  (Illumina)

treatment_protocol: Cells were cultured with or without 5% FBS for 48 hours.

value: ovarian cancer

value: Serum starved


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 1


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 3

value: ORIN1001 (IRE1a RNase inhibitor)


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 1


title: Ovcar8, Serum starved, rep 2


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 2


title: Ovcar8, FBS, rep 3

value: +FBS


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 3

value: Vehicle


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 2


title: Ovcar8, FBS, rep 2


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 3

value: none (input)


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 1


title: Ovcar8, FBS, rep 1


title: 2153L GEMM TNBC Combo, Input, biol rep 2


title: Ovcar8, control, rep 3

treatment_protocol: Cells were treated for 72h with 10mM sodium acetate

value: control


title: 2153L GEMM TNBC Combo, Input, biol rep 3

value: 2153L GEMM TNBC tumor


title: Ovcar8, acetate, rep 3

value: 10mM sodium acetate


title: Ovcar8, control, rep 2


title: 2153L GEMM TNBC Combo, Input, biol rep 1

value: Bulk Tumor cells

value: p53 knocckout


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 1


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 3


title: Ovcar8, control, rep 1


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 2


title: Ath embryo, wild-type, br3

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA3 version 3.4.4
Quality-filtered reads corresponding to rRNA were removed, and the remaining reads were mapped to Arabidopsis primary transcripts (Athaliana_167_transcript_primaryTranscriptOnly.fa.gz downloaded from phytozome) using bowtie v0.12.7, with parameters -v 2 -5 10 -3 23 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. TMM-normalized counts are obtained using the EdgeR package v3.10.5 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Assembly: TAIR10
Supplementary files format and content: EMB_***-br*.counts.txt, tab-delimited text files countaining the raw counts for each samples.
Supplementary files format and content: Ath-EMB.norm.counts.txt, tab-delimited text file containing TMM-normalized count values for all the samples in the Series.

organism: Arabidopsis thaliana

source_name: 8  DAP embryos

growth_protocol: Plants were grown in a Conviron chamber under 16h day/8h night with fluorescent lamps at 20°C and 50-70% humidity.

extract_protocol:
Total RNA was isolated using the RNAqueous-Micro total RNA isolation kit (Life Technologies) following the manufacturer's instructions.
RNA-Seq libraries were prepared using Tecan Ovation RNA-Seq System V2 using 50 ng of total RNA, and double-stranded cDNA was fragmented to ~200 bp using a Covaris E220.  End repair, A-tailing, adapter ligation and PCR enrichment were performed according to Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, using NEXTflex ChIP-Seq Barcodes (BiooScientific).

treatment_protocol: Embryos were dissected out of seeds, 8 days after pollination.   25-30 embryos were harvested for each biological replicate.

value: 8  DAP embryos

tag: ecotype

value: wild-type


title: Ovcar8, Serum starved, rep 1


title: Ath embryo, wild-type, br1


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 2


title: Ath embryo, wild-type, br2


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 1


title: Ath embryo, wri1-1 mutant, br3


title: 2153L GEMM TNBC Vehicle, Input, biol rep 3


title: 2153L GEMM TNBC Vehicle, Input, biol rep 2


title: 2153L GEMM TNBC Vehicle, Input, biol rep 1


title: Ath embryo, wri1-1 mutant, br1


title: Ath, protoplast, GmWRI1, br3

data_processing:
Basecalls performed using RTA3 version 3.4.4
Quality-filtered reads corresponding to rRNA were removed, and the remaining reads were mapped to Arabidopsis primary transcripts (Athaliana_167_transcript_primaryTranscriptOnly.fa.gz downloaded from phytozome) using bowtie v0.12.7, with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. TMM-normalized counts are obtained using the EdgeR package v3.10.5 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Assembly: TAIR10
Supplementary files format and content: Ath-***-br*.counts.txt, tab-delimited text files countaining the raw counts for each samples.
Supplementary files format and content: Ath-WRI1OX.TMMnorm.counts.txt, tab-delimited text file containing TMM-normalized count values for all the samples in the Series.

source_name: leaf mesophyll protoplasts

treatment_protocol: Arabidopsis leaf protoplasts were prepared, transfected and incubated as described in Jo et al., PNAS 2020, 117-2: 1223-1232.

value: leaf mesophyll protoplasts


title: Ovcar8, acetate, rep 2


title: Ovcar8, acetate, rep 1


title: Ath, protoplast, GmWRI1, br2


title: Liver cells, Ctr, Day5, Biorep3

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

data_processing:
Base calling and demultiplexing: bcl2fastq2 2.20.0
Adaptor trimming of TrueSeq universal adapter AGATCGGAAGAG: cutadapt 1.16 with --e 0.05 --match-read-wildcards --minimum-length 15
Trimmed sequence reads were mapped to GRCm39 (Ensembl_v103) using STAR 2.7.3.a
Read count extraction was done with STAR 2.7.3.a --quantMode GeneCounts considering uniquely mapping reads only.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

growth_protocol: DLK+ positive hepatoblasts were isolated from time-pregnant (E13.5) mice. Hepatoblasts were plated in matrigel-coated wells in expansion media: DMEM/F-12, GlutaMAX supplement (Thermo Fisher Scientific; cat. no. 31331028), 10% FBS, 1× ITS-X (GIBCO BRL; cat. no. 51500–056), 0.1 µM dexamethasone (Sigma-Aldrich; cat. no D1756-25MG), 10 mM nicotinamide (Sigma-Aldrich; cat. no. N0636-100G), 10 ng/ml human HGF (in-house production), and 10 ng/ml mouse EGF (in-house production). After 24h, the cells were overlaid with differentiation media: MCDB131 (Thermo Fisher Scientific: cat. No. 10372019), 2 mM L-glutamine (Thermo Fisher Scientific: cat. No. M11-004) 0.25x ITS-X and 0.1 µM dexamethasone, containing Matrigel (Corning; cat. no. 356231) to a final concentration of 5% v/v. Cells were cultured for 5 d at 37°C, 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  300 ng input total RNA enrichment by poly-dT pull down with NEBNext Poly(A), fragmented to 350 nt, with Ultra II Directional RNA Lib Prep from ILL RNA with NEB adaptor (0.6µM); 12 PCR cycles; FA, following manufacturer's protocols.

treatment_protocol: Hepatoblasts were reverse-transfected with Mock (lipofectamine only), siScrambled-Rab35#4 or siRab35#4. Transfection was performed using Lipofectamine RNAiMax and a final concentration of 10 nM siRNA.

value: Liver

value: Scrambled Rab35 siRNA (control)

tag: time

value: Day 5


title: Ath, protoplast, mCherry, br3

tag: treatment


title: Liver cells, Ctr, Day4, Biorep3

tag: genotype

value: Day 4


title: Liver cells, Ctr, Day5, Biorep2


title: Ath, protoplast, mCherry, br2


title: Liver cells, Ctr, Day4, Biorep2


title: Ath, protoplast, GmWRI1, br1


title: Liver cells, Ctr, Day4, Biorep1


title: Ath, protoplast, mCherry, br1


title: Liver cells, Ctr, Day5, Biorep1


title: Nutrient stravations, Mphd9-14, 0% sucrose starvation, Rep 3

city: Singapore

first: Yating

last: Dong

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M. polymorpha v5.1; K. nitens v1.1
Supplementary files format and content: comma-separated values file includes raw read counts for each sample

organism: Marchantia polymorpha

source_name: Whole gemmaling

growth_protocol: Marchantia polymorpha L.  liverworts were axenically cultivated from gemmae on half-strength Gamborg’s B5 medium (hereafter 1⁄2 B5) containing 1% (w/v) plant agar under continuous white LED light (50-60 µmol m-2 s-1) at 22°C. Klebsormidium nitensalgae cultures were grown on C medium agar plates under continuous light (10 µmol m-2 s-1) at 22°C

extract_protocol:
RNA was extracted using the QIAGEN Plant RNeasy kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol: For nutrient treatment experiments, M. polymorpha gemmae and K. nitens were grown in axenic liquid culture with full Yamagami medium for seven days on an orbital shaker; afterwards, gemmalings were shifted into respective modified Yamagami media (nitrogen deprivation: 1% of the recommended concentrations of NaNO3 and KNO3, phosphate deprivation: 1% of recommended KH2PO4, sucrose deprivation: 0% of recommended sucrose). After five days of deprivation, culture media of M. polymorpha were replaced with full Yamagami medium for recovery periods for 6 h, 24 h, and 72 h, respectively.

value: Whole gemmaling

value: 0% Sucrose_5d


title: Nutrient stravations, Mphd9-14, 0% sucrose starvation, Rep 1


title: Liver cells, Ctr, Day3, Biorep2

value: Day 3


title: Nutrient stravations, Mphd9-14, 0% sucrose starvation, Rep 2


title: Liver cells, Ctr, Day3, Biorep3


title: Liver cells, Ctr, Day3, Biorep1


title: Ath embryo, wri1-1 mutant, br2


title: Nutrient starvations, Mphd9-14, 1% phosphate starvation, Rep 3

value: 1% Phosphate_5d


title: Nutrient starvations, Mphd9-14, 1% phosphate starvation, Rep 2


title: NOMO-1, sgUSP8-2, D6, rep1

city: Cold Spring Harbor

first: Nicholas

last: Tonks

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description:
USP8_sg6_Rep1_S12
DESeq2_input_USP8_NOMO1.txt

data_processing:
Sequencing reads were mapped to the human reference genome (hg38) using Hisat2 2.1.0 with default settings.
Differentially expressed genes were analyzed using counts from HTSeq-count (version 0.13.5).
Only genes that have at least 10 reads in total were then fed into DESeq2 with masking structural RNAs and non-coding RNAs for calculating fold changes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: NOMO-1 acute myeloid leukemia cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq sample prep kit v2 following manufacturer's protocols.

treatment_protocol:
NOMO-1 cells were infected with indicated sgRNA vectors, and culture for 5-6 days.
On Day 3, the cells were spun down and resuspended in fresh media. The percentage of infected cells were determined using Guava easyCyte Flow Cytometer (Millipore) to measure the GFP+ cell population. Only samples with >90% GFP+ were kept culture and heavested on Day 5 or Day6.

value: Acute myeloid leukemia

value: USP8 knockout

value: sgRNA infection

value: Day 6


title: NOMO-1, sgUSP8-1, D6, rep3

description:
USP8_sg4_Rep3_S17
DESeq2_input_USP8_NOMO1.txt


title: NOMO-1, sgUSP8-1, D6, rep2

description:
USP8_sg4_Rep2_S14
DESeq2_input_USP8_NOMO1.txt


title: Liver cells, Ctr, Day2, Biorep3

value: Day 2


title: NOMO-1, sgUSP8-2, D6, rep3

description:
USP8_sg6_Rep3_S18
DESeq2_input_USP8_NOMO1.txt


title: NOMO-1, sgNEG control_for_USP8, D6, rep3

description:
USP8_rosa_Rep3_S16
DESeq2_input_USP8_NOMO1.txt

value: sgRNA negative control


title: Liver cells, Ctr, Day2, Biorep2


title: Liver cells, Ctr, Day2, Biorep1


title: NOMO-1, sgNEG control_for_USP8, D6, rep2

description:
USP8_Rosa_Rep2_S13
DESeq2_input_USP8_NOMO1.txt


title: Nutrient starvations, Mphd9-14, 1% nitrate starvation, Rep 1

value: 1% Nitrate_5d


title: NOMO-1, sgUBAP-2, D6, rep2

description:
UBAP1_sg6_Rep2_S6
DESeq2_input_UBAP1_NOMO1.txt

value: UBAP1 knockout


title: NOMO-1, sgUSP8-1, D6, rep1

description:
USP8_sg4_Rep1_S11
DESeq2_input_USP8_NOMO1.txt


title: NOMO-1, sgNEG control_for_USP8, D6, rep1

description:
USP8_Rosa_Rep1_S10
DESeq2_input_USP8_NOMO1.txt


title: Liver cells, Ctr, Day1, Biorep2

value: Day 1


title: Nutrient starvations, Mphd9-14, 1% nitrate starvation, Rep 3


title: Liver cells, Ctr, Day1, Biorep3

value: Liver


title: Liver cells, Rab35 KD, Day5, Biorep3

value: Rab35 siRNA


title: Nutrient starvations, Mphd9-14, control, Rep 2

value: Full Yamagami


title: Nutrient starvations, Mphd9-14, control, Rep 3


title: Nutrient starvations, Mphd9-14, 1% nitrate starvation, Rep 2


title: Nutrient starvations, Mphd9-14, 1% phosphate starvation, Rep 1


title: NOMO-1, sgUSP8-2, D6, rep2

description:
USP8_sg6_Rep2_S15
DESeq2_input_USP8_NOMO1.txt


title: Liver cells, Ctr, Day1, Biorep1

value: Scrambled Rab35 siRNA (control)


title: NOMO-1, sgUBAP-1, D6, rep3

description:
UBAP1_sg3_Rep3_S8
DESeq2_input_UBAP1_NOMO1.txt


title: Nutrient starvations, Mperf20-21, 0% sucrose starvation, Rep 2

value: Whole gemmaling


title: NOMO-1, sgNEG control_for_UBAP-1, D6, rep3

description:
UBAP1_Rosa_Rep3_S7
DESeq2_input_UBAP1_NOMO1.txt


title: Liver cells, Rab35 KD, Day5, Biorep2

value: Day 5


title: Liver cells, Rab35 KD, Day4, Biorep2

value: Day 4


title: NOMO-1, sgUBAP-2, D6, rep1

description:
UBAP1_sg6_Rep1_S3
DESeq2_input_UBAP1_NOMO1.txt


title: Liver cells, Rab35 KD, Day5, Biorep1


title: Liver cells, Rab35 KD, Day4, Biorep3


title: Nutrient starvations, Mphd9-14, control, Rep 1


title: NOMO-1, sgNEG control_for_UBAP-1, D6, rep2

description:
UBAP1_Rosa_Rep2_S4
DESeq2_input_UBAP1_NOMO1.txt


title: Nutrient starvations, Mperf20-21, 1% phosphate starvation, Rep 3

value: 1% Phosphate_5d


title: Liver cells, Rab35 KD, Day4, Biorep1


title: NOMO-1, sgUBAP-1, D6, rep2

description:
UBAP1_sg3_Rep2_S5
DESeq2_input_UBAP1_NOMO1.txt

value: Acute myeloid leukemia


title: NOMO-1, sgUBAP-1, D6, rep1

description:
UBAP1_sg3_Rep1_S2
DESeq2_input_UBAP1_NOMO1.txt


title: NOMO-1, sgNEG control_for_UBAP-1, D6, rep1

description:
UBAP1_Rosa_Rep1_S1
DESeq2_input_UBAP1_NOMO1.txt


title: Nutrient starvations, Mperf20-21, 1% phosphate starvation, Rep 1


title: Nutrient starvations, Mperf20-21, 0% sucrose starvation, Rep 1

value: 0% Sucrose_5d


title: Liver cells, Rab35 KD, Day3, Biorep2

value: Day 3


title: Nutrient starvations, Mperf20-21, 1% nitrate starvation, Rep 3


title: Nutrient starvations, Mperf20-21, 1% nitrate starvation, Rep 2


title: NOMO-1, sgTSG101-2, D6, rep1

description:
Tsg101_sg247_Rep1_S3
DESeq2_input_Tsg101_NOMO1.txt

value: TSG101 knockout

value: sgRNA infection

value: Day 6


title: NOMO-1, sgTSG101-2, D6, rep3

description:
Tsg101_sg247_Rep3_S9
DESeq2_input_Tsg101_NOMO1.txt


title: NOMO-1, sgTSG101-1, D6, rep3

description:
Tsg101_sg75_Rep3_S8
DESeq2_input_Tsg101_NOMO1.txt


title: Liver cells, Rab35 KD, Day3, Biorep1


title: NOMO-1, sgTSG101-2, D6, rep2

description:
Tsg101_sg247_Rep2_S6
DESeq2_input_Tsg101_NOMO1.txt


title: Nutrient starvations, Mperf20-21, 1% nitrate starvation, Rep 1

value: 1% Nitrate_5d


title: Liver cells, Rab35 KD, Day2, Biorep2

value: Day 2


title: Liver cells, Rab35 KD, Day2, Biorep1


title: NOMO-1, sgTSG101-1, D6, rep2

description:
Tsg101_sg75_Rep2_S5
DESeq2_input_Tsg101_NOMO1.txt


title: Liver cells, Rab35 KD, Day2, Biorep3


title: Nutrient starvations, Mperf20-21, control, Rep 2


title: Nutrient starvations, Mperf20-21, control, Rep 3


title: NOMO-1, sgTSG101-1, D6, rep1

description:
Tsg101_sg75_Rep1_S2
DESeq2_input_Tsg101_NOMO1.txt


title: NOMO-1, sgNEG control_for_TSG101, D6, rep3

description:
Tsg101_rosa_Rep3_S7
DESeq2_input_Tsg101_NOMO1.txt

value: sgRNA negative control


title: Liver cells, Rab35 KD, Day1, Biorep2

value: Liver

value: Day 1


title: Liver cells, Rab35 KD, Day1, Biorep3

value: Rab35 siRNA


title: Nutrient starvations, Mperf20-21, control, Rep 1

value: Full Yamagami


title: NOMO-1, sgNEG control_for_TSG101, D6, rep2

description:
Tsg101_rosa_Rep2_S4
DESeq2_input_Tsg101_NOMO1.txt


title: Liver cells, Rab35 KD, Day1, Biorep1


title: NOMO-1, sgNEG control_for_TSG101, D6, rep1

description:
Tsg101_rosa_Rep1_S1
DESeq2_input_Tsg101_NOMO1.txt


title: Liver cells, Rab35 KD, Day3, Biorep3


title: Nutrient starvations, Mpcsd-2, 0% sucrose starvation, Rep 2

value: Whole gemmaling


title: Nutrient starvations, Mpcsd-2, 0% sucrose starvation, Rep 1


title: Liver cells, Mock, Day5, Biorep3

value: WT

value: Mock

value: Day 5


title: Liver cells, Mock, Day5, Biorep2


title: Nutrient starvations, Mpcsd-2, 1% phosphate starvation, Rep 3

value: 1% Phosphate_5d


title: NOMO-1, sgPTPN23-2, D6, rep3-2nd-exp

description:
PTPN23_sg2_Rep3_S18
DESeq2_input_PTPN23_NOMO1.txt

value: Acute myeloid leukemia

value: PTPN23 knockout


title: NOMO-1, sgPTPN23-2, D6, rep2-2nd-exp

description:
PTPN23_sg2_Rep2_S15
DESeq2_input_PTPN23_NOMO1.txt


title: SaCas9-AAV non-targeting gRNA, 30 Day Treatment in vivo; Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
Briefly, reads were binned into editing event categories where + 20 bp from the expected Cas9 cleavage site was analyzed for an editing event. This included unedited (Wt) reads, or reads containing insertions/deletions (indels), AAV-integration, unresolved double-stranded breaks, translocations, or foreign DNA integration.
Assembly: mm10
Supplementary files format and content: The read counds Excel sheet contains sample metadata as well as counts for different read types, such as: unedited reads, AAV integration reads, indel readss, translocation reads, DSB reads at the gRNA site, and foreign DNA integration reads.
Library strategy: AMP-seq

molecule: genomic DNA

source_name: Neurons

growth_protocol: Neurons used in AMP-seq experiments were derived from E15.5 (gestational day 15.5) C57BL/6J embryos.

extract_protocol:
All genomic DNA extractions were performed using DNeasy Blood & Tissue Kit (Qiagen #69504).
KAPA HyperPlus Kit (Roche #KK8514). Prep method was based off of AMP-seq (https://www.nature.com/articles/nm.3729). Sequenced on the Illumina MiniSeq using MiniSeq Mid Output Kit.

treatment_protocol: Neurons were transduced with NmCas9-AAV-gRNA or with SaCas9-AAV-gRNA virus on day-in-vitro (DIV) 3 and collected on DIV 10. For in vivo experiments, C57BL/6J mice were bilaterally i.c.v. (intracerebroventricularly) injected on P1 with SaCas9-AAV and collected on P30.

tag: experiment type

value: in vivo

tag: developmental stage

value: P1 (post-natal day 1)

value: Neurons

tag: strain

tag: agent

tag: viral day


title: Nutrient starvations, Mpcsd-2, 1% phosphate starvation, Rep 2


title: Liver cells, Mock, Day5, Biorep1


title: NOMO-1, sgPTPN23-2, D6, rep1-2nd-exp

description:
PTPN23_sg2_Rep1_S12
DESeq2_input_PTPN23_NOMO1.txt

value: sgRNA infection

value: Day 6


title: NOMO-1, sgPTPN23-1, D6, rep3-2nd-exp

description:
PTPN23_sg1_Rep3_S17
DESeq2_input_PTPN23_NOMO1.txt


title: SaCas9-AAV non-targeting gRNA, 30 Day Treatment in vivo; Rep1


title: Liver cells, Mock, Day4, Biorep2

value: Day 4


title: Liver cells, Mock, Day4, Biorep3

value: Liver


title: Nutrient starvations, Mpcsd-2, 1% nitrate starvation, Rep 3

value: 1% Nitrate_5d


title: Nutrient starvations, Mpcsd-2, 0% sucrose starvation, Rep 3

value: 0% Sucrose_5d


title: SaCas9-AAV non-targeting gRNA, 7 Day Treatment in vitro; Rep2

value: in vitro

value: E15.5 (gestational day 15.5)


title: Nutrient starvations, Mpcsd-2, 1% nitrate starvation, Rep 2

value: Whole gemmaling


title: NOMO-1, sgPTPN23-1, D6, rep2-2nd-exp

description:
PTPN23_sg1_Rep2_S14
DESeq2_input_PTPN23_NOMO1.txt


title: Nutrient starvations, Mpcsd-2, 1% nitrate starvation, Rep 1


title: NOMO-1, sgNEG control_for_PTPN23, D6, rep3

description:
PTPN23_rosa_Rep3_S16
DESeq2_input_PTPN23_NOMO1.txt

value: sgRNA negative control


title: Liver cells, Mock, Day3, Biorep3

value: WT

value: Mock

value: Day 3


title: SaCas9-AAV non-targeting gRNA, 7 Day Treatment in vitro; Rep1


title: SaCas9-AAV gRNA, 30 Day Treatment in vivo; Rep3


title: Liver cells, Mock, Day3, Biorep1


title: SaCas9-AAV non-targeting gRNA, 30 Day Treatment in vivo; Rep2


title: Liver cells, Mock, Day3, Biorep2


title: Nutrient starvations, Mpcsd-2, control, Rep 2

value: Full Yamagami


title: Nutrient starvations, Mpcsd-2, 1% phosphate starvation, Rep 1

value: 1% Phosphate_5d


title: SaCas9-AAV non-targeting gRNA, 7 Day Treatment in vitro; Rep3


title: SaCas9-AAV gRNA, 30 Day Treatment in vivo; Rep2

value: in vivo

value: P1 (post-natal day 1)


title: Liver cells, Mock, Day4, Biorep1


title: SaCas9-AAV gRNA, 30 Day Treatment in vivo; Rep1

value: Neurons


title: Liver cells, Mock, Day2, Biorep3

value: Day 2


title: Control conditions, Marchantia polymorpha Mphd9-14, Rep3


title: NOMO-1, sgPTPN23-1, D6, rep1-2nd-exp

description:
PTPN23_sg1_Rep1_S11
DESeq2_input_PTPN23_NOMO1.txt

value: Acute myeloid leukemia

value: PTPN23 knockout

value: sgRNA infection

value: Day 6


title: Liver cells, Mock, Day2, Biorep1

value: Liver


title: NOMO-1, sgHGS-2, D6, rep3

description:
HGS_sg59_Rep3_S18
DESeq2_input_HGS_NOMO1.txt

value: HGS knockout


title: NOMO-1, sgHGS-2, D6, rep2

description:
HGS_sg59_Rep2_S15
DESeq2_input_HGS_NOMO1.txt


title: NOMO-1, sgNEG control_for_PTPN23, D6, rep1

description:
PTPN23_rosa_Rep1_S10
DESeq2_input_PTPN23_NOMO1.txt


title: Control conditions, Marchantia polymorpha Mphd9-14, Rep2

value: Whole gemmaling


title: SaCas9-AAV gRNA, 7 Day Treatment in vitro; Rep3

value: in vitro

value: E15.5 (gestational day 15.5)


title: Nutrient starvations, Mpcsd-2, control, Rep 3


title: SaCas9-AAV gRNA, 7 Day Treatment in vitro; Rep2


title: NOMO-1, sgNEG control_for_PTPN23, D6, rep2

description:
PTPN23_rosa_Rep2_S13
DESeq2_input_PTPN23_NOMO1.txt

value: sgRNA negative control


title: Liver cells, Mock, Day1, Biorep3

value: WT

value: Mock

value: Day 1


title: NOMO-1, sgHGS-1, D6, rep3

description:
HGS_sg18_Rep3_S17
DESeq2_input_HGS_NOMO1.txt


title: SaCas9-AAV gRNA, 7 Day Treatment in vitro; Rep1


title: Control conditions, Marchantia polymorpha Mperf20-21, Rep3

value: Full Yamagami


title: Non-targeting gRNA 23, Timecourse; Rep3


title: Liver cells, Mock, Day1, Biorep2


title: Nutrient starvations, Mpcsd-2, control, Rep 1


title: Non-targeting gRNA 23, Timecourse; Rep2


title: CAM-E_ALG26_day3_r3

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: C 3-3

data_processing:
Raw data acquisition (HiSeq Control Software, HCS, HD 3.4.0.38) and base calling (Real-Time Analysis Software, RTA, 2.7.7) was performed on-instrument
Base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM).
Archive BAM files were demultiplexed into sample-specific, unaligned BAM files (Illumi-naSamDemux, 2.19.2-CeMM).
NGS reads were mapped to the Genome Reference Consortium GRCh38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR, 2.7.9a) utilizing the “basic” ensembl transcript annotation from version e100 (April 2020) as reference transcriptome.
STAR was run with options recommended by the ENCODE project. NGS read alignments overlapping ensembl transcript features were counted with the Bioconductor (3.14) Genomic Alignments (1.30.0) package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HepG2-NTCP HA:HBc were manteined in DMEM supplemented with 10% FBS, 1X non-essential amino acids, 50 µg/ml gentamicin, 250 µg/ml G418

extract_protocol:
Total RNA was extracted using ReliaPrep RNA Miniprep Systems (Promega)
RNA-seq libraries were prepared with the NEB-Next® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA)

treatment_protocol: Cells were treated with the CAM compound at 1µM for 2 or 3 days in DMSO 2%

value: day 3

value: CAM-E ALG28


title: Non-targeting gRNA 23, Timecourse; Rep1

value: Neurons


title: Liver cells, Mock, Day1, Biorep1

data_processing:
Base calling and demultiplexing: bcl2fastq2 2.20.0
Adaptor trimming of TrueSeq universal adapter AGATCGGAAGAG: cutadapt 1.16 with --e 0.05 --match-read-wildcards --minimum-length 15
Trimmed sequence reads were mapped to GRCm39 (Ensembl_v103) using STAR 2.7.3.a
Read count extraction was done with STAR 2.7.3.a --quantMode GeneCounts considering uniquely mapping reads only.


title: Control conditions, Marchantia polymorpha Mperf20-21, Rep1


title: CAM-E_ALG26_day3_r2

description: C 2-3

value: CAM-E ALG27


title: Control conditions, Marchantia polymorpha Mperf20-21, Rep2


title: Control conditions, Marchantia polymorpha Mpcsd-2, Rep3


title: Liver cells, Mock, Day2, Biorep2

value: Day 2


title: NOMO-1, sgHGS-2, D6, rep1

description:
HGS_sg59_Rep1_S12
DESeq2_input_HGS_NOMO1.txt

value: Acute myeloid leukemia

value: sgRNA infection


title: NOMO-1, sgHGS-1, D6, rep1

description:
HGS_sg18_Rep1_S11
DESeq2_input_HGS_NOMO1.txt

value: Day 6


title: NmCas9-AAV gRNA 23, no virus; Rep3


title: NOMO-1, sgNEG control_for_HGS, D6, rep2

description:
HGS_rosa_Rep2_S13
DESeq2_input_HGS_NOMO1.txt


title: CAM-E_ALG26_day3_r1

description: C 1-3

value: CAM-E ALG26


title: NmCas9-AAV gRNA 23, no virus; Rep2


title: Control conditions, Marchantia polymorpha Mpcsd-2, Rep2

value: Whole gemmaling


title: NOMO-1, sgNEG control_for_HGS, D6, rep1

description:
HGS_rosa_Rep1_S10
DESeq2_input_HGS_NOMO1.txt


title: CAM-At_ALG5398_day3_r3

description: A 3-3

value: CAM-At ALG5400


title: Control conditions, Marchantia polymorpha Mpcsd-2, Rep1


title: NmCas9-AAV gRNA 23, no virus; Rep1

value: in vitro

value: E15.5 (gestational day 15.5)


title: NOMO-1, sgCLTC-2, D6, rep3

description:
CLTC_sg529_Rep3_S9
DESeq2_input_CLTC_NOMO1.txt

value: CLTC knockout


title: CAM-At_ALG5398_day3_r2

description: A 2-3

value: CAM-At ALG5399


title: NmCas9-AAV gRNA 23, Timecourse Day 7; Rep3


title: NOMO-1, sgNEG control_for_HGS, D6, rep3

description:
HGS_rosa_Rep3_S16
DESeq2_input_HGS_NOMO1.txt

value: sgRNA negative control


title: Control conditions, Marchantia polymorpha WT, Rep2

value: Full Yamagami


title: NmCas9-AAV gRNA 23, Timecourse Day 7; Rep2


title: CAM-At_ALG5398_day3_r1

description: A 1-3

value: day 3

value: CAM-At ALG5398


title: NmCas9-AAV gRNA 23, Timecourse Day 7; Rep1

value: Neurons


title: CAM-Ah_RG7907_day3_r3

description: R 3-3

value: CAM-Ah RG7909


title: CAM-Ah_RG7907_day3_r2

description: R 2-3

value: CAM-Ah RG7908


title: NOMO-1, sgCLTC-2, D6, rep1

description:
CLTC_sg529_Rep1_S3
DESeq2_input_CLTC_NOMO1.txt

value: Acute myeloid leukemia


title: NOMO-1, sgCLTC-1, D6, rep3

description:
CLTC_sg124_Rep3_S8
DESeq2_input_CLTC_NOMO1.txt

value: sgRNA infection


title: NmCas9-AAV gRNA 23, Timecourse Day 6; Rep3


title: Control conditions, Marchantia polymorpha Mphd9-14, Rep1


title: NmCas9-AAV gRNA 23, Timecourse Day 6; Rep2


title: Marchantia polymorpha, 72h Sucrose resupply to starved plants, Rep 3


title: NOMO-1, sgNEG control_for_CLTC, D6, rep3

description:
CLTC_rosa_Rep3_S7
DESeq2_input_CLTC_NOMO1.txt

value: Day 6


title: Marchantia polymorpha, 72h Sucrose resupply to starved plants, Rep 1


title: NOMO-1, sgCLTC-1, D6, rep1

description:
CLTC_sg124_Rep1_S2
DESeq2_input_CLTC_NOMO1.txt


title: Control conditions, Marchantia polymorpha WT, Rep3


title: DMSO_day3_r2

description: D 2-3

value: DMSO


title: NmCas9-AAV gRNA 23, Timecourse Day 6; Rep1


title: NOMO-1, sgNEG control_for_CLTC, D6, rep2

description:
CLTC_rosa_Rep2_S4
DESeq2_input_CLTC_NOMO1.txt


title: DMSO_day3_r3

description: D 3-3


title: NmCas9-AAV gRNA 23, Timecourse Day 5; Rep3


title: NOMO-1, sgHGS-1, D6, rep2

description:
HGS_sg18_Rep2_S14
DESeq2_input_HGS_NOMO1.txt

value: HGS knockout


title: Marchantia polymorpha, 24h Sucrose resupply to starved plants, Rep 3

value: Whole gemmaling


title: DMSO_day3_r1

description: D 1-3


title: NOMO-1, sgCLTC-2, D6, rep2

description:
CLTC_sg529_Rep2_S6
DESeq2_input_CLTC_NOMO1.txt


title: Control conditions, Marchantia polymorpha WT, Rep1


title: Marchantia polymorpha, 24h Sucrose resupply to starved plants, Rep 2


title: NmCas9-AAV gRNA 23, Timecourse Day 5; Rep2

value: in vitro


title: CAM-E_ALG26_day2_r3

description: C 3-2

value: day 2

value: CAM-E ALG28


title: CAM-Ah_RG7907_day3_r1

description: R 1-3

value: CAM-Ah RG7907


title: NOMO-1, sgCLTC-1, D6, rep2

description:
CLTC_sg124_Rep2_S5
DESeq2_input_CLTC_NOMO1.txt

value: CLTC knockout


title: NOMO-1, sgNEG control_for_CLTC, D6, rep1

description:
CLTC_rosa_Rep1_S1
DESeq2_input_CLTC_NOMO1.txt

value: sgRNA negative control


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D18, rep2

description:
TKO18_S18
combined_counts_D18.csv

value: CASP8-/-/RIPK3-/-/GSDMD-/- triple KO, PTPN23 KO

value: Day 18


title: CAM-E_ALG26_day2_r2

description: C 2-2

value: CAM-E ALG27


title: NmCas9-AAV gRNA 23, Timecourse Day 4; Rep3

value: E15.5 (gestational day 15.5)

value: Neurons


title: Marchantia polymorpha, 24h Sucrose resupply to starved plants, Rep 1


title: Marchantia polymorpha,  6h Sucrose resupply to starved plants, Rep 3


title: NmCas9-AAV gRNA 23, Timecourse Day 5; Rep1


title: Marchantia polymorpha, 72h Sucrose resupply to starved plants, Rep 2


title: CAM-E_ALG26_day2_r1

description: C 1-2

value: CAM-E ALG26


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D18, rep2

description:
TKO17_S17
combined_counts_D18.csv

value: Acute myeloid leukemia

value: sgRNA infection


title: Marchantia polymorpha,  6h Sucrose resupply to starved plants, Rep 2


title: Marchantia polymorpha,  6h Sucrose resupply to starved plants, Rep 1


title: NmCas9-AAV gRNA 23, Timecourse Day 4; Rep2


title: CAM-At_ALG5398_day2_r3

description: A 3-2

value: CAM-At ALG5400


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgNEG control, D18, rep2

description:
TKO16_S16
combined_counts_D18.csv

value: CASP8-/-/RIPK3-/-/GSDMD-/- triple KO, sgRNA negative control


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D18, rep1

description:
TKO15_S15
combined_counts_D18.csv


title: Marchantia polymorpha, 72h Phosphate resupply to starved plants, Rep 3

value: Whole gemmaling


title: NmCas9-AAV gRNA 23, Timecourse Day 3; Rep3

value: in vitro


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D18, rep1

description:
TKO14_S14
combined_counts_D18.csv


title: CAM-At_ALG5398_day2_r1

description: A 1-2

value: day 2

value: CAM-At ALG5398


title: NmCas9-AAV gRNA 23, Timecourse Day 3; Rep2


title: Marchantia polymorpha, 72h Phosphate resupply to starved plants, Rep 2


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgNEG control, D18, rep1

description:
TKO13_S13
combined_counts_D18.csv


title: CAM-Ah_RG7907_day2_r3

description: R 3-2

value: CAM-Ah RG7909


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D12, rep2

description:
TKO12_S12
combined_counts_D12.csv

value: Day 12


title: CAM-Ah_RG7907_day2_r2

description: R 2-2

value: CAM-Ah RG7908


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D12, rep2

description:
TKO11_S11
combined_counts_D12.csv

value: CASP8-/-/RIPK3-/-/GSDMD-/- triple KO, PTPN23 KO


title: Marchantia polymorpha, 24h Phosphate resupply to starved plants, Rep 3


title: CAM-Ah_RG7907_day2_r1

description: R 1-2

value: CAM-Ah RG7907


title: NmCas9-AAV gRNA 23, Timecourse Day 2; Rep2


title: Marchantia polymorpha, 72h Phosphate resupply to starved plants, Rep 1


title: Marchantia polymorpha, 24h Phosphate resupply to starved plants, Rep 2


title: NmCas9-AAV gRNA 23, Timecourse Day 4; Rep1


title: DMSO_day2_r3

description: D 3-2

value: DMSO


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgNEG control, D12, rep2

description:
TKO10_S10
combined_counts_D12.csv


title: NmCas9-AAV gRNA 23, Timecourse Day 3; Rep1

value: E15.5 (gestational day 15.5)


title: NmCas9-AAV gRNA 23, Timecourse Day 2; Rep1

value: Neurons


title: Marchantia polymorpha, 24h Phosphate resupply to starved plants, Rep 1


title: DMSO_day2_r2

description: D 2-2


title: CAM-At_ALG5398_day2_r2

description: A 2-2

value: CAM-At ALG5399


title: Marchantia polymorpha,  6h Phosphate resupply to starved plants, Rep 3


title: Nutrient starvations, Mperf20-21, 1% phosphate starvation, Rep 2

value: 1% Phosphate_5d


title: NmCas9-AAV gRNA 23, Timecourse Day 2; Rep3


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D12, rep1

description:
TKO08_S8
combined_counts_D12.csv

value: Acute myeloid leukemia

value: sgRNA infection


title: NmCas9-AAV gRNA 23, Timecourse Day 1; Rep3


title: DMSO_day2_r1

description: D 1-2


title: Marchantia polymorpha,  6h Phosphate resupply to starved plants, Rep 2


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D6, rep2

description:
TKO06_S6
combined_counts_D6.csv


title: NmCas9-AAV gRNA 23, Timecourse Day 1; Rep2


title: Gm.27hai.biorep3.run2

city: Kannapolis

first: Tzung-Fu

last: Hsieh

address: Tzung-Fu Hsieh, 600 Laureate Way

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
Illumina raw reads were first trimmed at 5' and 3' ends with the positions error rates > 0.5%, trimmed 10 bases average error rate > 0.1% and trimmed the adapter using trimmomatic (v0.38). The trimmed RNA reads were mapped to soybean reference genome (v1.1; https://phytozome-next.jgi.doe.gov) using Hisat2.ESeq2 was used to identify differentially expressed genes.
Assembly: soybean reference genome v1.1
Supplementary files format and content: tab-delimited text file of normalized count matrix

organism: Glycine max

source_name: whole seed

growth_protocol: Long day condition (16 hours light, 8 hours dark) at 22 °C

extract_protocol:
Embryos were collected from early, mid and late desiccation, mature dry seeds, and 3hai (hour after imbibition), 16hai and 27hai. Total RNA was extracted using RNAeasy kit (Qiagen) plus in-column DNase digestion.
Illumina cDNA libraries were constructed with the Illumina Tru-Seq RNA Prep kit per manufacturer’s instruction.

value: whole seed

value: Williams 82

value: Gm seed at 27 hours after imbibition


title: Marchantia polymorpha,  6h Phosphate resupply to starved plants, Rep 1

value: Whole gemmaling


title: NmCas9-AAV gRNA 23, Timecourse Day 1; Rep1

value: in vitro


title: Marchantia polymorpha, 72h Nitrate resupply to starved plants, Rep 3


title: Gm.27hai.biorep3.run1


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgNEG control, D6, rep2

description:
TKO04_S4
combined_counts_D6.csv

value: CASP8-/-/RIPK3-/-/GSDMD-/- triple KO, sgRNA negative control

value: Day 6


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D12, rep1

description:
TKO09_S9
combined_counts_D12.csv

value: Day 12


title: Non-targeting gRNA 25, 7 Day Treatment; Rep2


title: Non-targeting gRNA 25, 7 Day Treatment; Rep3


title: Gm.27hai.biorep1.run1


title: Non-targeting gRNA 25, 7 Day Treatment; Rep1


title: Marchantia polymorpha, 72h Nitrate resupply to starved plants, Rep 2


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-2, D6, rep1

description:
TKO03_S3
combined_counts_D6.csv

value: CASP8-/-/RIPK3-/-/GSDMD-/- triple KO, PTPN23 KO


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D6, rep1

description:
TKO02_S2
combined_counts_D6.csv


title: Gm.16hai.biorep3.run1

value: Gm seed at 16 hours after imbibition


title: Marchantia polymorpha, 72h Nitrate resupply to starved plants, Rep 1


title: Non-targeting gRNA 23, 7 Day Treatment; Rep3


title: Gm.16hai.biorep2.run1


title: Marchantia polymorpha, 24h Nitrate resupply to starved plants, Rep 2


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgNEG control, D6, rep1

description:
TKO01_S1
combined_counts_D6.csv


title: Non-targeting gRNA 23, 7 Day Treatment; Rep2


title: NOMO-1, sgPTPN23-2, D6, rep2

description:
NOMO-1_N23-sg2_S21
NOMO-1_D6_N23-sg2_exp2.txt

value: PTPN23 knockout


title: Marchantia polymorpha, 24h Nitrate resupply to starved plants, Rep 1


title: Gm.16hai.biorep1.run1


title: Non-targeting gRNA 23, 7 Day Treatment; Rep1

value: E15.5 (gestational day 15.5)


title: Non-targeting gRNA 21, 7 Day Treatment; Rep3

value: Neurons


title: NOMO-1 CASP8-/-/RIPK3-/-/GSDMD-/-, sgPTPN23-1, D6, rep2

description:
TKO05_S5
combined_counts_D6.csv


title: Marchantia polymorpha,  6h Nitrate resupply to starved plants, Rep 3


title: Gm.3hai.biorep3.run1

value: Gm seed at 3 hours after imbibition


title: NOMO-1, sgNEG control, D6, rep2

description:
NOMO-1_sgNEG_S19
NOMO-1_D6_N23-sg1_exp1.txt

value: sgRNA negative control


title: Gm.27hai.biorep2.run1


title: Marchantia polymorpha,  6h Nitrate resupply to starved plants, Rep 2


title: Gm.3hai.biorep2.run1


title: NOMO-1, sgPTPN23-1, D6, rep2

description:
NOMO-1_N23-sg1_S20
NOMO-1_D6_N23-sg1_exp1.txt

value: Acute myeloid leukemia


title: NOMO-1, sgPTPN23-2, D6, rep1

description:
NOMO-1_N23-sg2_S9
NOMO-1_D6_N23-sg2_exp2.txt

value: sgRNA infection


title: Marchantia polymorpha, 24h Nitrate resupply to starved plants, Rep 3


title: Gm.3hai.biorep1.run1

value: whole seed


title: Marchantia polymorpha,  6h Nitrate resupply to starved plants, Rep 1


title: Non-targeting gRNA 21, 7 Day Treatment; Rep1


title: Marchantia polymorpha, 0% Sucrose starvation, 5d, Rep 3

value: 0% Sucrose_5d


title: NOMO-1, sgPTPN23-1, D6, rep1

description:
NOMO-1_N23-sg1_S8
NOMO-1_D6_N23-sg1_exp1.txt


title: Gm.ld.biorep3.run1

value: Williams 82

value: Gm seed at late desiccation stage


title: NOMO-1, sgNEG control, D6, rep1

description:
NOMO-1_sgNEG_S7
NOMO-1_D6_N23-sg1_exp1.txt


title: NmCas9-AAV gRNA 25, 7 Day Treatment; Rep3

value: in vitro


title: Marchantia polymorpha, 0% Sucrose starvation, 5d, Rep 2

value: Whole gemmaling


title: Gm.ld.biorep2.run1


title: NmCas9-AAV gRNA 25, 7 Day Treatment; Rep1


title: NmCas9-AAV gRNA 25, 7 Day Treatment; Rep2


title: Gm.ld.biorep1.run1


title: NmCas9-AAV gRNA 23, 7 Day Treatment; Rep3


title: Gm.md.biorep3.run1

value: Gm seed at mid desiccation stage


title: Marchantia polymorpha, 0% Sucrose starvation, 5d, Rep 1


title: Gm.md.biorep1.run1


title: Gm.md.biorep2.run1


title: NmCas9-AAV gRNA 23, 7 Day Treatment; Rep2


title: Gm.ed.biorep3.run1

value: Gm seed at early desiccation stage


title: Marchantia polymorpha, 1% Nitrate starvation, 5d, Rep 3

value: 1% Nitrate_5d


title: NmCas9-AAV gRNA 23+AZD7648, 7 Day Treatment; Rep3


title: Gm.ed.biorep2.run2


title: PEO1 treated with Prexasertib 20 nM C

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR to the reference genome UCSC hg38 with default parameters.
Reads that aligned to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: hg38
Supplementary files format and content: raw counts in tab-delimited text file

growth_protocol: COV362  and PEO1 were grown in DMEM with 10% heat-inactivated Fetal Bovine Serum (FBS), 100 𝜇M nonessential amino acids, 10 𝜇g/mL insulin, 100 units/mL penicillin G, 100 𝜇g/mL streptomycin, and 2 mM glutamine

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: COV362  and PEO1 were treated with 20 nM Prexasertib before RNA collection


title: NmCas9-AAV gRNA 23+AZD7648, 7 Day Treatment; Rep2


title: Marchantia polymorpha, 1% Nitrate starvation, 5d, Rep 2


title: PEO1 treated with Prexasertib 20 nM B


title: Non-targeting gRNA 21, 7 Day Treatment; Rep2


title: Gm.ed.biorep2.run1


title: Marchantia polymorpha, 1% Nitrate starvation, 5d, Rep 1


title: Marchantia polymorpha, untreated control, Rep 3

value: Full Yamagami


title: Marchantia polymorpha, 1% Phosphate starvation, 5d, Rep 2

value: 1% Phosphate_5d


title: Marchantia polymorpha, 1% Phosphate starvation, 5d, Rep 3


title: Gm.ed.biorep1.run1


title: NmCas9-AAV gRNA 21, 7 Day Treatment; Rep3

value: E15.5 (gestational day 15.5)


title: Marchantia polymorpha, 1% Phosphate starvation, 5d, Rep 1


title: Gm.dry.biorep3.run2

value: Gm seed at dry seed stage


title: NmCas9-AAV gRNA 21, 7 Day Treatment; Rep2

value: Neurons


title: PEO1 DMSO vehicle C

source_name: Parental


title: Gm.dry.biorep3.run1


title: Marchantia polymorpha, untreated control, Rep 2


title: NmCas9-AAV gRNA 21, 7 Day Treatment; Rep1


title: PEO1 DMSO vehicle A


title: Gm.dry.biorep2.run2


title: Knockout_rep3

city: East Lansing

first: Qiang

last: Guo

address: 612 Wilson Rd

department: MSU-DOE Plant Research Laboratory

institute: Michigan State University

data_processing:
Reads assessed for quality and filtered with FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.25 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Pseudomonas syringae pv. syringae UMAF0158 genome downloaded from Pseudomonas Genome Database with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Assembly: Pseudomonas_syringae_UMAF0158_3878
Supplementary files format and content: expression data (mgo_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary files format and content: count data (mgo_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

organism: Pseudomonas syringae pv. syringae

source_name: Bacteria

extract_protocol:
Tubes of 5 mL cultures of Pss UMAF0158 wildtype and Δmgo1 were inoculated with 10 μL of overnight culture and grown for 24 hr. Three biological replicates each of wildtype and Δmgo1 were grown. After 24 hr, 1 mL of each culture was removed for RNA extraction. For RNA extraction, cells were harvested by centrifugation for 30 min at 4˚C, 3500 x g. RNA was extracted with TRIzol (ThermoFisher Scientific) and purified using Direct-zol™ RNA Miniprep Plus kit (Zymo Research), as per the manufacturer’s protocol.
Sequencing libraries were prepared using the Novogene Prokaryotic RNA Library kit according to the manufacturer's instructions.

value: Bacteria

value: delta mgo


title: Marchantia polymorpha, untreated control, Rep 1


title: Gm.dry.biorep2.run1


title: COV362 treated with Prexasertib 20 nM C


title: whole heart, tak1+/+ wild-type, replicate #3

city: Copenhagen

first: Lars

middle: Allan

last: Larsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
After quality filtering, reads were aligned to reference sequence (GCF_000002035.6_GRCz11) using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%, average mapping ratio with genes was 74.56%. In total 23966 genes were identified.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: Matrix txt file. Columns: gene_id  (NCBI); gene_symbol; tpm_mut_1; tpm_mut_2; tpm_mut_3; tpm_WT_1; tpm_WT_2; tpm_WT_3. Data is shown as transcripts per million (TPM).

organism: Danio rerio

source_name: Whole heart, 3 dpf

extract_protocol:
RNA isolation using Qiagen Rneasy micro kit
Bulk RNAseq was performed as a service by BGI, China. Samples were paired end-sequenced using the DNBSEQ platform.

value: Whole heart, 3 dpf


title: whole heart, tak1+/+ wild-type, replicate #2


title: Gm.dry.biorep1.run1

value: whole seed


title: whole heart, tak1+/+ wild-type, replicate #1


title: COV362 treated with Prexasertib 20 nM B


title: Knockout_rep2


title: COV362 treated with Prexasertib 20 nM A


title: Knockout_rep1


title: COV362 DMSO vehicle C


title: whole heart, tak1-/- mutant, replicate #2


title: P-Sp, E9.5

city: Kumamoto

first: Saori

last: Morino-Koga

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

data_processing:
The fastq files were aligned, filtered, and counted by the cellranger count (v7.0.0) (10x Genomics).
Assembly: mm10-2020-A
Supplementary files format and content: tab-separated value files and matrix files

source_name: dorsal aorta

extract_protocol:
The P-Sp was dissociated using 0.25% trypsin-EDTA. Single cells were suspended in 0.04% BSA/PBS.
Library construction was performed by using the Chromium Single Cell 3' v3 kit (10x Genomics).

value: dorsal aorta

value: P-Sp-derived cells


title: PEO1 DMSO vehicle B


title: Wildtype_rep2

value: Wildtype


title: COV362 DMSO vehicle B


title: STZ-HFHC, 2nd-1-1-3, replicate 1, sNuc Seq

city: Seoul

first: Jung Hoon

last: Cha

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: College of Medicine, The Catholic University of Korea

data_processing:
Single-cell gene expression data were analyzed using Cell Ranger v7.0.1 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Initially, raw BCL files from Illumina HiSeqXten were demultiplexed, generating FASTQ files through the 'cellranger mkfastq' tool.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: liver

extract_protocol:
Nuclei were prepared from approximately 100 mg of frozen mouse liver tissue using the Singulator 100 system (S2 Genomics). Following dissociation, debris were eliminated through a Percoll gradient. The nuclei concentration was then evaluated using a LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems), and nuclei morphology was scrutinized through microscopy.
Libraries were generated using the Chromium controller in adherence to the 10× Chromium Next GEM Single Cell 3’ v3.1 protocol (CG000315). In summary, cell suspensions were diluted with nuclease-free water to attain a targeted cell count of 10,000. The cell suspension was mixed with a master mix and loaded onto a Chromium Next GEM chip G along with Single Cell 3’ v3.1 Gel Beads and Partitioning Oil. Within droplets, RNA transcripts from individual cells were uniquely barcoded and reverse transcribed. The cDNA molecules were pooled, underwent end repair, had a single ‘A’ base added, and the adapters were then ligated. Following purification and PCR enrichment, the final cDNA library was created. Quantification of the purified libraries was performed using quantitative real-time polymerase chain reaction (qRT-PCR) according to the qPCR Quantification Protocol Guide (KAPA), and their quality was assessed using the Agilent Technologies 4200 TapeStation (Agilent Technologies). The libraries were then sequenced on the HiSeq platform (Illumina), adhering to the read length specifications provided in the user guide.

value: liver

tag: disease state

value: MASH-related liver fibrosis


title: Wildtype_rep3


title: Wildtype_rep1


title: COV362 DMSO vehicle A


title: ND, 3rd-4-1-2, sNuc Seq

value: normal


title: whole heart, tak1-/- mutant, replicate #3


title: STZ-HFHC, 2nd-1-2-3, replicate 2, sNuc Seq


title: whole heart, tak1-/- mutant, replicate #1


title: ECMO_33_R (expression)

status: Public on Oct 15 2024

type: RNA

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data were generated by GenomeStudio v2011.1 software. Then the data were normalized using quantile normalization.

label: biotin

source_name: PBMC at Removal

label_protocol: cRNA were prepared with TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Congestive heart failure

tag: age

tag: gender

value: M

tag: outcome

value: Success

value: PBMC

value: Removal


title: ECMO_32_R (expression)

value: Acute myocardial infarction


title: ECMO_27_R (expression)

value: Arrhythmia


title: ECMO_19_R (expression)


title: ECMO_28_R (expression)

value: Dilated cardiomyopathy


title: ECMO_39_R (expression)

value: F


title: ECMO_8_R (expression)

value: Acute myocarditis

value: Failure


title: ECMO_10_R (expression)


title: ECMO_41_2 (expression)

source_name: PBMC at 2hr


title: ECMO_22_R (expression)


title: ECMO_42_2 (expression)


title: ECMO_42_R (expression)


title: ECMO_38_R (expression)


title: ECMO_40_2 (expression)


title: ECMO_37_2 (expression)

value: Dilated cardiomyopathy, DCMP


title: ECMO_34_2 (expression)

value: Aortic dissection


title: ECMO_39_2 (expression)


title: ECMO_6_R (expression)


title: ECMO_35_2 (expression)


title: ECMO_36_2 (expression)


title: ECMO_14_R (expression)


title: ECMO_32_2 (expression)


title: ECMO_31_2 (expression)


title: ECMO_30_2 (expression)


title: ECMO_7_R (expression)


title: ECMO_38_2 (expression)


title: ECMO_33_2 (expression)


title: ECMO_24_2 (expression)


title: ECMO_27_2 (expression)


title: ECMO_23_2 (expression)


title: ECMO_22_2 (expression)


title: ECMO_14_2 (expression)


title: ECMO_17_2 (expression)


title: ECMO_13_2 (expression)


title: ECMO_10_2 (expression)


title: ECMO_7_2 (expression)


title: ECMO_28_2 (expression)


title: ECMO_25_2 (expression)


title: ECMO_29_2 (expression)

value: failure


title: ECMO_20_2 (expression)


title: ECMO_11_2 (expression)


title: ECMO_19_2 (expression)


title: ECMO_21_2 (expression)


title: ECMO_6_2 (expression)


title: ECMO_8_2 (expression)


title: ECMO_39_0 (expression)

source_name: PBMC at 0hr


title: ECMO_40_0 (expression)


title: PEO1 treated with Prexasertib 20 nM A

tag: cell line


title: NmCas9-AAV gRNA 23+AZD7648, 7 Day Treatment; Rep1

value: in vitro

value: E15.5 (gestational day 15.5)

value: Neurons


title: NmCas9-AAV gRNA 23, 7 Day Treatment; Rep1


title: ECMO_38_0 (expression)


title: ECMO_36_0 (expression)


title: ECMO_22_0 (expression)


title: ECMO_29_0 (expression)


title: ECMO_30_0 (expression)


title: ECMO_23_0 (expression)

value: Congestive heart failure


title: ECMO_24_0 (expression)

value: M


title: ECMO_31_0 (expression)

value: Success


title: ECMO_34_0 (expression)

value: PBMC


title: ECMO_37_0 (expression)


title: ECMO_33_0 (expression)


title: ECMO_26_0 (expression)


title: ECMO_41_0 (expression)


title: ECMO_42_0 (expression)


title: ECMO_35_0 (expression)


title: ECMO_14_0 (expression)


title: ECMO_27_0 (expression)


title: ECMO_19_0 (expression)


title: ECMO_10_0 (expression)


title: ECMO_20_0 (expression)


title: ECMO_28_0 (expression)


title: ECMO_21_0 (expression)


title: ECMO_17_0 (expression)


title: ECMO_25_0 (expression)


title: ECMO_7_0 (expression)


title: ECMO_13_0 (expression)


title: ECMO_32_0 (expression)


title: ECMO_8_0 (expression)


title: ECMO_16_0 (expression)


title: ECMO_11_0 (expression)


title: RIP 4

city: Columbia

first: Lei

last: Lei

state: MO

address: 920 East Campus Dr

department: of Obstetrics, Gynecology and Women's Health

institute: University of Missouri School of Medicine

description: Sample_113848 RIP 4

data_processing:
Sequencing results were analyzed using Tuxedo/Cuffdiff2 (with DE at gene and isoform level)
Assembly: we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10)
Supplementary files format and content: tab-delimited text file includes raw counts of all samples

source_name: mouse ovary

extract_protocol:
Magna RIPTM RNA-binding protein immunoprecipitation kit (Sigma-Aldrich 17-700) was used to isolate RNAs that bind with DCP1A
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2- Pico input Mammalian

tag: tissue

value: mouse ovary


title: RIP 3

description: Sample_113847 RIP 3


title: input 4

description: Sample_113844 input 4


title: RIP 2

description: Sample_113846 RIP 2


title: input 2

description: Sample_113842 input 2


title: input 1

description: Sample_113841 input 1


title: WT bud (10 hpf) charged tRNA-seqrep 3

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.3.8) using the parameters: --species Drer --cluster-id 0.93 --threads 40 --min-cov 0.001 --deconv-cov-ratio 0.4 --max-mismatches 0.075 --remap --remap-mismatches 0.075  --max-multi 10 max-multi 6 --remap --remap-mismatches 0.075 --crosstalks.
Assembly: GRCz11
Supplementary files format and content: csv; mim-tRNAseq generated CCA proportions

source_name: 10 hpf embryos

extract_protocol:
Total RNA from D.rerio embryos collected at the sphere (4 hpf) or bud (10 hpf) stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta-elimination (Behrens and Nedialkova, 2022).
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens and Nedialkova, 2022) and sequenced on an Illumina NovaSeq 6000 platform.

value: 10 hpf embryos


title: WT bud (10 hpf) charged tRNA-seqrep 2


title: LPS+ApoA1 treatment-3

city: Stanford

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

institute: Stanford University

data_processing:
Adapter sequences and low-quality base calls (Phred score < 30 at ends) were trimmed using Cutadapt v1.8.1. Trimmed reads were aligned to the reference genome using STAR 2.7.10b with comprehensive gene annotations from GENCODE release vM30. Gene-level transcript abundances were quantified with RSEM v1.3.1. RNA-Seq read counts and Transcripts Per Million (TPM) values were obtained from RSEM output and imported into R software for further analysis.
Assembly: mm10
Supplementary files format and content: count table (CSV)
Supplementary files format and content: TPM (CSV)

organism: Rattus norvegicus

source_name: Primary cells

extract_protocol:
RNA was extract using Rneasy plus micro kit (qiagen)
RNA libraries for RNA-seq were prepared by Novogene

value: Primary cells

value: microglia

value: wild type


title: LPS+ApoA1 treatment-4


title: LPS treatment-4


title: WT sphere (4 hpf) charged tRNA-seqrep 3

source_name: 4 hpf embryos

value: 4 hpf embryos


title: LPS treatment-2


title: LPS+ApoA1 treatment-1


title: WT sphere (4 hpf) charged tRNA-seqrep 1


title: LPS+ApoA1 treatment-2


title: WT sphere (4 hpf) charged tRNA-seqrep 2


title: input 3

description: Sample_113843 input 3


title: RIP 1

description: Sample_113845 RIP 1


title: LPS treatment-1


title: ApoA1 treatment-4


title: ApoA1 treatment-3


title: LPS treatment-3


title: ECMO_6_0 (expression)

value: Acute myocarditis

value: F


title: ApoA1 treatment-2


title: Control-4


title: Control-3


title: ApoA1 treatment-1


title: NPCs, shNC_2

city: Xi'an

first: Liangwei

last: Mei

state: Shaanxi

address: 127 Changle West Road

department: Orthopaedics

institute: Xijing Hospital, the Fourth Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: rno Ensembl_v101
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values and counts for each Sample

source_name: NP cells, shNC

growth_protocol: NP tissues were isolated from the lumbar IVD of 4-week-old male Sprague-Dawley rats. Next, the tissues were diced into small pieces and treated with 0.025% collagenase II at 37°C for 4 h. NPCs were cultured in DMEM/F12 medium with 10% FBS in a constant temperature incubator containing 5% CO2 at 37°C. Cultured medium was changed every 2 days. Cells from passages 3–5 were used in the following experiments.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NPCs were transfected with Bmal1 shRNA or its negative control lentivirus for 72 hours

value: Sprague-Dawley

value: Nucleus pulposus cells

value: transfection with negative control shRNA lentivirus for 72 hours


title: NPCs, shNC_1


title: NPCs, shNC_3


title: Control-1


title: WT bud (10 hpf) charged tRNA-seqrep 1


title: Control-2


title: NPCs, shBmal1_3

source_name: NP cells, shBmal1

value: transfection with Bmal1 shRNA lentivirus for 72 hours


title: NPCs, shBmal1_1


title: NPCs, shBmal1_2


title: B10siSNRPB-YFP-3

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

description: replicate 3b

data_processing:
For alignment and quantification of gene.tpm and psi files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step
Assembly: hg38
Supplementary files format and content: contains whippet derived gene expression information in transcripts per million per gene
Supplementary files format and content: contains whippet-derived percentage splie in

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin (Invitrogen).

extract_protocol:
RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Depletions were performed with siRNA from Thermofisher Scientific (silencer select) and independently validated with siRNA from Dharmacon (Dharmacon siGenome-SMARTpool). The non-targeting siRNA from Thermofisher Scientific (silencer select) was used as the siRNA control. Transfections were performed with HiPerFect transfection reagent (Qiagen, #301707)

value: HeLa

value: si SNRPB


title: A10siSNRPB-YFP-3

description: replicate 3a


title: A2siSNRPB-YFP-1

description: replicate 1a


title: A6siSNRPB-YFP-2

description: replicate 2a


title: B2siSNRPB-YFP-1

description: replicate 1b


title: B5siCtrl-YFP-2

description: replicate 2b

value: si CTRL


title: B1siCtrl-YFP-1

description: replicate 1b


title: R300_duct

city: bethesda

first: Efsun

last: Arda

state: Maryland

address: 41 medlars drive

institute: National Institutes of Health

data_processing:
Raw reads Mapping: HiC pro
Loop calling: hichipper and FitHiChIP
Assembly: hg38
Supplementary files format and content: tab-delimited text file include consensus loops with pair-ended tags (PETs) for each cell type
Library strategy: HiChIP

source_name: duct

extract_protocol:
Sorted cells are fixed with 1% formaldehyde for 10 minutes at room temperature, after quenching, cell lysis, in situ chromatin digestion and proximity ligation, the ligated chromatin was extracted from nuclei following the protocol described in Mumbach et al (PMID: 27643841)
custom DNA libraries were prepared following the protocol described in Mumbach et al (PMID: 27643841)

value: duct

tag: sample origin

value: Pancreas

tag: disease status

value: normal

tag: Sex

value: Female

tag: bmi


title: SAMN10977276_delta

source_name: delta

tag: cell type

value: delta

value: Male


title: R299_alpha

source_name: alpha

value: alpha


title: SAMN10977276_beta

source_name: beta

value: beta


title: A1siCtrl-YFP-1

description: replicate 1a

tag: treatment


title: A5siCtrl-YFP-2

description: replicate 2a


title: SAMN10977276_alpha


title: SAMN10913630_beta


title: SAMN10913630_delta


title: SAMN10913630_alpha


title: R303_delta


title: R303_beta


title: SAMN10737781_beta


title: SAMN10737781_alpha


title: R303_alpha


title: SAMN10391370_delta.


title: SAMN10391370_beta.


title: SAMN10737781_delta


title: B9siCtrl-YFP-3

description: replicate 3b


title: A9siCtrl-YFP-3

description: replicate 3a


title: B6siSNRPB-YFP-2

description: replicate 2b


title: SAMN10391370_delta

data_processing:
Raw reads were processed using PEPATAC package (PMID: 34859208)
Homer Suite was used to generate counts table
Assembly: hg38
Supplementary files format and content: tab-delimited file containing consensus peaks with normalized counts in each donor and cell type

extract_protocol:
sorted cells were transposed following steps described in Corces et al (PMID: 28846090), then transcposed DNA fragments were purified using a Zymo DNA Clean and Concentrator-5 Kit
custom DNA libraries were prepared following the protocol described in Corces et al (PMID: 28846090).

tag: dsease status


title: R290_duct.


title: SAMN10391370_alpha


title: SAMN10391370_beta


title: Drosophila_melanogaster_ag_NG_z21_131017_I1125

city: Davis

first: Ben

last: Hopkins

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

organism: Drosophila melanogaster

source_name: accessory glands

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

value: accessory glands

tag: sample id

tag: library name

tag: strain information


title: R299_beta.


title: Drosophila_melanogaster_testes_NG_z22_130917_I1135

source_name: testes

value: testes


title: R290_duct


title: SAMN10391370_alpha.


title: Drosophila_melanogaster_ag_NG_z21_130917_I1135


title: R290_acinar.

source_name: acinar

value: acinar


title: Negative control 3

first: Elena

last: Grueso-Navarro

state: Ciudad Real

address: Vereda de Socuéllamos s/n

department: Gastroenterology

country: Spain

institute: Hospital General de Tomelloso

data_processing:
raw reads processing included quality control analysis with multiQC v1.6 tool
trimming for Illumina adapters, and alignment to human genome using BWA (Burrow-Wheeler aligner)
Gene quantification by means HTseq software(3) was performed using gencode v.26 as annotation database
To determine the overall microRNA (miRNA) and transfer RNA-Related Fragments (tRFs) composition for each sample, miRge3.0 pipeline(5) from processed reads from no outliers against a set of sRNA annotation libraries was used to obtain their tabulated counts.
Assembly: gencode v.26
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Blood plasma

extract_protocol:
Total RNA was isolated from EV samples using Total RNA Purification Kit (Norgen Biotek, Ontario, Canada) and treated with DNAse with RNAse-free DNAse I Kit (Norgen Biotek) to eliminate contaminant DNA according to manufacturer’s protocol.
Sequencing libraries were prepared following the manufacturer’s protocol for “NEXTflex™ Small RNA-Seq Kit v3” (Bioo Scientific Corporation, Austin, TX, USA).

value: Blood plasma


title: Blood plasma EVs, EoE.Basal ID 124


title: Blood plasma EVs, EoE.Basal ID 117


title: Negative control 2


title: Blood plasma EVs, EoE.Basal ID 122


title: Negative control 1


title: Blood plasma EVs, EoE.Basal ID 121


title: Blood plasma EVs, EoE.Basal ID 112


title: Blood plasma EVs, EoE.Basal ID 116


title: Blood plasma EVs, EoE.Basal ID 111


title: Blood plasma EVs, EoE.Basal ID 110


title: Blood plasma EVs, EoE.Basal ID 106


title: Blood plasma EVs, EoE.Basal ID 114


title: Blood plasma EVs, EoE.Basal ID 104


title: Blood plasma EVs, Control


title: Blood plasma EVs, EoE.Basal ID 101


title: R299_beta


title: Drosophila_melanogaster_testes_NG_z22_131017_I1125


title: Blood plasma EVs, EoE.Basal ID 98


title: Blood plasma EVs, EoE.Basal ID 100


title: Blood plasma EVs, EoE.Basal ID 95


title: Blood plasma EVs, EoE.Basal ID 87


title: Blood plasma EVs, EoE.Basal ID 96


title: Blood plasma EVs, EoE.Basal ID 94


title: Blood plasma EVs, Control ID 85


title: Blood plasma EVs, EoE.Basal ID 120


title: Blood plasma EVs, Control ID 83


title: Blood plasma EVs, Control ID 84


title: Blood plasma EVs, Control ID 82


title: Blood plasma EVs, Control ID 81


title: Blood plasma EVs, Control ID 80


title: Blood plasma EVs, Control ID 79


title: Blood plasma EVs, Control ID 78


title: Blood plasma EVs, EoE.Basal ID 66


title: Blood plasma EVs, Control ID 71


title: Blood plasma EVs, EoE.Basal ID 70


title: Blood plasma EVs, Control ID 75


title: Blood plasma EVs, Control ID 74


title: Blood plasma EVs, EoE.Basal ID 59


title: Blood plasma EVs, EoE.Basal ID 60


title: Blood plasma EVs, EoE.Basal ID 64


title: Blood plasma EVs, EoE.Basal ID 77


title: Blood plasma EVs, EoE.Pos.tx ID 53


title: Blood plasma EVs, EoE.Basal ID 58


title: Blood plasma EVs, Control ID 55


title: Blood plasma EVs, EoE.Basal ID 97


title: Blood plasma EVs, EoE.Pos.tx ID 51


title: Blood plasma EVs, EoE.Pos.tx ID 46


title: Blood plasma EVs, EoE.Basal ID 45


title: Blood plasma EVs, EoE.Pos.tx ID 44


title: Blood plasma EVs, EoE.Basal ID 72


title: Blood plasma EVs, EoE.Basal ID 39


title: Blood plasma EVs, EoE.Pos.tx ID 35


title: Blood plasma EVs, EoE.Pos.tx ID 42


title: Blood plasma EVs, EoE.Pos.tx ID 43


title: Blood plasma EVs, EoE.Pos.tx ID 38


title: Blood plasma EVs, EoE.Basal ID 31


title: Blood plasma EVs, EoE.Basal ID 30


title: Blood plasma EVs, EoE.Pos.tx ID 22


title: Blood plasma EVs, EoE.Pos.tx ID 21


title: Blood plasma EVs, Control ID 26