title: C08N

status: Public on Oct 22 2024

city: fukukoka

first: Jinghui

address: 3-1-1 maidashi fukuoka

country: Japan

institute: kyushu university

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
Assembly: human
Supplementary files format and content: Tab-separated values files and matrix files generated by Cell Ranger program.

source_name: Adjacent normal mucosa

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1 the Chromium Next GEM Single Cell 5′ Kit v2 for Dual Index (10x Genomics). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct the 3’ and 5’ gene library.
The libraries were sequenced on DNBSEQ-G400 (MGI Tech).

tag: sample id

value: Adjacent normal mucosa

tag: colon operation_date

tag: stage (ptmn)

tag: gender

value: not applicable


title: C08T

type: SRA

last: Zhang

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

source_name: Colon cancer

tag: tissue

value: Colon cancer

tag: age

value: Male

tag: treatment

value: Tacrolimus, Mycophenolate Mofetil, Steroids


title: C11N


title: C09T

value: Female


title: C11T


title: C10T

value: Ciclosporin, Mycophenolate Mofetil, Steroids


title: C10N


title: CON_TNF_Med_2

type: RNA

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R, log2 transformed and quantile normalized.

label: Biotin

source_name: human chondrocytes (Ref. P10970, Innoprot®)

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: All cell types were cultured in a mix of serum-free DMEM (Hyclone®) and 1% penicillin/streptomycin (Hyclone®).

extract_protocol: GeneMATRIX universal RNA purification kit (EURx®) following the manufacturer’s instructions

treatment_protocol: Inflamed chondrocytes were treated with CM derived from mesenchymal stem cells cultures.

value: chondrocytes were treated with TNF (25 ng/mL) and CM (50 μg/mL)

tag: cell type

value: Group 4 (CM-treated TNF-inflamed chondrocytes)


title: PDAC Cancer Replicate1

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

country: USA

institute: Purdue University

library_source: transcriptomic

data_processing:
Data quality control and filtering was performed with FastX.
Read-mapping against the human (mm10) genome was performed with STAR.
Raw read counts for each gene from each replicate were determined using HTSeq.
Differential expression analysis was performed with R-package edgeR .
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Pancreas

growth_protocol:
The Plk1 knock-in mouse (Plk1LSL) was designed by the Xiaoqi Liu lab at Purdue University, and constructed by Taconic, Germany.
Plk1LSL mice were subsequently obtained from these recombinant ES cells. Mist1Cre/+/KrasG12D/+ mice were generated by the Konieczny lab at Purdue University, whereas Rosa26CreERt2 mice were purchased from the Jackson Laboratory.
To generate Mist1CreER/+/Plk1LSL mice, we crossed the Plk1LSL line to Mist1CreER/+ line.
To generate Mist1CreER/+/KrasG12D/+/Plk1LSL mice, we crossed the Mist1CreER/+/KrasG12D/+ line to the Plk1LSL line.
To generate Rosa26CreERt2/Plk1LSL mice, we crossed the Plk1LSL line to Rosa26CreERt2 line.

extract_protocol:
Mice were sacrificed and pancreata samples were harvested for RNA-Seq, following the final caerulein injection.
Total RNA was extracted from tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Acute pancreatitis was induced by caerulein via intraperitoneal (i.p) injections. Adult mice (6-8 wk) were given i.p. injections of caerulein (Sigma-Aldrich, St. Louis, MO) every 8 hours for two consecutive days (50 μg/kg body weight), with control mice receiving phosphate buffered saline (PBS).
Caerulein injection was administrated to induce accurate pancreatitis (AP) and chronic pancreatitis (CP) in Mist1CreER/+ and Mist1CreER/+/Plk1LSL mice 2 d and 7 d post-treatment, respectively and PanIN in Mist1CreER/+/KrasG12D/+ and Mist1CreER/+/KrasG12D/+/Plk1LSL mice 25 d post-acute pancreatitis.

tag: strain

value: Mist1CreER+/KrasG12D/+/p53R172H/+  mice

value: Pancreas

value: PDAC Cancer

tag: genotype


title: PDAC Cancer Replicate2


title: PDAC Cancer Replicate3


title: AT_MSC_3

source_name: Human adipose-derived mesenchymal stem cells (Ref. P10763, Innoprot®)

value: ASCs cultured in a mix of serum-free DMEM (Hyclone®) and 1% penicillin/streptomycin (Hyclone®)

value: Group 2 (ASC control samples)


title: CON_TNF_2

value: chondrocytes cultured in a mix of serum-free DMEM (Hyclone®) and 1% penicillin/streptomycin (Hyclone®) plus TNF (25 ng/mL)

value: Group 3 (TNF-inflamed chondrocytes)


title: CON_TNF_Med_1


title: CON_TNF_Med_3


title: Mist1-CRE/+;Plk1+ PanIN (Day 25) Tam+Cae (treated) Replicate2

value: Mist1CreER/+/Plk1LSL mice


title: Mist1-CRE/+;Plk1+ PanIN (Day 25) Tam+Cae (treated) Replicate1


title: Cond_1

value: chondrocytes cultured in a mix of serum-free DMEM (Hyclone®) and 1% penicillin/streptomycin (Hyclone®)

value: Group 1 (non-inflamed chondrocytes)


title: CON_TNF_3


title: AT_MSC_2


title: CON_TNF_1


title: AT_MSC_1


title: Cond_3


title: Mist1-CRE/+ PanIN (Day 25) Tam+Cae (treated) Replicate2

value: Mist1CreER/+ mice


title: Mist1-CRE/+ Acute pancreatitis (Day 2) Tam+Cae (treated) Replicate2

value: Mist1-CRE/+ Acute pancreatitis (Day 2) Tam+Cae- (treated)


title: Mist1-CRE/+ Acute pancreatitis (Day 2) Tam+Cae (treated) Replicate1


title: Mist1-CRE/+;Plk1+ Acute pancreatitis Tam+PBS (untreated) Replicate1


title: Mist1-CRE/+ PanIN (Day 25) Tam+Cae (treated) Replicate1


title: Mist1-CRE/+;Plk1+ Acute pancreatitis (Day 2) Tam+Cae- (treated) Replicate1


title: Mist1-CRE/+;Plk1+ Acute pancreatitis (Day 2) Tam+Cae- (treated) Replicate2


title: Mist1-CRE/+;Plk1+ Acute pancreatitis Tam+PBS (untreated) Replicate2


title: Mist1-CRE/+ Acute pancreatitis Tam+PBS (untreated) Replicate2


title: PDAC Cancer Replicate4


title: Mist1-CRE/+ Acute pancreatitis Tam+PBS (untreated) Replicate1


title: Cond_2


title: Vehicle(DMSO) -3

status: Public on Oct 23 2024

city: Xia Men

first: Yu

last: Luo

address: zhenhai Road

country: China

institute: the fiirst affiliated hospital of Xiamen University

description:
FPKM_allsamples
Raw_gene_counts_matrix

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: 786-O renal cancer cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 786-O cells were treated with 10uM Everolimus, 1.5uM SGI-1027, 5uM Everolimus combined with1.5uM SGI-1027, or vehicle (DMSO) for 24 hours. Each processing group contains three replicates.

tag: cell line

value: Human renal cancer cell line

value: WT

value: DMSO


title: RB754 worms, atRA, rep 3

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

description:
alignments/tretinoin/B12_RB754_TRET_3.bam
RB754_featureCounts.txt

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in paired-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 104)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans strains N2-PD1073, PS3551 [hsf-1(sy441)], and RB754 [aak-2(ok524)] were maintained on nematode growth medium (NGM) plates seeded with Escherichia coli OP50-1 at 20˚C.

extract_protocol:
To generate populations for RNA sequencing, we pooled animals from 4 plates to generate populations of ~200 animals, on day four of adulthood. RNA was collected using standard techniques.
RNA libraries for RNA-seq were prepared with the KAPA mRNA HyperPrep Kit.

treatment_protocol: Tretinoin (all-trans retinoic acid) (Sigma-Aldrich PHR1187) was obtained as a solid and dissolved in DMSO (dimethyl sulfoxide) to obtain a stock solution. DMSO stock solutions were mixed with water to form a working solution before being added to plates. In-plate concentrations were calculated by presuming the final volume to be equal to that of the volume of agar. For 150 µM atRA plates, stock solutions formed precipitates at working solution concentrations, requiring working solutions to be prepared individually for each plate.

value: whole worm

value: adult day 4

value: all-trans retinoic acid


title: RB754 worms, atRA, rep 2

description:
alignments/tretinoin/F10_RB754_TRET_2.bam
RB754_featureCounts.txt


title: RB754 worms, DMSO, rep 3

description:
alignments/tretinoin/A12_RB754_DMSO_3.bam
RB754_featureCounts.txt

value: DMSO control


title: RB754 worms, DMSO, rep 1

description:
alignments/tretinoin/B10_RB754_DMSO_1.bam
RB754_featureCounts.txt


title: RB754 worms, atRA, rep 4

description:
alignments/tretinoin/H10_RB754_TRET_4.bam
RB754_featureCounts.txt


title: PS3551 worms, DMSO, rep 1

description:
alignments/tretinoin/A10_PS3551_DMSO_1.bam
PS3551_featureCounts.txt


title: PS3551 worms, DMSO, rep 2

description:
alignments/tretinoin/E10_PS3551_DMSO_2.bam
PS3551_featureCounts.txt


title: PS3551 worms, DMSO, rep 3

description:
alignments/tretinoin/C12_PS3551_DMSO_3.bam
PS3551_featureCounts.txt


title: N2 worms, DMSO, rep 4

description:
alignments/tretinoin/D11_N2_DMSO_4.bam
N2_featureCounts.txt


title: N2 worms, DMSO, rep 2

description:
alignments/tretinoin/F11_N2_DMSO_2.bam
N2_featureCounts.txt


title: N2 worms, atRA, rep 3

description:
alignments/tretinoin/G11_N2_TRET_3.bam
N2_featureCounts.txt


title: PS3551 worms, DMSO, rep 4

description:
alignments/tretinoin/G12_PS3551_DMSO_4.bam
PS3551_featureCounts.txt


title: PS3551 worms, atRA, rep 1

description:
alignments/tretinoin/C10_PS3551_TRET_1.bam
PS3551_featureCounts.txt


title: PS3551 worms, atRA, rep 2

description:
alignments/tretinoin/G10_PS3551_TRET_2.bam
PS3551_featureCounts.txt


title: N2 worms, atRA, rep 4

description:
alignments/tretinoin/A11_N2_TRET_4.bam
N2_featureCounts.txt


title: PS3551 worms, atRA, rep 3

description:
alignments/tretinoin/D12_PS3551_TRET_3.bam
PS3551_featureCounts.txt


title: N2 worms, atRA, rep 2

description:
alignments/tretinoin/B11_N2_TRET_2.bam
N2_featureCounts.txt


title: N2 worms, atRA, rep 1

description:
alignments/tretinoin/H11_N2_TRET_1.bam
N2_featureCounts.txt


title: Mutant3

city: Portland

first: Supender

last: Kaur

state: Oregon

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology and Immuno

institute: Oregon health and science university

description: Mutant animals on PA14-24HOURS

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Caenorhabditis elegans genome WS220
The  htseq-count were further analyesd for the  differentially expressed features from count tables using DESeq2
Genome_build: Caenorhabditis elegans genome WS220
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample ...

source_name: Whole organism

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to young adult stage at 20oC

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and added to the P.aeruginosa PA14 seeded plates at 25℃ for 24 hours . After that worms were washed with M9  thrice to get rid of bacteris and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: Whole organism

value: Young adults


title: N2 worms, DMSO, rep 1

description:
alignments/tretinoin/C11_N2_DMSO_1.bam
N2_featureCounts.txt


title: RB754 worms, DMSO, rep 2

description:
alignments/tretinoin/H12_RB754_DMSO_2.bam
RB754_featureCounts.txt


title: RB754 worms, atRA, rep 1

description:
alignments/tretinoin/D10_RB754_TRET_1.bam
RB754_featureCounts.txt


title: RB754 worms, DMSO, rep 4

description:
alignments/tretinoin/E12_RB754_DMSO_4.bam
RB754_featureCounts.txt


title: Mutant2

description: Mutant animals on PA14-24HOURS


title: Mutant1

description: Mutant animals on PA14-24HOURS


title: Control3

description: Control animals on PA14-24HOURS


title: Control2

description: Control animals on PA14-24HOURS


title: N2 worms, DMSO, rep 3

description:
alignments/tretinoin/E11_N2_DMSO_3.bam
N2_featureCounts.txt


title: Control1

description: Control animals on PA14-24HOURS


title: Donor 3, baseline multiome chromatin accessibility

city: Somerville

first: Daniel

last: Burkhardt

state: Massachusetts

address: 101 South Street 6th Floor

institute: Cellarity

library_source: genomic single cell

data_processing:
For multiome data, Cell Ranger ARC (v2.0) mkfastq was used to generate all demultiplexed FASTQ files from the raw sequencing data.  Cell Ranger ARC count was used to align transcriptome reads to the human GRCh38 genome reference provided by 10X Genomics and generate all downstream count matrices.
Assembly: hg38
Supplementary files format and content: Single-cell RNA expression and multiome objects are stored as AnnData objects, where observation metadata can be found in .obs and feature metadaata can be found in .var.

molecule: genomic DNA

source_name: blood

extract_protocol: Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide

value: blood

value: PBMC

tag: ethnicity

value: caucasian

tag: Sex

value: male

tag: vendor

value: AllCells, LLC


title: Donor 3, hashtags for perturbation sample 12

data_processing:
For perturbation data, Cell Ranger (v5.0.1) mkfastq was used to generate demultiplexed FASTQ files from the raw sequencing data. Cell Ranger count was used to align transcriptome reads to the human GRCh38 genome reference, identify corresponding feature barcode reads according to a csv reference file containing all the relevant information needed for downstream processing, and quantify gene and UMI counts.
Assembly: hg38
Supplementary files format and content: Single-cell RNA expression and multiome objects are stored as AnnData objects, where observation metadata can be found in .obs and feature metadaata can be found in .var.

molecule: polyA RNA

extract_protocol: Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry) with Feature Barcoding

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, CGM-097, SLx-2119, Nefazodone, STK219801, TPCA-1, MGCD-265, Masitinib, CEP-18770 (Delanzomib), Ceritinib


title: Donor 3, hashtags for perturbation sample 13

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Clemastine, YK 4-279, Buspirone, Midostaurin, CEP-37440, GSK256066, GSK-1070916, Ricolinostat, Bosutinib


title: Donor 3, hashed perturbation sample 14

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Imatinib, SCH-58261, Colforsin, MLN 2238, Tivantinib, Tosedostat, R428, Oxybenzone, Vandetanib


title: Donor 3, hashed perturbation sample 12


title: Donor 3, hashtags for perturbation sample 15

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Tipifarnib, BX 912, Doxorubicin, PF-03814735, AZD4547, Prednisolone, Colchicine, ABT-199 (GDC-0199), Mometasone Furoate


title: Donor 3, hashed perturbation sample 11

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, TGX 221, Pitavastatin Calcium, ABT737, PRT-062607, AZ628, AZD-8330, Saracatinib, RG7112, Lamivudine


title: Donor 3, hashed perturbation sample 10

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Azacitidine, TR-14035, Nilotinib, AT 7867, OSI-930, GO-6976, CC-401, Resminostat, Crizotinib


title: Donor 3, hashtags for perturbation sample 9

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Riociguat, CHIR-99021, Defactinib, BI-D1870, AZD3514, HMN-214, Decitabine, LDN 193189, Cabozantinib


title: Donor 3, hashtags for perturbation sample 14


title: Donor 3, hashed perturbation sample 13


title: Donor 3, hashtags for perturbation sample 11


title: Donor 3, hashtags for perturbation sample 6

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AT13387, PF-04691502, Perhexiline, UNII-BXU45ZH6LI, RVX-208, Ketoconazole, LY2090314, Vardenafil, Dasatinib


title: Donor 3, hashed perturbation sample 9


title: Donor 3, baseline multiome gene expression


title: Donor 3, hashtags for perturbation sample 10


title: Donor 3, hashtags for perturbation sample 8

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Oprozomib (ONX 0912), Alogliptin, Penfluridol, Quizartinib, RN-486, PD-0325901, IMD-0354, Canertinib, Idelalisib


title: Donor 3, hashtags for perturbation sample 4

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, BMS-265246, Ruxolitinib, Pomalidomide, Dovitinib, AVL-292, Navitoclax, TL_HRAS26, Proscillaridin A;Proscillaridin-A, Vorinostat


title: Donor 3, hashtags for perturbation sample 7

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Desloratadine, Dactolisib, BMS-536924, IKK Inhibitor VII, Amiodarone, Isoniazid, Alvocidib, Disulfiram, Flutamide


title: Donor 3, hashtags for perturbation sample 5

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AMD-070 (hydrochloride), Sgc-cbp30, FK 866, Chlorpheniramine, Scriptaid, BAY 61-3606, Methotrexate, Palbociclib, Trametinib


title: Donor 3, hashtags for perturbation sample 3

value: blood

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Topotecan, BAY 87-2243, Phenylbutazone, K-02288, BMS-777607, Porcn Inhibitor III, BMS-387032, IN1451, Raloxifene


title: Donor 3, hashtags for perturbation sample 2

value: PBMC

value: caucasian

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, 5-(9-Isopropyl-8-methyl-2-morpholino-9H-purin-6-yl)pyrimidin-2-amine, O-Demethylated Adapalene, Protriptyline, I-BET151, Foretinib, GW843682X, CGP 60474, Ixabepilone, Linagliptin


title: Donor 3, hashtags for perturbation sample 1

value: male

value: AllCells, LLC

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Atorvastatin, Ganetespib (STA-9090), Clomipramine, Sunitinib, Tivozanib, Tamatinib, TIE2 Kinase Inhibitor, MK-5108, Lapatinib


title: Donor 3, hashtags for perturbation sample 16

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, RG7090, GLPG0634, Mubritinib (TAK 165), Vanoxerine, SB525334, HYDROXYUREA, Tacalcitol, Selumetinib, Clotrimazole


title: Donor 3, hashed perturbation sample 8


title: Donor 3, hashed perturbation sample 16


title: Donor 3, hashed perturbation sample 1


title: Donor 3, hashed perturbation sample 3


title: Donor 3, hashed perturbation sample 4


title: Donor 3, hashed perturbation sample 6


title: Donor 2, baseline multiome chromatin accessibility


title: Donor 2, baseline multiome gene expression


title: Donor 2, hashtags for perturbation sample 16


title: Donor 3, hashed perturbation sample 2


title: Donor 2, hashtags for perturbation sample 12

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, CGM-097, SLx-2119, Nefazodone, STK219801, TPCA-1, MGCD-265, Masitinib, CEP-18770 (Delanzomib), Ceritinib


title: Donor 2, hashtags for perturbation sample 14

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Imatinib, SCH-58261, Colforsin, MLN 2238, Tivantinib, Tosedostat, R428, Oxybenzone, Vandetanib


title: Donor 2, hashtags for perturbation sample 13

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Clemastine, YK 4-279, Buspirone, Midostaurin, CEP-37440, GSK256066, GSK-1070916, Ricolinostat, Bosutinib


title: Donor 2, hashtags for perturbation sample 11

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, TGX 221, Pitavastatin Calcium, ABT737, PRT-062607, AZ628, AZD-8330, Saracatinib, RG7112, Lamivudine


title: Donor 2, hashtags for perturbation sample 10

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Azacitidine, TR-14035, Nilotinib, AT 7867, OSI-930, GO-6976, CC-401, Resminostat, Crizotinib


title: Donor 2, hashtags for perturbation sample 15

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Tipifarnib, BX 912, Doxorubicin, PF-03814735, AZD4547, Prednisolone, Colchicine, ABT-199 (GDC-0199), Mometasone Furoate


title: Donor 2, hashtags for perturbation sample 9

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Riociguat, CHIR-99021, Defactinib, BI-D1870, AZD3514, HMN-214, Decitabine, LDN 193189, Cabozantinib


title: Donor 2, hashed perturbation sample 16


title: PS3551 worms, atRA, rep 4

description:
alignments/tretinoin/F12_PS3551_TRET_4.bam
PS3551_featureCounts.txt

value: whole worm

value: adult day 4

value: all-trans retinoic acid


title: Donor 2, hashed perturbation sample 15

value: blood

value: PBMC


title: Donor 2, hashed perturbation sample 13

value: caucasian


title: Donor 2, hashtags for perturbation sample 8

value: male

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Oprozomib (ONX 0912), Alogliptin, Penfluridol, Quizartinib, RN-486, PD-0325901, IMD-0354, Canertinib, Idelalisib


title: Donor 2, hashed perturbation sample 10

value: AllCells, LLC


title: Donor 3, hashed perturbation sample 15


title: Donor 2, hashed perturbation sample 11


title: Donor 3, hashed perturbation sample 7

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Desloratadine, Dactolisib, BMS-536924, IKK Inhibitor VII, Amiodarone, Isoniazid, Alvocidib, Disulfiram, Flutamide


title: Donor 2, hashed perturbation sample 9


title: Donor 3, hashed perturbation sample 5

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AMD-070 (hydrochloride), Sgc-cbp30, FK 866, Chlorpheniramine, Scriptaid, BAY 61-3606, Methotrexate, Palbociclib, Trametinib


title: Donor 2, hashtags for perturbation sample 7


title: Donor 2, hashtags for perturbation sample 6

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AT13387, PF-04691502, Perhexiline, UNII-BXU45ZH6LI, RVX-208, Ketoconazole, LY2090314, Vardenafil, Dasatinib


title: Donor 2, hashtags for perturbation sample 4

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, BMS-265246, Ruxolitinib, Pomalidomide, Dovitinib, AVL-292, Navitoclax, TL_HRAS26, Proscillaridin A;Proscillaridin-A, Vorinostat


title: Donor 2, hashed perturbation sample 7


title: Donor 2, hashtags for perturbation sample 5


title: Donor 2, hashed perturbation sample 8


title: Donor 2, hashed perturbation sample 6


title: Donor 2, hashed perturbation sample 4


title: Donor 2, hashed perturbation sample 3

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Topotecan, BAY 87-2243, Phenylbutazone, K-02288, BMS-777607, Porcn Inhibitor III, BMS-387032, IN1451, Raloxifene


title: Donor 2, hashed perturbation sample 5


title: Donor 2, hashtags for perturbation sample 2

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, 5-(9-Isopropyl-8-methyl-2-morpholino-9H-purin-6-yl)pyrimidin-2-amine, O-Demethylated Adapalene, Protriptyline, I-BET151, Foretinib, GW843682X, CGP 60474, Ixabepilone, Linagliptin


title: Donor 2, hashed perturbation sample 2


title: Donor 2, hashtags for perturbation sample 3


title: Donor 1, baseline multiome chromatin accessibility

value: female


title: Donor 2, hashed perturbation sample 14

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Imatinib, SCH-58261, Colforsin, MLN 2238, Tivantinib, Tosedostat, R428, Oxybenzone, Vandetanib


title: Donor 1, baseline multiome gene expression


title: Donor 2, hashed perturbation sample 1

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Atorvastatin, Ganetespib (STA-9090), Clomipramine, Sunitinib, Tivozanib, Tamatinib, TIE2 Kinase Inhibitor, MK-5108, Lapatinib


title: Donor 2, hashed perturbation sample 12

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, CGM-097, SLx-2119, Nefazodone, STK219801, TPCA-1, MGCD-265, Masitinib, CEP-18770 (Delanzomib), Ceritinib


title: Donor 1, hashtags for perturbation sample 16

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, RG7090, GLPG0634, Mubritinib (TAK 165), Vanoxerine, SB525334, HYDROXYUREA, Tacalcitol, Selumetinib, Clotrimazole


title: Donor 1, hashtags for perturbation sample 15

value: blood

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Tipifarnib, BX 912, Doxorubicin, PF-03814735, AZD4547, Prednisolone, Colchicine, ABT-199 (GDC-0199), Mometasone Furoate


title: Donor 1, hashtags for perturbation sample 13

value: PBMC

value: caucasian

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Clemastine, YK 4-279, Buspirone, Midostaurin, CEP-37440, GSK256066, GSK-1070916, Ricolinostat, Bosutinib


title: Donor 1, hashtags for perturbation sample 14

value: AllCells, LLC


title: Donor 1, hashed perturbation sample 16


title: Donor 1, hashtags for perturbation sample 11

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, TGX 221, Pitavastatin Calcium, ABT737, PRT-062607, AZ628, AZD-8330, Saracatinib, RG7112, Lamivudine


title: Donor 1, hashtags for perturbation sample 9

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Riociguat, CHIR-99021, Defactinib, BI-D1870, AZD3514, HMN-214, Decitabine, LDN 193189, Cabozantinib


title: Donor 1, hashtags for perturbation sample 10

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Azacitidine, TR-14035, Nilotinib, AT 7867, OSI-930, GO-6976, CC-401, Resminostat, Crizotinib


title: Donor 2, hashtags for perturbation sample 1

value: male


title: Donor 1, hashed perturbation sample 15


title: A_Sum

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Bos Taurus reference genome (ARS-UCD1.2) using Bowtie2 (2.2.2)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as transcripts per million (TPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: ARS-UCD1.2
Supplementary files format and content: xlsx file include TPM values for each sample

organism: Bos taurus

source_name: Oocyte

extract_protocol:
Total RNA was isolated from oocytes using an RNeasy Plus Micro Kit, according to the manufacturer’s protocol. To remove genomic DNA contaminants, on-column DNA digestion was performed using RNase-free Dnase.
RNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

value: Oocyte

value: Summer


title: Donor 1, hashed perturbation sample 12

value: female


title: Donor 1, hashed perturbation sample 14

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Imatinib, SCH-58261, Colforsin, MLN 2238, Tivantinib, Tosedostat, R428, Oxybenzone, Vandetanib


title: Donor 1, hashed perturbation sample 11


title: Donor 1, hashed perturbation sample 13


title: Donor 1, hashed perturbation sample 10


title: Donor 1, hashed perturbation sample 9


title: Donor 1, hashtags for perturbation sample 8

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Oprozomib (ONX 0912), Alogliptin, Penfluridol, Quizartinib, RN-486, PD-0325901, IMD-0354, Canertinib, Idelalisib


title: Donor 1, hashtags for perturbation sample 5

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AMD-070 (hydrochloride), Sgc-cbp30, FK 866, Chlorpheniramine, Scriptaid, BAY 61-3606, Methotrexate, Palbociclib, Trametinib


title: Donor 1, hashtags for perturbation sample 7

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Desloratadine, Dactolisib, BMS-536924, IKK Inhibitor VII, Amiodarone, Isoniazid, Alvocidib, Disulfiram, Flutamide


title: Donor 1, hashtags for perturbation sample 6

value: blood

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, AT13387, PF-04691502, Perhexiline, UNII-BXU45ZH6LI, RVX-208, Ketoconazole, LY2090314, Vardenafil, Dasatinib


title: Donor 1, hashtags for perturbation sample 3

value: PBMC

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Topotecan, BAY 87-2243, Phenylbutazone, K-02288, BMS-777607, Porcn Inhibitor III, BMS-387032, IN1451, Raloxifene


title: Donor 1, hashtags for perturbation sample 4

value: caucasian

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, BMS-265246, Ruxolitinib, Pomalidomide, Dovitinib, AVL-292, Navitoclax, TL_HRAS26, Proscillaridin A;Proscillaridin-A, Vorinostat


title: Donor 1, hashed perturbation sample 8

value: AllCells, LLC


title: Donor 1, hashtags for perturbation sample 1

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, Atorvastatin, Ganetespib (STA-9090), Clomipramine, Sunitinib, Tivozanib, Tamatinib, TIE2 Kinase Inhibitor, MK-5108, Lapatinib


title: Donor 1, hashtags for perturbation sample 12

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, CGM-097, SLx-2119, Nefazodone, STK219801, TPCA-1, MGCD-265, Masitinib, CEP-18770 (Delanzomib), Ceritinib


title: Untreated - Rep 1

city: Philadelphia

first: Francisco

middle: J

last: Albicoro

state: PA

address: 3440 N Broad St

institute: Temple University

data_processing:
Raw reads were subjected to quality control using FastQC.
Trimming of low-quality bases was performed using Sickle.
Reads were aligned to the Salmonella Typhimurium LT2 genome (NC_003197) using EDGE-pro which then calculated the RPKM values.
The raw counts were then normalized using the DESeq2 package in R.
Differential expression analysis was performed using the DESeq2 package in R with a false discovery rate (FDR) of 0.05 and P value of less than 0.05 used to determine significance.
Assembly: Salmonella Typhimurium LT2 genome (NC_003197)
Supplementary files format and content: Table S1 is an excel file containing differential gene expresion analysis of untreated vs treated samples

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: bacteria cell pellet

extract_protocol:
Total RNA was extracted using the hot phenol. RNA quality and quantity were assessed using a nanodrop (Thermo Scientific, USA).
All library construction were prepared according to the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA).

value: bacteria cell pellet

value: untreated


title: Donor 1, hashed perturbation sample 5


title: Donor 1, hashed perturbation sample 7


title: Donor 1, hashed perturbation sample 6


title: Donor 1, hashed perturbation sample 3


title: Donor 1, hashed perturbation sample 2

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, 5-(9-Isopropyl-8-methyl-2-morpholino-9H-purin-6-yl)pyrimidin-2-amine, O-Demethylated Adapalene, Protriptyline, I-BET151, Foretinib, GW843682X, CGP 60474, Ixabepilone, Linagliptin


title: Donor 1, hashed perturbation sample 1

value: female


title: SAMSEN4

city: London

first: Simak

last: Ali

state: London

address: 1/F ICTEM, Hammersmith Hospital

department: Cancer

country: United Kingdom

institute: Imperial College London

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads. Clean reads were aligned to the Homo Sapiens(GRCh38/hg38) reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCh38/hg38
Supplementary files format and content: xls file includes gene counts for each biological samples

source_name: Prostate

growth_protocol: 22Rv1 cells are cultued in RPMI-medium (Sigma-Aldrich R8757)  containing 10% FCS (Sigma-Aldrich F9665), and 1% penicillin, streptomycin and L-glutamine solution (Sigma-Aldrich G1146).

extract_protocol:
RNA was extracted using RNeasy PluS Mini Kit (Qiagen 74134)
RNA samples were sent to Novogene (UK) for polyA mRNA enrichment, cDNA library preparation and paired-end Illumina sequencing.

treatment_protocol: 300,000 of SAMRES and SAMSEN cells were seeded into each well on a 6-well plate in RPMI-medium in the absence of Samuraciclib. Cells were lysed and RNA was extracted 72 hours following cell seeeding.

value: Prostate

value: Prostate cancer cells

tag: phenotype

value: Samuraciclib-Sensitive

value: Cultured in RPMI, 10%, PS L-Glu


title: SAMSEN5


title: SAMSEN3


title: SAMSEN6


title: SAMSEN1


title: SAMSEN2


title: SAMRES6

value: 22Rv1 Samuraciclib-resistant

value: Samuraciclib-Resistant


title: SAMRES4


title: Donor 1, hashtags for perturbation sample 2

value: blood

value: PBMC


title: SAMRES5


title: SAMRES3


title: SAMRES1


title: PBMC LPS 3

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Raw paired-end FASTQ reads were trimmed using Trim Galore! v 0.6.6 with Cutadapt v 3.4 to remove library adapter sequences and low-quality bases (using command “-g 20 -length 20”). The trimmed reads were then aligned by STAR v2.79a to the hg38 reference genome.
Gene/smORF counts were quantified from the aligned reads using HOMER analyzeRepeats, with the smORFs appended to the annotated reference GTF file.
Assembly: GRCh38.p13
Supplementary files format and content: A counts file generated using HOMER, where the first 8 columns contain annotation information such as feature (gene/smORF) ID and coordinates, and the remaining columns contain the counts of each feature

source_name: PBMC

growth_protocol: Cells were seeded into 6 well plates according to the following densities: CCD18-Co cells (ATCC, Cat# CRL-1459) 0.47 x 106 cells/1.5mL of EMEM + 10% FBS/well (x 2 wells), CaCo2 cells (ATCC, Cat# HTB-37) 0.51 x 106 cells/1.5mL of EMEM + 10% FBS/well (x 2 wells), HCEC-1CT cells (ABM, Cat# T0715) 1.5 x 106 cells/1.7mL of DMEM + 2%FBS, 20ng/mL hEGF (Sigma-Aldrich, Cat# E9644), 10ug/mL Insulin (Sigma-Aldrich, Cat# I9278), 2ug/mL Apo-Transferrin (Sigma-Aldrich, Cat# T2036), 5nM Sodium-Selenite (Sigma-Aldrich, Cat# S5261), 1ug/mL Hydrocortisone (Sigma-Aldrich, Cat# H0396),  PBMC (Hemacare, Cat# PB009C-3, lot:20063132) (4 x 106 cells/4 mL RPMI + 2% human serum) (x 2 wells).

extract_protocol:
Two wells of each sample were pooled and stored at -80°C until sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library preparation used the NEBNext Ultra II RNA Library Prep Kit for Illumina. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on NovaSeq6000, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on a NovaSeq6000 and paired-end reads were generated.

treatment_protocol: Cells were then treated with following stimulants (all 1uL/mL of media) for 24hr before being harvested: LPS (100ng/mL) (Sigma-Aldrich, Cat# L4391-1MG), IL-22 (10ng/mL) (RnD Bio, Cat# 782-IL), TNFa (10ng/mL) (RnD Bio, Cat#210-TA-005), IFN-g (10ng/mL) (RnD Bio, Cat#285-IF-100), IL-1b (10ng/mL) (RnD Bio, Cat#201-LB010), OSM (10ng/mL) (RnD Bio, Cat# 295-OM-010) and TGFb (10ng/mL) (RnD Bio, Cat#240-B-010). After 24hr, cells were washed with PBS followed by addition of 500uL TRIZOL to each well.

value: LPS


title: PBMC LPS 2


title: SAMRES2


title: Donor 1, hashed perturbation sample 4

value: caucasian

value: Belinostat, Dabrafenib, Dimethyl Sulfoxide, BMS-265246, Ruxolitinib, Pomalidomide, Dovitinib, AVL-292, Navitoclax, TL_HRAS26, Proscillaridin A;Proscillaridin-A, Vorinostat


title: PBMC LPS 1


title: PBMC anti-CD3/CD28 1


title: PBMC anti-CD3/CD28 3


title: PBMC Naive 2

value: Naive


title: PBMC Naive 1


title: CCD-18Co 10 ng/mL TGFb 2

value: 10 ng/mL TGFb


title: PBMC Naive 3


title: PBMC anti-CD3/CD28 2


title: Water - Empty control replicate 1

city: San Francisco

first: Leah

last: Dorman

state: CA

address: 499 Illinois St

department: Data Science

institute: CZBiohub

data_processing:
Following demultiplexing, the sequenced reads were aligned to the human genome GRCh38 (hg38) version 41 and the KSHV genome GQ994935.1.
STAR alignment with the following parameters: STAR --runMode alignReads --outReadsUnmapped Fastx --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMattributes NH   HI   NM   MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
samtools sort
HTSeq quantification with the following parameters: htseq-count -f bam -r pos -s yes -t exon --nonunique none -m intersection-nonempty -i gene_id
Sum duplicate genes; remove samples with <10 non-ERCC counts; remove genes with <100 counts; normalize with VSD; run DESeq2
Assembly: GRCh38 (hg38) and KSHV GQ994935.1
Supplementary files format and content: KSHV_aligned_counts.csv: CSV file with unfiltered htseq counts per sample with gene name and ensembl ID
Supplementary files format and content: KSHV_z_scores_viralgenes.csv: CSV file with normalized and scaled viral counts per sample
Supplementary files format and content: KSHV_filtered_counts.csv: CSV file with filtered htseq counts per sample with gene name only
Supplementary files format and content: KSHV_dds_object.rds: RDS object (R; readRDS) with raw and normalized counts and sample information metadata.

growth_protocol: iSLK.219 cells were grown in Dulbecco's modified Eagle medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS, 200 µM of L-glutamine, and 100 U/mL of penicillin and streptomycin, and 10 μg/mL of puromycin (Invivogen, San Diego, CA, USA).

extract_protocol:
Total cellular and viral RNA was isolated from iSLK.219 cells at 72h post reactivation in the presence or absence of 10µM HA15, using the RNAeasy Plus Mini kit (QIAGEN 74134) following manufacturers' recommendations, including a DNAse treatment step.
RNA sequencing libraries were generated using the NEBNext Ultra II RNA Library Prep Kit (New England BioLabs E7760) and sequenced using a 150bp paired-end protocol on an Illumina NextSeq 550 instrument.

treatment_protocol: Exogenous RTA expression was induced in iSLK.219 and TREx-BCBL-1-RTA cells by treatment with 1 μg/mL of doxycycline (Fisher Scientific, Waltham, MA, USA). To prevent viral DNA replication (Fig 1C), these cells were induced with Dox in the presence of phosphonoformate (PFA) 100µM (Sigma Aldrich P6801). Viral reactivation was evaluated by microscopy detection of the PAN-RFP reporter and immunoblot for viral proteins.

tag: virus


title: Lytic KSHV, HA15 treated, biological replicate 3

value: KSHV

value: 72 hrs post 1 ug/mL Dox; 10 um HA15


title: Lytic KSHV, DMSO treated, biological replicate 3

value: 72 hrs post 1 ug/mL Dox; DMSO


title: CCD-18Co 10 ng/mL TGFb 3


title: CCD-18Co 10 ng/mL TGFb 1


title: Latent KSHV, HA15 treated, biological replicate 3

value: 10 um HA15


title: Water - Empty control replicate 2


title: Latent KSHV, DMSO treated, biological replicate 3

value: DMSO


title: CCD-18Co 10 ng/mL OSM 3

value: 10 ng/mL OSM


title: CCD-18Co 10 ng/mL OSM 2


title: Latent KSHV, HA15 treated, biological replicate 2


title: CCD-18Co 10 ng/mL IL-1b 3

value: 10 ng/mL IL-1b


title: CCD-18Co 10 ng/mL OSM 1


title: Latent KSHV, DMSO treated, biological replicate 2


title: CCD-18Co 10 ng/mL IL-1b 2


title: CCD-18Co 10 ng/mL IL-1b 1


title: Lytic KSHV, HA15 treated, biological replicate 1


title: Latent KSHV, HA15 treated, biological replicate 1


title: CCD-18Co 10 ng/mL TNFa 1

value: 10 ng/mL TNFa


title: Lytic KSHV, HA15 treated, biological replicate 2


title: CCD-18Co Naive 3


title: CCD-18Co Naive 2


title: CCD-18Co 10 ng/mL TNFa 2


title: Sperm, control, rep4

city: Barcelona

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

institute: IDIBAPS

data_processing:
SPORTS1.1 was used to trim, map and annotate fragments
Reads were trimmed and filtered for low quality base-pairs. In addition, reads with a length shorter than 15bp or greater than 45bp were excluded from the analysis
Reads were mapped using Bowtie  to mouse reference genome (mm10) and small RNA annotation databases (provided by SPORTS1.1 for mus musculus species).
SPORTS1.1 output files were used to generate normalized RPM counts for the different small RNA biotypes annotations per sample and fragment length. Small RNA biotype abundance per experimental group was calculated averaging the previous values.
Assembly: mm10
Supplementary files format and content: “<sample>_output.txt”: A 6 column table file including annotation information for every unique sequence.
Supplementary files format and content: “<sample>_summary.txt”: A 3 column table file including reads number of each major- and sub- classes.

source_name: Mature sperm

growth_protocol: Mice were housed in a controlled environment, maintaining a temperature range of 20-24ºC and a 12-hour light-dark cycle. The mice's health condition was constantly evaluated.

extract_protocol:
Four hours post-administration, mature sperm was harvested from the caudae epididymides, and RNAs were extracted from the sperm. These RNAs were then used to prepare a small non-coding RNA (sncRNA) library, which was subsequently sequenced.
Small non coding RNA library were generated with 100ng of RNA with NEXTFLEX Small RNA-Seq kit v4 with UDIs

treatment_protocol: We bilaterally injected an activator DREADD adeno-associated viral (AAV-hM3Dq-mCherry) vector into the arcuate nucleus of the hypothalamus (ARH) in both AgrpCre/+ and Agrp+/+. The DREADD ligand, Clozapine-N-Oxide (CNO), was administered to AgrpCre/+ (activated) and Agrp+/+ (control) mice in the absence of food.

value: Mature sperm

value: Agrp +/+

value: DREADD ligand + CNO


title: Latent KSHV, DMSO treated, biological replicate 1


title: Sperm, control, rep3


title: Caco-2 10 ng/mL IFNg 3

value: 10 ng/mL IFNg


title: Caco-2 10 ng/mL IFNg 1


title: CCD-18Co Naive 1


title: Sperm, AgRP_activated, rep3

value: Agrp Cre/+


title: Sperm, control, rep2


title: Sperm, control, rep1


title: Sperm, AgRP_activated, rep4


title: Caco-2 10 ng/mL TNFa 2


title: Caco-2 10 ng/mL TNFa 3


title: Sperm, AgRP_activated, rep2


title: Lytic KSHV, DMSO treated, biological replicate 2


title: CCD-18Co 10 ng/mL TNFa 3


title: Lytic KSHV, DMSO treated, biological replicate 1


title: Sperm, AgRP_activated, rep1


title: Caco-2 10 ng/mL TNFa 1


title: tumor, Cbfb(het) RS519

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

data_processing:
Bascalling: RTA 2.11.3
Alignment: STAR 2.7.0f
FPKM was calculated using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing expected_count, TPM, FPKM values for each sample

source_name: spontaneous tumor from mammary gland

growth_protocol: RNA was extracted from freshly isolated tumors.

extract_protocol:
Use Trizol
TruSeq Stranded mRNA Library Prep

treatment_protocol: No treatment

value: spontaneous tumor from mammary gland

tag: repeat


title: Caco-2 10 ng/mL IL-22 3

value: 10 ng/mL IL-22


title: tumor, Cbfb(wt) RS516

value: MMTV-Cre(+);Cbfb(wt);Pikca(H1047R, het)


title: tumor, Cbfb(het) RS514


title: Caco-2 100 ng/mL LPS 3

value: 100 ng/mL LPS


title: tumor, Cbfb(het) RS511


title: Caco-2 100 ng/mL LPS 2


title: Caco-2 10 ng/mL IFNg 2


title: Caco-2 Naive 3

value: Naive


title: tumor, Cbfb(het) RS512


title: tumor, Cbfb(wt) RS510


title: Caco-2 Naive 1


title: Caco-2 Naive 2


title: HCEC-1CT 10 ng/mL IFNg 3


title: tumor, Cbfb(het) RS508


title: HCEC-1CT 10 ng/mL IFNg 2


title: tumor, Cbfb(wt) RS509


title: tumor, Cbfb(het) RS506


title: tumor, Cbfb(het) RS507


title: HCEC-1CT 10 ng/mL TNFa 3


title: HCEC-1CT 10 ng/mL IFNg 1


title: tumor, Cbfb(het) RS505


title: Caco-2 10 ng/mL IL-22 1


title: tumor, Cbfb(homo) RS518


title: HCEC-1CT 10 ng/mL TNFa 2


title: tumor, Cbfb(het) RS504


title: tumor, Cbfb(het) RS503


title: Caco-2 10 ng/mL IL-22 2


title: tumor, Cbfb(het) RS515


title: HCEC-1CT 10 ng/mL IL-22 2


title: HCEC-1CT 10 ng/mL IL-22 1


title: Caco-2 100 ng/mL LPS 1


title: tumor, Cbfb(het) RS501


title: PBS_B-Glucan+IFNG Gene Expression

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Demultiplexing, barcode processing, and count aggregation were performed using cellranger (pipeline v7.0.0, https://support.10xgenomics.com)
Demultiplexing hashtag oligonucleotides was done with the default Seurat HTOdemux pipeline (two samples have been multiplexed together in one rxn)
Assembly: mm10
Supplementary files format and content: tsv values and matrix file

source_name: Omentum

extract_protocol:
immune cells (minus B cells, CD45+CD19-) were sorted from omentum tumor samples (3 mice/group) and pooled. Samples were uniquely barcoded using TotalSeq-B mouse hashtag antibodies.
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics), according to manufacturer’s instructions.

value: Omentum

value: KPCA murine ovarian cancer cells

value: Wildtype

value: PBS or b-glucan+IFNg


title: PBS_B-Glucan+IFNG Antibody Capture


title: HCEC-1CT 100 ng/mL LPS 2


title: HCEC-1CT 100 ng/mL LPS 3


title: HCEC-1CT 10 ng/mL IL-22 3


title: IFNG_B-Glucan Antibody capture

value: CD45+CD19- immune cells

value: IFNg or b-glucan


title: HCEC-1CT 100 ng/mL LPS 1


title: IFNG_B-Glucan Gene Expression


title: HCEC-1CT Naive 1


title: HCEC-1CT Naive 2


title: tumor, Cbfb(het) RS499


title: HCEC-1CT 10 ng/mL TNFa 1

value: 10 ng/mL TNFa


title: JFL111

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

data_processing:
Sequenced reads were trimmed to remove low-quality bases at ends and were then mapped to the reference genome (GRCm39) using STAR.
Counts were filtered and normalized using DESeq2.
Assembly: Homo Sapiens - HUman (GRCh38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: Prostate carcinoma

growth_protocol: LNCaP cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1x glutamine, 1x pen/strep

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Library preparations and sequencing were conducted at Genewiz (AZENTA)

treatment_protocol: Enzalutamide 10 micromolar during 72 h.

value: Prostate carcinoma

value: LNCaP

value: Epithelial

value: sgPRKCI

value: Enzalutamide 72 hours


title: tumor, Cbfb(het) RS502

value: spontaneous tumor from mammary gland


title: JFL110


title: GM19209_cyto_rep1

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

data_processing:
Basecalling + poly(A) tail length estimation (Dorado v0.7.0)
Alignment (minimap2)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab/nano-COP)
Assembly: GRCh38
Supplementary files format and content: *_hg38_multi_introns_isoforms_counts.withSKP.RefSeq.txt: text files containing the read count for full-length splicing statuses
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_read_counts_per_gene_and_allele.RefSeq_all.txt: text file containing the read counts per allele
Library strategy: Direct RNA nanopore sequencing

molecule: cytoplasmic RNA

source_name: Lymphoblastoid cell line

extract_protocol:
Cellular fractionation to separate cytoplasm and chromatin, Qiazol extraction to isolate cytoplasmic and chromatin-associated RNA
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)

value: Lymphoblastoid cell line


title: GM19099_cyto_rep1


title: GM18870_cyto_rep1


title: GM19102_cyto_rep1


title: GM19223_cyto_rep1


title: GM19152_cyto_rep1


title: GM19144_cyto_rep1


title: RNSC-9

description: LNCaP sg Control stimulated with Enzalutamide for 72 h, replicate 3

data_processing:
Sequenced reads were trimmed to remove low-quality bases at ends with bbduk, and mapped to the reference genome (GRCh38) using STAR with option quantMode
Counts were filtered and normalized using DESeq2.
Assembly: Homo Sapiens - Human (GRCh38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

growth_protocol: LNCaP cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 1x glutamine, 1x pen/strep

treatment_protocol: Enzalutamide 10 uM for 72 h.

value: sgControl


title: GM18522_cyto_rep1


title: GM18853_cyto_rep1


title: JFL107


title: JFL108


title: RNSC-11

description: LNCaP sgPRKCI stimulated with Enzalutamide for 72 h, replicate 2


title: HCEC-1CT Naive 3


title: GM18861_cyto_rep1


title: GM18510_cyto_rep1


title: GM18870_chr_rep2b

library_source: other

molecule: other


title: RNSC-10

description: LNCaP sgPRKCI stimulated with Enzalutamide for 72 h, replicate 1


title: RNSC-7

description: LNCaP sg Control stimulated with Enzalutamide for 72 h, replicate 1


title: RNSC-12

description: LNCaP sgPRKCI stimulated with Enzalutamide for 72 h, replicate 3


title: SMA_PVMusc08

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

data_processing:
nf-core rnaseq
Deseq2 for differential expression analysis
Assembly: hg38
Supplementary files format and content: salmon.merged.gene_counts.tsv; tab delimited gene counts from salmon
Supplementary files format and content: salmon.merged.gene_tpm.tsv; tab delimited gene tpm from salmon
Supplementary files format and content: salmon.merged.transcript_counts.tsv; tab delmited transcript counts

source_name: paravetebral muscle

extract_protocol:
Qiagen RNAeasy kit
Takara SMART-seq v4 kit for low-input samples

value: paravetebral muscle

value: M


title: GM18870_chr_rep1


title: RNSC-8

description: LNCaP sg Control stimulated with Enzalutamide for 72 h, replicate 2


title: GM19099_chr_rep2b


title: GM18870_chr_rep2a


title: SMA_PVMusc05

value: F


title: GM19099_chr_rep2a


title: JFL109


title: SMA_PVMusc07


title: JFL112


title: SMA_PVMusc06


title: SMA_PVMusc03


title: SMA_PVMusc04


title: GM19223_chr_rep1c


title: SMA_PVMusc02


title: Control_PVMusc06

value: control


title: Control_PVMusc07


title: Control_PVMusc05


title: SMA_PVMusc01


title: GM19223_chr_rep1b


title: GM19099_chr_rep1


title: GM18501_cyto_rep1


title: Control_PVMusc03


title: GM19102_chr_rep1


title: Control_PVMusc02


title: GM19102_chr_rep3


title: Control_PVMusc01


title: GM19223_chr_rep1a


title: GM19102_chr_rep2


title: Primary melanocytes, rep2

city: Oklahoma City

first: Jeffrey

middle: Don

last: McBride

state: OK

address: 1000 NE 13th St

department: Dermatology

institute: University of Oklahoma

data_processing:
The .fastq files were run through the DRAGEN RNA v4.2.4 app on Illumina’s Basespace using default settings.
Differential expression was performed using Illumina’s DRAGEN Differential Expression v4.2.4 app in Basespace using default settings.
Assembly: Human GRCh38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: HEM

growth_protocol:
Human melanoma cell lines A375 (ATCC) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin, 50 µg/ml streptomycin. Primary epidermal melanocytes (ATCC) were cultured in dermal cell basal medium supplemented with Adult Melanocyte Growth Kit.  Primary dermal fibroblasts (ATCC)  were cultured in fibroblast basal medium supplemented with fibroblast growth kit.   Primary dermal microvascular endothelial cells were cultured in vascular cell basal medium supplemented with endothelial cell growth kit.
Cell cultures were maintained in a humidified atmosphere of 5% CO2 and 37 °C.

extract_protocol:
Qiagen Rneasy Mini kit
NEBNext Poly(A) mRNA Magnetic Isolation Module & IDT xGen Broad Range RNA Library Kit

treatment_protocol: Human melanoma A375 cells were cultured until they reached 80% confluency. The cells were then washed several times with PBS and switched to serum-free DMEM media for 72 hours to minimize protein contamination from serum. The medium was collected and centrifuged at 3,000 x g for 15 minutes to remove cellular debris, followed by ultrafiltration using 100 kDa filters (Amico Ultra-15, Millipore) at 4,000 x g for 15 minutes. PM, PF and EN cells were incubated with the collected condition medium for 72h respectively. Different groups of cells were collected separately and  performed RNAseq.

value: HEM

value: Primary epidermal melanocytes (ATCC)

value: WT

value: no treatment


title: Primary melanocytes, rep1


title: Primary melanocytes treated w/A375 PRAME +/+, rep1

value: Extracellular vesicle treatment from A375 PRAME +/+


title: Primary fibroblast treated w/A375 PRAME +/+, rep2

source_name: HDF

value: HDF

value: Primary dermal fibroblasts (ATCC)


title: Primary melanocytes treated w/A375 PRAME +/+, rep2


title: Primary melanocytes, rep3


title: Primary melanocytes treated w/A375 PRAME +/+, rep3


title: Primary fibroblast treated w/A375 PRAME +/+, rep3


title: Primary fibroblasts, rep3


title: Primary fibroblast treated w/A375 PRAME +/+, rep1


title: WIL750-1B

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
Data were processed using a previoulsy published method[https://pubmed.ncbi.nlm.nih.gov/24972667/]. In brief, reads were quality controlled using FASTQC. Reads were mapped against hg38 genome using STAR aligner. HT-Seq was utilized to analyzed the aligned reads and generate gene-wise counts using Ensemble version 78 transcriptome. Extracted read data was processed using edgeR software. Timmed means of M-values method was utilized to normalized reads that were provided in the file named 20231208-For-GEO-Raw-Counts.tsv".
Assembly: hg38
Supplementary files format and content: 20231208-For-GEO-Raw-Counts.tsv; tab-delimited; Raw gene-count matrix

source_name: Skeletal muscle

extract_protocol:
mRNA was extracted using Trizol and stored in RNAlater.
mRNA library was constructed using Illumina TruSeq Stranded kit following manufacturer's recommendations.
Paired end library strategy was utilized

value: Skeletal muscle

value: older

value: female

tag: training time_point

value: rest


title: WOO670-1B

value: male


title: WIL750-2B


title: WOO670-2B


title: Control_PVMusc04


title: WAL630-2B


title: WAL630-1B


title: A375 PRAME +/+ melanoma cells, rep3

value: Human melanoma cell lines A375 (ATCC)

value: WT - PRAME +/+


title: Primary fibroblasts, rep1


title: WAL360-1B


title: WAL360-2B


title: VU819-3B

value: young


title: A375 PRAME +/+ melanoma cells, rep2


title: A375 PRAME +/+ melanoma cells, rep1


title: VU819-2B


title: VEL570-2B


title: VAS331-1B


title: VEL570-1B


title: TOQ897-2B


title: VU819-1B


title: VAS331-3B


title: TOQ897-1B


title: Primary fibroblasts, rep2


title: TOB905-3B


title: Blastocyst pool 42

city: Knoxville

first: Sarah

middle: E

last: Moorey

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

data_processing:
Only forward (R1) reads were used as input for data processing since reverse (R2) reads from the SMART-Seq v4 3’ DE Kit are not informative beyond indexing.
Assess quality of raw reads using FastQC; subsequent read trimming and filtering using fastp.
Reassess trimmed reads using FastQC;  map to the bovine genome (ARS-UCD2.0) using STAR.
Sort and index alignments using SAMtools, and alignment quality control was performed with QualiMap.
Assembly: Bos taurus genome ARS-UCD2.0
Supplementary files format and content: csv that includes raw count data for each sample

source_name: blastocyst

extract_protocol:
Total RNA was isolated from pools of 2 blastocysts with stage score 7 and quality score 1 (IETS) using an optimized TRIzol protocol.
Approximately 250 pg total RNA was used as input for reverse transcription, and cDNA amplification was performed using the SMART-Seq v4 3 DE Kit following the manufacturers protocol with volumes adjusted to complete procedures using half reactions. Approximately 500 pg cDNA was utilized for library preparation using the Illumina Nextera XT DNA Sample Preparation Kit and following the manufacturers protocol.

value: blastocyst


title: Blastocyst pool 6


title: Blastocyst pool 9


title: Blastocyst pool 45


title: Blastocyst pool 5


title: Blastocyst pool 46


title: Blastocyst pool 38


title: Blastocyst pool 44


title: Blastocyst pool 36


title: TOB905-2B


title: VAS331-2B


title: Blastocyst pool 35


title: Blastocyst pool 33


title: TOB905-1B


title: Blastocyst pool 41


title: THO540-2B


title: Blastocyst pool 31


title: THO540-3B


title: THO540-1B


title: TAT896-2B


title: STA359-1B


title: TAT896-1B


title: SOR358-2B


title: Blastocyst pool 26


title: Blastocyst pool 25


title: SOG782-1B


title: Blastocyst pool 15


title: Blastocyst pool 23


title: SOR358-1B


title: STA359-2B


title: Blastocyst pool 21


title: Blastocyst pool 19


title: SOG782-2B


title: Blastocyst pool 22


title: SMI659-1B


title: SMI659-2B


title: Blastocyst pool 14


title: Blastocyst pool 32


title: Blastocyst pool 1


title: SIM306-1B


title: Blastocyst pool 24


title: SIE949-2B


title: Blastocyst pool 13


title: SIM306-2B


title: SIE949-1B


title: Blastocyst pool 28


title: HAP

city: jinan

first: wang

last: qiang

address: West Wenhua Road.

institute: Qilu Hospital.

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: All cells in the tissue

value: pancreas

value: 6-8 weeks old


title: SEN231-2B


title: AP

description: 10x Genomics


title: MDU9_Nbr1KO3

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were filtered and normalized using DESeq2.
Assembly: Mus musculus - mouse (GRCm39)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: liver

growth_protocol: Hepatic stellate cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1x glutamine, 1x pen/strep during 4 days.

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: basal conditions

value: liver

value: hepatic stellate cells

value: Nbr1 knock-out


title: SEN231-1B


title: HFD

description: 10x Genomics


title: Blastocyst pool 12


title: MDU8_Nbr1KO2


title: NFD

description: 10x Genomics


title: MDU3_WT3

value: wild type


title: RYD739-2B


title: RYD039-2B


title: SCH279-1B


title: MDU7_Nbr1KO1


title: YK15_Nbr1Sqstm1DKO3

data_processing:
Sequenced reads were trimmed to remove low-quality bases at ends and were then mapped to the reference genome (GRCm39) using STAR.
Counts were filtered and normalized using DESeq2.
Assembly: Mus musculus - mouse (GRCm39)
Supplementary files format and content: normCounts matrix with gene expression value for all samples.

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Library preparations and sequencing were conducted at Genomics Core at Sanford Burnham Prebys Medical Discovery Institute.

value: Nbr1-Sqstm1 double-knock-out


title: ROT236-1B

value: Skeletal muscle


title: ROT236-2B

value: older


title: YK13_Nbr1Sqstm1DKO1


title: RYD039-1B

value: female


title: RIE102-1B

value: rest


title: MDU1_WT1


title: SCH279-2B

value: male


title: YK9_Sqstm1KO3

value: Sqstm1 knock-out


title: RIC717-3B


title: RIE102-2B


title: YK7_Sqstm1KO1


title: RIC717-2B


title: RIC717-1B


title: YK8_Sqstm1KO2


title: RYD739-1B


title: RAY806-1B


title: YK14_Nbr1Sqstm1DKO2


title: YK1_WT1


title: MDU2_WT2


title: YK3_WT3


title: POI944-2B


title: PET517-2B


title: Sperm H3.1/2/t Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (--quality 20 --illumina --stringency 3 )
Trimmed reads were then aligned to the mouse genome build mm10 using STAR (version 2.5.0a) with settings (--alignIntronMin 1 --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 1000 --outFilterMatchNminOverLread 0.85)
Aligned reads were deduplicated using SAMtools (version 1.10) with standard settings
Uniquely mapped reads were counted on genomic regions using the function qCount (mapqMin = 255L) from QuasR package (version 1.36.0).
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package (version 1.36.0) with standard settings

source_name: sperm cells

extract_protocol:
For sperm cell sorting, mouse cauda epididymides were dissected into a Petri dish and fat patches were removed with forceps and scissors. Each epididymis was punctured with a needle and carefully squeezed into 100 ul of PBS with the help of two forceps. Sperm was transferred into an Eppendorf tube and was allowed to liquefy at room temperature for 5 minutes. To break sperm tails, cells were briefly sonicated with a Brandson Tip digital sonicator with 10% amplitude and 3 cycles of 0.5 sec ON / 2 sec OFF. Cells were stained with 2 ul/ml Hoechst 33342 (H3570, ThermoFisher) for 1h at 25°C with constant shaking and protected from light. Sperm cells were filtered through a 40 μm Nylon filter into 5 ml polypropylene tubes.Sperm cells (500.000 per reaction) were FACS sorted in Eppendorf® LoBind microcentrifuge tubes. The cells were pelleted at 6000g for 5 minutes at 4°C in a benchtop centrifuge. The pellet was snap frozen in liquid nitrogen and stored at –80°C freezer until further processing. The pellet was thawed on ice and resuspended in 500 μl PBS. 50mM DTT was added for 2 hours at 21°C to reduce disulfide bonds of protamine. 100mM N-Ethylmaleinimid was added for 30 minutes at 21°C to modify the cysteine residues. The cells were pelleted at 6000g for 5 minutes at 4°C in a benchtop centrifuge and washed once with 600 μl PBS. Cells were resuspended in 50 μl Lysis buffer (20 mM Tris-HCl pH 7.5, 60 mM KCl, 5mM MgCl2, 0.1 mM EGTA, 300 mM Sucrose, ,0.5 mM DTT, 0.25 % Igepal, 0.5% sodium deoxycholate, 1X EDTA-free protease inhibitor cocktail) and incubated for 30 minutes at 21°C. 50 μl of MNAse digestion buffer (5 gelUnits/μl Micrococcal Nuclease (NEB M0247S), 2X Micrococcal Nuclease buffer) was added to the sample for 15 minutes at 37°C to fragment the chromatin. Reaction was stopped by addition of 5 μl 500 uM EDTA and the sample was centrifuged at 16000g for 10 minutes at 4°C in a benchtop centrifuge. The supernatant chromatin was pre-cleared with 10 μl of 1:1 protein A: protein G Dynabeads (Thermo Fisher Scientific, 10001D and 10003D). The precleared chromatin sample was incubated with 0.5 μg of anti-H3K4me3 (Millipore 17-614) or 1 μg anti-nucleosome (44) provided by J. van der Vlag) or 1 μg anti-H3.3 (Cosmo Bio CE-040B) or 1 μg anti-H3.1/2/t (63) provided by J. van der Vlag) conjugated with 10 μl of 1:1 protein A:protein G Dynabeads overnight at 4 °C on a rotator. Chromatin-Antibody-Dynabeads complexes were washed once with 500 μl of ChIP buffer, 3 times with 1ml of Low Salt wash buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and 3 times with 1 ml High Salt buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 250 mM NaCl). Chromatin was eluted in 40 μl of Elution buffer (100 mM NaHCO3 and 1% SDS) for 90 minutes at 65 °C. DNA from eluted material was purified by phenol-chloroform, ethanol-precipitation and resuspended in 25 μl nuclease free H2O.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645L)

value: sperm cells

tag: chip antibody

value: Sperm

value: Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg


title: RAY806-2B


title: Sperm H3.1/2/t Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2


title: PET517-1B

value: young


title: POI944-1B


title: Sperm H3.1/2/t Dnmt3a f/+ ; Dnmt3b f/+  rep 1

value: Dnmt3a f/+ ; Dnmt3b f/+


title: PEC280-2B


title: Sperm H3.3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: PAT977-3B


title: PAT977-2B


title: Sperm H3.3 Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: PAR397-2B


title: PAT977-1B


title: PEC280-1B


title: Sperm Nucleosome Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2

value: anti-Nucleosome


title: Sperm Nucleosome Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: Sperm H3.3 Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: PAR397-1B


title: Sperm H3.1/2/t Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: YK2_WT2

value: liver


title: Sperm Nucleosome Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: NOB524-2B


title: MOZ641-2B


title: NOB524-1B


title: Sperm H3K4me3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2


title: Sperm H3.3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2


title: MOZ641-1B


title: MAR474-3B


title: Sperm H3K4me3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: Sperm H3K4me3 Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: Sperm Nucleosome Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: Sperm H3K4me3 Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: MAR474-1B


title: Differentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with parameters (--clip_R1 3 --quality 20 --illumina --stringency 3)
Trimmed reads were then aligned to the mouse genome build mm10 using STAR (version 2.5.0a) with settings (--outFilterMismatchNmax 6)
Duplicated reads were marked/removed using python script nudup.py from NuGEN Technologies (version 2.2) from with settings (-s 8, -l 8) using UMIs (R2 fastq file, 8bp reads).
Uniquely mapped reads were counted on genes (TxDb.Mmusculus.UCSC.mm10.knownGene) using the function qCount (mapqMin = 255L) from QuasR package (version 1.36.0).
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package (version 1.36.0).

source_name: spermatogonia

extract_protocol:
For spermatogonia, testicular cell suspension was prepared by incubation of seminiferous tubules in 200 U/ml Collagenase type I (Worthington Biochemical LS004196), 5 μg/ml DNAse I (Roche 10104159001), and 0.05%Trypsin (Gibco 25200056) in GBSS (Sigma G9779) as described in (60). Cells were stained with 1/200 anti-CD117/c-kit PE (eBioscience 12-1171-83), anti-CD324/E-Cadherin eFluor 660 (eBioscience 50-3249-82) and anti-CD49f/Integrin alpha 6 PE-Cyanine7 (eBioscience 25-0459-82) for 1 hour at 32oC with constant shaking and protected from light. After washing cells were incubated with 20 μg/ml with Hoechst 33342 (Thermo Fischer Scientific H3570) for 1 hour at 32oC with constant shaking and protected from light and then with 30nM DRAQ7 (Biostatus DR71000) for 5 minutes on bench. The stained cells were strained through a 40 μm nylon filter into 5 ml polypropylene tubes and were sorted on a BD FACSAria III cell sorter fitted with a 70 μm nozzle (Becton Dickinson) using a 375nm laser to excite Hoechst 33342, a 561nm laser to excite PE and PE-Cy7 and a 633nm laser to excite DRAQ7 and eFluor600. Cells were first gated for FSC and SSC to exclude debris. Then the live cells were selected based on the absence of DRAQ7 signal detected using 755LP, 780/60BP. Then we gated for cells positive for Hoechst 33342 emission which was detected using a 670LP (Hoechst-Red) and 450/20 BP (Hoechst-Blue). We gated for the Hoechst-Redlow and Hoechst-Bluemid population which is enriched for 2N spermatogonia. Fluorescence for PE was detected using a 582/15BP filter, for PE-Cy7 was detected using 735LP,780/60BP filter and for eFluor660 using a 660/20BP filter. Undifferentiated spermatogonia were sorted as CD324high, CD49fhigh, CD117low and differentiated spermatogonia were sorted as CD324low, CD49flow, CD117high. RNA from Spermatogonia (10.000 per sample) was extracted with Single Cell RNA Purification Kit (Norgen, 51800) .
Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen, 0501-32)

value: spermatogonia

value: Differentiated Spermatogonia


title: LOP737-2B


title: Differentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: LOP737-1B


title: LIN580-1B


title: Differentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 3


title: Differentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: LAW733-2B


title: Differentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: Undifferentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 3

value: Undifferentiated Spermatogonia


title: Undifferentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2


title: LAW733-1B


title: LAM977-3B


title: LAM977-2B


title: Undifferentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 3


title: Undifferentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: Undifferentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: MAR474-2B


title: KOS224-1B


title: LAM977-1B


title: Differentiated Spermatogonia Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 3


title: Sperm Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with parameters (--quality 20 --illumina --stringency 3 )
Trimmed sequence reads were aligned to the mouse genome build mm10 using the qAlign function from the QuasR package with parameter (bisulfite="dir")
Methylated and unmethylated read counts for each CpG were extracted from the BAM files using the function qMeth from the QuasR package.
Assembly: mm10
Supplementary files format and content: BigWig files (*.bw) processed files were generated for methylation levels of each CpG (files ending with *MethylationLevel.bw) and total number of reads covering each CpG (*TotalNReads.bw).
Library strategy: EM-seq

source_name: Sperm

extract_protocol:
For sperm cell sorting, mouse cauda epididymides were dissected into a Petri dish and fat patches were removed with forceps and scissors. Each epididymis was punctured with a needle and carefully squeezed into 100 ul of PBS with the help of two forceps. Sperm was transferred into an Eppendorf tube and was allowed to liquefy at room temperature for 5 minutes. To break sperm tails, cells were briefly sonicated with a Brandson Tip digital sonicator with 10% amplitude and 3 cycles of 0.5 sec ON / 2 sec OFF. Cells were stained with 2 ul/ml Hoechst 33342 (H3570, ThermoFisher) for 1h at 25°C with constant shaking and protected from light. Sperm cells were filtered through a 40 μm Nylon filter into 5 ml polypropylene tubes. Sperm cells were sorted for 1C DNA content. Pellets of 1 million sperm cells were incubated in 200μl of DNA extraction buffer (20mM Tris-HCl pH 7.5, 300mM NaCl, 2% SDS, 10mM EDTA, 200 μg/ml Proteinase K) for 16 hours at 55oC. An equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) solution was added to the samples. After a vigorous vortexing for 30 seconds and centrifugation at 16.000g for 10 minutes, the upper aqueous phase was transferred to new tubes. 0.05 μg/μl glycogen, 1/10 volume of 3M sodium acetate and 2.5 volumes of 100% ethanol were added, and the samples were incubated fot 2 hours at -80oC. DNA precipitated by centrifugation at 16000g for 30m minutes at 4oC. DNA pellet was washed once with 70% ethanol and resuspended in 20 μl. DNA was further purified using 2 volumes of Ampure XP beads (Beckman Coulter). Genomic DNA (100ng per reaction) was sheared to an average fragment size of 400 bp using the Covaris S220 instrument.
The sheared DNA was used as input for the NEBNext Enzymatic Methyl-seq (NEB E7120) following the manufacturer’s instructions except for doubling the reaction incubation times. The libraries were amplified for 5 cycles and sequenced in 2x75-bp paired-end mode with NextSeq 500 sequencing technology (Illumina), per the manufacturer’s recommendations.


title: JAS115-2B


title: KOS224-2B


title: LIN580-2B


title: Undifferentiated Spermatogonia Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: Sperm Dnmt3a f/+ ; Dnmt3b f/+  rep 2


title: Sperm Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg rep 1


title: Sperm Dnmt3a f/+ ; Dnmt3b f/+  rep 1


title: C9_Injured_posAxin2

city: Boston

first: Mor

last: Grinstein

state: MA

address: 2114 Cambrisge street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

description: processed data file: TPM_SalmonSMARTSeq

data_processing:
For SMART-seq bulk RNA-seq samples, gene expression was quantified using Salmon (version 0.13.1) using the mm10 transcriptome (Ensembl 92, 2018-10-10). To identify differentially expressed genes in a pairwise manner, the statistical package DESeq2 (version 1.24.0) was utilized. Genes were classified as differentially expressed based on a 2-fold change in expression value and false discovery rates (FDR) below 0.05.
For single cell RNA-sequencing samples, raw demultiplexed fastq files were merged and trimmed using Trimmomatic. Trimmed reads were then aligned to the mm10 mouse genome build and processed using Cellranger. Raw feature-barcode matrices were analyzed downstream using Seurat and SCANPy to identify cell type clusters and cluster marker expression.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts for Salmon-aligned SMART-seq bulk samples (A1-A8)
Supplementary_files_format_and_content: TPM_SalmonSMARTSeq: Normalized counts for samples B10-C11
Supplementary_files_format_and_content: Raw cellranger output files for barcodes, features, and barcode-feature matrices

source_name: Injured

extract_protocol:
For SMART-seq samples: Fresh isolated tendons were collected from mouse forelimbs and hindlimbs or from injured Achilles tendons (10 dpi) and dissociated as described (Grinstein et al., 2019; Grinstein et al., 2018). The cells were sorted using BD FACSARIA II. CD31-APC, CD45-APC Cy7 cells were excluded. The Axin2TdTom and the Axin2- cells were sorted separately into 96-well plates into TCL buffer, 200-1000 cells of  Axin2TdTom / Axin2-  cells were sorted into each well, and stored at -80 ̊C.
For single cell RNA-sequencing samples: Achilles tendons were freshly isolated from 4 adult mice (3-4 months of age), 8 tendons total for homeostasis, and 3 tendons total from 3 adult mice (3-4 months of age) for 10 days post injury.  Tendons were dissociated as described (Grinstein et al., 2019; Grinstein et al., 2018). Cells were sorted using BD FACSARIA II. CD31-APC, CD45-APCCy7 and TER-119/Erythroid APC-Cy7 cells were excluded.  Immediately following FACS, cells were loaded to the 10X platform using Chromium next GEM single cells 3’ reagents kit V3.1.
SMART seq libraries were generated using the Nextera XT library prep kit (Illumina), pooled, and sequenced on NextSeq 500 sequencer, using 38 bp PE reads, and resulted in approximately 30 million 75 bp reads per sample. For 10x single cell sequencing, libraries were generated using the 10x V3 library kit and run on the 10x Chromium system. Libraries were sequenced on a Nextseq 500 and Novaseq 6000.

value: pos Axin2

value: achilles

value: 3-5 months


title: HUI996-1B

value: Skeletal muscle


title: HOO917-2B

value: older

value: female


title: C11_uninjuredcontralateral_posAxin2

description: processed data file: TPM_SalmonSMARTSeq

source_name: uninjured contralateral


title: HOO917-3B


title: C8_uninjuredcontralateral_negAxin2

description: processed data file: TPM_SalmonSMARTSeq

value: neg Axin2


title: C7_uninjuredcontralateral_posAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: JAS115-1B

value: male

value: rest


title: MOC1_10dayspostinjury_Axin2+TdTomatocells

source_name: 10 days post injury

value: Axin2+ TdTomato cells


title: HOO343-1B


title: HUI996-2B

value: young


title: C5_injured_posAxin2

description: processed data file: TPM_SalmonSMARTSeq

source_name: injured


title: C6_injured_negAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: HOO917-1B


title: HEI605-2B


title: C4_contralateral_negAxin2

description: processed data file: TPM_SalmonSMARTSeq

source_name: contralateral


title: HEI605-3B


title: C3_uninjuredcontralateral_posAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: HEI348-3B


title: HEI348-2B


title: HEI348-1B


title: HEI605-1B


title: B12_uninjuredcontralateral_posAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: HAN172-2B


title: C2_injured_posAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: B11_injured_negAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: B10_injured_posAxin2

description: processed data file: TPM_SalmonSMARTSeq


title: C1_Uninjuredcontralateral_negAxin2

description: processed data file: TPM_SalmonSMARTSeq

source_name: Uninjured contralateral


title: HAN171-1B


title: HAN171-2B


title: A8_homeostasis_negAxin2

description: processed data file: normalized_counts

source_name: homeostasis


title: HAL405-1B


title: A6_homeostasis_negAxin2

description: processed data file: normalized_counts


title: HAL405-2B


title: A4_homeostasis_negAxin2

description: processed data file: normalized_counts


title: A3_homeostasis_posAxin2

description: processed data file: normalized_counts


title: A5_homeostasis_posAxin2

description: processed data file: normalized_counts


title: HAL404-1B


title: HAB770-2B


title: HAB770-1B


title: A2_homeostasis_negAxin2

description: processed data file: normalized_counts


title: A1_homeostasis_posAxin2

description: processed data file: normalized_counts


title: HAN172-1B


title: DZI988-3B


title: GER864-1B


title: 134 αSyn PFFs+IFNγ

city: Kuopio

first: Jonna

middle: Elisa

last: Niskanen

address: Neulaniementie 2

department: A.I.Virtanen Institute of Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Sequences have been aligned and quantified using the nf-core pipeline. Precisely, running the following command: nextflow run nf-core/rnaseq -r 3.8.1 -profile docker --input /media/lg/extHD2/Backup/Sarka_micr_counts/samplesheet1.csv --outdir /media/lg/extHD2/Backup/Sarka_micr_counts/p1/. --genome GRCh38 --max_cpus 16 --skip_bigwig –skip_rseqc
Count data were prepared following the workflow defined by Law et al. We filtered out lowly expressed molecules in any condition using the function “filterByExpr” to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for batch effect due to differences in library preparation by performing a principal component analysis and unsupervised consensus clustering with Cola.
We corrected the batch effect with combat_seq.  We followed limma and edgeR pipeline for the downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt

source_name: iPSC derived human microglia

growth_protocol: Cells differentiated from human iPSCs using the Hematopoietic Kit (StemCell Technologies, 05310) and differentiation protocol from Abud et al 2017, McQuade et al 2018

extract_protocol:
RNA was extracted directly using RNeasy MiniKit (Qiagen, 74104), then further purified and concentrated with RNA Clean & Concentrate (Zymo Research, R1013) before library preparation.
The ribosomal RNA was removed using the RiboCop rRNA Depletion Kit (Lexogen, 144.24) then the CorAll Total RNA-seq Library Prep Kit (Lexogen, K09596) was used to prepare dual indexing.

treatment_protocol: Post maturation Media changed to assay media with only IL34 100ng/ml and MCSF 25ng/ml, with or without IFNγ 20 ng/ml for 24h, then αSyn PFFs 0.5µM were added (or equivalent amount of media) for additional 4h

value: iPSC derived human microglia

value: microglia

value: Mad6 cl1

value: control/healthy

value: αSyn PFFs 0.5µM 4h + IFNγ 20ng/ml 28h


title: A7_homeostasis_posAxin2

description: processed data file: normalized_counts


title: EGG745-1B


title: 104 αSyn PFFs+IFNγ

value: LL190 cl 5


title: 117 αSyn PFFs+IFNγ


title: HAL404-2B


title: DZI988-2B


title: EGG745-2B


title: 102 αSyn PFFs+IFNγ


title: DUD877-3B


title: 100 αSyn PFFs+IFNγ


title: DUD877-2B


title: DZI988-1B


title: GER864-2B


title: 141 αSyn PFFs+IFNγ


title: DUD877-1B


title: 130 IFNγ

value: IFNγ 20ng/ml 28h


title: DOW515-2B


title: 97 IFNγ


title: 96 IFNγ


title: DOD388-3B


title: 132 IFNγ


title: DOW515-3B


title: 139 αSyn PFFs

value: αSyn PFFs 0.5µM 4h


title: 99 IFNγ


title: DOD388-2B


title: DIE776-2B


title: 138 αSyn PFFs


title: DOD388-1B


title: 136 αSyn PFFs


title: 131 IFNγ


title: 137 αSyn PFFs


title: DIE776-1B


title: DEU843-2B


title: 128 αSyn PFFs


title: 126 control

value: control/untreated


title: DOW515-1B

value: Skeletal muscle


title: DEU843-1B

value: older


title: DER052-2B

value: female


title: DER052-1B


title: DER052-3B


title: 88 control


title: 89 control


title: 91 control


title: 127 control


title: Wildtype, rep2

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

data_processing:
read alignment with hisat2-2.2.0 inclluding --dta option
alignment sorting and bam conversion usign samtools 1.19.2
transcript abundance estimation using StringTie v2.2.1
Assembly: AmexG_v6
Supplementary files format and content: Cu1.gtf - StringTie read count summary for copper phenotype pool 1
Supplementary files format and content: Cu2.gtf - StringTie read count summary for copper phenotype pool 2
Supplementary files format and content: WT1.gtf - StringTie read count summary for willdtype phenotype pool 1
Supplementary files format and content: WT2.gtf - StringTie read count summary for willdtype phenotype pool 1

organism: Ambystoma mexicanum

source_name: tail tip

extract_protocol:
RNA was isolated with TRIzol and then further purified using a QIAGEN RNeasy Mini Kit with DNase treatment
poly-A selected libraries prepared by Novogene

value: tail tip

value: WT


title: 90 control


title: DAV433-2B


title: DAV433-3B


title: AsPC-1 cells treated with 6-Diazo-5-oxo-l-norleucine (DON), Rep3

city: La Jolla

first: Cosimo

last: Commisso

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Read data were processed in BaseSpace
Reads were aligned to Homo sapiens genome (hg19) using STAR aligner with default settings
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: Pancreas

growth_protocol: Cells were cultured in the following media: AsPC-1 in RPMI (Corning) supplemented with 10% fetal bovine serum (FBS), 20 mM HEPES and 1 mM sodium pyruvate and HPAF-II and HEK-293T cells in DMEM (Corning) with 10% FBS and 20mM HEPES

extract_protocol:
Poly(A) RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and barcoded libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).
RNA-seq libraries were pooled and single-end sequenced (1x75 bp) on the Illumina NextSeq 500 using the High-Output V2 Kit (Illumina)

treatment_protocol: AsPC-1 cells were treated with either vehicle or DON for 24 hours in serum-free media

value: Pancreas

value: 6-Diazo-5-oxo-l-norleucine (DON)


title: 103 αSyn PFFs+IFNγ


title: AsPC-1 cells treated with 6-Diazo-5-oxo-l-norleucine (DON), Rep2


title: AsPC-1 cells treated with vehicle, Rep2

value: Vehicle


title: Copper, rep2

value: Cu


title: DAV433-1B

source_name: Skeletal muscle

value: young

value: rest


title: CUR267-3B


title: Wildtype, rep1


title: AsPC-1 cells treated with vehicle, Rep3


title: AsPC-1 cells treated with vehicle, Rep1


title: CUR267-2B


title: 5CG18

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
CircRNAs were identified and quantified using A-tailing reads by CARP28. Candidate circRNA identification was performed by applying four different algorithms with default parameters (CIRCexplorer2, CIRI-quant, find_circ and MapSplice) on A-tailing RNA-seq reads. Candidate circRNAs identified in each sample were pooled and “CARP PseudoRef” was utilized to construct a pseudo-reference covering 149bp of the flanking BSJ site for each candidate circRNA. RNA-seq reads were aligned to the pseudo-reference to detect candidate BSJ reads by “CARP Mapping.” “CARP Remap” was used to detect and filter out false reads that could also be mapped to the genome or transcriptome. The remaining reads were used for circRNA quantification by “CARP ReadsCount.”
Normalized reads count for each circRNA obtained by “CARP ReadsCount” were used for DE circRNA analysis by Z-Test approached used in our published circMeta algorithm82. Significant DE circRNAs were defined by FDR < 0.05.
CircRNA full-length was determined by “CARP CircAS” using A-tailing RNA-seq data. Junction reads in the circRNA body were summarized and Z-test was used for circRNA isoform switch detection using P < 0.05 and |Inclusion level difference| > 20% as cutoff.
Sequencing reads from the control library were aligned to mm9 by TopHat 2.1.0 using default parameters. Aligned bam files were used for DE genes between 5xFAD and CTL at each time point using Cuffdiff. DE genes were defined by q-value < 0.05.
Assembly: mm9
Supplementary files format and content: CircRNA expression in A-tailing library are stored in CircRNA.5mCTL.5mFAD.7mCTL.7mFAD.txt
Supplementary files format and content: Gene expression in non-treated libearies are stored in Gene.5mCTL.5mFAD.7mCTL.7mFAD.txt

source_name: Cortex

extract_protocol:
Mouse brain cortex samples or cell pellets were homogenized in 1mL TRIzol (Invitrogen) and incubated at room temperature for 5min. 200µL Chloroform was added in sample’s tube, thoroughly mixed, and incubated at room temperature for 15min. Next, all samples were centrifuged at 13,000g for 20min at 4ºC.  The total RNA was precipitated in 60µL NaAc (3M, pH 5.2), 4µL glycogen (5 mg/mL), and 600µL 100% Isopropanol for at least 30min at -80ºC with 600µL supernatant.
4µL E-PAP and 40U RNase inhibitor were added to 10µg total RNA in a 50µL reaction by following the poly(A) tailing kit (Thermo Fisher Scientific). The reactions were incubated for 1hour at 37ºC, purified and eluted with 25µL nuclease-free water. For the RNase R treatment, the RNA products were treated with 10U RNase R, 3µL 10X RNase R Buffer with specific LiCl (0.2M Tris–HCl pH 8.0, 1mM MgCl2, and 1M LiCl), and 80U RiboLock RNase Inhibitor (40 U/μL, Thermo Fisher Scientific). Finally, the RNA products were purified and eluted in 30µL nuclease-free water to proceed the rRNA-depleted RNA-seq library.
We used the Qubit RNA High Sensitivity Assay to quantify the A-tailing RNA y ) and the Bioanalyzer 2100 Eukaryote Total RNA Pico to value the quality of the A-tailing RNA. The Ribo-Zero rRNA Removal Kit was used to deplete ribosomal RNAs and the NEBNext UltraTM RNA Library Prep Kit was used to prepare libraries.

value: Cortex

value: NO


title: 5CG17


title: Copper, rep1


title: 5CG16


title: 5CG15


title: COR775-2B


title: KO9 WGBS

city: Valencia

first: Natalia

last: Tapia

state: València

address: Jaime Roig 11

institute: Spanish National Research Council

data_processing:
FastQC (fastqc_v0.11.8) was used to perform basic statistics on the quality of the raw reads.
Reads were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ; MINLEN:36)
Bismark software (version 0.24.0; Krueger et al., 2011) was used to perform alignments of bisulfite-treated reads to the reference genome. The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead et al., 2012).
Sequence reads that produced a unique best alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read was inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones.
Assembly: grcm38
Supplementary files format and content: bigwig

source_name: E18.5 isolated villi from intestinal epithelium

growth_protocol: Tissue, no cell culture.

extract_protocol:
Genomic DNA was extracted using QIAamp DNA micro kit (Qiagen) and bisulfite treated using EZ DNA Methylation Gold Kit (Zymo Research).
Genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treated to generate single strand DNA. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. The library was ready after size selection and PCR amplification.

treatment_protocol: The villi of E18.5  intestinal epithelium was isolated as follows. Briefly, the small intestine was dissected from E18.5 embryos, opened longitudinally, and placed on ice-cold PBS containing 30mM EDTA and 1.5mM DTT for 20min on ice. Next, the intestine was transferred to a tube containing 30mM EDTA in PBS, incubated at 37ºC for 10min and, then, vigorously shaken for 30s to release the intestinal epithelium from the lamina propia. After removing the intact intestinal muscle, the villi suspension was used for DNA extraction and WGBS.

value: C57BL6/JRccHsd N>5

value: Tet3 knockout


title: 5CG13


title: AsPC-1 cells treated with 6-Diazo-5-oxo-l-norleucine (DON), Rep1


title: KO4 WGBS

value: E18.5 isolated villi from intestinal epithelium


title: CLO122-2B

value: male


title: 5CG10


title: 5CG11