title: TS50_5_DMSO_5_CEBP_a

value: anti-CEBPA (C15410225 from Diagenode)


title: IonXpress_006: Full visible spectrum 1h

status: Public on Nov 28 2023

type: SRA

city: Cajamar

first: Juliana

last: Lago

state: SP

address: Via de Acesso, KM30,5, Prédio C

department: R&D

country: Brazil

institute: Natura Cosméticos S/A

description: 3D skin samples exposed to blue wavelength light, for 1 hour, simulating acute exposure

library_source: transcriptomic

data_processing:
Software Version: Torrent Suite 5.10.0; host figo; ion-analysis 5.10.10-1; ion-dbreports 5.10.26-1; ion-gpu 5.10.0-1; ion-pipeline 5.10.8-1; ion-torrentpy 5.10.8-1; ion-torrentr 5.10.9-1; S5 Script 0.1.31; LiveView 2389; DataCollect 3602; OIA 51000; OS 34; Graphi
Run Name R 2018 09 06 22 44 33 user S5-CEC-75; Run Date Oct. 4, 2018, 3:15 p.m.; Run Flows 500
Chip Type 540; Chip Data tiled; Chip Lot Number QSC156; Chip Wafer 19; Barcode Set IonXpress
Analysis Args Analysis {args-json /opt/ion/config/args 540 analysis.json; Pre-BaseCaller BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0; {max-phasing-levels 2 {wells-normalization on; Calibration Args Calibration; BaseCaller Args BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0; {max-phasing-levels 2 {num-unfiltered 1000 {barcode-filter-postpone 1; {wells-normalization on; Alignment Args tmap mapall -q 50000 ... stage1 map4; IonStats Args ionstats alignment; Analysis Parameters default
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The mRNA from 3D skin was extracted using MINI KIT PURELINK PURIFIC RNA 50 PREPS (INVITROGEN) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard NGS platform (ION chef e ION5S) protocols:
A26325: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit
Q32852: Qubit™ RNA high sensitivity (HS), broad range (BR) and extended range (XR) Assay Kits
468802: Ion Library TaqMan® Quantitation Kit
A27759: ION 540 kit-Chef

treatment_protocol: 3D skin samples, in triplicate, was irradiated using LED light

tag: tissue

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

tag: treatment

value: full spectrum 1h


title: RNA_seq _X1

city: TaiAn

first: min

last: zhang

state: ShanDong

address: 61 Daizong Street

department: College of Animal Science and Technology

country: China

institute: ShanDongAgricultural University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The sequences were processed and analyzed by GENEWIZ.
Hisat2 (v2.0.1) was used to index reference genome sequence. And, clean data were aligned to reference genome via software Hisat2 (v2.0.1).

organism: Mus musculus

source_name: cumulus cells

extract_protocol:
Total RNA was extracted from CC samples using RNeasy Mini Kit (Qiagen) or miRNeasy Mini Kit (Qiagen) for mRNA and miRNA sequencing, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: granulosa cells in the antral follicles

tag: strain

value: Mice of Kunming

value: untreated


title: TS163_04_6h_CCS1477_100nM_rep1

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38

source_name: THP1 cells

growth_protocol: Human AML cell lines were obtained from ATCC and the DSMZ cell repositories and cultured in RPMI containing 10% FBS supplemented with 2mM L-glutamine.

extract_protocol:
Total RNA was extracted from THP1 cells treated with either DMSO or CCS1477 using the RNeasy Plus Mini Kit (Qiagen, 74134), according to manufacturer’s instructions. RNA quality was analyzed using the Agilent Bioanalyzer.
Libraries were prepared using the Agilent Sureselect pA. Then, libraries were sequenced using the Novaseq SP sequencing system (Illumina) with 30 million reads per sample.

treatment_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

tag: time point

tag: agent

tag: cell line


title: IonXpress_003: Blue wavelenght 2h

description: 3D skin samples exposed to blue wavelength light, for 2 hours, simulating acute exposure

value: blue 2h


title: TS163_03_6h_DMSO_rep2

value: DMSO


title: TS173_06_Sample_F_treatment_timepoint4_Cycle4_Day1

library_source: transcriptomic single cell

data_processing:
Reads were processed using the CellRanger (version 5.0.1)  10x demultiplexing pipeline using  'mkfastq' (parameters:  jobmode=local, localcores=16, localmem=60, barcode-mismatches=1), then 'count' (parameters: transcriptome=GRCh38-2020-A, jobmode=local, localmem=1990, localcores=32)
Assembly: GRCh38

source_name: Cryopreserved patient sample from bone marrow

growth_protocol: Cells were acquired from cryopreserved samples, so no growth protocol was utilized.

extract_protocol:
Cryopreserved patient samples from bone marrow or blood from the patient pre and post treatment with CCS1477 were thawed and immediately counted. The cells were not processed further, but were washed in 0.04% BSA/PBS and submitted for single-cell RNA seq library preparation.
The libraries were prepared using the Chromium Single Cell 3’ Reagent Kit using v3.1 chemistry.

value: blood


title: IonXpress_002: Blue wavelength 1h

source_name: 3D skin samples exposed to blue wavelength light, for 1 hour, simulating acute exposure

value: blue 1h


title: TS173_05_Sample_E_treatment_timepoint2_Cycle2_Day3


title: RNA_seq _F2

value: treated with FSH and FBS for 18 hours


title: IonXpress_004: Blue wavelenght 4h

description: 3D skin samples exposed to blue wavelength light, for 4 hours, simulating acute exposure

value: blue 4h


title: TS163_02_6h_CCS1477_100nM_rep2


title: IonXpress_001: Negative control

description: 3D skin samples non-exposed

source_name: 3D skin samples non-exposed

value: control


title: TS173_04_Sample_D_screening_pretreatment

source_name: Cryopreserved patient sample from blood


title: TS163_01_6h_DMSO_rep1


title: RNA_seq _F3


title: KMS11,shScramble,rep 2

status: Public on Nov 27 2023

city: Tianjin

first: Peixia

last: Tang

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Data filtering:The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0).
Reference gene mapping:The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5).The expression level of genes was calculated by RSEM (v1.2.8).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include fpkm,tpm and read count values for each Sample.

source_name: cell

growth_protocol: All human MM cell lines were grown in complete culture medium (RPMI 1640) supplemented with 10% FBS and 100 IU/mL penicillin in tissue culture flasks at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen).
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: cell

value: multiple myeloma cell lines

tag: genotype

value: WT


title: KMS11,shScramble,rep 3


title: KMS11,shScramble,rep 1


title: RNA_seq _F1


title: fenster2020-CTCTCTAT

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

state: PA

address: 5000 Forbes Ave

department: Computational Biology

country: USA

institute: Carnegie Mellon University

description:
inDrops v3
S1_1

data_processing:
The demultiplexing was performed using a custom shell script. Reads were aligned to the rheMac10 genome and counted at cell and gene level with STARsolo using a reference annotation lifted from the human genome to the rheMac10 genome.
To combine cells together across samples, we normalize the UMI counts with the variance-stabilizing SCTransform and glmGamPoi on each sample 7,8 and jointly embed cells across samples with reciprocal PCA integration 6 as outlined in https://satijalab.org/seurat/articles/integration_rpca.html. In this joint embedding, we over-clustered the dataset with FindClusters(algorithm = 2, resolution = 1)and removed any cluster with more than 10% of cells flagged by miQC, scds, or DropletQC as low-quality biased-clusters in the data.
We annotated our cells from the human striatum to a recently published high-resolution snRNA-seq reference dataset of the non-human primate striatum 9 using Seurat v4. We downloaded the monkey snRNA-seq processed, annotated gene UMI counts for all cells and MSNs from GSE167920. He, Kleyman et al. had aligned the snRNA-seq reads to the rheMac10 genome using the GRCh38 gene annotation liftover to rheMac10, so the gene-wise labels represent the UMI counts on the rheMac10 genome most orthologous to human. For both full nuclei and MSN subset datasets, we re-processed the macaque cells with SCTransform , glmGamPoi, and reciprocal PCA with default parameters as above to enable label transfer using the most recent integration algorithms in Seurat.
To transfer cell annotations from the reference macaque striatum dataset to the human striatum cells, we perform two label transfers at increasing resolutions: one with all cells and another with just MSNs. As He, Kleyman et al. described, the differences between transcriptionally and anatomically distinct MSN subtypes are subtle, so we split the annotations into two steps to optimally annotate the cells. The first label transfers the cell classes (Oligodendrocytes, MSNs, Interneurons, etc.) from the macaque to the human dataset with the Seurat functions FindTransferAnchors(reduction = ‘rpca’) and TransferData. Next, we identified cells or cell clusters that were labeled as MSNs and transferred MSN subtype labels (D1.Striosome, D2.Striomsome, etc.) from the macaque to human datasets. We filtered out cells where the cell class or cell subtype labels have max prediction scores less than 0.5 as these tend to represent noisy predictions due to low quality cells from either datasets. We confirmed accurate label transfer at the cell class and cell subtype levels with published marker genes and similar proportions across subjects and samples.
Even with the robust cutoffs that we applied to this dataset to remove likely low quality or doublet cells, we find a residual subset of the data that contain these cells. Upon clustering, doublet cells tend to project into the UMAP space as long streaks between two well-defined cell types. Low-quality cell types would project into the UMAP space as amorphous cell types without clear boundaries. Using these embedding features, we selected these clusters with Seurat’s FindClusters(resolution = 1) function, confirmed that they have the indicative QC metrics, and removed them from analyses.
Assembly: rheMac10
Supplementary files format and content: Annotated seurat h5 object with raw, processed, and integrated gene counts by cell aggregating samples across the entire dataset

organism: Macaca mulatta

source_name: nucleus accumbens

extract_protocol:
After sacrifice, brains were rapidly dissected into slabs and frozen on metal plates in liquid nitrogen vapor. Time between animal sacrifice and tissue freezing was between 1-2 hours for all animals. Brains were kept stored at -80 C until punching, when they were punched on a microtome with guidance from a macaque anatomist (Dr. S. Haber). Punches were stored at -80 C until the day of nuclear isolation and encapsulation.
Nuclei were isolated as in previous studies130, with minor modifications. Punches were placed into buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5mM spermidine, protease inhibitors) and placed in a Dounce homogenizer for 10 strokes each with loose and tight pestles. A 5% IGEPAL solution was added to a final concentration of 0.3% followed by five additional dounce strokes, then the lysate was filtered through a 40-μm strainer. Nuclei were mixed with an equal volume of 50% iodixanol and then layered on top of an iodixanol gradient of 40% and 30% layers in a 2 mL dolphin microcentrifuge tube. Nuclei were spun by centrifuging at 10,000 x g for 4 min at 4°C and then collected by aspiration at the interface of the 30% and 40% iodixanol layers. Nuclear concentration and prep quality were ascertained by loading on a hemocytometer and were diluted to a concentration of 80-100K and 15% iodixanol with Buffer HB prior to loading on InDrops platform. Single-nuclei suspensions were encapsulated into droplets, lysed, and the RNA within each droplet was reverse-transcribed using a unique nucleotide barcode as described previously131. Approximately 6,000 nuclei, in two batches of 3,000 nuclei each were processed per library and sequenced on Illumina NovaSeq 6000 chips (at a density of approximately 20,000 reads/nucleus).

treatment_protocol: Each morphine-treated subject was trained to come to the front of the enclosure for twice daily intramuscular (IM) injections (<0.5 cc) of morphine sulfate (NIDA Drug Supply Program) dissolved in 0.9% saline. Injections were administered at 09:30 and 17:00 hours. A gradual dosing escalation method (0.5 log unit increase every 3 days) was used to achieve the terminal dosage of 9 mg/kg/day (i.e., 4.5 mg/kg, BID). This dosage was selected to produce moderate opioid dependence128,129. All subjects received approximately 1500 mg of morphine over the 5-6-month period of chronic dosing. On the last day and approximately 3 hrs following the last IM morphine injection, each subject received an IM injection of ketamine (10 mg/kg) followed by 5.0 ml IV of a pentobarbital-based euthanasia solution (Beuthanasia-D).

tag: Sex

value: F

tag: weight (kg)

value: morphine

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

value: ~1500 mg/kg morphine (2018)

tag: pair

value: B


title: BS-seq hira groupA biol Rep1

city: Cold Spring Harbor

first: Jonathan

last: Cahn

state: NY

address: 1 Bungtown Rd

institute: CSHL

description: each biological replicates from each group (A or B) were grown and processed at the same time

library_source: genomic

data_processing:
Adapter trimming with cutadapt
Genome alignement with Bismark v0.22.3
Deduplication with deduplicate_bismark
Methylation values extracted with bismark_methylation_extractor
Bedgraphs made with custom awk statement on the CX_report
Bigwig made with bedGraphToBigWig from UCSC-kent tools
Assembly: TAIR10
Supplementary files format and content: Bigwig files representating methylation level for each cytosine sequence context (CG, CHG, CHH)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium and transferred to soil after 7 days.

extract_protocol:
Genomic DNA (gDNA) was extracted from rosette leaves of 3-4 plants for each genotype with Nucleon PhytoPure Genomic DNA Extraction Kits.
1 μg gDNA samples were sheared to an average size of 400 bp using a Covaris S220 focused-ultrasonicator. BS-seq libraries were made using the NEXTFLEX Bisulfite Library Prep Kit

tag: tissue

value: Rosette leaves

value: leaves

value: Bisufite treatment


title: BS-seq ddm1 groupA biol Rep1


title: KMS11,shCRIP1,rep 3

value: CRIP1 knockdown


title: BS-seq WT groupA biol Rep1

value: wild-type


title: KMS11,shCRIP1,rep 1


title: Staphylococcus aureus M6, replicate 2

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

description: Target, replicate 2

data_processing:
The quality of RNA sequencing raw data was checked using FastQC (v0.11.9). They were trimmed using Trimmomatic (v0.39).
The trimmed data were mapped to the whole genome sequences of each strain using bowtie2 (v2.4.5).
The mapping data were assigned read counts to each gene using HTSeq (v1.99.2).
To compare transcription levels between strains, an orthologous search was performed using OrthoFinder (v2.5.5), and the S. aureus IFM15 gene with the highest score was assigned to each gene of S. aureus M6.
Afterwards, filtering and trimmed mean of M-values (TMM) normalization were performed using the edgeR (v3.36.0) package of the R (v4.1.3) language.
Assembly: IFM15.gbf and M6.gbf as supplementary file
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes edgeR result for each sample.

organism: Staphylococcus aureus

source_name: miccro-organism from human's cheek

extract_protocol:
To harvest cells, cultures were centrifuged at 15,000 x g for 1 min. TRIzol™ Reagent (0.7532 mL) was added to bacterial pellets that had been stored at -80℃. RNA extraction was subsequently performed according to the manufacturer’s instructions with the following modifications. To obtain RNA from S. aureus, we added glass beads and vortexed for 1 minute, before placing the sample on ice for 1 minute and repeating this process 10 times.
Protocol for rRNA depletion using NEBNext rRNA Depletion Kit (Bacteria), TruSeq Stranded Total RNA Reference Guide (1000000040499 v00)

tag: cultivar

value: miccro-organism from human's cheek


title: Staphylococcus aureus IFM15, replicate 1

description: Control, replicate 1


title: Staphylococcus aureus M6, replicate 3

description: Target, replicate 3


title: Staphylococcus aureus IFM15, replicate 3

description: Control, replicate 3


title: KMS11,shCRIP1,rep 2


title: Staphylococcus aureus M6, replicate 1

description: Target, replicate 1


title: Staphylococcus aureus IFM15, replicate 2

description: Control, replicate 2


title: swi6T278Kepe1D_9me3_tet

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA
Supplementary files format and content: bedgraph

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: YEA, -tet conditions grown to log phase at 32C, +tet conditions grown to log phase for 24 hours in tetracycline

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

tag: chip antibody

value: plus tet


title: swi6T278Yepe1D_9me3_tet

tag: treatment


title: swi6T278Kepe1D_9me3_minustet

value: minus tet


title: WT_9me3_tet


title: swi6T278Y_9me3_tet


title: swi6T278K_9me3_minustet


title: swi6T278Y_9me3_minustet


title: epe1D_9me3_minustet


title: WT_9me3_minustet


title: swi6T278K_9me3_tet


title: swi6T278Yepe1D_9me3_minustet


title: clr4D_9me3_minustet


title: swi6T278KYepe1D_9me2_tet


title: swi6T278K_9me2_tet


title: swi6T278Yepe1D_9me2_tet


title: epe1D_9me2_tet


title: swi6T278Y_9me2_tet


title: clr4D_9me2_tet


title: WT_9me2_tet


title: swi6T278Kepe1D_9me2_minustet


title: clr4D_9me3_tet


title: swi6T278Yepe1D_9me2_minustet


title: swi6T278Y_9me2_minustet


title: WT_9me2_minustet


title: epe1D_9me2_minustet


title: clr4D_9me2_minustet


title: Soft-Glass_3

city: LYON

first: Romain

last: DEBRET

address: 7 passage du Vercors

country: France

institute: CNRS

description: Gene_ID;Soft_1 Glass_1;Soft-Glass_1;Soft_2;Glass_2;Soft-Glass_2;Soft_3;Glass_3;Soft-Glass_3

data_processing:
Reads were aligned to the human reference genome hg19 using the Ion Torrent RNASeqAnalysis plugin. Two consecutive alignments were achieved through the STAR and Bowtie2 programs to generate the BAM files.
Reads over genes were determined using the R/Bioconductor “Rsubread” software package to create a count matrix.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: skin

growth_protocol: Human primary keratinocytes were maintained in complete KGM2 medium (Promocell) supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA quantity and purity were verified using 2200 TapeStation system.
Library preparation was performed using mRNA-Seq Library Prep Kit Lexogen following the manufacturer’s instructions. Libraries were validated on TapeStation – HSD1000 ScreenTape®Dosage.
WARNING: In contrast to most other library preparation protocols, SENSE libraries generate reads in a strand orientation opposite to the genomic reference.

treatment_protocol:
Cells were seeded for 72h on glass coverslips coated with type-I collagen (Glass), or on polyacrylamide hydrogel (4 kPa) functionalized with type-I collagen (Soft).
Cells were preconditionned for 72h on soft hydrogels prior transfer on collagen-coated glass coverslips for 24h (Soft-Glass).

value: skin

value: primary keratinocytes

tag: cell type

value: epithelial cells


title: Soft-Glass_2


title: Glass_3

value: glass


title: Soft_1

value: soft


title: Soft_2


title: Soft-Glass_1


title: mouse kidney, UUO7D, 5AZA, sample 1 [5aza1]

city: AUGUSTA

first: Qingqing

last: Wei

state: Georgia

address: 1460 Laney Walker Blvd.

department: Cellular Biology & Anatomy

institute: Augusta University

data_processing:
To map the sequencing reads from RRBS, the mouse genome (mm9) was indexed by converting all C’s and G’s to T’s and A’s, respectively, which results in two different reference databases representing both strands. The cleaned reads was used to map to each of the two reference databases using Bowtie (Langmead et al., 2009) after converting all C’s to T’s. For each read, an in-house script computed the best of all alignments for the different loci using two different reference databases based on the number of mismatches after realigning the original read and reference sequences. Another in-house script determined the methylation status of each cytosine residue by comparing the bisulfite-converted sequence to the reference sequence. The third script piled reads for each cytosine in the reference genome and counted the numbers of reads that contained methylated and unmethylated cytosines, respectively. Finally the methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined. CpGs with < 5 reads were filtered out for further analyses. We used windows of length 200bp with an overlap of 100bp between to identify differentially methylated regions (DMRs) by summing the numbers of methylated and unmethylated CpGs in reads, respectively.
Methylation calculation: The methylation level [(# of methylated)/(# of methylated + # of unmethylated)] was calculated after measuring the amount of methylation (CG->CG) and unmethylation (CG->TG) in the CpG position. Only CpGs that are covered by at least 10 sequencing reads were included.
Assembly: mm9
Supplementary files format and content: bed

source_name: Kidney

extract_protocol:
The genomic DNA samples were extracted from mouse kidney cortex and outer medulla with QIAmp DNA Blood Mini kit from Qiagen (Germantown, MD) according to the manufacturer’s manual.
RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications. For each sample, 1  g genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20  l reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2  l premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20  l reaction containing 1  l concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 ?m of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

treatment_protocol: For UUO surgery, mice were anesthetized and the left ureter was ligated twice with suture and a cut was made between the two ligations. The sham-operated mice experienced similar surgery operations but without ureter ligation . For 5AZA treatment, 1mg/kg/day 5AZA in saline was administered through I.P. injection.

value: Kidney

tag: strain

value: male

value: wild type


title: mouse kidney, UUO7D, 5AZA, sample 2 [5aza2]


title: Soft_3


title: mouse kidney, UUO7D, sample 2 [Saline2]

value: UUO+saline


title: mouse kidney, UUO7D, sample 1 [Saline1]


title: mouse kidney, sham for kidney ischemia/reperfusion  [Sham48h]

value: sham


title: Glass_2


title: si-Suclg2_2 [DS2]

city: shanghai

first: xiaomin

address: 800 Xiang Yin Road

institute: National Key Laboratory of  Medical Immunology & Institute of Immunology, Naval Military Medical University

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute  using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: diffDC transfected with si-nc or si-Suclg2 mRNA.GeneDiffExp.xlsx

source_name: BMDC

growth_protocol: Bone marrow cells from  C57/BL6 mice were cultured with GM-CSF and IL-4 for 6 days and stimulated with LPS for 24 hours to generate bone-marrow derived DC (BMDC). CD11c+ BMDC were isolated by anti-mouse CD11c magbeads to generate maDC. maDC were then cocultured with spleen stroma cells for 9 days to generate diffDC. And then diffDCs were transfected with si-Suclg2 or si-nc.

extract_protocol:
diffDCs transfected with si-Suclg2 or si-nc were collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by  Beijing Genomics Institute  using Illumina HiSeq platform.

value: BMDC


title: si-Suclg2_4 [DS4]


title: si-Suclg2_3 [DS3]


title: mouse kidney, sham sample 1 for UUO7D [Sham]


title: si-nc_4 [DN4]

value: si-nc


title: si-nc_3 [DN3]


title: si-Suclg2_1 [DS1]


title: si-nc_2 [DN2]


title: swi6T278K_9me2_minustet


title: diffDC_3

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute  using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).
Supplementary files format and content: mm10

growth_protocol: Bone marrow cells from  C57/BL6 mice were cultured with GM-CSF and IL-4 for 6 days and stimulated with LPS for 24 hours to generate bone-marrow derived DC (BMDC). CD11c+ BMDC were isolated by anti-mouse CD11c magbeads to generate maDC. maDC were then cocultured with spleen stroma cells for 9 days to generate diffDC.

extract_protocol:
maDC and diffDC were collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by  Beijing Genomics Institute  using Illumina HiSeq platform.


title: si-nc_1 [DN1]


title: diffDC_2


title: diffDC_1


title: maDC_3


title: maDC_2


title: IonXpress_008: Full visible spectrum 4h

source_name: 3D skin samples exposed to blue wavelength light, for 4 hours, simulating acute exposure

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

value: full spectrum 4h


title: Glass_1

tag: cell line


title: maDC_1

tag: genotype


title: NarS_T380A_2

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

molecule: polyA RNA

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) strains with either vector pDTCF_empty vector (EV) or pDTCF_NarS_T380D or pDTCF_NarS_T380A were grown to an OD600 of ~0.3 in Middlebrook 7H9 medium (Difco) with 0.2 % glycerol, 10% OADC supplement and 0.05% Tween80 medium. Cultures were then induced with 100ng/ml anhydrotetracycline and were further allowed to grow till stationary phase.

extract_protocol:
The bacteria were harvested at the indicated timepoint and the RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, cell pellets were resuspended in Trizol and lysed by bead beating for 30sec at 6m/s for three cycles with intermittent cooling on ice. Cell debris were pelleted at 20,000g for 1min, and the supernatant was transferred to a heavy phase lock gel tube containing 300 µl chloroform. The tubes were inverted for 2min and centrifuged at 20,000g for 5min. RNA in the aqueous phase was precipitated using 300 μl isopropanol and 300 μl high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was purified using QIAGEN RNeasy kit and ribosomal RNA was depleted using the Ribo-Zero rRNA removal magnetic kit (Illumina) according to manufacturer's instructions.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit.

value: NarS T380A induced


title: NarS_T380A_1


title: S7AHUn3

city: Montreal

first: Jason

last: Tanny

state: Quebec

address: 3655 Prom Sir William Osler room 132

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Quality of the reads was determined using FastQC prior to and after trimming with TrimGalore (0.6.6) (Babraham Institute Bioinformatics https://www.bioinformatics.babraham.ac.uk/).
The trimmed reads were then aligned to a reference genome consisting of the S. pombe ASM294v2 genome combined with the ERCC RNA Spike-In transcripts. Alignment was with STAR (2.7.8a)
S. pombe transcripts were assembled using StringTie (2.1.5) and normalized to the spike-in RNA using RUVSeq (1.30.0)
Differential expression was assessed using DESeq2 (1.36.0)
Assembly: ASM294v2
Supplementary files format and content: gtf file (output from StringTie)

source_name: h- rpb1-S7A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210

growth_protocol: S. pombe cells were grown to OD600 of 0.2 in 50 mL YES at 30oC and then split into two 25 mL cultures.

extract_protocol:
Total RNA was extracted using a hot phenol method, followed by purification using the RNeasy Mini Kit (Qiagen). Quality of the RNA samples (RIN score >7) was verified on the Agilent 2100 Bioanalyzer using the RNA 6000 kit (Agilent, cat# 5067-1513). 1 μg of each RNA sample was then used for poly(A) selection and library preparation. Poly(A) selection was conducted using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Libraries were prepared with 0.1 μg poly(A) RNA using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: HU was added to one of the cultures to a final concentration of 12 mM, and incubation was continued for 4 hours. Cells were then harvested by centrifugation at 4oC, washed once with distilled water, and frozen at -80oC.

value: 12 mM HU


title: S7AHUn1

value: h- rpb1-S7A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: NarS_T380D_2

value: NarS T380D induced


title: S7Auntreatedn2

value: control


title: S7Auntreatedn3


title: T4AHUn3

source_name: h- rpb1-T4A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: EV_IND_3

value: Empty vector induced


title: T4AHUn2

value: h- rpb1-T4A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: T4AHUn1


title: T4Auntreatedn3


title: S7AHUn2


title: T4Auntreatedn1


title: S2AHUn3

source_name: h- rpb1-S2A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: S7Auntreatedn1


title: EV_IND_1


title: T4Auntreatedn2


title: S2AHUn1

value: h- rpb1-S2A::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: S2Auntreatedn3


title: S2Auntreatedn2


title: S2AHUn2


title: NarS_T380D_1


title: EV_IND_2


title: S2Auntreatedn1


title: Y1FHUn3

source_name: h- rpb1-Y1F::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: Y1Funtreatedn3

value: h- rpb1-Y1F::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210


title: Y1FHUn1


title: Y1FHUn2


title: Y1Funtreatedn1


title: Y1Funtreatedn2


title: rpb1WTHUn2

source_name: h- rpb1-WT::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 (marker placed 3’ of rpb1+)

value: h- rpb1-WT::natMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 (marker placed 3' of rpb1+)


title: rpb1WTuntreatedn1


title: rpb1WTuntreatedn3


title: rpb1WTuntreatedn2


title: rpb1WTHUn1


title: cds1HUn3

source_name: h- cds1∆::ura4+ leu1-32 ura4-D18

value: h- cds1{delta}::ura4+ leu1-32 ura4-D18


title: cds1HUn2


title: cds1untreatedn3


title: cds1untreatedn2


title: WTHUn2

value: WT


title: WTHUn3


title: cds1untreatedn1


title: WTuntreatedn3


title: WTuntreatedn1


title: WTuntreatedn2


title: brl1HUn2

source_name: h- brl1∆::hphMX4 ade6-M210

value: h- brl1{delta}::hphMX4 ade6-M210


title: brl1HUn1


title: brl1untreatedn3


title: brl1untreatedn2


title: brl1untreatedn1


title: set2HUn2

source_name: h- set2∆::hphMX6 ade6

value: h- set2{delta}::hphMX6 ade6


title: set2HUn1


title: set2HUn3


title: rpb1WTHUn3


title: cds1HUn1


title: set2untreatedn3


title: set2untreatedn2


title: WTHUn1


title: prf1HUn2

source_name: h- prf1∆::hphMX4 ade6

value: h- prf1{delta}::hphMX4 ade6


title: prf1untreatedn2


title: prf1HUn1


title: prf1HUn3


title: prf1untreatedn3


title: prf1untreatedn1


title: brl1HUn3


title: IGROV-1, PromethION, Rep 1

city: South San Francisco

last: Sterne-Weiler

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
Nanopore reads were aligned to the reference genome using minimap2 (v2.24-r1122)
Transcript expression quantification was performed using Isosceles (v0.0.3), using the Ensembl 90 annotations
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file containing the mapping between Isosceles transcript IDs and Ensembl gene and transcript IDs
Supplementary files format and content: comma-delimited text files containing Isosceles transcript read count and TPM quantifications for each sample

extract_protocol:
RNA was purified using Qiagen’s RNeasy Plus Mini kit (Cat. #74134) according to manufacturer’s instructions.
Library preparation for nanopore sequencing was performed according to the LSK-110 kit protocol with the exception of the end-repair step time which was increased to 30 min.


title: set1HUn2

source_name: h+ set1∆::kanMX6 ade6+ leu1-32 ura4-D18

value: h+ set1{delta}::kanMX6 ade6+ leu1-32 ura4-D18


title: IGROV-1, PromethION, Rep 2


title: Cell line mix, PromethION

data_processing:
The Illumina sequencing data was preprocessed using CellRanger (v6.0.1).
The Nanopore sequencing data was preprocessed using the Sicelore workflow (v2.0)
Transcript expression quantification was performed using Isosceles (v0.0.3), using the Ensembl 90 annotations
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file containing the mapping between Isosceles transcript IDs and Ensembl gene and transcript IDs
Supplementary files format and content: text file containing CellRanger filtered barcodes for Illumina data
Supplementary files format and content: text files and matrix file containing Isosceles transcript read count quantifications for Nanopore data

source_name: Mix (IGROV1, SK-OV-3, COV504)

extract_protocol:
IGROV1, SK-OV-3 and COV504 cells were trypsinized and pooled together at a 1:1:1 ratio at a concentration of 1000 cells / μl and submitted for single cell long read sequencing.
Illumina whole transcriptome dual-indexed library was prepared using the standard 10x Genomics protocol. Library preparation for nanopore sequencing was performed according to the LSK-110 kit protocol with the exception of the end-repair step time which was increased to 30 min.

value: Mix (IGROV1, SK-OV-3, COV504)


title: COV504, PromethION


title: SK-OV-3, PromethION


title: set1HUn3


title: set1untreatedn3


title: set1HUn1


title: OVTOKO, PromethION

source_name: OVTOKO

value: OVTOKO


title: COV362, PromethION


title: OVKATE, PromethION

source_name: OVKATE

value: OVKATE


title: set1untreatedn1


title: set2untreatedn1


title: OVMANA, PromethION

source_name: OVMANA

value: OVMANA


title: Col-0, rep 3

city: Norwich

first: Hannah

middle: Rae

last: Thomas

address: Norwich Research Park, Colney Lane

department: Cell and Developmental Biology

institute: John Innes Centre

data_processing:
Library quality was accessed with Fastqc v0.11.9 and Mulitqc v1.9
Libraries were trimmed using Trimmomatic v0.39.
Libraries were aligned to the Arabidopsis genome using Hisat2 v2.2.0.
Libraries were converted to SAM and BAM files using Samtools v1.11.
Transcripts were assembled using Htseq v0.5.4.
Assembly: TAIR10 https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Supplementary files format and content: text file which includes raw counts for each individual sample

source_name: leaf

growth_protocol: Arabidopsis thaliana lines, Columbia-0 wild-type,35S:ChEC127-GFP, and 35S:ChEC132-GFP, were grown on MS media (1% sucrose, 0.8% agar) for 4 weeks at 10:14h light:dark conditions at 22 °C.

extract_protocol:
Two leaves from three plants for each sample were harvested. Three biological replicates for each genotype  were collected.
Leaves were flash frozen in liquid nitrogen. Leaf tissue was homogenised using a Genogrinder.
RNA was extracted from leaf tissue using the Qiagen Plant RNeasy mini kit.
Rigorous treatment with Turbo DNase was undertaken to remove genomic DNA contamination.
Libraries were constructed by Novogene Co., Ltd using Illumina NovaSeq 6000, with 10M read depth.

value: leaf


title: K119RHUn3

source_name: h- htb1-K119R::kanMX6 ade6+ leu1-32 ura4-D18

value: 12 mM HU


title: K119RHUn2

value: h- htb1-K119R::kanMX6 ade6+ leu1-32 ura4-D18


title: Col-0, rep 2


title: K119RHUn1


title: Col-0, rep 1


title: ChEC132-GFP, rep 1


title: epe1D_9me3_tet

source_name: yeast cells

value: plus tet


title: K119Runtreatedn2

value: control


title: set1untreatedn2


title: ChEC132-GFP, rep 2


title: K119RIPHUn2

description:
1196_IP_HU_n2
1196_IPINratio_HU_n2_SESscaled.bw

data_processing:
Quality of the reads was determined using FastQC prior to and after trimming with TrimGalore (0.6.6)(Babraham Institute Bioinformatics https://www.bioinformatics.babraham.ac.uk/).
The trimmed reads were aligned to the reference S. pombe ASM294v2 genome using bowtie2
Aligned, deduplicated bam files were sorted and indexed in samtools
The deeptools package (version 2.0) was then used to derive bigWig files corresponding to IP/input ratios for each sample, and to scale based on read depth using the SES method.
A median genic Rpb3-HA occupancy across all protein-coding genes was computed for each bigWig file; this value was set to 1 for the wild-type control and used to scale the other bigWig files using wiggletools
Assembly: ASM294v2
Supplementary files format and content: bigWig

source_name: h? htb-K119R::kanMX6 rpb3-HA:kanMX6

growth_protocol: S. pombe strains expressing rpb3-HA were grown to OD600 of 0.2 in 100 mL YES at 30oC and then split into two 50 mL cultures.

extract_protocol:
1.5x10^7 cells from each sample were then crosslinked with 1% formaldehyde. Extracts were prepared by bead beating and were sonicated in a Bioruptor (Diagenode; UCD-200).
ChIP-seq libraries were prepared with 2 ng of input or IP DNA using the NEBNext Ultra II DNA Library kit for Illumina (New England Biolabs).

treatment_protocol: HU was added to one of the cultures to a final concentration of 12 mM, and incubation was continued for 4 hours.

value: h? htb-K119R::kanMX6 rpb3-HA:kanMX6

value: HA (Millipore Sigma Roche ROAHA


title: K119RIPHUn1

description:
1196_IP_HU_n1
1196_IPINratio_HU_n1_SESscaled.bw


title: K119RIPuntreatedn2

description:
1196_IP_C_n2
1196_IPINratio_C_n2_SESscaled.bw


title: ChEC127-GFP, rep 2


title: ChEC127-GFP, rep 3


title: K119RinputHUn1

description:
1196_IN_HU_n1
1196_IPINratio_HU_n1_SESscaled.bw


title: ChEC127-GFP, rep 1


title: K119RinputHUn2

description:
1196_IN_HU_n2
1196_IPINratio_HU_n2_SESscaled.bw


title: K119Rinputuntreatedn2

description:
1196_IN_C_n2
1196_IPINratio_C_n2_SESscaled.bw


title: Gene Expression

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description:
10x Genomics
Seurat_object.rds

data_processing:
*library strategy: ECCITE-seq
Cellranger v5.0.0 count and aggr functions to aggregate reads across sequncing lanes into a single set of barcodes.tsv.gz, features.tsv gz and matrix.mtx.gz
Assembly: NOT PROVIDED
Supplementary files format and content: Seurat_object.rds

source_name: lung

extract_protocol:
CD45+ cells were sorted from lungs digested into a singlce cell suspension.  Single cells were encapsulated in gel-beads=in emulsion using the 10x controller with a chromium single cell 5'GEM library and gel bead kit
ECCITE-seq and hashing protocol  described by Stoeckius et al, Mimitou et al, Buus et al  was used to generate an antibody-derived tag(ADT/hashtag oligo (HTO) library, a 5' gene expression library, and a VDJ-TCR library

value: lung

value: lung tumor

value: Keap1 R470C or WT


title: Hashing

description:
10x Genomics
Seurat_object.rds


title: K119Runtreatedn3


title: K119Runtreatedn1


title: WOM_NCD_rep4

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Sample Fastq files were aligned to the mouse reference genome GRCm38.p6 (GCA_000001635.8) using TopHat 2.1.1
Mapped reads were filtered for unique mapping to the genome.  The number of unique reads mapping to each gene (GencodeM24 annotation) was counted with  HTSeq-count (0.9.1, -t exon and –m union)
Assembly: GRCm38.p6 (GCA_000001635.8)
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

source_name: Whole Olfactory Mucosa

extract_protocol:
Whole Olfactory mucosa tissue was homogenized in Trizol reagent (Qiagen) using the OMNI tissue homogenizer (TH) (OMNI International). Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen), according to the manufacturer’s protocol.
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina)

treatment_protocol: normal chow diet (NCD): #8604 Teklad Rodent diet - Envigo, high-fat diet (HFD): #D12492 - Research Diets Inc, synthetic control diet (SCD): #D12450B - Research Diets Inc

value: Whole Olfactory Mucosa

value: NCD

tag: animal


title: WOM_NCD_rep3


title: ChEC132-GFP, rep 3


title: brl1IPHUn1

description:
1170_IP_HU_n1
1170_IPINratio_HU_n1_SESscaled.bw

source_name: h? brl1∆::hphMX4; rpb3-HA:kanMX6

value: h? brl1{delta}::hphMX4; rpb3-HA:kanMX6


title: K119Rinputuntreatedn1

description:
1196_IN_C_n1
1196_IPINratio_C_n1_SESscaled.bw


title: TCR

description:
10x Genomics
Seurat_object.rds


title: WOM_NCD_rep2


title: brl1inputHUn2

description:
1170_IN_HU_n2
1170_IPINratio_HU_n2_SESscaled.bw


title: Protein Expression

description:
10x Genomics
Seurat_object.rds


title: WOM_HFD_rep4

value: HFD


title: K119RIPuntreatedn1

description:
1196_IP_C_n1
1196_IPINratio_C_n1_SESscaled.bw


title: brl1inputHUn1

description:
1170_IN_HU_n1
1170_IPINratio_HU_n1_SESscaled.bw


title: WOM_HFD_rep3


title: brl1IPuntreatedn1

description:
1170_IP_C_n1
1170_IPINratio_C_n1_SESscaled.bw


title: brl1inputuntreatedn2

description:
1170_IN_C_n2
1170_IPINratio_C_n2_SESscaled.bw


title: brl1inputuntreatedn1

description:
1170_IN_C_n1
1170_IPINratio_C_n1_SESscaled.bw


title: WOM_SCD_rep4

value: SCD


title: WOM_HFD_rep1


title: WOM_SCD_rep2


title: prf1IPHUn2

description:
1169_IP_HU_n2
1169_IPINratio_HU_n2_SESscaled.bw

source_name: h? prf1∆::hphMX4; rpb3-HA:kanMX6

value: h? prf1{delta}::hphMX4; rpb3-HA:kanMX6


title: WOM_HFD_rep2


title: WOM_SCD_rep3


title: WOM_SCD_rep1


title: prf1IPuntreatedn2

description:
1169_IP_C_n2
1169_IPINratio_C_n2_SESscaled.bw


title: BS_NCD_rep4

source_name: brain

extract_protocol:
Cerebellum, cortex or Brain Stem tissues were homogenized in Trizol reagent (Qiagen) using the OMNI tissue homogenizer (TH) (OMNI International). Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen), according to the manufacturer’s protocol.
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina)

value: brain

tag: organ

value: BS


title: prf1IPHUn1

description:
1169_IP_HU_n1
1169_IPINratio_HU_n1_SESscaled.bw

value: 12 mM HU


title: prf1inputHUn2

description:
1169_IN_HU_n2
1169_IPINratio_HU_n2_SESscaled.bw


title: brl1IPuntreatedn2

description:
1170_IP_C_n2
1170_IPINratio_C_n2_SESscaled.bw


title: S7AIPHUn2

description:
1168_IP_HU_n2
1168_IPINratio_HU_n2_SESscaled.bw

source_name: h? rpb1-S7A::natMX6; rpb3-HA:kanMX6

value: h? rpb1-S7A::natMX6; rpb3-HA:kanMX6


title: prf1inputuntreatedn1

description:
1169_IN_C_n1
1169_IPINratio_C_n1_SESscaled.bw


title: prf1IPuntreatedn1

description:
1169_IP_C_n1
1169_IPINratio_C_n1_SESscaled.bw


title: BS_NCD_rep3


title: OB_NCD_rep4

value: OB


title: Male, 6-month-old, control 5

city: Richmond

first: Steven

middle: Joshua

last: Meas

email: stevenmeas3@gmail.com, meass2@vcu.edu

state: VA

address: 70 S Madison St

institute: Virginia Commonwealth University, Richmond

data_processing:
BioJupies (https://maayanlab.cloud/biojupies/)
Supplementary files format and content: tab-delimited file including raw counts per Sample

source_name: marrow-flushed tibia

extract_protocol:
Bone marrow flushed tibias were stored in RNAlater (Sigma-Aldrich, R0901-500ML) overnight at 4ºC before removing solution and storing at -80ºC until ready for processing. Frozen bones were ground with a mortar and pestle in liquid nitrogen and bone dust was homogenized in bead mill tubes (FisherBrand, 15-340-151) in Trizol (Thermo Fisher, 15596026). RNA was extracted using RNEasy Mini Kit (Qiagen, 74104).
RNAseq library was prepared (Illumina stranded mRNA prep) and performed on Nextseq 2000 P3 – 200 cycles (up to 1.1 billion reads) (Illumina).

value: marrow-flushed tibia

tag: gender

value: Male

tag: age

value: WT

value: control


title: Cerebellum_NCD_rep3

value: Cerebellum


title: Cortex_NCD_rep3

value: Cortex


title: prf1inputuntreatedn2

description:
1169_IN_C_n2
1169_IPINratio_C_n2_SESscaled.bw

value: HA (Millipore Sigma Roche ROAHA


title: prf1inputHUn1

description:
1169_IN_HU_n1
1169_IPINratio_HU_n1_SESscaled.bw


title: OB_NCD_rep3

value: NCD


title: Male, 6-month-old, control 4


title: S7AIPuntreatedn2

description:
1168_IP_C_n2
1168_IPINratio_C_n2_SESscaled.bw


title: OB_NCD_rep2


title: S7AinputHUn1

description:
1168_IN_HU_n1
1168_IPINratio_HU_n1_SESscaled.bw


title: S7Ainputuntreatedn2

description:
1168_IN_C_n2
1168_IPINratio_C_n2_SESscaled.bw


title: Male, 6-month-old, control 3


title: BS_NCD_rep2


title: Cerebellum_NCD_rep2


title: S7AIPuntreatedn1

description:
1168_IP_C_n1
1168_IPINratio_C_n1_SESscaled.bw


title: S7Ainputuntreatedn1

description:
1168_IN_C_n1
1168_IPINratio_C_n1_SESscaled.bw


title: Cortex_NCD_rep2


title: T4AIPHUn2

description:
1167_IP_HU_n2
1167_IPINratio_HU_n2_SESscaled.bw

source_name: h? rpb1-T4A::natMX6; rpb3-HA:kanMX6

value: h? rpb1-T4A::natMX6; rpb3-HA:kanMX6


title: Male, 6-month-old, control 1


title: Male, 6-month-old, control 2


title: S7AIPHUn1

description:
1168_IP_HU_n1
1168_IPINratio_HU_n1_SESscaled.bw


title: OB_NCD_rep1


title: T4AIPHUn1

description:
1167_IP_HU_n1
1167_IPINratio_HU_n1_SESscaled.bw


title: Male, 6-month-old, HLU 5

value: HLU


title: S7AinputHUn2

description:
1168_IN_HU_n2
1168_IPINratio_HU_n2_SESscaled.bw


title: T4AinputHUn2

description:
1167_IN_HU_n2
1167_IPINratio_HU_n2_SESscaled.bw


title: T4AIPuntreatedn1

description:
1167_IP_C_n1
1167_IPINratio_C_n1_SESscaled.bw


title: Cerebellum_NCD_rep1


title: Male, 6-month-old, HLU 4


title: Male, 6-month-old, HLU 2


title: S2AIPHUn1

description:
1166_IP_HU_n1
1166_IPINratio_HU_n1_SESscaled.bw

source_name: h? rpb1-S2A::natMX6; rpb3-HA:kanMX6

value: h? rpb1-S2A::natMX6; rpb3-HA:kanMX6


title: S2AIPuntreatedn2

description:
1166_IP_C_n2
1166_IPINratio_C_n2_SESscaled.bw


title: Cortex_NCD_rep1


title: Male, 6-month-old, HLU 1


title: BS_HFD_rep4

value: HFD


title: S2AinputHUn1

description:
1166_IN_HU_n1
1166_IPINratio_HU_n1_SESscaled.bw


title: BS_SCD_rep4

value: brain

value: SCD


title: Female, 6-month-old, control 4

value: Female


title: T4AinputHUn1

description:
1167_IN_HU_n1
1167_IPINratio_HU_n1_SESscaled.bw

value: 12 mM HU


title: S2AIPuntreatedn1

description:
1166_IP_C_n1
1166_IPINratio_C_n1_SESscaled.bw


title: OB_HFD_rep3

value: OB


title: S2AIPHUn2

description:
1166_IP_HU_n2
1166_IPINratio_HU_n2_SESscaled.bw


title: S2Ainputuntreatedn2

description:
1166_IN_C_n2
1166_IPINratio_C_n2_SESscaled.bw


title: Female, 6-month-old, control 3

value: marrow-flushed tibia


title: Male, 6-month-old, HLU 3

value: Male


title: T4AIPuntreatedn2

description:
1167_IP_C_n2
1167_IPINratio_C_n2_SESscaled.bw


title: S2Ainputuntreatedn1

description:
1166_IN_C_n1
1166_IPINratio_C_n1_SESscaled.bw


title: BS_NCD_rep1

value: BS


title: BS_HFD_rep3


title: Y1FIPHUn2

description:
1165_IP_HU_n2
1165_IPINratio_HU_n2_SESscaled.bw

source_name: h? rpb1-Y1F::natMX6; rpb3-HA:kanMX6

value: h? rpb1-Y1F::natMX6; rpb3-HA:kanMX6


title: Y1FIPHUn1

description:
1165_IP_HU_n1
1165_IPINratio_HU_n1_SESscaled.bw


title: Female, 6-month-old, control 2

value: WT

value: control


title: Female, 6-month-old, control 1


title: Cerebellum_HFD_rep3

value: Cerebellum


title: Y1FIPuntreatedn2

description:
1165_IP_C_n2
1165_IPINratio_C_n2_SESscaled.bw

value: HA (Millipore Sigma Roche ROAHA


title: Male, 22-month old, control 10

value: 22-month old


title: Cortex_HFD_rep3

value: Cortex


title: Y1FinputHUn2

description:
1165_IN_HU_n2
1165_IPINratio_HU_n2_SESscaled.bw


title: T4Ainputuntreatedn2

description:
1167_IN_C_n2
1167_IPINratio_C_n2_SESscaled.bw

value: h? rpb1-T4A::natMX6; rpb3-HA:kanMX6


title: Y1FinputHUn1

description:
1165_IN_HU_n1
1165_IPINratio_HU_n1_SESscaled.bw


title: S2AinputHUn2

description:
1166_IN_HU_n2
1166_IPINratio_HU_n2_SESscaled.bw

value: h? rpb1-S2A::natMX6; rpb3-HA:kanMX6


title: OB_HFD_rep2

value: brain

value: HFD


title: Male, 22-month old, control 9


title: BS_HFD_rep2


title: Y1Finputuntreatedn2

description:
1165_IN_C_n2
1165_IPINratio_C_n2_SESscaled.bw


title: Male, 22-month old, control 8


title: UCP1high3

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: University of Ulm

data_processing:
Next-generation sequencing (NGS) analysis was performed on the BGISEQ-500 platform by BGI Genomics Inc. (Cambridge, MA, USA), generating ~26.2 million reads per sample. Firstly,we remove the reads mapped to rRNA and get raw data. Sequencing reads were checked to remove low-quality, adaptor-polluted and unknown base reads before downstream analyses. After filtering, the clean reads were mapped to the reference genome using HISAT.
On average, 96.8% of reads were mapped, and the uniformity of the mapping result for each sample suggested that the samples were comparable. We mapped clean reads to reference transcripts using Bowtie2, then calculated the gene expression level for each sample with RSEM.
Sequencing data saturation analysis was used to measure whether the depth of sequencing data was sufficient for bioinformatics analysis. Based on their gene expression levels, we identified differentially-expressed genes (DEGs) between sample groups. We used the DEseq2 algorithm to detect the DEGs.
Assembly: not provided
Supplementary files format and content: DEGs.

source_name: adipose tissue

extract_protocol:
Total RNA extraction using TRIZOL extraction reagent. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads.
Library was validated on the Agilent Technologies 2100 bioanalyzer.
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

value: adipose tissue

value: adipocytes and stromal cells

value: IRF7 high


title: UCP1high1


title: UCP1high2


title: Y1Finputuntreatedn1

description:
1165_IN_C_n1
1164_IPINratio_C_n1_SESscaled.bw


title: UCP1low3

value: IRF7 low


title: Cortex_HFD_rep2


title: Male, 22-month old, control 6

value: marrow-flushed tibia

value: Male


title: WTIPHUn2

description:
1164_IP_HU_n2
1164_IPINratio_HU_n2_SESscaled.bw

source_name: h? rpb1-WT::natMX6; rpb3-HA:kanMX6

value: h? rpb1-WT::natMX6; rpb3-HA:kanMX6

value: 12 mM HU


title: Male, 22-month old, control 7

value: WT

value: control


title: Y1FIPuntreatedn1

description:
1165_IP_C_n1
1165_IPINratio_C_n1_SESscaled.bw

value: h? rpb1-Y1F::natMX6; rpb3-HA:kanMX6

value: HA (Millipore Sigma Roche ROAHA


title: Male, 22-month old, control 5

value: 22-month old


title: OB_HFD_rep1

value: OB


title: UCP1low1


title: Male, 22-month old, control 4


title: Male, 22-month old, control 3


title: Cerebellum_HFD_rep1

value: Cerebellum


title: Cortex_HFD_rep1

value: brain

value: Cortex


title: Atxn1 KO, rep3

city: Chuo-ku

first: Haruna

last: Takeda

state: Tokyo

address: 5-1-1 Tsukiji,

country: Japan

institute: National Cancer Center Japan

data_processing:
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.3.1 and STAR version 2.7.7a.
Reads were trimmed using trim_galore of Trim Galore version 0.6.7 and Cutadapt version 3.5.
The processed reads were mapped to the reference sequences and TPM (Transcripts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.3.1 and STAR version 2.7.10a.
Gene and isoform TPM values were extracted from TPM columns of RSEM result files.
Assembly: GRCm39
Supplementary files format and content: tab-deliminted text files include TPM values for each sample.

source_name: colon

extract_protocol:
Organoids embedded in Matrigel were dissolved in ISOGEN, and RNA was extracted following the protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat No. 7770)  following manufacturer's protocols.

treatment_protocol: Cas9 was intraduced by lenti-virus, then gRNA targeting Atxn1 or non-targeting gRNA were introduced by lenti-virus.

value: colon

value: organoid

value: epithelial cells

value: Atxn1 gRNA


title: Male, 22-month old, HLU 3

value: marrow-flushed tibia

value: HLU


title: WTinputHUn2

description:
1164_IN_HU_n2
1164_IPINratio_HU_n2_SESscaled.bw

value: h? rpb1-WT::natMX6; rpb3-HA:kanMX6


title: Cerebellum_HFD_rep2

value: HFD


title: Atxn1 KO, rep1


title: UCP1low2

value: adipose tissue

value: adipocytes and stromal cells

value: IRF7 low


title: BS_SCD_rep3

value: BS

value: SCD


title: control, rep3

value: non-target gRNA


title: WTinputuntreatedn2

description:
1164_IN_C_n2
1164_IPINratio_C_n2_SESscaled.bw

value: WT

value: HA (Millipore Sigma Roche ROAHA


title: Male, 22-month old, HLU 2

value: Male

value: 22-month old


title: WTinputHUn1

description:
1164_IN_HU_n1
1164_IPINratio_HU_n1_SESscaled.bw

value: 12 mM HU


title: control, rep2

value: colon

value: organoid

value: epithelial cells


title: BS_HFD_rep1

value: brain


title: WTIPuntreatedn2

description:
1164_IP_C_n2
1164_IPINratio_C_n2_SESscaled.bw

value: h? rpb1-WT::natMX6; rpb3-HA:kanMX6


title: Cerebellum_SCD_rep3

value: Cerebellum


title: WTinputuntreatedn1

description:
1164_IN_C_n1
1164_IPINratio_C_n1_SESscaled.bw


title: brl1IPHUn2

description:
1170_IP_HU_n2
1170_IPINratio_HU_n2_SESscaled.bw

value: h? brl1{delta}::hphMX4; rpb3-HA:kanMX6


title: Male, 22-month old, control 2

value: marrow-flushed tibia

value: control


title: WTIPuntreatedn1

description:
1164_IP_C_n1
1164_IPINratio_C_n1_SESscaled.bw


title: Atxn1 KO, rep2

value: Atxn1 gRNA


title: Cortex_SCD_rep3

value: Cortex

value: SCD


title: control, rep1

value: non-target gRNA


title: OB_SCD_rep2

value: OB


title: WTIPHUn1

description:
1164_IP_HU_n1
1164_IPINratio_HU_n1_SESscaled.bw

value: WT

value: HA (Millipore Sigma Roche ROAHA


title: BS-seq ddm1 groupB biol Rep2

description: each biological replicates from each group (A or B) were grown and processed at the same time

data_processing:
Adapter trimming with cutadapt
Genome alignement with Bismark v0.22.3
Deduplication with deduplicate_bismark
Methylation values extracted with bismark_methylation_extractor
Bedgraphs made with custom awk statement on the CX_report
Bigwig made with bedGraphToBigWig from UCSC-kent tools
Assembly: TAIR10
Supplementary files format and content: Bigwig files representating methylation level for each cytosine sequence context (CG, CHG, CHH)

source_name: Rosette leaves

extract_protocol:
Genomic DNA (gDNA) was extracted from rosette leaves of 3-4 plants for each genotype with Nucleon PhytoPure Genomic DNA Extraction Kits.
1 μg gDNA samples were sheared to an average size of 400 bp using a Covaris S220 focused-ultrasonicator. BS-seq libraries were made using the NEXTFLEX Bisulfite Library Prep Kit

value: Rosette leaves

value: leaves

value: Bisufite treatment


title: Female, 22-month-old, control 3

value: Female


title: BS_SCD_rep2

value: brain

value: BS


title: BS-seq atrx groupB biol Rep2


title: OB_SCD_rep3


title: Male, 22-month old, HLU 1

value: Male

value: 22-month old

value: HLU


title: Female, 22-month-old, control 2

value: marrow-flushed tibia

value: control


title: Female, 22-month-old, control 1


title: BS-seq WT groupB biol Rep2

value: wild-type


title: mouse olfactory bulb, 50 μm-spot, 3D, slide1

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Spatial transcriptomics

source_name: mouse olfactory bulb

extract_protocol:
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"

value: mouse olfactory bulb


title: mouse olfactory bulb, 50 μm-spot, 3D, slide2


title: KI_30W_3

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

department: Neuroscience

institute: Yale University

description:
10x Genomics
58242

data_processing:
CellRanger (mouse, v6.1.2; human, v7.0.0)
Preprocessing quality control including doublet detection using Scrublet
Normalization and square root transformation
BBKNN batch correction
Cell type annotation
Assembly: mm10 or GRCh38
Supplementary files format and content: h5ad files

molecule: nuclear RNA

source_name: Cerebellar cortex

extract_protocol:
Nuclei were isolated from frozen tissue as previously described.10 For mouse snRNA-seq, hemicerebella of three animals per genotype (WT and SCA1 KI) per timepoint (5, 12, 18, 24, and 30 weeks) were used, for a total of 30 animals. For human post-mortem samples, pieces of cerebellar cortex were harvested from frozen tissue of ten unique individuals per diagnosis (CTRL and SCA1), for a total of 20 human samples. Briefly, frozen mouse or human tissue was gently dounce homogenized in 2mL of ice-cold Nuclei EZ Prep buffer (Sigma; NUC101-1KT) with large clearance pestle “A” and then a small clearance pestle “B” for 25 strokes each, then incubated on ice for five minutes with an additional 2mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. Pelleted nuclei were then washed in 4mL of cold EZ Prep buffer, incubated on ice at five minutes, and centrifuged again at 500xg for five minutes at 4°C. Pelleted nuclei were then washed in 4mL of Nuclei Suspension Buffer (NSB) containing 1x phosphate buffered saline (PBS), 0.01% BSA, and 0.1% RNase inhibitor (Clontech/Takara; 2313B) and centrifuged at 500xg for five minutes at 4°C. Finally, nuclei were resuspended in 1mL of NSB, filtered through a 40mm cell strainer (Fisher Scientific; 22-363-547), and counted using a Countess II FL Cell Counter (Applied Biosystems; A27978). Single-nucleus suspensions were diluted to approximately 1000 nuclei per ml in NSB.
Libraries were prepared from diluted single-nucleus suspensions using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v.3 (mouse dataset) or v.3.1 (human dataset) through the Yale Center for Genome Analysis (YCGA). Briefly, 10,000 cells per sample were added to RT Master Mix, loaded on the Single Cell A Chip, and portioned with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing the following: an Illumina R1 sequence (read 1 sequencing primer), a 16-nucleotide barcode, a 12-nucleotide unique molecular identifier (UMI), and a 30-nucleotide poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers were released and mixed with the cell lysate and Master Mix. Incubation of the GEMs then produced barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were then used to remove leftover biochemical reagents from the post-GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction, and enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Libraries were sequenced using the NovaSeq6000 at the YCGA. Sample concentrations were normalized to 1.2nM and loaded onto an Illumina NovaSeq S4 flow cell at a concentration that yielded 20k-50k passing filter clusters per cell per sample. Samples were sequenced using paired-end sequencing on an Illumina NovaSeq6000 instrument according to Illumina protocols using 10x sequencing specifications. The 8bp index was read during an additional sequencing read that automatically followed the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor quality in real time. Signal intensities were converted to individual base calls during a run using the system’s Real Time Analysis (RTA) software. Base calls were transferred from the machine’s dedicated personal computer to the Yale high-performance computing cluster via a 1 Gigabit network mount for downstream analysis.
snRNA-seq

value: Cerebellar cortex

value: Atxn1 154Q/2Q knock-in

value: 30 weeks


title: Cerebellum_SCD_rep2

value: Cerebellum

value: SCD


title: BS-seq ddm1atrx groupB biol Rep1

address: 1 Bungtown Rd

institute: CSHL

value: Rosette leaves

value: leaves

value: ddm1-2 atrx-2


title: OB_SCD_rep1

value: brain

value: OB


title: BS-seq ddm1 groupB biol Rep1

value: Bisufite treatment


title: T4Ainputuntreatedn1

description:
1167_IN_C_n1
1167_IPINratio_C_n1_SESscaled.bw

value: h? rpb1-T4A::natMX6; rpb3-HA:kanMX6

value: HA (Millipore Sigma Roche ROAHA


title: Cortex_SCD_rep2

value: Cortex


title: Male, 22-month old, control 1

value: marrow-flushed tibia

value: Male

value: 22-month old

value: WT

value: control


title: KI_30W_1

description:
10x Genomics
58231

value: Cerebellar cortex

value: Atxn1 154Q/2Q knock-in

value: 30 weeks


title: BS_SCD_rep1

value: BS

value: SCD


title: BS-seq ddm1atrx groupB biol Rep2

value: Rosette leaves

value: leaves

value: ddm1-2 atrx-2


title: BS-seq atrx groupB biol Rep1

value: Bisufite treatment


title: Cerebellum_SCD_rep1

value: brain

value: Cerebellum


title: WT_30W_3

description:
10x Genomics
58232

value: Wild-type


title: BS-seq WT groupB biol Rep1

value: wild-type


title: KI_30W_2

description:
10x Genomics
58241


title: WT_30W_2

description:
10x Genomics
5822


title: WT_30W_1

description:
10x Genomics
5812


title: Cortex_SCD_rep1

value: Cortex


title: BS-seq ddm1hira groupA biol Rep2

value: ddm1-2 hira-1


title: KI_24W_3

description:
10x Genomics
20212

value: 24 weeks


title: BS-seq ddm1 groupA biol Rep2


title: BS-seq hira groupA biol Rep2


title: Primary tumor - single cell RNA seq

first: Joshua

middle: Caleb

last: Leinwand

address: 177 Fort Washington Ave, 7th Floor

department: Surgery

institute: Columbia University Irving Medical Center

description: Single cell RNA seq

data_processing:
For bulk RNA seq, Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated to normalize read count by dividing it by the gene length the the total number of reads mapped to protein-coding genes.
For single cell RNA seq, base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Bulk RNAseq: raw counts, fpkm counts, and normalized counts (all .csv files). Single cell RNAseq: genes-barcodes (.tsv files) and matrices (.mtx file)

source_name: Pancreatic tumor

extract_protocol:
For bulk RNA-seq, total RNA was extracted from fresh tissue using QIAGEN Rneasy Mini Kit, following the manufacturer's protocol. Single cell RNA sequencing was performed using the 10X Chromium platform, following manufacturer's protocol.
For bulk RNA seq, RNA libraries were prepared for sequencing using standard Illumina protocols. For single cell RNA seq, library construction was performed using the 10X Genomics platform using Chromium™ Single Cell 3' v2 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol

treatment_protocol: Mice were orthotopically injected with 100,000 murine FC1242 KPC pancreatic cancer cells, either orthotopically in the pancreas or metastatic to the liver. Tumors were harvested after 3 weeks, then either processed for bulk RNA sequencing, or FACS-sorted for CD45+ cells for single cell RNA sequencing via 10X platform.

value: Infiltrating CD45+ immune cells from primary tumor


title: Liver mets - bulk RNA seq rep_3

description:
Bulk RNA seq
m3

source_name: Metastatic liver tumor

value: Liver metastatic tumor tissue


title: Liver mets - bulk RNA seq rep_2

description:
Bulk RNA seq
m2


title: BS-seq WT groupA biol Rep2

first: Jonathan

last: Cahn


title: KI_24W_1

description:
10x Genomics
1589

value: Cerebellar cortex

value: Atxn1 154Q/2Q knock-in


title: KI_24W_2

description:
10x Genomics
2021


title: Liver mets - bulk RNA seq rep_1

description:
Bulk RNA seq
m1


title: Liver mets - single cell RNA seq

description: Single cell RNA seq

value: Infiltrating CD45+ immune cells from metastatic tumor


title: WT_24W_1

description:
10x Genomics
1974


title: SV-5

city: GuangZhou

first: Xiangwen

last: Diao

address: No.58 Zhongshan Second Road

institute: The First Affiliated Hospital，Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.  Seurat package (version: 4.0.3 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.  PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38
Supplementary files format and content: Single cell matrix files

source_name: peritoneal dialysis overnight effluent

extract_protocol:
Take 50ml abdominal dialysis solution and mix it upside down,then centrifuged at 400g for 8min. Discard the supernatant, add appropriate amount of red cell lysate according to the color of cell precipitation, and crack red cell for 5-10min,add 1640 medium to stop cracking red,400G centrifuge for 8min.After the supernatant was removed,the cell pellets was re-suspended in  PBS+0.04%BSA ,Pass 35µm cell sieve,centrifuged at 400G for 8min,and clean the cells twice in total.After the supernatant was removed,the cell pellets was re-suspended in  PBS+0.04%BSA,transferred into 1.5mlEP tube,blown and mixed with pipette,and 10ul cell suspension was taken for cell staining and counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 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.

treatment_protocol: We collected overnight effluent from 16 PD patients, including 6 SV patients, 6 patients in the LV_NOT_UF group, and 4 patients in the LV_UF group. SV group: patients received PD for less than 6 months. LV_NOT_UF group: patients received PD for more than 90 months and modified PET (Mod-PET) test showed that the ultrafiltration volume was greater than 400 mL. LV_UF group: patients received PD for more than 90 months, Mod-PET test showed that the ultrafiltration volume was less than 400 mL.

value: peritoneal dialysis overnight effluent

tag: Sex

value: M

value: SV


title: type 2 diabetes mellitus 11

type: RNA

city: Zheng Zhou

first: Zihao

last: Zhao

state: Henan

address: Jianshe Road 1

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

hyb_protocol: After 17 hours of hybridization at 65°C, the arrays were washed

scan_protocol: Scanned by Agilent Scanner G5761A

data_processing: Feature Extraction software (version 12.0.3.1, Agilent Technologies) was used to process raw images to extract raw data. Quantile normalization and subsequent processing were then performed using Genespring software (version 14.8, Agilent Technologies).

source_name: urinary extracellular vesicles

label_protocol: Affinity Script-RT kit and Promoter Primer were used to reverse-transcribe RNA into the first strand of cDNA, then Anti-sense Promoter was used to generate the second strand of cDNA, T7 RNA polymerase was added, and the second strand of cDNA was amplified to generate cRNA. It was then labeled with the fluorescent dye Cyanine-3-CTP (Cy3) and purified using the QIAGEN RNeasy Kit.

extract_protocol: Total RNA was extracted from EVs samples using Trizol reagent (Invitrogen, USA).

value: female


title: BS-seq ddm1hira groupA biol Rep1

city: Cold Spring Harbor

value: Rosette leaves

value: leaves

value: Bisufite treatment


title: SV-6

description: 10x Genomics


title: WT_24W_3

description:
10x Genomics
20202

value: Wild-type


title: type 2 diabetes mellitus 12


title: Primary tumor - bulk RNA seq rep_3

description:
Bulk RNA seq
p3

value: Pancreatic tumor tissue


title: type 2 diabetes mellitus 10

value: male


title: type 2 diabetes mellitus 9


title: Primary tumor - bulk RNA seq rep_2

description:
Bulk RNA seq
p2


title: WT_24W_2

description:
10x Genomics
2020


title: SV-4

description: 10x Genomics

value: F


title: KI_18W_3

description:
10x Genomics
65732

value: 18 weeks


title: Primary tumor - bulk RNA seq rep_1

description:
Bulk RNA seq
p1


title: type 2 diabetes mellitus 8


title: type 2 diabetes mellitus 5


title: SV-3

description: 10x Genomics


title: type 2 diabetes mellitus 6


title: type 2 diabetes mellitus 4


title: KI_18W_1

description:
10x Genomics
6571


title: KI_18W_2

description:
10x Genomics
65731


title: SV-2

description: 10x Genomics


title: Δ133p53α CAR T cells, CAR product, biological replicate 3

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result of mapping
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Peripheral Blood

growth_protocol: CAR T cells were maintained in R10 media and fed 300µL R10/well following day 3 tumor measurement

extract_protocol:
Total RNA was extracted from samples using column-based purification, followed by polyA selection to enrich for mRNA
Following purification, enriched mRNA was fragmented, followed by synthesis of first strand cDNA using reverse transcriptase and random primers. Second strand synthesis performed using SMM with DNA polymerase I and Rnase H.

treatment_protocol: CAR T cells were co-cultured in vitro at a 1 to 10 effector to target ratio with nalm6 leukemia cells, as described in the corresponding manuscript. "CAR product" samples represent the baseline CAR T cells prior to co-culture and we generated by isolating surface CAR+ T cells prior to co-culture, 4hrs post-thaw.

value: Peripheral Blood

value: Primary T cells

value: T cells

value: CAR product


title: WT CAR T cells, CAR product, biological replicate 2

value: WT


title: WT CAR T cells, CAR product, biological replicate 3


title: SV-1

description: 10x Genomics

value: peritoneal dialysis overnight effluent


title: LV_NOT_UF-6

description: 10x Genomics

value: LV_NOT UF


title: WT_18W_3

description:
10x Genomics
65702

value: Cerebellar cortex


title: type 2 diabetes mellitus 7


title: WT CAR T cells, CAR product, biological replicate 1


title: LV_NOT_UF-5

description: 10x Genomics


title: WT_18W_1

description:
10x Genomics
6569


title: KI_12W_3

description:
10x Genomics
2065

value: Atxn1 154Q/2Q knock-in

value: 12 weeks


title: WT_18W_2

description:
10x Genomics
65701


title: type 2 diabetic nephropathy 12

value: female


title: type 2 diabetes mellitus 1


title: type 2 diabetic nephropathy 11


title: LV_NOT_UF-3

description: 10x Genomics

value: M


title: type 2 diabetes mellitus 2


title: type 2 diabetic nephropathy 10


title: KI_12W_2

description:
10x Genomics
2063


title: Δ133p53α CAR T cells, mid-coculture, biological replicate 3

value: Tumor co-culture


title: Δ133p53α CAR T cells, CAR product, biological replicate 1


title: type 2 diabetic nephropathy 9


title: Δ133p53α CAR T cells, CAR product, biological replicate 2


title: LV_NOT_UF-1

description: 10x Genomics


title: LV_NOT_UF-4

description: 10x Genomics


title: KI_12W_1

description:
10x Genomics
22019


title: LV_NOT_UF-2

description: 10x Genomics


title: WT_12W_3

description:
10x Genomics
2062

value: Wild-type


title: WT_12W_2

description:
10x Genomics
2061


title: type 2 diabetic nephropathy 8

value: male


title: Δ133p53α CAR T cells, mid-coculture, biological replicate 2


title: LV_UF-4

description: 10x Genomics


title: WT_12W_1

description:
10x Genomics
22018


title: WT CAR T cells, mid-coculture, biological replicate 2


title: LV_UF-3

description: 10x Genomics

value: F


title: Δ133p53α CAR T cells, mid-coculture, biological replicate 1


title: LV_UF-2

description: 10x Genomics


title: WT CAR T cells, mid-coculture, biological replicate 3


title: KI_5W_3

description:
10x Genomics
72932

value: 5 weeks


title: type 2 diabetic nephropathy 7


title: type 2 diabetic nephropathy 6


title: KI_5W_2

description:
10x Genomics
72931


title: LV_UF-1

description: 10x Genomics


title: IGROV-1, MinION, Rep 2

first: Tim

extract_protocol:
RNA was purified using Qiagen’s RNeasy Plus Mini kit (Cat. #74134) according to manufacturer’s instructions.
Library preparation for nanopore sequencing was performed according to the LSK-110 kit protocol with the exception of the end-repair step time which was increased to 30 min.


title: type 2 diabetic nephropathy 4


title: KI_5W_1

description:
10x Genomics
7294


title: IGROV-1, MinION, Rep 1


title: WT_5W_3

description:
10x Genomics
72922


title: Donor 14 CD8 T cells CMV.A2 HELIOS NEG OKT3

city: Woluwé-Saint-Lambert

first: Damien

last: Neyens

state: Bruxelles

address: Avenue Hippocrate 74

country: Belgium

institute: De Duve Institute

data_processing:
Quality control
Files were trimmed with trimmomatic
alignet to GRCh38 human genome with HISAT2
Read counts were determined with featuresCount
Normalization of read counts and analysis of differentially expressed genes were performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Count_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)
Supplementary files format and content: Count_Subpop_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)
Supplementary files format and content: Count_Tetramer_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)

source_name: Blood

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (ref AM1975 Thermo Fisher Scientific)
SMART-Seq (Nextera XT DNA Library Preparation Kit (96 samples)  FC-131-1096, Illumina)

treatment_protocol: 5h coated anti-CD3 (clone OKT3 1ug/ml) activation

value: Blood

value: CD8 T cells

tag: marker

value: HELIOS NEG

tag: stimulation

tag: tetramer


title: type 2 diabetic nephropathy 3


title: type 2 diabetic nephropathy 5


title: Donor 14 CD8 T cells CMV.E HELIOS POS OKT3

tag: tissue

value: HELIOS POS


title: AG13156 early passage replicate 2

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For nascent strand peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: T2T
Supplementary files format and content: Bed file format of replication origin peaks
Supplementary files format and content: BigWig file format of replication origin locations
Library strategy: NS-seq

source_name: Skin

growth_protocol: Fibroblasts were grown in MEM medium, 15% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exonuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of NS samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).

treatment_protocol: Fibroblast cells were immortalized by human Telomerase Reverse Transcriptase protein (hTERT). Cells were then cultured on a cover glass and treated with and without EX527 (1uM for 48hr). The SIRT1 gene was deleted from the cancer cell lines using CRISPR-Cas9 targeting exon1.

value: Skin

value: Human skin fibroblast

value: early passage


title: WT_5W_2

description:
10x Genomics
72921

value: Cerebellar cortex


title: WT_5W_1

description:
10x Genomics
7202


title: AG04441 early passage replicate 2


title: Donor 14 CD8 T cells CMV.E HELIOS POS NS

value: NS


title: Cell line mix, Illumina

data_processing:
The Illumina sequencing data was preprocessed using CellRanger (v6.0.1).
The Nanopore sequencing data was preprocessed using the Sicelore workflow (v2.0)
Transcript expression quantification was performed using Isosceles (v0.0.3), using the Ensembl 90 annotations
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file containing the mapping between Isosceles transcript IDs and Ensembl gene and transcript IDs
Supplementary files format and content: text file containing CellRanger filtered barcodes for Illumina data
Supplementary files format and content: text files and matrix file containing Isosceles transcript read count quantifications for Nanopore data

source_name: Mix (IGROV1, SK-OV-3, COV504)

extract_protocol:
IGROV1, SK-OV-3 and COV504 cells were trypsinized and pooled together at a 1:1:1 ratio at a concentration of 1000 cells / μl and submitted for single cell long read sequencing.
Illumina whole transcriptome dual-indexed library was prepared using the standard 10x Genomics protocol. Library preparation for nanopore sequencing was performed according to the LSK-110 kit protocol with the exception of the end-repair step time which was increased to 30 min.

value: Mix (IGROV1, SK-OV-3, COV504)


title: AG04441 early passage replicate 1


title: Y_Fibs

city: Boston

first: Sergiy

last: Velychko

state: MA

address: 77 Avenue Louis Pasteur, Room 232

department: Genetics

institute: Harvard Medical School

data_processing:
NEBNExt ultra Directional RNA Kit with polyA enrichment was used for library preparation. Reads were aligned to the reference genome using CLC Genomics Workbench 12.0
Supplementary files format and content: TPM

extract_protocol: RNA-seq and RRBS were performed for human iPSC at passage 10-12, human ESCs (H6 and H9) at passage 35-36 grown in StemFlex media on Matrigel.

tag: sox variant


title: O_Fibs

tag: treatment


title: Donor 14 CD8 T cells CMV.E HELIOS NEG OKT3


title: type 2 diabetic nephropathy 1

value: female


title: hESC_H9

source_name: ESC

value: ESC


title: hESC_H6


title: type 2 diabetic nephropathy 2


title: AG04441 early passage with ex527 replicate 2

tag: cell type

value: early passage with ex527


title: WT CAR T cells, mid-coculture, biological replicate 1

value: Peripheral Blood

value: Primary T cells

value: T cells

value: WT

value: Tumor co-culture


title: Donor 14 CD8 T cells CMV.E HELIOS NEG NS

value: Blood

value: CD8 T cells


title: Y_iPSC_SOX2_17_5

source_name: iPSC

value: iPSC

value: male


title: AG04441 with hTERT (genomic control)

value: Skin

value: Human skin fibroblast

value: genomic control


title: Donor 14 CD8 T cells CMV.B7 HELIOS NEG OKT3

value: HELIOS NEG


title: 1NMPP1_2

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

description: Fresh frozen Spatial transcriptome Sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTAQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Reseq coding genes were quantified using Space Ranger's default settings
Seurat v3 was used for further analysis.  Spatial spots were manually registered to the following zones : (1) Tendon, (2) Mid (M)-Injury, (3) Peripheral (P)-Injury, and (4) Deep (D)-Injury.
To describe the spatially regulated gene signature within the tendon injury site, SpatialTime was performed using similar techniques as we recently described in bone tissues.  First, a reference point was drawn at the exact center of the injury site.  The SpatialTime of each spatial spot was generated based on their relative distance to this midpoint of the injury site.  To analyze the integration of spatial transcriptomics and scRNA data, we used Seurat.  Briefly, annotations from scRNA and Visium were queried between each other to obtain prediction scores of the spatial position of cell subclusters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: SPATIAL TRANSCRIPTOMICS

source_name: Injured tendon area

growth_protocol: Spatial sequencing: Longitudinal cryosections of the injury site were obtained TrkA^WT and TrkA^F592A animals at 14 d post-operative for spatial sequencing.  The Visium Spatial Gene Expression System (10X Genomics, Pleasanton, CA) was used.

extract_protocol:
Tissue samples were frozen, embedded in OCT, and stored at -80 °C.  Samples were sectioned at 10-μm thickness at -40 °C and transferred to the Visium slide.  Library preparation, clean up, and indexing was conducted using standard procedures.  Next, samples were subjected to sequencing using a NovaSeq S2 100 cycle (4.1B reads).
Spatial transcriptome sequencing libraries were prepared with 10x Visium Spatial Gene expression slides and reagents according to manufacturer's instructions

treatment_protocol: Before surgery, male and female 12 week old mice were given buprenorphine SR (1 mg/kg IP). Briefly, hair overlying the left lower leg was clipped, and the skin was aseptically prepared using alternating betadine and alcohol scrubs. Mice were anesthetized by isoflurane gas (1– 3% inh) for the duration of the experiment. After confirming deep anesthesia, a 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon allowing visualization of this structure from its proximal origin from the gastrocnemius muscle down to its insertion into the calcaneum. Then, the Achilles’ peritenon-tendon complex was circumferentially isolated from the adjacent tissues by blunt dissection. A punch biopsy (0.5 mm in diameter) was made approximately 2 mm proximal from the calcaneal insertion. The skin incision was closed with continuous 5-0 Vicryl absorbable suture, and the animal was monitored per established postoperative protocols. The tendon injury site was dissected from TrkA^WT and TrkA^F592A animals at 14 d post-tendon injury for spatial transcriptomics.

value: 12 weeks old

value: Tendon + injured area

value: Tenocytes + other celltypes in the injured site

value: TrkA F592A

tag: time

value: 14 d post-operative


title: AG04446 with hTERT (genomic control)


title: 1NMPP1_1


title: AG12851 with hTERT (genomic control)


title: PBS3

city: Nan Jing

first: pingwen

last: shao

address: 163 Xianlin Avenue, Qixia Distric

institute: Nanjing University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: xenograft

extract_protocol:
Total RNA was extracted from the tumor tissue of 4T1-bearing mice using TRIzol reagent according to the manufacturer’s protocol. To avoid the contamination of genomic DNA, RNA samples were treated with RNase-free DNase.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: xenograft

value: mammary gland

value: untreated


title: Y_iPSC_SOX2_17_4


title: Control_1

value: TrkA WT

value: Control


title: Donor 14 CD8 T cells CMV.B7 HELIOS NEG NS

value: Blood

value: CD8 T cells

value: NS


title: Y_iPSC_SOX2_17_2

value: iPSC

value: male


title: Y_iPSC_SOX2_17_3


title: AG13156 with hTERT (genomic control)

value: Skin

value: Human skin fibroblast

value: genomic control


title: PBS2

value: WT


title: PBS1


title: Donor 13 CD8 T cells CMV.E HELIOS POS NS

value: HELIOS POS


title: Donor 13 CD8 T cells CMV.E HELIOS NEG OKT3

value: HELIOS NEG


title: AG04446 (genomic control)


title: Y_iPSC_SOX2_17_1


title: Control_2

value: 12 weeks old

value: Tendon + injured area

value: Tenocytes + other celltypes in the injured site

value: 14 d post-operative


title: NV3

value: xenograft

value: mammary gland

value: NV treated


title: AG04441 (genomic control)


title: Y_iPSC_AV_5


title: Donor 13 CD8 T cells CMV.E HELIOS NEG NS

value: Blood

value: CD8 T cells


title: AG12851 (genomic control)


title: Donor 13 CD8 T cells CMV.E HELIOS POS OKT3


title: type 2 diabetes mellitus 3


title: NV2


title: Y_iPSC_AV_4

value: iPSC


title: Y_iPSC_AV_3

value: male


title: Donor 13 CD8 T cells CMVA2.B7 HELIOS NEG NS

value: NS


title: NV1


title: AG13156 (genomic control)

value: Skin

value: Human skin fibroblast


title: Donor 12 CD8 T cells CMV.E HELIOS POS OKT3


title: AG04441 early passage with ex527 replicate 1

value: early passage with ex527


title: 20_S20

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to GRCm38 (GENCODE M25) reference genome using STAR programs (Dobin et al., 2013) and RSEM (Li and Dewey, 2011) with default parameters. Expected_read counts were calculated using RSEM.
Supplementary files format and content: expected_count.txt

source_name: lung

extract_protocol:
RNA was isoltaed using Invitrogen Purelink RNA minikit. CDNA was isolated
cDNA was synthesided from RNA using SMARTer PCR cDNA Synthesis kit. Sequencing libraries were prepared using Nextera XT DNA library prepearation kit.
Samples were pooled at equimolar ratios.

value: lung

value: lung tumor

value: Keap1 R470C


title: Donor 13 CD8 T cells CMVA2.B7 HELIOS NEG OKT3

value: HELIOS NEG


title: 19_S19


title: Donor 12 CD8 T cells CMV.E HELIOS POS NS

value: HELIOS POS


title: Y_iPSC_AV_1


title: AG13156 with hTERT and ex527 replicate 2

value: with hTERT and ex527


title: AG13156 with hTERT and ex527 replicate 1


title: 18_S18


title: Donor 12 CD8 T cells CMV.E HELIOS NEG OKT3


title: Y_iPSC_WT_5


title: AG13156 with hTERT replicate 1

value: with hTERT


title: Y_iPSC_WT_3


title: Donor 12 CD8 T cells CMV.E HELIOS NEG NS


title: AG13156 with hTERT replicate 2


title: 16_S16

value: Keap1 WT


title: 17_S17


title: Y_iPSC_AV_2


title: Donor 12 CD8 T cells CMVA2.B7 HELIOS NEG OKT3


title: Donor 12 CD8 T cells CMVA2.B7 HELIOS NEG NS


title: Y_iPSC_WT_2


title: AG12851 with hTERT and ex527 replicate 2

value: AG12851 with hTERT and ex527


title: O_iPSC_SOX2_17_5


title: Donor 11 CD8 T cells CMV.E HELIOS POS OKT3

value: Blood


title: AG12851 with hTERT replicate 2

value: AG12851 with hTERT


title: Y_iPSC_WT_4

value: iPSC


title: Y_iPSC_WT_1

value: male


title: 15_S15


title: Donor 11 CD8 T cells CMV.E HELIOS NEG OKT3

value: CD8 T cells


title: Eif4enif1+/-_arrested_1cell_3

city: Beijing

first: Yuxi

last: Ding

address: D110, Medical Building, 30 Shuangqing Road

institute: Tsinghua University

description:
AR9
embryo_RNA_count_matrix

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
Reads were mapped to  mm10 whole genome using Hisat2 (v2.1.0) with default parameters.
Gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: arrested 1-cell embryo

extract_protocol:
For T&T seq transcriptome and RNA-seq data,mRNA was extracted by lysing oocytes or embryos in lysis buffer for direct reverse transcription  Vazyme Single Cell Full Length mRNA-Amplification Kit. For T&T-seq translatome data, ribosome-bound mRNAs were extracted using RiboLace Module 1 Kit following manufacturer's  guidelines and purified using VAHT RNA clean beads. The purified mRNAs were then reverse transcribed with Vazyme Single Cell Full Length mRNA-Amplification Kit. cDNAs were purified using VAHT DNA clean beads.
DNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's instructions.

value: arrested 1-cell embryo

value: in vitro cultured for 24 hours


title: AG12851 with hTERT replicate 1

value: Skin

value: Human skin fibroblast


title: Donor 14 CD8 T cells CMV.A2 HELIOS NEG NS

value: NS


title: AG04446 with hTERT and ex527 replicate 2


title: O_iPSC_SOX2_17_4


title: Eif4enif1+/-_arrested_1cell_2

description:
AR7
embryo_RNA_count_matrix