title: opossum, scRNAseq, 2

description: 10x genomics scRNA-seq

data_processing:
Assembly: ASM229v1
Single cell RNA-seq library alignment to Ensembl GRCm39 (mouse) or ASM229v1 (opossum) and quality control was performed using 10x Genomics Cell Ranger 6.0.1 with default parameters (Zheng et al., 2017). CellRanger filtered matrices were then used for further filtering with SoupX (Young and Behjati, 2020) using the standard settings and no additional clustering data. Strained SoupX count matrices were used for all downstream analyses.
Supplementary files format and content: scRNA-seq: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: bulk RNA-seq: tab-delimited text files with FPKM values by gene

extract_protocol:
Whole testis single cell suspension was diluted to 10,000 cells/mL and single cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Library Kit. Libraries were sequenced on an Illumina NovaSeq.
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.


title: Ribo_body_KO1_1

status: Public on Aug 16 2024

type: SRA

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: dm6
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

molecule: total RNA

organism: Drosophila melanogaster

source_name: body

extract_protocol:
Testes were dissected from 2-3-day-adult-males in ice-cold PBS with 100 µg/ml cycloheximide. Dissected testes were immediately frozen with liquid nitrogen and stored at −80°C. We prepared 600 pairs of testes per sample. We prepared two replicates from WT (y1 w1118) and Mettl1-KO (Mettl1KO1) males, respectively.
Ribo-seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

tag: tissue

value: body

tag: treatment


title: G361_Lyso_low, biol rep 3

city: Boston

first: Deyang

last: Yu

state: MA

address: 360 Longwood Ave.

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing reads were mapped to GRCh38.90 using HiSat2.1
Quantitation was based on genes as counts per million reads (CPM) using SeqMonk v48.2.
Assembly: GRCh38.90
Supplementary files format and content: tab delimited text file include raw counts for each sample

organism: Homo sapiens

growth_protocol: G361 lysohigh and lysolow cells were maintained in DMEM growth media supplemented with 10% FBS and 1x Penicillin-Streptomycin.

extract_protocol:
TRIzol chloroform RNA extraction
purification and fragmentation of mRNA using oligo (dT)-attached magnetic beads, cDNA synthesis and processing, followed by amplification and further purification for PE100 libraries

tag: cell line

tag: cell type

value: malignant melanoma cell line

tag: genotype

value: BRAF V600E mutant

value: Sorted by low lysotracker intentsity


title: opossum, scRNAseq, 1

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: 10x genomics scRNA-seq

library_source: transcriptomic single cell

organism: Monodelphis domestica

source_name: testis

growth_protocol: Animals were grown under standard laboratory conditions and euthanized at the indicated developmental time points.

value: testis

tag: age

value: adult


title: G361_Lyso_low, biol rep 2


title: CB2KO_rep2

city: Los Angeles

first: Benjamin

last: Hurrell

state: CA

address: 1450 Biggy Street

institute: USC

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

organism: Mus musculus

source_name: lung

growth_protocol: Cells were freshly isolated on day 4 from the lungs of mice treated for 3 consecutive days with  0.5µg rmIL-33 intranasally

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: Cnr2 KO


title: G361_Lyso_low, biol rep 4


title: CB2KO_rep3


title: opossum, 2M, 4

description: rRNA depleted RNA-seq

data_processing:
Assembly: ASM229v1
RNA-seq libraries were aligned using HISAT 2.2.1 (Kim et al., 2019) with Ensembl (Yates et al., 2020) release 104 as a reference and -data output type. Output files were converted from SAM format to sorted BAM format using SAMtools-1.12 (Danecek et al., 2021; Li et al., 2009; Murat et al., 2021). Raw count values and FPKM were obtained using StringTie 2.1.4 (Pertea et al., 2016) with the -e and -G options and Ensembl (Yates et al., 2020) ASM229 release 104 or GRCM39 release 104 reference files for opossum and mouse, respectively.
Supplementary files format and content: scRNA-seq: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: bulk RNA-seq: tab-delimited text files with FPKM values by gene

extract_protocol:
Bulk RNA-seq libraries were prepared usingKAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche # 08098140702) and sequenced on an Illumina NovaSeq
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.

value: 2 months


title: G361_Lyso_low, biol rep 1


title: G361_Lyso_high, biol rep 3

value: Sorted by high lysotracker intentsity


title: G361_Lyso_high, biol rep 4


title: WT_rep1


title: WT_rep3


title: CB2KO_rep1


title: G361_Lyso_high, biol rep 1


title: G361_Lyso_high, biol rep 2


title: WT_rep2


title: MMTV-PyMT  CD8T cells shMogat1-3

city: Hangzhou

first: Huan

last: Wei

address: sandun street

country: China

institute: westlake university

data_processing:
FastQC Trim Galore and Hisat2 were used, respectively, to check, trim and map the raw RNA-seq data.
Assembly: mm10
Supplementary files format and content: tab-delimited csv files includes raw TPM for each Sample

source_name: tumor

extract_protocol:
RNA was harvested using TRIZOL.1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA-seq(NR602)  Library Prep Kit following manufacture's protocols.

value: tumor

value: CD8 T cells

value: Mogat1 knockdown


title: MMTV-PyMT  CD8T cells shMogat1-2


title: Control mice, Spleen

city: Melbourne

first: Nikita

last: Potemkin

state: Vic

address: 792 Elizabeth St

department: The Peter Doherty Institute for Infection and Immunity

country: Australia

institute: University of Melbourne

description: instrument model: Chromium iX

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using the `count` function from CellRanger v7.0.0
Assembly: mm10
Supplementary files format and content: h5 barcode matrix files

source_name: Spleen

extract_protocol:
Spleens were digested with cocktail mix of Collagenase, Dispase and DNAse and cells of interest sorted then mixed in equal ratios and subjected to 10X chromium
Libraries were constructed according to manufacturer's instructions (single cells 3' v2 protocol, 10X genomics)

treatment_protocol: Mice were treated with DT and 24h later infected with LCMV Armstrong.

value: Spleen

value: tdTomato+ P14 cells, CD11c+ myeloid cells, CD11c- myeloid cells, CD157+PDPN+ stromal cells, CD157-PDPN- stromal cells, total splenocytes mixed in equal ratios

value: Cre-DTR

tag: infection

value: DT and LCMV Arm infection


title: FRC depleted mice, Spleen

description: instrument model: Chromium iX

value: Cre+DTR


title: MMTV-PyMT  CD8T cells shCTRL-3

value: WT

value: shCTRL


title: MMTV-PyMT  CD8T cells shCTRL-1


title: MMTV-PyMT  tumor cells shMogat1-4

value: MMTV-PyMT

value: breast cancer cells


title: MMTV-PyMT  tumor cells shMogat1-2


title: MMTV-PyMT  tumor cells shMogat1-1


title: MMTV-PyMT  tumor cells shCTRL-1


title: 48h PMMA_M1

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Healthy Environments and Consumer Safety Branch

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65°C and 10 rpm.

scan_protocol: Scanned on an Agilent G4900DA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.01.1 ). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung cell from transgenic mutamouse

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Cells were cultivated in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture (DMEM): F12 HAM (1:1) culture media, Life Technologies, Burlington, ON, Canada) supplemented with 2% fetal bovine serum (FBS, Life Technologies, Burlington, ON, Canada), 1 ng/mL human epidermal growth factor (EGF, Life Technologies, Burlington, ON, Canada), 1 U/mL penicillin G, and 1 µg/mL streptomycin (Life Technologies, Burlington, ON, Canada) at 37 °C, with 5% CO2.

extract_protocol: Total RNA was extracted from cell pellet collected after harvest of FE1 cell treated with various microplastic particles using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a NanoDrop one spectrophotometer (Thermofisher Scientific, Waltham, Massachusetts, USA) and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, California, USA), respectively.  RNA samples used for gene expression analysis by microarray had A260/280 ratios > 2.0 and RINs > 8.0.

treatment_protocol: FE1 cells were exposed to 0, 12.5, 25 and 50 mg/mL of 100 nm polystyrene (PS) or polyethylene terephthalate (PETE) or polymethyl methacrylate (PMMA) or polypropylene (PP-TW) or vehicle control for 48h.

value: FE1 cell from Mutamouse

value: PMMA

tag: time point

tag: dose

value: 25 ug/mL

source_name: universal mouse reference RNA

value: universal mouse reference RNA


title: MMTV-PyMT CD8T cells,week4-4

tag: timepoint


title: MMTV-PyMT  tumor cells shCTRL-2


title: MMTV-PyMT  tumor cells shCTRL-4


title: MMTV-PyMT  CD8T cells shCTRL-4


title: 48h PMMA_C3

value: 0 ug/mL


title: MMTV-PyMT  CD8T cells shMogat1-1

value: tumor


title: 48h 100 nm PS_H3

value: 100 nm PS

value: 50 ug/mL


title: 48h PETE_M3

value: PETE


title: 48h PP-TW_H3

value: PP-TW


title: 48h PPTW_M3


title: MMTV-PyMT CD8T cells,week4-3

value: CD8 T cells


title: 48h PMMA_M3


title: 48h 100 nm PS_L3


title: 48h PPTW_L3


title: 48h PPTW_H2


title: 48h PP-TW_C2


title: 48h PMMA_L3


title: 48h PPTW_C3


title: 48h 100 nm PS_M3


title: MMTV-PyMT CD8T cells,week3-4


title: MMTV-PyMT CD8T cells,week3-3


title: MMTV-PyMT CD8T cells,week4-2


title: MMTV-PyMT CD8T cells,week2-3


title: MMTV-PyMT CD8T cells,week3-1


title: MMTV-PyMT CD8T cells,week2-2


title: 48h PMMA_H3


title: 48h PPTW_L2


title: 48h PETE small_C3


title: MMTV-PyMT tumor cells,week4-2


title: MMTV-PyMT tumor cells,week4-4


title: MMTV-PyMT tumor cells,week4-3


title: MMTV-PyMT CD8T cells,week2-1


title: 48h PPTW_M1


title: 48h PPTW_C1


title: MMTV-PyMT tumor cells,week4-1


title: 48h PETE small_L3


title: 48h PPTW_M2


title: 48h PETE small_H3


title: 48h PPTW_L1


title: 48h PMMA_C2


title: 48h 100 nm PS_M2


title: 48h 100 nm PS_C3


title: MMTV-PyMT tumor cells,week3-4


title: MMTV-PyMT tumor cells,week3-3


title: MMTV-PyMT tumor cells,week2-1


title: 48h PMMA_M2


title: MMTV-PyMT tumor cells,week3-1


title: MMTV-PyMT tumor cells,week2-3


title: MMTV-PyMT tumor cells,week2-2


title: RAW-PE-CUR3

city: Chengdu

first: linke

last: Li

address: No.111, North Section 1, Erhuan Road, Jinniu District

institute: Southwest Jiaotong University

description: Cells were treated for 24 hours with LPS (100 ng/ml) and 2 mg/mL PE-CUR before harvesting.

data_processing:
Illumina NovaSeq 6000, 150 bp paired-end reads.
fastp, Removal of low-quality reads to retain clean reads.
HTSeq-count: Read counts, FPKM calculation
DESeq2: Q-value < 0.05, fold change > 2 or < 0.5; R: PCA, clustering, enrichment analysis; GSEA, StringTie2, Cuffcompare, ASprofile: alternative splicing; SAMtools, BCFtools: SNP/Indel calling; SnpEff: variant annotation
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include counts and FPKM values for each Sample.

growth_protocol: RAW 264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: RAW264.7 cells were plated in 24-well and treated them with 100 ng/mL lipopolysaccharide (LPS) and 2 mg/mL PE-CUR for 24 hours.

value: Bone marrow macrophage

value: wild type

value: LPS and PE-CUR


title: 48h 100 nm PS_H2


title: RAWLPS3

description: Cells were treated for 24 hours with LPS (100 ng/ml) before harvesting.

value: LPS


title: 48h PPTW_H1


title: RAW-PE-CUR1


title: 48h 100 nm PS_C2


title: RAW-PE-CUR2


title: RAWLPS1


title: 48h PETE small_M2


title: 48h PMMA_H1


title: 48h PMMA_L2


title: 48h PMMA_H2


title: 48h PETE small_L2


title: RAWLPS2


title: 48h PMMA_L1


title: P2C

city: Coimbatore

first: Rajasree

last: venkatachalam

state: Tamil Nadu

address: TNAU - RI Block, Tamil Nadu Agricultural University, Lawley Rd, P N Pudur,

country: India

institute: Tamil Nadu Agricultural University, Coimbatore, India

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to GCF_000004075.3 genome using Hisat2 aligner.
Read count extraction was done using featureCounts and normalization and DEG identification was done using Voom/limma R packages
Assembly: GCF_000004075.3
Supplementary files format and content: Tab delimited text file includes normalized counts for each sample

organism: Cucumis sativus

source_name: leaf

extract_protocol:
RNA is isolated using Qiagen RNeasy PowerPlant kit, where the plant tissue is homogenised using lysis buffer in a power bead tube. Then, transfer the lysate to a spin column for RNA binding, followed by washing and elution ofpurifiedRNA.
QIAseq stranded mRNA Enrichment for mRNA capture and then QIAseq Stranded RNA Library Kit for Librarypreparation

value: leaf

value: Susceptible Control


title: 48h PMMA_C1

value: FE1 cell from Mutamouse


title: E14 KO2

city: macau

first: YIWEI

last: QIAN

state: Other (Non U.S.)

address: Avenida Wai Long,Taipa,Macau

institute: macau university of science and technology

data_processing:
Original image data file from Illumina  is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts. In this step, clean data (clean reads) were obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content thecleandata were calculated. All the downstream analyses were based on thecleandata with high quality
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the referencegenome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the genemodel annotation file and thus a better mapping result than other non-splice mappingtools.
featureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene.  And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: E14 cell

extract_protocol:
RNA was harvested using theTransZol Up Plus RNA Kit (TransGen, ER501-01). 1 μg of total RNA was used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E14 cell

value: mouse embryonic stem cells

value: Npac knockout


title: P2V

value: Susceptible Virus inoculated


title: 48h PETE small_H1

value: universal mouse reference RNA


title: E14 KO1


title: 48h 100 nm PS_H1

value: 100 nm PS


title: E14 WT2

value: WT


title: P1V

value: Resistant Virus inoculated


title: 48h PETE small_L1

value: PETE


title: 48h PETE small_C1

value: 0 ug/mL


title: 48h PETE small_H2

value: 50 ug/mL


title: 48h PETE small_M1

value: 25 ug/mL


title: E14 WT1


title: P1C

value: Resistant Control


title: 48h 100 nm PS_C1


title: 48h 100 nm PS_L1


title: 48h 100 nm PS_M1


title: RNA_body_KO1_2

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: dm6
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: body


title: Cit_NP_LGJ_1f

city: Philadelphia

first: Makarand

middle: V

last: Risbud

state: PA

address: 1025 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description: K3Citrate sample 4

data_processing:
the sequence reads were aligned by STAR 2.7.11b, and counts data were retrieved by --quantMode option
Assembly: mm10
Supplementary files format and content: raw counts table

source_name: Nucleus Pulposus

extract_protocol:
Caudal NP tissues from control and K3Citrate cohorts (n=4 mice/cohort) were micro-dissected under a stereo microscope (Zeiss, Stemi 503) and immediately placed in RNAlater® Reagent (Invitrogen, Carlsbad, CA). Tissues were stored at -80°C until the time of RNA isolation, wherein they were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971), and RNA was extracted from the lysates using an RNeasy® Mini kit (Qiagen).
Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 50 ng of RNA and 14 cycles of final PCR amplification.  Library size was assessed using the 4200 TapeStation and the DNA D5000 ScreenTape assay (Agilent, Santa Clara, CA).  Library concentration was determined using the Qubit Fluorometer 2.0 (ThermoFisher Scientific, Waltham, MA).

treatment_protocol: Treatments for this study began when mice were 17 months old and have not yet developed disc calcifications. All animals in this study belonged to one of two treatment cohorts: control or K3Citrate. Mice in the control cohort received regular, untreated drinking water throughout the study. Mice in the K3Citrate cohort began receiving a continuous supplementation of 80 mM K3Citrate (Sigma-Aldrich, C3029) in their drinking water at 17 months-of-age. They received this continuous supplementation until the experiment’s conclusion. Mice were euthanized with CO2 asphyxiation.

value: Nucleus Pulposus

tag: strain

value: LG/J

value: 23 months

tag: Sex

value: female

value: 80 mM K3Citrate


title: RNA_body_KO1_1


title: MMTV-PyMT tumor cells,week3-2

value: tumor

value: MMTV-PyMT

value: breast cancer cells


title: Cit_NP_LGJ_2f

description: K3Citrate sample 3


title: RNA_body_KO2_1


title: femal hamsters, M5F56

city: Zhengzhou

first: Ying

last: Peng

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: ；The First Affiliated Hospital of Zhengzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM.
Assembly: BCM_Maur_2.0
Supplementary files format and content: Tab-delimited text file includes row counts for each sample

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: heart

extract_protocol:
Total RNA was extracted through trizol reagent
polyA probes were used to retrieve mRNA from total RNA, then fragment and add adaptor to build a library

value: heart


title: femal hamsters, M5F55


title: Cit_NP_LGJ_X3m

description: K3Citrate sample 1

value: male


title: RNA_body_KO2_2


title: RNA_body_WT1_1

value: CT


title: RNA_body_WT1_2


title: RNA_testis_WT2_2

value: testis


title: femal hamsters, M5F22


title: 48h PETE small_C2

value: FE1 cell from Mutamouse

value: PETE

value: 0 ug/mL

value: universal mouse reference RNA


title: RNA_testis_KO2_2


title: femal hamsters, M5F16


title: Unt_NP_LGJ_28m

description: Untreated control sample 4

value: Untreated Control


title: Cit_NP_LGJ_14m

description: K3Citrate sample 2

value: Nucleus Pulposus


title: RNA_testis_KO1_2


title: Unt_NP_LGJ_31f

description: Untreated control sample 3

value: LG/J


title: RNA_testis_WT1_2


title: Neocortex Chd8+/- 3

city: Manchester

first: Siddharth

last: Banka

address: Oxford Road

country: United Kingdom

institute: University of Manchester

library_source: genomic

data_processing:
RRBS single-end reads were trimmed using TrimGalore v0.4.4 with `--rrbs` option
Reads were aligned to reference mm39 genome using Bismark v0.20.0 aligner with option `--nucleotide_coverage`.
Aligned BAM files were sorted by coordinate using Samtools v1.9.
Reads mapped to Mitochondrial chromosomes or to unassembled contigs were removed.
Assembly: mm39
Supplementary files format and content: Methylation call files

molecule: genomic DNA

source_name: P5 neocortex

extract_protocol:
DNA was extracted using DNeasy DNA extraction (Qiagen, 69504) kit. DNA concentrations were checked using Qubit Fluorometry and 100ng of DNA was used for RRBS library preparation using the Premium RRBS kit (Diagenode, C02030032).
DNA was digested using MspI overnight at 37˚C after which adapters were ligated. Prior to quantification by qPCR, fragments were selected based on fragment size using AMPure XP beads (Beckman Coulter, A63880). For qPCR quantification, 1µl of size-selected library, LUNA Universal qPCR Master Mix (New England Biolabs, M3003), 3.5µl of nuclease free H2O, and 0.5µl primer mix (from the RRBS kit) transferred to 96-well PCR plate. Libraries were pooled based on the formula (17 x 2-ΔCt , where ΔCt = Ctmax –Ctsample). Pooled libraries were topped up with nuclease free H2O before clean up with AMPure XP beads. Bisulfite conversion was performed using BS Conversion reagent (from the Premium RRBS kit), before enrichment PCR, quality control and clean-up.

value: P5 neocortex


title: femal hamsters, M5F19


title: femal hamsters, M5F12


title: femal hamsters, M5F7


title: Neocortex WT 2


title: Neocortex Chd8+/- 2


title: Unt_NP_LGJ_X9m

description: Untreated control sample 1

value: 23 months


title: mouse_scRNAseq_3

description: 10x genomics scRNA-seq

data_processing:
Single cell RNA-seq library alignment to Ensembl GRCm39 (mouse) or ASM229v1 (opossum) and quality control was performed using 10x Genomics Cell Ranger 6.0.1 with default parameters (Zheng et al., 2017). CellRanger filtered matrices were then used for further filtering with SoupX (Young and Behjati, 2020) using the standard settings and no additional clustering data. Strained SoupX count matrices were used for all downstream analyses.
see data processing associated with each sample
Assembly: see information associated with each sample
Supplementary files format and content: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files

extract_protocol:
Whole testis single cell suspension was diluted to 10,000 cells/mL and single cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Library Kit. Libraries were sequenced on an Illumina NovaSeq.
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.
See protocols associated with each sample

value: adult

tag: genome build


title: Neocortex Chd8+/- 1


title: Irf3 fl/Δ Cre+, SeV infected, 5 dpi, mouse3

city: Lexington

first: Saurabh

last: Chattopadhyay

state: KY

address: 760, Press Avenue

institute: University of Kentucky

data_processing:
High throughput sequencing data from Illumina was transformed into sequenced reads (raw data) by CASAVA base recognition (Base calling).
Quality of downstream analysis was improved by removing reads with adapter contamination, more than 10% of uncertain nucleotides and more than 50% of low quality nucleotides (base quality <5)
Alignment of reads was then performed using HISAT2 to the reference genome GRCm38/mm10
featureCounts was used to the quantify the expression of genes in the samples in terms of raw counts for each sample
Assembly: Mus Musculus (GRCm38/mm10)
Supplementary files format and content: Tab-delimited xls file contains the raw counts for each sample with annotation of each gene
Supplementary files format and content: Tab-delimited xls file contains the fpkm values for each sample with annotation of each gene

source_name: Lung

extract_protocol:
The mouse lungs were homogenized using Trizol and total RNA was extracted using the phenol-chloroform method. The extracted RNA was then purified using the RNeasy plus mini kit.  The RNA was then sent to Novogene for library preperation and sequencing analysis.
After quality control tests, mRNA library was constructed using poly(A) tail capture via oligo(dT) magnetic beads and again tested for quality control. First cDNA strand was synthesized using random hexamers, after fragmentation. This was followed by second cDNA strand synthesis; dUTP for directional library, dTTP for non-directional library. Quantified libraries were pooled and sequenced on Illumina platform (NovaSeq 6000) with pair-end 150 base pairs sequencing strategy (PE150).

value: Lung

value: Irf3 fl/{delta} Cre+

value: SeV


title: Unt_NP_LGJ_33m

description: Untreated control sample 2


title: femal hamsters, M5F5

value: heart


title: 48h 100 nm PS_L2

value: 100 nm PS


title: HEK293T_LTR12C-target_VP64_H3K4me3_ChIP

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

data_processing:
Sequencing reads were aligned against the human GRCh37/hg19 reference genomeb by Bowtie2.
Peaks were called by MACS with q-value < 0.01.
The definitions of ERV elements were based on RepeatMasker.
Assembly: hg19
Supplementary files format and content: csv file. Signal peaks in transposable elements.

growth_protocol: HEK293T cells were mainteined in DMEM with 10%FBS and antibiotics.

extract_protocol:
Transfected cells were cross-linked with 1% formaldehyde for 10 min and the cross-linking was neutralized with 125 mM glycine for 5 min at room temperature. Cell pellets were lysed in 1% lysis buffer.
Sequencing libraries were prepared using TruSeq ChIP Library Prep Kit (Illumina)

treatment_protocol: Transfections were performed by Lipofectamine LTX Reagent (Termo Fisher Scientific) with 500ng plasmid constructs into HEK293T cells. The cells were harvested at 3 days after treatment.

tag: chip antibody

value: H3K4me3 antibody (Diagenode, C42D8)

value: Human Embryonic Kidney

value: WT

value: LTR12C-target CRISPRa (VP64)


title: HEK293T_LTR12C-target_VP64_WGBS

data_processing:
Sequencing reads were aligned against the human GRCh37/hg19 reference genomeb by BSMAP.
The DNA methylation levels at each CpG site were calculated as the ratio of methylated CpG and all CpG in uniquely mapped reads.
The definitions of ERV elements were based on RepeatMasker.
Assembly: hg19
Supplementary files format and content: BSMAP_Non-target_result.txt
Supplementary files format and content: BSMAP_LTR12C-target_result.txt

extract_protocol:
Genomic DNA from HEK293T after CRISPRa was purified using a DNAzol (Invitrogen)
Bisulfite conversion, library preparation, and sequencing were performed by the Van Andel Research Institute Genomics Core.


title: Irf3 fl/Δ Cre+, SeV infected, 5 dpi, mouse2


title: Telencephalon+POA, male, snRNA-seq, rep2

city: Atlanta

first: Larry

last: Young

state: GA

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, and gene counting was conducted using Cell Ranger software v6.0.1
Assembly: Nemo_v1
Supplementary files format and content: Seurat object of filtered and processed data saved as an rds file

molecule: nuclear RNA

organism: Amphiprion ocellaris

source_name: Telencephalon+POA

extract_protocol:
Frozen telencephalon tissue samples were incubated on ice for 30 minutes in chilled lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 1% Nonidet P40 Substitute, and Nuclease-free H2O) with gentle rotation. Following lysis, HAB medium (with 2% B27 and 0.5 mM Glutamax) was added and tissue was triturated using silanized glass Pasteur pipettes (500 μm internal diameter) to complete tissue dissociation. Samples were centrifuged (600rcf, 5 minutes, 4°C) and resuspended in chilled wash and resuspension buffer (1X PBS, 2% BSA, 0.2 U/μl RNase Inhibitor). Nuclei suspensions were filtered through 40 μm Flowmi® cell strainers and 30 μm MACS® SmartStrainers to remove debris and large nuclei aggregations. Finally, fluorescence activated cell sorting (FACS) was used to further purify samples. DAPI (1.0 μg/ml) was used as a nuclear stain and viable, intact nuclei singlets were selected and sorted into collection buffer (1X PBS, 2% BSA, 0.2 U/μl RNase Inhibitor) using a BD FACSAriaTM Fusion Cell Sorter.
Libraries were prepared according to manufacturer instructions (Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry (10X Genomics)). Single nuclei suspensions were loaded onto the 10x Genomics Chromium Controller and partitioned into individual GEMs (gel bead-in emulsion), each containing a single nucleus, a barcoded gel bead and master mix with reverse transcription (RT) reagents. Primers released from each gel bead include a 10X barcode, unique molecular identifier (UMI) and Illumina R1 primer. Partitioned nuclei were lysed and GEMs were incubated to produce full-length, barcoded cDNA. Barcoded cDNA were purified using Silane magnetic beads and amplified via PCR . Amplified cDNA was size-selected with SPRIselect. During final library construction, an Illumina R2 primer sequence, I5 and I7 paired-end construct sequences, and a sample index were added. Quality was assessed using high sensitivity DNA analysis on the Bioanalyzer 2100 system (Agilent) and libraries were quantified using Qubit 2.0 (Invitrogen).

value: Telencephalon+POA

value: male

value: adult (>1 year, reproductive)


title: Neocortex WT 1


title: Telencephalon+POA, male, snRNA-seq, rep1

description: 10x Genomics


title: HEK293T_LTR12C-target_VP64_H3K27ac_ChIP

value: H3K27ac antibody (Active Motif, MABI 0309)


title: HEK293T_LTR12C-target_VP64_HAtag_ChIP

value: HA-tag antibody (Cell Signaling, C29F4)


title: HEK293T_non-target_VP64_H3K27ac_ChIP

value: Non-target CRISPRa (VP64)


title: Neocortex WT 3

value: P5 neocortex


title: Telencephalon+POA, female, snRNA-seq, rep2

description: 10x Genomics

value: female


title: Telencephalon+POA, female, snRNA-seq, rep1

description: 10x Genomics


title: HEK293T_non-target_VP64_HAtag_ChIP


title: Irf3 fl/Δ Cre+, SeV infected, 5 dpi, mouse1

value: Lung


title: Irf3 fl/Δ Cre+, PBS treated, 5 days, mouse3

value: Irf3 fl/{delta} Cre+

value: PBS


title: HEK293T_LTR12C-target_p300_biol_rep2

data_processing:
Sequencing reads were aligned against the human hg19 reference genome using HISAT2.
The definitions of ERV elements were based on RepeatMasker.
RPKM values were calculated using uniquely mapped reads obtained from featureCounts.
Assembly: hg19
Supplementary files format and content: csv file. Expression level of transposable elements.

growth_protocol: HEK293T, MCF7, A2780 cells were mainteined in DMEM with 10%FBS and antibiotics. HCT116 cells were mainteined in McCoy's 5A with 10%FBS and antibiotics.

extract_protocol:
Total RNA from cell lines after CRISPRa was purified using a Direct-zol RNA MiniPrep Kit (Zymo Research).
cDNA linraries were prepared using KAPA RNA HyperPrep Kits and pooled using standard illumina protocols.

treatment_protocol:
HEK293T cells were treated with PBS (control) or 300 nM 5-aza-CdR for 24 h. The cells were harvested at 5 days after treatment.
Transfections were performed by Lipofectamine LTX Reagent (Termo Fisher Scientific) with 500ng plasmid constructs into HEK293T, HCT116, MCF7, or A2780 cells. The cells were harvested at 3 days after treatment.

value: LTR12C-target CRISPRa (p300)


title: HEK293T_LTR12C-target_p300_biol_rep3


title: HEK293T_non-target_VP64_WGBS


title: HEK293T_non-target_p300_biol_rep3

value: Non-target CRISPRa (p300)


title: Irf3 fl/Δ Cre+, PBS treated, 5 days, mouse2


title: HEK293T_LTR12C-target_p300_biol_rep1


title: Irf3 fl/Δ Cre+, PBS treated, 5 days, mouse1


title: HEK293T_non-target_p300_biol_rep2


title: MCF7_LTR12C-target_VP64_biol_rep2

value: Breast Carcinoma


title: MCF7_LTR12C-target_VP64_biol_rep3


title: Irf3 fl/Δ, SeV infected, 5 dpi, mouse3

value: Irf3 fl/{delta}

value: SeV


title: MCF7_LTR12C-target_VP64_biol_rep1

value: WT

value: LTR12C-target CRISPRa (VP64)


title: HEK293T_non-target_VP64_H3K4me3_ChIP

value: H3K4me3 antibody (Diagenode, C42D8)

value: Human Embryonic Kidney


title: Irf3 fl/Δ, SeV infected, 5 dpi, mouse2


title: Irf3 fl/Δ, SeV infected, 5 dpi, mouse1


title: MCF7_non-target_VP64_biol_rep1


title: A2780_LTR12C-target_VP64_biol_rep3

value: Ovarian Carcinoma


title: MCF7_non-target_VP64_biol_rep2


title: MCF7_non-target_VP64_biol_rep3


title: 2019_0204_Qg3

city: Fukuoka

first: Akiko

last: Satake

address: Motooka 744

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Custom Gene Expression 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities for each probe were calculated from the hybridization intensities using GeneSpring Software. The raw signal intensities of all samples were  normalized by the 75 percentile shift algorithm with the GeneSpring.
75 percentile shift normalized signal (log2).

organism: Quercus glauca

source_name: leaf and bud

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA from leaf and bud samples was extracted using hexadecyltrimethylammonium bromide (CTAB) buffer (3% CTAB, 1.4 M NaCl, 20 mM EDTA, 100 mM Tris–HCl pH 8.0, 0.2% b-mercaptoethanol) and was purified using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)

value: leaf and bud


title: Irf3 fl/Δ, PBS treated, 5 days, mouse3


title: Irf3 fl/Δ, PBS treated, 5 days, mouse2


title: A2780_LTR12C-target_VP64_biol_rep1


title: A2780_non-target_VP64_biol_rep2

value: Non-target CRISPRa (VP64)


title: HEK293T_non-target_p300_biol_rep1


title: 2019_0204_Qg2


title: A2780_non-target_VP64_biol_rep3


title: 2019_0109_Qg1


title: 2019_0109_Qg3


title: Irf3 fl/Δ, PBS treated, 5 days, mouse1


title: HCT116_LTR12C-target_VP64_biol_rep3

value: Colorectal Carcinoma


title: O_CTR5

first: Yishang

last: Yan

state: zhejiang

address: The Key Laboratory of Reproductive Genetics

institute: Zhejiang University

data_processing:
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4)  to map reads to the genome.The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: O_GDMVSO_CTR_Gene_differential_expression.xlsx

source_name: limb muscle

extract_protocol:
Total RNA was isolated and purified usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure. 1ug of total RNA was used for construction of sequencing libraries.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: skeletal muscle

value: limb muscle

value: cells mixture

value: injection of dissolving buffer at gestational day 6.5 and 12.5


title: A2780_non-target_VP64_biol_rep1


title: 2018_1213_Qg3


title: HCT116_LTR12C-target_VP64_biol_rep2


title: HCT116_non-target_VP64_biol_rep3


title: 2018_1213_Qg2


title: HCT116_LTR12C-target_VP64_biol_rep1


title: O_CTR3


title: HCT116_non-target_VP64_biol_rep2


title: O_CTR4


title: HEK293T_LTR12C-target_VP64_biol_rep3


title: A2780_LTR12C-target_VP64_biol_rep2


title: HCT116_non-target_VP64_biol_rep1


title: O_CTR2


title: HEK293T_LTR12C-target_VP64_biol_rep2


title: O_CTR1


title: HEK293T_LTR12C-target_VP64_biol_rep1


title: HEK293T_non-target_VP64_biol_rep3


title: HEK293T_non-target_VP64_biol_rep2


title: HEK293T_non-target_VP64_biol_rep1


title: HEK293T_5-Aza_biol_rep3


title: 2018_1213_Qg1


title: O_GDM4

value: injection of streptozocozin at gestational day 6.5 and 12.5


title: HEK293T_5-Aza_biol_rep2


title: 2018_1115_Qg3


title: 2018_1115_Qg2


title: 2018_1115_Qg1


title: 2018_1017_Qg3


title: O_GDM3


title: O_GDM2


title: HEK293T_PBS_biol_rep2

value: PBS


title: HEK293T_PBS_biol_rep1


title: REC-1, Ibrutinib Resistant, RNA-seq, Repeat 1

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.5) with parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 100000 --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 25  --chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.5.1) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input for gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files with read count; bigWig files for genome browser viewing

growth_protocol: RPMI 1640  supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol

extract_protocol:
24 hours post treatment with DMSO and 100nM ibrutinib followed by IgM stimulation for 5 min, parental and resistant cells were lysed with 350ul RLT Plus buffer supplemented with 2-mercaptoethanol and total RNA was isolated using the RNeasy Plus Micro Kit.
Strand-specific RNA-seq was performed on parental and ibrutinib-reistant Rec1 cells using SMARTer Stranded Total RNA Sample Prep kit.

treatment_protocol: Parental and resistant cells were tretated with DMSO (parental) or ibrutinib (reistant) for 24 hours followed by BCR crosslinking with IgM for 5min.

value: Mantle Cell Lymphoma

value: Ibrutinib


title: REC-1, Ibrutinib Resistant, RNA-seq, Repeat 2


title: REC-1, Ibrutinib Resistant, RNA-seq, Repeat 3


title: 2018_1017_Qg2


title: 2018_1017_Qg1


title: 2019_0204_Qg1


title: 2018_0919_Qg3


title: O_GDM1


title: O_GDM5


title: REC-1, DMSO, RNA-seq, Repeat 3

value: DMSO


title: 2019_0109_Qg2


title: HEK293T_5-Aza_biol_rep1

value: WT


title: REC-1, DMSO, RNA-seq, Repeat 2


title: pLN, 1313259_05, TCR

city: Gainesville

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: D1
pLN_1313259_05_barcodes.tsv.gz
pLN_1313259_05_features.tsv.gz
pLN_1313259_05_matrix.mtx.gz

data_processing:
Raw sequence reads were processed using Cell Ranger multi (v. 3.0.0) with gene expression libraries (mm10-2020-A) and V(D)J libraries (GRCm38-alts-ensemble-7.0.0) aligned to mouse reference assemblies
Assembly: mm10-2020-A (GEX) and GRCm38-alts-ensembl-7.0.0 (TCR)
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_contig_annotations.csv: High-level annotations of high-confidence contigs from cell-associated barcodes

source_name: pLN

extract_protocol:
Single-cell suspensions of pancreatic draining lymph nodes (pLN; 3x Isotype, 5x ⍺-CD226) and collagenase-digested pancreas (3x Isotype, 2x ⍺-CD226), isolated from treated mice around 12 weeks of age, were enriched for CD3+ T cells using the Mouse T cell EasySep Kit. Enriched cells underwent Fc-blocking and 30 minutes of staining with oligonucleotide-tagged antibodies at 4˚C for CITE-seq. Approximately 5,000 cells were used to generate Gel Beads In-Emulsions (GEMs) with a 10x Chromium Controller and the Chromium NEXT GEM Single Cell 5' Kit v2.
Gene expression, V(D)J, and feature barcode libraries were prepared according to manufacturer's instructions (single cell 5' v2 protocol, 10x Genomics)

treatment_protocol: NOD mice received three total doses of either an IgG2a Isotype Control or ⍺-CD226 mAb, with 200 µg doses administered via IP injection at the following ages: 49 days, 53 days, and 56 days.

value: NOD/ShiLtJ

value: Female

value: pLN

tag: time

value: 88 Days

tag: library type

value: TCR


title: REC-1, DMSO, RNA-seq, Repeat 1


title: HEK293T_PBS_biol_rep3

value: Human Embryonic Kidney


title: REC-1, Ibrutinib Resistant, ATAC, Repeat 2

data_processing:
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 5 --phred33 --gzip --stringency 5 -e 0.1 --length 20 --paired. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 12. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.29.1) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 369).
Assembly: hg19
Supplementary files format and content: bigWig files for genome browser viewing

extract_protocol:
ATAC-seq assay was performed as previously described (PMID: 30745086). Briefly, 50,000 cells were pelleted at 800 x g and washed with 50 μl of ice cold 1 x PBS (Corning cat# 21031CV), followed by 2min treatment with 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal cat# CA-630). Pelleted nuclei were resuspended in 50 μl of transposition buffer (25 μl of 2 x TD buffer, 22.5ul of molecular biology grade water and 2.5 μl Tn5 transposase (Illumina cat# FC-121-1030) to tag the accessible chromatin for 45min at 37°C.
Tagmented DNA was purified with MinElute Reaction Cleanup kit and amplified with 5 cycles. Additional number of PCR cycles was determined from the side reaction and ranged from 8-9 total cycles of PCR. Libraries were purified using QiaQuick PCR purification kit.

treatment_protocol: Parental and resistant cells were respectively tretated with DMSO (parental) and ibrutinib (reistant)  for 24 hours followed by BCR crosslinking with IgM for 5min.


title: 2018_0919_Qg1

value: leaf and bud


title: REC-1, Ibrutinib Resistant, ATAC, Repeat 1


title: REC-1, Ibrutinib Resistant, ATAC, Repeat 3


title: pLN, 1313259_04, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A11
pLN_1313259_04_barcodes.tsv.gz
pLN_1313259_04_features.tsv.gz
pLN_1313259_04_matrix.mtx.gz

library_source: other

molecule: protein

value: 87 Days

value: ADT

tag: adt

value: TotalSeq-C0001 anti-mouse CD4, TotalSeq-C0002 anti-mouse CD8⍺, TotalSeq-C0073 anti-mouse CD44, TotalSeq-C0112 anti-mouse CD62L, TotalSeq-C0848 anti-mouse TIGIT


title: 2018_0919_Qg2

tag: tissue


title: pLN, 1313259_05, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: B1
pLN_1313259_05_barcodes.tsv.gz
pLN_1313259_05_features.tsv.gz
pLN_1313259_05_matrix.mtx.gz

tag: treatment


title: Kidney C_9

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Fastq Files were aligned to the hg38 genome using HISAT2
Counts table was produced using Rsubread
Normalisation was perfomed using DESeq2
Assembly: hg38

source_name: Kidney

growth_protocol: Samples were preserved by QUOD, Universty of Oxford

extract_protocol:
RNA was extracted from bladders using Ambion RNA mini kit
Libraries were produced using Illumina TruSeq total RNA

value: Kidney

tag: delayed graft function

value: NO

tag: person id


title: pLN, 1313259_04, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A11
pLN_1313259_04_barcodes.tsv.gz
pLN_1313259_04_features.tsv.gz
pLN_1313259_04_matrix.mtx.gz

value: mRNA


title: REC-1, DMSO, ATAC, Repeat 2

tag: cell line

tag: cell type

value: Mantle Cell Lymphoma


title: pLN, 1313259_04, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C11
pLN_1313259_04_barcodes.tsv.gz
pLN_1313259_04_features.tsv.gz
pLN_1313259_04_matrix.mtx.gz


title: REC-1, DMSO, ATAC, Repeat 1


title: 2018_0821_Qg1


title: Kidney C_95

value: Yes


title: 2018_0725_Qg3


title: Kidney C_97


title: 2018_0725_Qg2


title: 2018_0821_Qg2


title: Kidney C_99


title: Kidney C_93


title: pLN, 1313259_03, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C10
pLN_1313259_03_barcodes.tsv.gz
pLN_1313259_03_features.tsv.gz
pLN_1313259_03_matrix.mtx.gz


title: pLN, 1313259_05, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: B1
pLN_1313259_05_barcodes.tsv.gz
pLN_1313259_05_features.tsv.gz
pLN_1313259_05_matrix.mtx.gz


title: Kidney C_92


title: 2018_0725_Qg1


title: pLN, 1313259_03, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A10
pLN_1313259_03_barcodes.tsv.gz
pLN_1313259_03_features.tsv.gz
pLN_1313259_03_matrix.mtx.gz


title: REC-1, DMSO, ATAC, Repeat 3

value: DMSO


title: Kidney C_89


title: Kidney C_86


title: Kidney C_88


title: pLN, 1313259_02, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A3
pLN_1313259_02_barcodes.tsv.gz
pLN_1313259_02_features.tsv.gz
pLN_1313259_02_matrix.mtx.gz

value: 86 Days


title: 2018_0627_Qg2


title: pLN, 1313259_03, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A10
pLN_1313259_03_barcodes.tsv.gz
pLN_1313259_03_features.tsv.gz
pLN_1313259_03_matrix.mtx.gz

value: NOD/ShiLtJ


title: Kidney C_82


title: pLN, 1313259_02, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C3
pLN_1313259_02_barcodes.tsv.gz
pLN_1313259_02_features.tsv.gz
pLN_1313259_02_matrix.mtx.gz

value: Female


title: Kidney C_79

value: Unknown


title: Kidney C_77


title: Kidney C_78


title: 2018_0627_Qg1


title: 2018_0821_Qg3


title: pLN, 1313259_02, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A3
pLN_1313259_02_barcodes.tsv.gz
pLN_1313259_02_features.tsv.gz
pLN_1313259_02_matrix.mtx.gz

value: pLN


title: Kidney C_76


title: Kidney C_74


title: Kidney C_70


title: Kidney C_75


title: pLN, 1313259_01, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A2
pLN_1313259_01_barcodes.tsv.gz
pLN_1313259_01_features.tsv.gz
pLN_1313259_01_matrix.mtx.gz


title: 2018_0627_Qg3


title: Kidney C_73


title: pLN, 1313259_01, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C2
pLN_1313259_01_barcodes.tsv.gz
pLN_1313259_01_features.tsv.gz
pLN_1313259_01_matrix.mtx.gz

value: TCR


title: Kidney C_63


title: Kidney C_62


title: Kidney C_61


title: pLN, 1313258_04, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A9
pLN_1313258_04_barcodes.tsv.gz
pLN_1313258_04_features.tsv.gz
pLN_1313258_04_matrix.mtx.gz

value: IgG2a Isotype


title: pLN, 1313259_01, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A2
pLN_1313259_01_barcodes.tsv.gz
pLN_1313259_01_features.tsv.gz
pLN_1313259_01_matrix.mtx.gz


title: Kidney C_5


title: 2018_0531_Qg3

value: leaf and bud


title: 2018_0531_Qg2


title: Kidney C_59


title: 2018_0501_Qg3


title: 2018_0501_Qg1


title: pLN, 1313258_04, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C9
pLN_1313258_04_barcodes.tsv.gz
pLN_1313258_04_features.tsv.gz
pLN_1313258_04_matrix.mtx.gz

value: 87 Days


title: Kidney C_58


title: 2018_0404_Qg3


title: 2018_0531_Qg1


title: 2018_0501_Qg2


title: pLN, 1313258_04, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A9
pLN_1313258_04_barcodes.tsv.gz
pLN_1313258_04_features.tsv.gz
pLN_1313258_04_matrix.mtx.gz


title: Kidney C_54


title: Kidney C_4


title: Kidney C_49


title: pLN, 1313258_03, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: E1
pLN_1313258_03_barcodes.tsv.gz
pLN_1313258_03_features.tsv.gz
pLN_1313258_03_matrix.mtx.gz


title: pLN, 1313258_03, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A8
pLN_1313258_03_barcodes.tsv.gz
pLN_1313258_03_features.tsv.gz
pLN_1313258_03_matrix.mtx.gz

value: ADT


title: Kidney C_47


title: pLN, 1313258_03, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A8
pLN_1313258_03_barcodes.tsv.gz
pLN_1313258_03_features.tsv.gz
pLN_1313258_03_matrix.mtx.gz


title: 2018_0404_Qg2


title: 2018_0404_Qg1


title: 2018_0309_Qg3


title: Kidney C_46


title: pLN, 1313258_01, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A1
pLN_1313258_01_barcodes.tsv.gz
pLN_1313258_01_features.tsv.gz
pLN_1313258_01_matrix.mtx.gz

value: TotalSeq-C0001 anti-mouse CD4, TotalSeq-C0002 anti-mouse CD8⍺, TotalSeq-C0073 anti-mouse CD44, TotalSeq-C0112 anti-mouse CD62L, TotalSeq-C0848 anti-mouse TIGIT


title: Kidney C_55

value: Kidney


title: 2018_0309_Qg1


title: Kidney C_399

value: NO


title: Kidney C_41


title: pLN, 1313258_01, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C1
pLN_1313258_01_barcodes.tsv.gz
pLN_1313258_01_features.tsv.gz
pLN_1313258_01_matrix.mtx.gz


title: Kidney C_394


title: pLN, 1313258_01, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A1
pLN_1313258_01_barcodes.tsv.gz
pLN_1313258_01_features.tsv.gz
pLN_1313258_01_matrix.mtx.gz

value: mRNA


title: Kidney C_393


title: 2018_0208_Qg3


title: Kidney C_53


title: Pancreas, 1313259_05, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: B3
Pan_1313259_05_barcodes.tsv.gz
Pan_1313259_05_features.tsv.gz
Pan_1313259_05_matrix.mtx.gz

source_name: Pancreas

value: Pancreas

value: 88 Days


title: 2018_0208_Qg2


title: 2018_0309_Qg2


title: Kidney C_38

value: Yes


title: Pancreas, 1313259_05, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: D3
Pan_1313259_05_barcodes.tsv.gz
Pan_1313259_05_features.tsv.gz
Pan_1313259_05_matrix.mtx.gz


title: Kidney C_388


title: Kidney C_390


title: Kidney C_51


title: Kidney C_387


title: Kidney C_42


title: Pancreas, 1313259_01, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A6
Pan_1313259_01_barcodes.tsv.gz
Pan_1313259_01_features.tsv.gz
Pan_1313259_01_matrix.mtx.gz

value: 86 Days


title: Kidney C_396


title: Pancreas, 1313259_05, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: B3
Pan_1313259_05_barcodes.tsv.gz
Pan_1313259_05_features.tsv.gz
Pan_1313259_05_matrix.mtx.gz

value: NOD/ShiLtJ


title: Kidney C_398


title: 2018_0114_Qg3


title: 2018_0114_Qg2


title: Kidney C_382


title: Kidney C_392


title: Pancreas, 1313259_01, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C6
Pan_1313259_01_barcodes.tsv.gz
Pan_1313259_01_features.tsv.gz
Pan_1313259_01_matrix.mtx.gz

value: Female


title: 2018_0114_Qg1


title: Kidney C_386


title: 2017_1213_Qg3


title: Kidney C_37


title: Pancreas, 1313259_01, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A6
Pan_1313259_01_barcodes.tsv.gz
Pan_1313259_01_features.tsv.gz
Pan_1313259_01_matrix.mtx.gz


title: 2017_1213_Qg2


title: Kidney C_389

value: Unknown


title: Kidney C_379


title: Kidney C_373


title: Pancreas, 1313258_05, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: B2
Pan_1313258_05_barcodes.tsv.gz
Pan_1313258_05_features.tsv.gz
Pan_1313258_05_matrix.mtx.gz


title: Kidney C_378


title: Pancreas, 1313258_05, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: D2
Pan_1313258_05_barcodes.tsv.gz
Pan_1313258_05_features.tsv.gz
Pan_1313258_05_matrix.mtx.gz


title: Kidney C_370


title: Kidney C_385


title: Kidney C_369


title: Kidney C_36


title: Kidney C_368


title: 2017_1213_Qg1


title: 2017_1115_Qg3


title: Pancreas, 1313258_05, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: B2
Pan_1313258_05_barcodes.tsv.gz
Pan_1313258_05_features.tsv.gz
Pan_1313258_05_matrix.mtx.gz


title: Kidney C_367


title: Kidney C_363


title: Pancreas, 1313258_02, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A5
Pan_1313258_02_barcodes.tsv.gz
Pan_1313258_02_features.tsv.gz
Pan_1313258_02_matrix.mtx.gz


title: Kidney C_35


title: Kidney C_366


title: 2017_1115_Qg1


title: Pancreas, 1313258_02, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C5
Pan_1313258_02_barcodes.tsv.gz
Pan_1313258_02_features.tsv.gz
Pan_1313258_02_matrix.mtx.gz


title: Kidney C_359


title: 2017_1018_Qg3


title: 2018_0208_Qg1


title: Kidney C_357


title: 2017_1018_Qg2


title: 2017_1115_Qg2


title: Kidney C_356


title: Kidney C_355


title: 2017_1018_Qg1


title: Pancreas, 1313258_01, ADT

description:
instrument model: NovaSeq X Plus
10x Genomics Cell Surface Protein Library
ADT: read1 file contains cell barcode and UMI; read2 file contains antibody derived tag reads
Dual Index Kit TN, Set A; Index ID: A4
Pan_1313258_01_barcodes.tsv.gz
Pan_1313258_01_features.tsv.gz
Pan_1313258_01_matrix.mtx.gz


title: Kidney C_348


title: Pancreas, 1313258_01, TCR

description:
instrument model: NovaSeq X Plus
10x Genomics V(D)J (5' v2 mRNA) Library
TCR: read1 file contains cell barcode and UMI; read2 file contains V(D)J-amplified transcripts
Dual Index Kit TT, Set A; Index ID: C4
Pan_1313258_01_barcodes.tsv.gz
Pan_1313258_01_features.tsv.gz
Pan_1313258_01_matrix.mtx.gz


title: Kidney C_347


title: Kidney C_346


title: Kidney C_345


title: Kidney C_344


title: ONC_NGF2,scRNAseq

city: Guangzhou

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

description: LNP-NGF injected+ ONC

data_processing:
Illumina BCL files were converted to fastq files by using 10X Genomics Cell Ranger pipeline mkfastq function
Cellranger count function was used to generate Gene-Barcode matrices from the FASTQ files, which uses the STAR algorithm to map high-quality reads to the human reference genome (mm9), then performs UMI counting.
Matrix table with raw gene-cell counts for every sample
Assembly: mm9
Supplementary files format and content: matrix  files

source_name: retina

extract_protocol:
Single cellsof retina tissueswere isolated by using Neuronal Isolation Enzyme (with papain)(Thermo Fisher,#88285)
The libraries were constructedusing the Chromium platform and Chromium Single Cell 3′ v2 chemistry. Briefly, cellular suspensions were loaded on a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA) forGEMs Generation and Barcoding.Single cell RNA-Seq libraries were prepared using the Chromium Single Cell Library Kit (10x Genomics, Pleasanton, CA).

treatment_protocol: Optic nerve entrapment was performed on ONC samples, and LNP-NGF was injected into the vitreous cavity of ONC_NGF samples and optic nerve entrapment was performed.

value: retina

value: Goblet cell

value: LNP-NGF injected+ ONC


title: 2017_0920_Qg2

value: leaf and bud


title: Pancreas, 1313258_02, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A5
Pan_1313258_02_barcodes.tsv.gz
Pan_1313258_02_features.tsv.gz
Pan_1313258_02_matrix.mtx.gz

value: IgG2a Isotype


title: Kidney C_340


title: 2017_0824_Qg3


title: Kidney C_342


title: ONC2,scRNAseq

description: ONC

value: ONC


title: 2017_0920_Qg1


title: Kidney C_33


title: Kidney C_338


title: Pancreas, 1313258_01, GEX

description:
instrument model: NovaSeq X Plus
10x Genomics GEX (5' v2 mRNA) Library
GEX: read1 file contains cell barcode and UMI; read2 file contains gene expression transcripts
Dual Index Kit TT, Set A; Index ID: A4
Pan_1313258_01_barcodes.tsv.gz
Pan_1313258_01_features.tsv.gz
Pan_1313258_01_matrix.mtx.gz


title: 2017_0824_Qg1


title: ONC1,scRNAseq

description: ONC


title: CTR2,scRNAseq


title: 2017_0920_Qg3


title: CTR1,scRNAseq


title: ONC_NGF1,scRNAseq

description: LNP-NGF injected+ ONC


title: Kidney C_354


title: Kidney C_332


title: 2017_0824_Qg2


title: Kidney C_335


title: KrTB-109

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was employed for basecalling.
The sequenced reads underwent trimming to eliminate low-quality bases and adapter sequences using cutadapt. Subsequently, these reads were mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
The extraction of raw read counts was accomplished through HTSeq-count v0.11.2.
Differential expression analysis was conducted using the BioJupies package at https://maayanlab.cloud/biojupies/
Assembly: mouse GRCm38
Supplementary files format and content: excel file including gene name, normalized log scale fold changes (KrTB+DOX vs. KrTB) for each gene

source_name: Tongue Epithelia

extract_protocol:
Qiagen's RNEasy Micro kit (Cat # 74004)
The preparation of RNA libraries utilized the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), following the protocols provided by the manufacturer. The libraries were sequenced with pair-end 51bp reads on the NovaSeq6000 sequencer.

treatment_protocol: Water and water+doxycycline (2 mg/mL)

value: Tongue epithelia tissue

value: KrTB+DOX


title: Kidney C_329

value: Kidney

value: NO


title: Kidney C_334


title: 2017_0726_Qg2


title: Kidney C_339


title: KrTB-108


title: Kidney C_336


title: 2017_0628_Qg3


title: KrTB-106


title: 2017_0726_Qg3


title: Kidney C_318


title: KrTB-104


title: Kidney C_319


title: Kidney C_31


title: Kidney C_317


title: Kidney C_32


title: 2017_0601_Qg3


title: 2017_0628_Qg1


title: Kidney C_316


title: KrTB-130

value: KrTB


title: 2017_0726_Qg1


title: Kidney C_325


title: 2017_0628_Qg2


title: Kidney C_310


title: Kidney C_324


title: KrTB-127


title: Kidney C_308


title: Kidney C_302


title: Kidney C_300


title: Kidney C_297


title: 2017_0601_Qg2


title: Kidney C_292


title: KrTB-121


title: mouse heart, WT_3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes row counts for each sample

value: heart

tag: genotype

value: WT


title: 2017_0503_Qg3


title: 2017_0601_Qg1


title: Kidney C_291


title: Kidney C_28

value: Yes


title: Kidney C_288


title: KrTB-128


title: 2017_0503_Qg2


title: Kidney C_284


title: Kidney C_283


title: mouse heart, WT_1


title: Kidney C_282


title: mouse heart, WT_2


title: 2017_0503_Qg1


title: Kidney C_279


title: Kidney C_280


title: Donor_4_Edited_2

city: South San Francisco

first: Dayue

last: Chen

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
Fourteen TotalSeq oligo-conjugated antibodies from Biolegend were used for cell-surface protein analysis
A minimum of 40 million paired-end read FASTQ files were processed by Tapestri Genome Editing Pipeline on the Genentech High Performance Computing (HPC).
Paired-end reads were trimmed by Cutadapt (22,23)to remove sequencing adaptors and discard short reads (< 30bp).
Trimmed reads were mapped to human hg38 reference genome by BWA-mem and cell calling was performed by Tapestri Cellfinder to split bam files per identified cell barcode
The cells are genotyped using the GATK (24)with a joint calling approach that follows GATK Best Practices recommendations
Assembly: hg38
Supplementary files format and content: tab-separated values
Library strategy: scDNA Amplicon and CITE-Seq

molecule: other

source_name: primary T-cells

extract_protocol:
Cryopreserved CGT products were thawed using 37 °C Prime XV media, followed by 3 washes with pre-warmed PBS at 37°C. Cell pellets were resuspended in Cell Staining Buffer (CSB, BioLegend, no. 420201), at 25,000 cells per μl in a total volume of 40 μl. The cell suspension was blocked using TruStain FcX (BioLegend) and Blocking Buffer (Mission Bio) for 15 min on ice and then stained with the pool of 14 oligo-conjugated antibodies for 30 min on ice followed by multiple washes with the CSB according to the Tapestri Single-Cell DNA + Protein Sequencing User Guide. Cells were counted and resuspended in Cell Buffer (Mission Bio) at 4,000 cells per μl and deposited on a Tapestri microfluidics cartridge
Single cells were encapsulated in the encapsulation oil (Mission Bio) with Lysis Buffer (Mission Bio) to create a cell emulsion. The cell-identifying barcode then integrated into each amplicon as part of a triple-primer PCR system. DNA PCR products were then isolated and purified with Ampure XP beads (Beckam Coulter) and the supernatants were kept to capture the protein library. 2 μl (5 μM) biotin oligo (Mission Bio) was added to the protein PCR product at 96 °C for 5 min followed by incubation on ice for 5 min. The protein PCR product is then extracted using Streptavidin beads (Mission Bio) followed by adding protein indices. Both DNA and protein libraries were purified by Ampure XP beads, and the final concentration measured by Qubit (1x high sensitivity dsDNA kit, Invitrogen). All libraries were quantified by Agilent 2100 bioanalyzer (DNA 1000 kit -Agilent Technologies)

value: primary T-cells


title: Kidney C_277


title: Kidney C_275


title: Donor_4_Edited_1


title: Donor_4_NC_2


title: Kidney C_274


title: Kidney C_272


title: Donor_3_NC_2


title: ApcMin, adjacent normal, biol rep5

city: College. Station

first: David

last: Threadgill

state: Texas

address: 400 Bizzell St

department: Cell Biology and Genetics

institute: Texas A&M University

data_processing:
Sequence reads were trimmed of adapter sequences and low-quality bases using Trimmomatic following the authors recommendations
Filtered reads were aligned to mouse assembly mm39 using HISAT2 version 2.2.1
Raw transcript counts were generated using HTSeq version 2.0.2
Read counts were normalized, and gene expression analyses were performed using DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text file contains raw counts

source_name: Adjacent non-tumor epithelium

growth_protocol: Mice were housed five per cage, fed Purina Mills Lab Diet 2919 and water ad libidum, and maintained at 22°C under a 12-hr light cycle

extract_protocol:
Total RNA from tumors and adjacent normal tissue was isolated using Maxwell LEV simplyRNA Tissue Kit (Promega AS1280) according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer's instructions

value: Adjacent non-tumor epithelium

tag: age

value: 100 days


title: Donor_3_NC_1


title: Kidney C_268


title: Kidney C_267


title: ApcMin, adjacent normal, biol rep2


title: Donor_4_NC_1


title: ApcMin, adjacent normal, biol rep3


title: Donor_3_Edited_2


title: Donor_3_Edited_1


title: ApcMin, adjacent normal, biol rep1


title: Kidney C_266


title: Kidney C_264


title: Kidney C_263


title: ApcMin, tumor, biol rep5

source_name: Colorectal tumor

value: Colorectal tumor


title: Kidney C_261


title: Donor_2_NC_1


title: Kidney C_262


title: Donor_2_NC_2


title: Kidney C_260


title: ApcMin, tumor, biol rep3


title: ApcMin, tumor, biol rep4


title: Kidney C_253

value: Unknown


title: ApcMin, tumor, biol rep2


title: Donor_2_Edited_1


title: Kidney C_255


title: Donor_2_Edited_2


title: Kidney C_245


title: Kidney C_25


title: Kidney C_265


title: ApcMin, tumor, biol rep1


title: Donor_1_NC_2


title: Kidney C_244


title: Erbb2-deficient ApcMin, adjacent normal, biol rep5


title: Kidney C_23


title: Kidney C_238


title: Kidney C_239


title: Erbb2-deficient ApcMin, adjacent normal, biol rep4


title: Donor_1_NC_1


title: Donor_1_Edited_2


title: Kidney C_237


title: Erbb2-deficient ApcMin, adjacent normal, biol rep2


title: Donor_1_Edited_1


title: Kidney C_223


title: Erbb2-deficient ApcMin, adjacent normal, biol rep3


title: SHAM replicate 5, human organoid

city: Baltimore

last: Hackam

state: MD

address: 1800 Orleans Street

department: Pediatric Surgery

description:
10x Genomics
processed_seurat.Rds

data_processing:
Alignment, filtering, barcode counting, and UMI counting were done with the count function of Cell Ranger 6.1.1.
All following steps performed in Seurat.
Assembly: GRCh38
Supplementary files format and content: UMI counts produced from cell ranger included as tab-separated value (TSV) files and matrices.
Supplementary files format and content: Fully processed Seurat also included as an R object (Rds).

source_name: intestinal organoid

extract_protocol:
Xenotransplants dissociated into single-cell suspension using Accumax (Sigma).
Library constructed by Johns Hopkins University School of Medicine Single Cell & Transcriptomics Core according to the manufacturers protocol. (3' Single Cell 10X Genomics)

value: intestinal organoid

value: SHAM


title: Kidney C_224


title: Kidney C_222


title: Kidney C_221


title: Kidney C_219


title: Kidney C_220


title: Kidney C_24


title: Kidney C_218


title: Kidney C_217


title: Erbb2-deficient ApcMin, tumor, biol rep5


title: SHAM replicate 4, human organoid

institute: Johns Hopkins University School of Medicine

description:
10x Genomics
processed_seurat.Rds


title: SHAM replicate 3-2, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Erbb2-deficient ApcMin, tumor, biol rep4


title: Kidney C_216


title: Kidney C_213


title: Kidney C_212


title: Kidney C_210


title: Erbb2-deficient ApcMin, adjacent normal, biol rep1


title: SHAM replicate 2, human organoid

description:
10x Genomics
processed_seurat.Rds


title: SHAM replicate 1, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Kidney C_199


title: Kidney C_201


title: Het_DOX_3

city: Shanghai

first: Fei

last: Xu

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: Heart

value: Otub1 +/-

value: DOX 2 weeks


title: SBS replicate 5, human organoid

description:
10x Genomics
processed_seurat.Rds

value: SBS


title: Erbb2-deficient ApcMin, tumor, biol rep3


title: Kidney C_197

value: Kidney


title: Kidney C_198

value: NO


title: Kidney C_196


title: Kidney C_214


title: Het_DOX_2


title: Kidney C_191


title: SBS replicate 3, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Het_DOX_1


title: Erbb2-deficient ApcMin, tumor, biol rep1


title: Kidney C_178


title: SHAM replicate 3-1, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Kidney C_179


title: WT_DOX_3

value: Otub1 +/+


title: SBS replicate 2, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Kidney C_177


title: SBS replicate 1, human organoid

description:
10x Genomics
processed_seurat.Rds


title: SBS replicate 4, human organoid

description:
10x Genomics
processed_seurat.Rds


title: Kidney C_174


title: Kidney C_172


title: Kidney C_168


title: BP-CTB_1344_11

city: La Jolla

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

description:
GeoMx spatial transcriptome sequencing
Normalized_Q3_Dataset2_060222_for_GEO.xlsx
Normalized_spatial_data.xlsx
rmorey_GNP_config.ini.txt
rmorey_LabWorksheet.csv
rmorey_SeqCodeIndices.csv

data_processing:
Fastq files were converted into DCC files following the GeoMx NGS pipeline
DCC files were uploaded to the GeoMx DSP to generate the initial, spatially resolved, dataset
Gene counts were mapped to specific ROIs and normalized using Q3 normalization strategy in keeping with NanoString GeoMx recommendations. (https://nanostring.com/resources/introduction-to-geomx-normalization-cta-whitepaper/)
dcc-metadata = false; save-interim-files = false; quality-trim-score = 20; 2color-trimming = True; adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; adapter-trim-match-length = 10; adapter-trim-max-mismatch = 3; barcode-max-mismatch = 1; stitching-max-mismatch = 2; dedup-hd = 1; threads = 4
Assembly: GRCh38
Supplementary files format and content: Normalized_Q3_Dataset2_060222_for_GEO.xlsx - excel file with segment, target, and BioProbe properties along with the count matrix
Supplementary files format and content: Normalized_spatial_data.xlsx - excel file with normalized count matrix
Supplementary files format and content: rmorey_GNP_config.ini.txt - text file with process information, AOI list and target barcodes
Supplementary files format and content: rmorey_LabWorksheet.csv - csv file with sample ID and metadata
Supplementary files format and content: .dcc - digital count files
Supplementary files format and content: rmorey_SeqCodeIndices.csv - csv file with sample ID and i7 and i5 indexes
Library strategy: Spatial Transcriptomics

source_name: Basal Plate placenta

extract_protocol:
Sections were deparaffinized and incubated overnight with the Whole Transcriptomic Assay UV-cleavable biological probes according to manufacturer’s instructions. Samples were stained with CONFIRM® anti-EGFR (5B7) Rabbit Monoclonal Primary Antibody  (Ventana #790-4347, 1:20 dilution) and anti-HLA-G (4H48) mouse primary antibody (Abcam #ab52455, 1:1000 dilution) for 2 hours followed by secondary staining for 1h with Alexa Fluor anti-rabbit-647 (Life Technologies, 1:500 dilution), Alexa Fluor anti-mouse-594 (Life Technologies, 1:500 dilution), and SYTO13 (Nanostring, 1:10 dilution) for nuclei staining. Slides were scanned on a GeoMx digital spatial profiler machine r. Based on the morphology markers, areas of interest (AOIs) containing at least EGFR+/HLA-G- 100 nuclei were manually selected.
Spatial transcriptomic libraries were prepared with GeoMx reagents according to the manufacturer’s protocol - Direct PCR

treatment_protocol: Normal formalin-fixed paraffin-embedded placental blocks at 6-week gestational age with visible embryonic sac were selected so that the basal and chorionic areas were identifiable. 5μm sections were mounted on SuperFrostTM Plus slides and used within 2 weeks.

value: Basal Plate placenta

tag: placenta block

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

value: stained for EGFR and HLA-g


title: Kidney C_320

tag: tissue

tag: delayed graft function

value: Yes

tag: person id


title: Kidney C_175


title: Kidney C_187


title: BP-CTB_1344_12

tag: cell type

tag: treatment


title: WT_DOX_1

tag: genotype


title: mouse, scRNAseq, 2

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

institute: Yale University

description: 10x genomics scRNA-seq

data_processing:
Assembly: mm39
Single cell RNA-seq library alignment to Ensembl GRCm39 (mouse) or ASM229v1 (opossum) and quality control was performed using 10x Genomics Cell Ranger 6.0.1 with default parameters (Zheng et al., 2017). CellRanger filtered matrices were then used for further filtering with SoupX (Young and Behjati, 2020) using the standard settings and no additional clustering data. Strained SoupX count matrices were used for all downstream analyses.
Supplementary files format and content: scRNA-seq: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: bulk RNA-seq: tab-delimited text files with FPKM values by gene

source_name: testis

extract_protocol:
Whole testis single cell suspension was diluted to 10,000 cells/mL and single cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Library Kit. Libraries were sequenced on an Illumina NovaSeq.
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.

value: testis

tag: strain

tag: age

value: adult


title: Kidney C_164


title: BP-CTB_1344_10

state: CA

tag: placenta block

tag: roi number

tag: area

tag: nucleicount


title: Kidney C_158


title: Kidney C_330


title: Kidney C_163


title: Kidney C_161


title: Kidney C_153


title: Kidney C_154


title: mouse, scRNAseq, 1

description: 10x genomics scRNA-seq


title: Kidney C_152


title: Kidney C_151


title: nuclear RNA Mettl3 CKO mESCs rep2

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

description: non-ribosome RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014), then aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0) with ‘--rna-strandness R -k 5’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq (Anders et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

source_name: Embryonic stem cells

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.

extract_protocol:
The nuclear fraction was separated and total RNA was purified by Trizol. Non-ribosome RNA was purified with RiboMinus transcriptome isolation kit.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
nuclear RNA-seq

value: mouse embryonic stem cells


title: BP-CTB_1344_6

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: WT_DOX_2


title: Kidney C_150


title: Kidney C_147


title: nuclear RNA Mettl3 Control mESCs rep1

description: non-ribosome RNA


title: Kidney C_148


title: Kidney C_146


title: BP-CTB_1344_5

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: nuclear RNA Mettl14 CKO mESCs rep2

description: non-ribosome RNA

tag: cell type


title: Kidney C_140

tag: tissue

tag: delayed graft function

tag: person id


title: BP-CTB_1344_8

tag: treatment


title: BP-CTB_1344_3

tag: placenta block


title: Kidney C_134


title: BP-CTB_1344_4

tag: roi number


title: nuclear RNA Mettl14 CKO mESCs rep1

description: non-ribosome RNA

tag: strain


title: Kidney C_132


title: Kidney C_139


title: Kidney C_128


title: BP-CTB_1344_2

tag: area

tag: nucleicount


title: nuclear RNA Mettl3 CKO mESCs rep1

description: non-ribosome RNA


title: BP-CTB_1344_1

tag: roicoordinatex

tag: roicoordinatey


title: Kidney C_125


title: Kidney C_121


title: nuclear RNA Mettl14 Control mESCs rep2

description: non-ribosome RNA


title: nuclear RNA Mettl14 Control mESCs rep1

description: non-ribosome RNA


title: nuclear RNA Mettl3 Control mESCs rep2

description: non-ribosome RNA


title: CP-CTB_1347_8

source_name: chorionic plate placenta

value: chorionic plate placenta

tag: rawreads

tag: alignedreads


title: Kidney C_120


title: Nasent RNA Eu 60min Mettl14 CKO mESCs rep2

description: nascent polyA RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014) and aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific)  HISAT (version 2.1.0) with ‘--rna-strandness R -k 5’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq (Anders et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

extract_protocol:
Total RNA was purified by Trizol and nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen). Before constructing libraries ERCC RNA spike-in control (Ambion) was added to each sample (0.01 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
nascent RNA-seq

treatment_protocol: Eight 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, 5-ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, 20 min and 10 min before trypsinization collection.

tag: eu treatment time (min)


title: ApcMin, adjacent normal, biol rep4

value: Adjacent non-tumor epithelium

tag: genotype

value: WT

tag: age

value: 100 days


title: Kidney C_118


title: Nasent RNA Eu 60min Mettl14 CKO mESCs rep1

description: nascent polyA RNA

tag: cell type


title: CP-CTB_1347_7

tag: tissue

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Kidney C_119

tag: delayed graft function

value: Unknown

tag: person id


title: Kidney C_115


title: Kidney C_129


title: CP-CTB_1347_6

tag: placenta block

tag: roi number

tag: area

tag: treatment


title: Nasent RNA Eu 30min Mettl14 CKO mESCs rep2

description: nascent polyA RNA

tag: strain


title: Kidney C_113


title: Kidney C_114