title: P21_C7D22 [RNA-Seq]

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

data_processing:
Adapters trimmed using Picard (paramters MarkIlluminaAdapters: ADAPTERS=PAIRED_END ADAPTERS=INDEXED  ADAPTERS=NEXTERA_V1 ADAPTERS=NEXTERA_V2 ADAPTERS=DUAL_INDEXED; parameters SamToFastq: CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2 INTERLEAVE=false NON_PF=true)
Reads aligned to GRCh38 primary assembly reference using STAR (parameters: --quantMode GeneCounts)
Count matrices obtained using Subreads' featureCounts (parameters: -B -T)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone Marrow

extract_protocol:
CD34+ cells from patients undergoing treatment with azacitidine were collected at two or four timepoints (pre-/post-treatment), and DNA and RNA extracted using the Qiagen AllPrep kit.
RNA was amplified using a SMARTer kit (Takara) and polyA selected mRNA sequencing libraries prepared and sequenced at NovogeneAIT Singapore

value: Bone Marrow

value: CD34+ HSPC

value: MDS

tag: group

value: responder

value: oral azacitidine x 21 days


title: THP-1, M0+LPS+IFN-γ+iMSCs, rep3

status: Public on Apr 01 2025

type: SRA

city: Beijing

first: Liang

last: Chen

address: No.22, Zhongguancun South Avenue, Haidian District

department: Department of Periodontology

country: China

institute: Peking University School and Hospital of Stomatology

description:
Library name: Sample 15
M1-CM-3

library_source: transcriptomic

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to human genome (GRCh38) using the Hisat2. HTseq was used to get gene counts and FPKM method was used to determine the gene expression.
Assembly: GRCh38
Supplementary files format and content: xlsx files for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: THP-1 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 0.05 nM 2-mercaptoethanol at 37°C in a 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent.
The cDNA libraries for each RNA sample were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China) following the manufacturer’s instructions

treatment_protocol: To induce differentiation into M0 macrophages, THP-1 cells were exposed to 100 ng/mL Phorbol 12-Myristate 13-Acetate (PMA) for 48 hours. Subsequently, PMA was removed by medium exchange, and M0 macrophages were polarized into the M1 phenotype by incubation with 20 ng/mL IFN-γ and 100 ng/mL LPS from P. gingivalis for an additional 48 hours. For the co-culture of macrophages with iMSCs, THP-1 cells were seeded at a density of 1 × 106 cells per well in six-well plates and differentiated into M0 macrophages using PMA. iMSCs were then plated in the upper chamber of Transwell inserts to establish a co-culture system. LPS and IFN-γ were added to the system to sustain the macrophage activation process for 48 hours.

tag: tissue

value: Peripheral blood

tag: cell line

tag: cell type

value: monocyte

tag: genotype

value: WT

tag: treatment

value: M0 macrophages co-cultured with iMSCs under LPS+IFN-γ stimulation for 48 hours


title: P3_100pM

city: Kansas City

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

country: USA

institute: University of Kansas Medical Center

data_processing:
After concatenation, fastq files were checked for QC using fastqc. Reads were aligned using hg38 and Bowtie2.
Assembly: hg38
Supplementary files format and content: Raw counts after alignment to hg38 using Bowtie2

source_name: T-cells

extract_protocol:
RNA was harvested at 72 hrs of activation of T-cells (Untreated and 100pM RTA-408 treated). Total RNA was extracted using RNeasy Plus Micro kit (Qiagen). 1.5ug of RNA was used for construction of sequencing libraries.
100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries.

value: T-cells


title: THP-1, M0 macrophages, rep2

description:
Library name: Sample 2
M0-2

value: Stimulated with PMA for 48 hours to differentiate into M0 macrophages


title: THP-1, M0 macrophages, rep1

description:
Library name: Sample 1
M0-1


title: P21_C1D8 [RNA-Seq]

molecule: polyA RNA

tag: disease

value: injected azacitidine x 7 days


title: P21_C1D1 [RNA-Seq]

value: Diagnosis


title: T24 cells, oeRNF112, rep3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: T24 cells were maintained in  RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: Tumor cells


title: P21_C7D1 [RNA-Seq]

value: injected azacitidine x 6 cycles plus with no drug


title: P1_100pM


title: THP-1, M0+iMSCs, rep4

description:
Library name: Sample 8
M0-CM-4

value: M0 macrophages co-cultured with iMSCs for 48 hours


title: T24 cells, oeRNF112, rep2


title: P13_C7D1 [RNA-Seq]


title: THP-1, M0+iMSCs, rep3

description:
Library name: Sample 7
M0-CM-3


title: Healthy control 1.1

city: Paris

first: Thomas

last: Poisot

address: 1 Avenue Claude Vellefaux

country: France

institute: INSERM

description:
HC1 was sequenced in two stages
count_matrix_HC1.csv

library_source: transcriptomic single cell

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed from raw FASTQ files to count matrices using Cytonaut v1.4 (https://cytonaut-scipio.bio) with Cytonaut's pre-processing module v6.12.6.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools double-checked by manual inspection.
The provided processed data is composed of one count matrix per sample at full sequencing depth.
Data post-processing (filtering, normalization, HVG, batch correction, PCA, 2D embedding, clustering, DGE) was performed using Seurat v4.3.0.1
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38). Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A; Species: Homo_sapiens; Genome Source: ensembl; Genome Version: GRCh38; Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/; Annotation Source: ensembl; Annotation Version: 99; Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Comma Separated Values (CSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: skin

extract_protocol:
Patients included were adults and had a diagnosis of histologically proven lGVHD from the dermatology and hematology departments of Saint Louis Hospital, Paris, France. Skin biopsies were obtained using 4 mm punch and normal skin were obtained from healthy donors undergoing breast plastic surgery. Skin biopsies were transferred in NaCl 9‰ and immediately digested for 4h30 at 37°C using whole skin dissociation kit (Miltenyi) according to the manufacturer protocol. Single cell suspension obtained was then processed with Asteria kit (Scipio Bioscience) with 30,000 cells input in 2 kits for each sample to generate 3' enriched cDNA with corresponding cell barcode.
The cell barcoded cDNA was fragmented, end-repaired then adapter was ligated to the extremities using NEBNext Ultra II FS DNA libary kit for illumina. Selective amplification of cDNA fragment containing the cell barcode was done with custum P5-R1 library primer from Asteria kit and indexed P7-R2 primier from NEBNext Mulitplex Oligos kit. Libraries were sequenced on the illumina NovaSeq 6000 sequencer to generate paired-end read. 25 bases for read1 and 70 bases for read2. read1 contains cell barcode and read2 contains 3' sequence of cDNA.

value: skin

value: Healthy


title: T24 cells, Vector, rep3

value: vector


title: P13_C1D8 [RNA-Seq]

value: Bone Marrow

value: CD34+ HSPC

value: MDS


title: T24 cells, Vector, rep1


title: chow4

city: Shanghai

first: Yinkun

last: Fu

address: chongqing Rd

department: school of medicine

institute: shanghai jiaotong university

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA were extracted from brown adipose tissue using  Trizol method.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Liver


title: T24 cells, Vector, rep2


title: P25_C1D1 [RNA-Seq]

value: AML

value: non-responder


title: chow3


title: P22_C7D1 [RNA-Seq]


title: chow2


title: chow1


title: P22_C7D22 [RNA-Seq]

value: oral azacitidine x 21 days


title: P22_C1D8 [RNA-Seq]


title: P25_C1D8 [RNA-Seq]


title: HFMCD4


title: P18_C1D8 [RNA-Seq]

value: responder


title: HFMCD3


title: P22_C1D1 [RNA-Seq]


title: P18_C1D1 [RNA-Seq]


title: T24 cells, oeRNF112, rep1


title: cKO_3

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

description: Library name: Sample 17

data_processing:
trimming with Cutadapt
mappping with RNA star
read counts measured with featureCounts
Differential gene expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: Excel file containing the results of the DEG_seq analysis

source_name: conditional KO animal 3

extract_protocol:
RNeasy kit (Qiagen)
PolyA enrichment

value: E12 Embryonic Cortex

value: Emx1 Cre/+; Zbtb7a fl/fl (cKO)


title: HFMCD2


title: HFMCD1


title: cKO_2

description: Library name: Sample 15

source_name: conditional KO animal 2


title: P17_C7D1 [RNA-Seq]


title: P17_C1D8 [RNA-Seq]

value: injected azacitidine x 7 days


title: P17_C1D1 [RNA-Seq]

value: Diagnosis


title: cKO_1

description: Library name: Sample 13

source_name: conditional KO animal 1


title: P13_C7D22 [RNA-Seq]


title: cHet_3

description: Library name: Sample 11

source_name: conditional heterozygous animal 3

value: Emx1 Cre/+; Zbtb7a fl/+ (cHet)


title: cHet_2

description: Library name: Sample 9

source_name: conditional heterozygous animal 2


title: P15_C7D1 [RNA-Seq]

value: injected azacitidine x 6 cycles plus with no drug


title: P15_C7D22 [RNA-Seq]


title: WT_3

description: Library name: Sample 5

source_name: Wildtype animal 3

value: Emx1 Cre/ +; Zbtb7a +/+ (WT)


title: WT_2

description: Library name: Sample 2

source_name: Wildtype animal 2


title: P15_C1D8 [RNA-Seq]


title: P28_C1D8 [RNA-Seq]


title: WT_1

description: Library name: Sample 1

source_name: Wildtype animal 1


title: P28_C1D1 [RNA-Seq]


title: P01_C1D8 [RNA-Seq]


title: ATAC-seq, round sperm, Daxx knockdown, biol rep2

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

description: Library name: Sample 31

library_source: genomic

data_processing:
Quality assessment and adaptor sequences removement of raw data were using Trim Galore (parameters: --paired --length 25 --clip_R1 15 --clip_R2 15)，reads were aligned to the UCSC mm39 genome using Bowtie2(2.5.4). Duplicated reads were also removed using Sambamba(1.0.1). Peak calling was performed using MACS2 (v2.2.7.1) , and annotation was carried out using HOMER(5.1)
Assembly: UCSC mm39
Supplementary files format and content: narrowPeak file includes peaks information for each Sample

molecule: genomic DNA

source_name: testis

extract_protocol:
We collected meiosis cells and RS from adult mice via FACS , and cells were washed twice with cold PBS. To prepare nuclei, cells were lysed with cold lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40], maintained on ice for 10 min, and centrifuged at 500g for 5 min at 4°C.
After carefully removing the suspension, we resuspended the pellet in the transposase reaction mix (TD501, Vazyme) and incubated it at 37°C for 10 min. Fragments were then immediately purified with ATAC DNA Extract Beads, and library amplification was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

value: testis

value: round sperm

value: DAXX knockdown


title: ATAC-seq, round sperm, Daxx knockdown, biol rep3

description: Library name: Sample 32


title: P01_C1D1 [RNA-Seq]

value: Bone Marrow

value: CD34+ HSPC


title: ATAC-seq, round sperm, Daxx knockdown, biol rep1

description: Library name: Sample 30


title: P14_C1D8 [RNA-Seq]


title: P13_C1D1 [RNA-Seq]

value: MDS


title: P17_C7D22 [RNA-Seq]


title: ATAC-seq, round sperm, Wild type, biol rep3

description: Library name: Sample 29

value: WT


title: P14_C1D1 [RNA-Seq]

value: AML


title: P16_C7D22 [RNA-Seq]

value: CMML

value: non-responder

value: oral azacitidine x 21 days


title: ATAC-seq, round sperm, Wild type, biol rep2

description: Library name: Sample 28


title: P16_C7D1 [RNA-Seq]


title: ATAC-seq, round sperm, Wild type, biol rep1

description: Library name: Sample 27


title: P16_C1D8 [RNA-Seq]


title: cHet_1

description: Library name: Sample 7

source_name: conditional heterozygous animal 1

value: E12 Embryonic Cortex


title: P16_C1D1 [RNA-Seq]


title: ATAC-seq, meiotic cells, Daxx knockdown, biol rep2

description: Library name: Sample 25

value: meiotic cells


title: ATAC-seq, meiotic cells, Daxx knockdown, biol rep3

description: Library name: Sample 26


title: ATAC-seq, meiotic cells, Daxx knockdown, biol rep1

description: Library name: Sample 24


title: P15_C1D1 [RNA-Seq]

value: responder

value: Diagnosis


title: ATAC-seq, meiotic cells, Wild type, biol rep2

description: Library name: Sample 22


title: ATAC-seq, meiotic cells, Wild type, biol rep3

description: Library name: Sample 23


title: P10_C7D1 [RNA-Seq]

value: injected azacitidine x 6 cycles plus with no drug


title: P10_C1D8 [RNA-Seq]

value: injected azacitidine x 7 days


title: P10_C1D1 [RNA-Seq]


title: ATAC-seq, meiotic cells, Wild type, biol rep1

description: Library name: Sample 21

value: testis


title: P10_C7D22 [RNA-Seq]


title: smallRNA-seq, round sperm, Daxx knockdown, biol rep2

description: Library name: Sample 20

data_processing:
Adaptor sequences were removed from 3′ end of the raw fastq file using cutadapt with parameters(-m 16 --trimmed-only). Then these reads were aligned to non-coding RNAs, piRNA clusters,  genomic transposable element sequences retrieved from RepeatMasker and  mouse genome(UCSC mm39)
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited txt file includes the sequence, length, count, annotation, sample ID, and condition of small RNAs identified in this study.

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively.
Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between18~40 bp were ready for sequencing.

value: round sperm


title: smallRNA-seq, round sperm, Daxx knockdown, biol rep1

description: Library name: Sample 19

value: DAXX knockdown


title: P09_C7D22 [RNA-Seq]

value: Bone Marrow


title: smallRNA-seq, meiotic cells, Daxx knockdown, biol rep2

description: Library name: Sample 16


title: P09_C7D1 [RNA-Seq]

value: CD34+ HSPC


title: smallRNA-seq, round sperm, Wild type, biol rep2

description: Library name: Sample 18


title: P09_C1D1 [RNA-Seq]

value: MDS


title: smallRNA-seq, round sperm, Wild type, biol rep1

description: Library name: Sample 17

value: WT


title: P38_C1D1 [RNA-Seq]


title: P09_C1D8 [RNA-Seq]


title: smallRNA-seq, meiotic cells, Daxx knockdown, biol rep1

description: Library name: Sample 15


title: P27_C1D8 [RNA-Seq]


title: P27_C1D1 [RNA-Seq]


title: P04_C1D8 [RNA-Seq]

value: AML


title: P04_C1D1 [RNA-Seq]


title: P19_C1D8 [RNA-Seq]

value: CMML


title: P38_C1D8 [RNA-Seq]

value: non-responder


title: P24_C1D1 [RNA-Seq]


title: Bone marrow, mRNA vaccine, Biol rep2

city: Seoul

first: Jae-Hun

last: Ahn

address: Daehak-ro 101, Jongro-gu

department: Biomedical Research Institute

country: South Korea

institute: Seoul National Universty Hospital

description:
Library name: 69TIIIF043
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the custom reference using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: The reference genome sequence is Mus musculus (mm10) from the NCBI Genome assembly with an added SARS-CoV2 Spike protein sequence.
Supplementary files format and content: TAB file including FPKMTPM

source_name: Bone marrow (Femur)

growth_protocol: Six-week-old CrlOri:CD1(ICR) female mice (Specific Pathogen Free condition) were used for this expermient.

extract_protocol:
Total RNA was extracted by RNeasy Plus mini kit (QIAGEN).
A library was independently prepared with 0.5ug of total RNA for each sample by Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., San Diego, CA, USA, #20020599)

treatment_protocol: A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, bone marrow tissue was harvested from the left side femur followed by RBC lysed and kept in RNAlater at -80°C

value: Bone marrow (Femur)

value: mRNA vaccine


title: Bone marrow, LNP, Biol rep 1

description:
Library name: 69TIIF037
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue

value: LNP


title: Bone marrow, mRNA vaccine, Biol rep1

description:
Library name: 69TIIIF042
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: Bone marrow, LNP, Biol rep 2

description:
Library name: 69TIIF038
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: P24_C1D8 [RNA-Seq]


title: Bone marrow, LNP, Biol rep 3

description:
Library name: 69TIIF039
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: Bone marrow, mRNA vaccine, Biol rep3

description:
Library name: 69TIIIF044
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: Bone marrow, mRNA, Biol rep 3

description:
Library name: 69TIF035
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue

value: mRNA


title: Bone marrow, mRNA, Biol rep 2

description:
Library name: 69TIF033
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: P21_C7D1

data_processing:
Raw RRBS data in fastq format were quality and adapter trimmed according to the manufacturer’s guide using trim_galore (0.6.4) and a custom trimming script.
The trimmed fastq files were then aligned to a bisulfite converted genome (hg38) using Bismark (0.22.3) and methylation status at each CpG locus were extracted.
Bigwig files were generated using ucsc bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: Coverage file from bismark containing genomic location, sequencing coverage and number of methylated/unmethylated Cytosines.

extract_protocol:
CD34+ cells from patients undergoing treatment with azacitidine were collected at two or four timepoints (pre-/post-treatment), and DNA and RNA extracted using the Qiagen AllPrep kit.
RRBS libraries were constructed from 50ng genomic DNA using an Ovation RRBS Methyl-Seq system (Tecan). Bisulphite conversion was performed using the Epitect Fast DNA Bisulfite kit (Qiagen) and libraries amplified using the Ovation RRBS Methyl-Seq system (Tecan).

value: responder


title: P21_C7D22

value: oral azacitidine x 21 days


title: Bone marrow, mRNA, Biol rep 1

description:
Library name: 69TIF031
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: Bone marrow, D-PBS, Biol rep 3

description:
Library name: 69CF029
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue

value: D-PBS


title: P21_C1D1

value: Diagnosis


title: P13_C7D22


title: P13_C7D1

value: injected azacitidine x 6 cycles plus with no drug


title: smallRNA-seq, meiotic cells, Wild type, biol rep2

description: Library name: Sample 14

value: testis

value: meiotic cells


title: CFPSS2_rep

city: New York

first: Ryan

middle: D

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

description:
Library name: CFPSS2_rep
10x Genomics

data_processing:
Raw paired-end reads were processed using Cell Ranger v.7.0.0 to map reads to the mm10 genome in intron mode.
Counts matrices where then filtered and analyzed with Seurat as described in Methods.
Assembly: Assembly: mm10 reference genome
Supplementary files format and content: WT_SS_CFPSS_Figure5.rds is an rds file loadable in Seurat containing the subset of cells used in Figure 5 and S6.

source_name: GI tract, small intestine to colon

growth_protocol: Ednrb-s/s male mice were crossed to Ret-CFP/+ Ednrb-s/+ female mice and resulting progeny were collected at sample timepoints embryonic day post coital 14.5 (E14.5).

extract_protocol:
Entire intestine from stomach to anal pore (E14.5) was collected from embryos, rinsed in 1X PBS, and singularized into individual cells using Accumax and mechanical pipetting. Cells were then turned into scRNA-Seq libraries using standard 10X Genomics 3' scRNA-Seq protocols. For P0, tissue was dissected, rinsed in cold 1X PBS, and snap-frozen in liquid N2. Single nuclei were then isolated using 10X Chromium single nuclei isolation kit. 20k nuclei were then used as input into the standard 10X Genomics scRNA-Seq library pipeline.
3' 10X Genomics

value: GI tract, small intestine to colon

tag: mouse line

value: Ret-CFP/+ Ednrb-s/s

tag: Sex

value: female

tag: time


title: Bone marrow, D-PBS, Biol rep 2

description:
Library name: 69CF028
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue


title: smallRNA-seq, meiotic cells, Wild type, biol rep1

description: Library name: Sample 13

value: WT


title: P13_C1D8

source_name: Bone Marrow

value: Bone Marrow

value: CD34+ HSPC

value: MDS

value: injected azacitidine x 7 days


title: CFPSS1_rep

description:
Library name: CFPSS1_rep
10x Genomics


title: P19_C1D1 [RNA-Seq]

value: CMML


title: P13_C1D1


title: P25_C1D8

value: AML

value: non-responder


title: CFPSS2

description:
Library name: CFPSS2
10x Genomics


title: P25_C1D1


title: SS2

description:
Library name: SS2
10x Genomics

value: Ednrb-s/s


title: SS1

description:
Library name: SS1
10x Genomics


title: CFPSS1

description:
Library name: CFPSS1
10x Genomics


title: P22_C7D1


title: P22_C1D1


title: WSB/EiJ, female, Sham-c

city: East Orange

first: Bruce

middle: A.

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

description:
Library name: 287
Column name in BlastStrainsRPKMs.xlsx

data_processing:
CLC Genomics Workbench v. 20.0.3
Assembly: Mus musculus C57BL/6J (GRCm39)
Supplementary files format and content: Excel file with raw RPKM for each sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated with an Rneasy Mini Plus Kit (Qiagen)
NEBNext Ultra RNA library prep kit for Illumina (New England BioLabs)

value: hippocampus

tag: strain

value: WSB/EiJ

value: Sham


title: WSB/EiJ, female, Blast-b

description:
Library name: 286
Column name in BlastStrainsRPKMs.xlsx

value: Blast


title: WSB/EiJ, male, Blast-c

description:
Library name: 289
Column name in BlastStrainsRPKMs.xlsx

value: male


title: WSB/EiJ, female, Blast-c

description:
Library name: 288
Column name in BlastStrainsRPKMs.xlsx


title: P22_C1D8


title: P18_C1D1

value: responder

value: Diagnosis


title: WSB/EiJ, female, Sham-b

description:
Library name: 285
Column name in BlastStrainsRPKMs.xlsx

value: female


title: P21_C1D8


title: P18_C1D8


title: P17_C7D1

value: injected azacitidine x 6 cycles plus with no drug


title: Bone marrow, D-PBS, Biol rep 1

description:
Library name: 69CF027
To quantify the Spike protein-coding mRNA levels, Spike protein coding sequence was also detected in bone marrow tissue

value: Bone marrow (Femur)

value: D-PBS


title: WSB/EiJ, male, Blast-b

description:
Library name: 282
Column name in BlastStrainsRPKMs.xlsx


title: P17_C1D1

value: Bone Marrow

value: CD34+ HSPC

value: MDS


title: P17_C1D8

value: injected azacitidine x 7 days


title: WSB/EiJ, female, Sham-a

description:
Library name: 283
Column name in BlastStrainsRPKMs.xlsx


title: WSB/EiJ, female, Blast-a

description:
Library name: 284
Column name in BlastStrainsRPKMs.xlsx


title: WSB/EiJ, male, Sham-c

description:
Library name: 281
Column name in BlastStrainsRPKMs.xlsx


title: P15_C7D1


title: WSB/EiJ, male, Sham-b

description:
Library name: 279
Column name in BlastStrainsRPKMs.xlsx


title: P22_C7D22

value: AML

value: non-responder

value: oral azacitidine x 21 days


title: WSB/EiJ, male, Blast-a

description:
Library name: 278
Column name in BlastStrainsRPKMs.xlsx

value: hippocampus

value: WSB/EiJ


title: P15_C1D8


title: P15_C1D1


title: P28_C1D8


title: P28_C1D1


title: P17_C7D22


title: PWK/PhJ, female, Blast-c

description:
Library name: 276
Column name in BlastStrainsRPKMs.xlsx

value: PWK/PhJ

value: Blast


title: PWK/PhJ, female, Sham-b

description:
Library name: 273
Column name in BlastStrainsRPKMs.xlsx

value: Sham


title: P01_C1D8

value: responder


title: P16_C7D22

value: CMML


title: PWK/PhJ, male, Blast-c

description:
Library name: 270
Column name in BlastStrainsRPKMs.xlsx

value: male


title: P14_C1D1

value: Diagnosis


title: P01_C1D1


title: PWK/PhJ, female, Sham-a

description:
Library name: 271
Column name in BlastStrainsRPKMs.xlsx

value: female


title: PWK/PhJ, female, Blast-b

description:
Library name: 274
Column name in BlastStrainsRPKMs.xlsx


title: PWK/PhJ, female, Blast-a

description:
Library name: 272
Column name in BlastStrainsRPKMs.xlsx


title: PWK/PhJ, male, Sham-c

description:
Library name: 269
Column name in BlastStrainsRPKMs.xlsx


title: P14_C1D8

value: Bone Marrow


title: P16_C1D8

value: CD34+ HSPC


title: P15_C7D22

value: MDS


title: PWK/PhJ, male, Blast-b

description:
Library name: 268
Column name in BlastStrainsRPKMs.xlsx


title: P16_C7D1

value: injected azacitidine x 6 cycles plus with no drug


title: PWK/PhJ, male, Sham-b

description:
Library name: 267
Column name in BlastStrainsRPKMs.xlsx


title: P16_C1D1


title: P10_C7D22


title: PWK/PhJ, male, Blast-a

description:
Library name: 266
Column name in BlastStrainsRPKMs.xlsx


title: WSB/EiJ, male, Sham-a

description:
Library name: 277
Column name in BlastStrainsRPKMs.xlsx


title: P10_C7D1


title: PWK/PhJ, male, Sham-a

description:
Library name: 265
Column name in BlastStrainsRPKMs.xlsx


title: P10_C1D8

value: injected azacitidine x 7 days


title: PWK/PhJ, female, Sham-c

description:
Library name: 275
Column name in BlastStrainsRPKMs.xlsx


title: CAST/EiJ, female, Blast-b

description:
Library name: 262
Column name in BlastStrainsRPKMs.xlsx

value: CAST/EiJ


title: P10_C1D1


title: CAST/EiJ, female, Sham-c

description:
Library name: 263
Column name in BlastStrainsRPKMs.xlsx


title: P38_C1D8

value: non-responder


title: CAST/EiJ, male, Blast-c

description:
Library name: 258
Column name in BlastStrainsRPKMs.xlsx

value: hippocampus


title: P38_C1D1


title: P09_C7D1


title: CAST/EiJ, female, Blast-a

description:
Library name: 260
Column name in BlastStrainsRPKMs.xlsx


title: P09_C7D22

value: oral azacitidine x 21 days


title: CAST/EiJ, female, Sham-b

description:
Library name: 261
Column name in BlastStrainsRPKMs.xlsx


title: CAST/EiJ, male, Sham-c

description:
Library name: 257
Column name in BlastStrainsRPKMs.xlsx


title: P09_C1D8


title: P09_C1D1


title: CAST/EiJ, female, Sham-a

description:
Library name: 259
Column name in BlastStrainsRPKMs.xlsx


title: P27_C1D1


title: CAST/EiJ, male, Sham-b

description:
Library name: 255
Column name in BlastStrainsRPKMs.xlsx


title: P04_C1D8

value: AML


title: CAST/EiJ, male, Blast-b

description:
Library name: 256
Column name in BlastStrainsRPKMs.xlsx

value: Blast


title: CAST/EiJ, male, Blast-a

description:
Library name: 254
Column name in BlastStrainsRPKMs.xlsx


title: CAST/EiJ, male, Sham-a

description:
Library name: 253
Column name in BlastStrainsRPKMs.xlsx

value: Sham


title: P04_C1D1

value: responder


title: CAST/EiJ, female, Blast-c

description:
Library name: 264
Column name in BlastStrainsRPKMs.xlsx


title: P19_C1D8

value: CMML


title: 129S1/SvlmJ, female, Blast-c

description:
Library name: 252
Column name in BlastStrainsRPKMs.xlsx


title: 129S1/SvlmJ, female, Sham-b

description:
Library name: 249
Column name in BlastStrainsRPKMs.xlsx


title: P19_C1D1


title: 129S1/SvlmJ, female, Sham-c

description:
Library name: 251
Column name in BlastStrainsRPKMs.xlsx


title: 129S1/SvlmJ, female, Sham-a

description:
Library name: 247
Column name in BlastStrainsRPKMs.xlsx


title: P24_C1D8


title: 6237, 4 regional samples, snRNAseq

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

country: Canada

institute: Princess Margaret Cancer Centre

description: Combinatorial indexing, sample information for each cell listed in sample column in plate1_cell_metadata.csv

data_processing:
Sample demultiplexing, cell barcode demultiplexing, read alignment, gene count aggregation were conducted using SplitPipe v1.0.4
Assembly: hg38
Supplementary files format and content: Matrix files and comma-separated value file

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei were dissociated from frozen tissue using Chromium Nuclei Isolation Kit (10x Genomics; PN-1000493). Tissue was dissociated using a pestle in a pre-chilled dissociation tube containing lysis buffer, and the mixture was then filtered through a Nuclei Isolation Column. The flow-through was collected, vortexed, and subsequently resuspended in Debris Removal Buffer, followed by repetitive washing to collect the nuclei pellet for subsequent nuclei fixation.
Nuclei barcoding, cDNA preparation and library construction were performed following the Evercode WT User Manual (Parse Biosciences). Fixed and permeabilized nuclei were loaded into 12 wells of the Round 1 Plate. RNA was reverse transcribed with oligo(dT) and random hexamer primers containing a well-specific barcode. The nuclei were pooled and loaded into the Round 2 Plate to ligate the second well-specific barcode adapter. The process was repeated for the Round 3 Plate to ligate the third well-specific barcode adapter with an additional Illumina R2 sequence and biotin. After 3 rounds of barcoding, the nuclei were split into sub-libraries and lysed. Biotinylated cDNA was captured via streptavidin beads and the TSO adapter via template switch reaction. The  cDNAThe cDNA was amplified with primers specific to R2 and TSO, and fragmented following end-repair and A-tailing. The Illumina TruSeq R1 adapter was ligated to the 5’ of cDNA. The sequencing library was amplified for Round 4 barcoding to add P5 and P7 adapters via the UDI-WT Plate. 6234, 6240, 6245 were processed following similar process as described in Evercode WT mini Usermini User Manual.

value: brain

value: GBM patient


title: SS1_rep

description:
Library name: SS1_rep
10x Genomics

value: GI tract, small intestine to colon

value: Ednrb-s/s

value: female


title: 129S1/SvlmJ, female, Blast-b

description:
Library name: 250
Column name in BlastStrainsRPKMs.xlsx


title: 129S1/SvlmJ, male, Blast-b

description:
Library name: 244
Column name in BlastStrainsRPKMs.xlsx

value: male


title: 129S1/SvlmJ, male, Sham-a

description:
Library name: 241
Column name in BlastStrainsRPKMs.xlsx


title: shHELLS-2, G4-ChIP, rep1

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
Raw reads of ChIP-seq data were aligned to human hg38 reference genome using Bowtie2 (v2.4.5)9. Heatmap and metagene profile were generated by deeptools (v3.5.1)10 plotHeatmap and plotProfile, respectively. Genome coverage bigwig files for Integrative Genomics Viewer visualization were generated by deeptools (v3.5.1)10 bamCoverage using RPKM for the normalization.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
G4-ChIP was conducted by following previously described procedures with slight modifications, using the custom-purified BG4 antibody7. Briefly, the chromatin samples were sonicated and diluted in a blocking buffer containing 25 mM HEPES (pH 7.5), 10.5 mM NaCl, 110 mM KCl, 1 mM MgCl2, and 1% BSA, and treated with RNase A. Subsequently, the chromatin samples were incubated with 500 ng of the BG4 antibody under rotation at 1400 rpm for 1.5 hr at 16°C. Pre-blocked Anti-Flag M2 magnetic beads (Sigma, M8823) were added to the mixture, which was then incubated under the same conditions for 1 hr. After washing the beads with ice-cold washing buffer (10 mM Tris, pH 7.4, 100 mM KCl, 0.1% Tween 20) for 6 cycles, the DNA was eluted with TE buffer containing proteinase K while rotating at 1400 rpm for 6 hr at 65 °C. The eluted DNA was purified using the DNA Clean and Concentrator-5 kit (Zymo).
ChIP-seq library was prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB) following the manufacturer’s instruction.
The purified DNA libraries were subsequently quantified using an Agilent 2100 Bioanalyzer and multiplexed for sequencing at Genomics Research and Technology Hub (Nova-seq 6000, GRT Hub, UC Irvine) with 100-bp paired-end sequencing.

value: Human Bone Osteosarcoma Epithelial Cells

tag: chip antibody


title: 129S1/SvlmJ, female, Blast-a

description:
Library name: 248
Column name in BlastStrainsRPKMs.xlsx


title: 129S1/SvlmJ, male, Blast-c

description:
Library name: 246
Column name in BlastStrainsRPKMs.xlsx


title: shHELLS-2, G4-ChIP, rep3


title: 129S1/SvlmJ, male, Sham-c

description:
Library name: 245
Column name in BlastStrainsRPKMs.xlsx


title: P27_C1D8

value: Bone Marrow

value: CD34+ HSPC

value: MDS

value: injected azacitidine x 7 days


title: 129S1/SvlmJ, male, Sham-b

description:
Library name: 243
Column name in BlastStrainsRPKMs.xlsx

value: hippocampus


title: NZO/HlLtJ, female, Blast-c

description:
Library name: 240
Column name in BlastStrainsRPKMs.xlsx

value: NZO/HlLtJ


title: shHELLS-2, G4-ChIP, rep2


title: 6234, 6240, 4 regional samples, snRNAseq

description: Combinatorial indexing, sample information for each cell listed in sample column in plate2_cell_metadata.csv


title: NZO/HlLtJ, female, Sham-c

description:
Library name: 239
Column name in BlastStrainsRPKMs.xlsx


title: P24_C1D1

value: AML

value: non-responder

value: Diagnosis


title: 129S1/SvlmJ, male, Blast-a

description:
Library name: 242
Column name in BlastStrainsRPKMs.xlsx

value: Blast


title: shHELLS-1, G4-ChIP, rep3


title: NZO/HlLtJ, female, Blast-b

description:
Library name: 238
Column name in BlastStrainsRPKMs.xlsx


title: shHELLS-1, G4-ChIP, rep2


title: 6245, 3 regional samples, snRNAseq

description: Combinatorial indexing, sample information for each cell listed in sample column in plate3_cell_metadata.csv

value: brain


title: NZO/HlLtJ, female, Sham-b

description:
Library name: 237
Column name in BlastStrainsRPKMs.xlsx

value: Sham


title: shHELLS-2, G4-ChIP


title: NZO/HlLtJ, female, Blast-a

description:
Library name: 236
Column name in BlastStrainsRPKMs.xlsx


title: shCtrl, G4-ChIP, rep1


title: NZO/HlLtJ, female, Sham-a

description:
Library name: 235
Column name in BlastStrainsRPKMs.xlsx


title: shHELLS-1, G4-ChIP, rep1


title: shCtrl, G4-ChIP

description: Input-Ctrl


title: shCtrl, G4-ChIP, rep3


title: shCtrl, G4-ChIP, rep2


title: NZO/HlLtJ, male, Blast-c

description:
Library name: 234
Column name in BlastStrainsRPKMs.xlsx


title: SK-N-BE(2),shBCAT1#2,rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells


title: shHELLS-1, G4-ChIP


title: NZO/HlLtJ, male, Sham-c

description:
Library name: 233
Column name in BlastStrainsRPKMs.xlsx


title: NZO/HlLtJ, male, Sham-b

description:
Library name: 231
Column name in BlastStrainsRPKMs.xlsx


title: SK-N-BE(2),shControl,rep1

value: shNC


title: D4_Dox_ATAC_r2

city: Boston

first: Danyang

state: Massachusetts

address: 300 longwood ave

department: Cardiology

institute: Boston Children's Hospital

description:
D4_D1_filtered_peak_bc_matrix.h5
D4_D1_fragments.tsv.gz
D4_D1_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
scRNA FASTQ files were processed with the 10× Genomics CellRanger pipeline
scATAC FASTQ files were processed with the 10× Genomics CellRanger ATAC pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files

source_name: iPSC

extract_protocol:
scRNA libraries and scATAC libraries were prepared according to the 10x genomics protocol
scRNA library was generated according to manufacturer’s protocol (10× Genomics Chromium Single Cell 3′ Library v3.1). scATAC library was generated according to manufacturer’s protocol (10× Genomics Chromium Single Cell ATAC Kit v2).

value: iPSC

value: induced pluripotent stem cells

tag: day

value: Dox


title: NZO/HlLtJ, male, Sham-a

description:
Library name: 229
Column name in BlastStrainsRPKMs.xlsx

value: male


title: SK-N-BE(2),shBCAT1#2,rep1


title: NZO/HlLtJ, male, Blast-a

description:
Library name: 230
Column name in BlastStrainsRPKMs.xlsx


title: A/J, female, Blast-c

description:
Library name: 228
Column name in BlastStrainsRPKMs.xlsx

value: A/J

value: female


title: SK-N-BE(2),shControl,rep2


title: NZO/HlLtJ, male, Blast-b

description:
Library name: 232
Column name in BlastStrainsRPKMs.xlsx


title: D4_ctrl_ATAC_r2

description:
D4_C1_filtered_peak_bc_matrix.h5
D4_C1_fragments.tsv.gz
D4_C1_fragments.tsv.gz.tbi

value: control


title: A/J, female, Sham-c

description:
Library name: 227
Column name in BlastStrainsRPKMs.xlsx

value: hippocampus


title: A/J, female, Sham-b

description:
Library name: 225
Column name in BlastStrainsRPKMs.xlsx


title: SK-N-BE(2),shBCAT1#1,rep2


title: D3_5_ctrl_ATAC_r2

description:
D35_C1_filtered_peak_bc_matrix.h5
D35_C1_fragments.tsv.gz
D35_C1_fragments.tsv.gz.tbi


title: A/J, female, Blast-b

description:
Library name: 226
Column name in BlastStrainsRPKMs.xlsx


title: A/J, female, Blast-a

description:
Library name: 224
Column name in BlastStrainsRPKMs.xlsx


title: D2_ATAC_r2

description:
D2_1_filtered_peak_bc_matrix.h5
D2_1_fragments.tsv.gz
D2_1_fragments.tsv.gz.tbi


title: D3_5_Dox_ATAC_r2

description:
D35_D1_filtered_peak_bc_matrix.h5
D35_D1_fragments.tsv.gz
D35_D1_fragments.tsv.gz.tbi


title: A/J, male, Blast-c

description:
Library name: 222
Column name in BlastStrainsRPKMs.xlsx


title: A/J, female, Sham-a

description:
Library name: 223
Column name in BlastStrainsRPKMs.xlsx


title: D3_ctrl_ATAC_r1

description:
D3_C1_filtered_peak_bc_matrix.h5
D3_C1_fragments.tsv.gz
D3_C1_fragments.tsv.gz.tbi


title: A/J, male, Sham-b

description:
Library name: 219
Column name in BlastStrainsRPKMs.xlsx


title: SK-N-BE(2),shBCAT1#1,rep1


title: A/J, male, Sham-c

description:
Library name: 221
Column name in BlastStrainsRPKMs.xlsx


title: D3_Dox_ATAC_r1

description:
D3_D1_filtered_peak_bc_matrix.h5
D3_D1_fragments.tsv.gz
D3_D1_fragments.tsv.gz.tbi


title: D2_ATAC_r1


title: D3_5_Dox_ATAC_r1


title: D4_ctrl_ATAC_r1


title: A/J, male, Sham-a

description:
Library name: 217
Column name in BlastStrainsRPKMs.xlsx


title: D3_5_ctrl_ATAC_r1


title: NOD/ShiLtJ, female, Blast-c

description:
Library name: 216
Column name in BlastStrainsRPKMs.xlsx

value: NOD/ShiLtJ


title: A/J, male, Blast-a

description:
Library name: 218
Column name in BlastStrainsRPKMs.xlsx


title: NOD/ShiLtJ, female, Blast-b

description:
Library name: 214
Column name in BlastStrainsRPKMs.xlsx


title: D4_Dox_ATAC_r1

description:
D4_D1_filtered_peak_bc_matrix.h5
D4_D1_fragments.tsv.gz
D4_D1_fragments.tsv.gz.tbi


title: NOD/ShiLtJ, female, Sham-b

description:
Library name: 213
Column name in BlastStrainsRPKMs.xlsx


title: NOD/ShiLtJ, female, Sham-c

description:
Library name: 215
Column name in BlastStrainsRPKMs.xlsx


title: Dox_D4_RNA_r2


title: Dox_D3_RNA_r2


title: A/J, male, Blast-b

description:
Library name: 220
Column name in BlastStrainsRPKMs.xlsx


title: Dox_D4_RNA_r1


title: NOD/ShiLtJ, female, Sham-a

description:
Library name: 211
Column name in BlastStrainsRPKMs.xlsx


title: Dox_D3_5_RNA_r2


title: NOD/ShiLtJ, male, Blast-c

description:
Library name: 210
Column name in BlastStrainsRPKMs.xlsx


title: Dox_D2_RNA_r2


title: Dox_D3_RNA_r1


title: NOD/ShiLtJ, male, Blast-b

description:
Library name: 208
Column name in BlastStrainsRPKMs.xlsx


title: Dox_D2_RNA_r1


title: ctrl_D4_RNA_r2


title: NOD/ShiLtJ, male, Sham-c

description:
Library name: 209
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D3_RNA_r2


title: NOD/ShiLtJ, male, Blast-a

description:
Library name: 206
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D3_5_RNA_r2

description: C1_D35_filtered_feature_bc_matrix.tar.gz


title: C57Bl/6J, female, Blast-c

description:
Library name: 204
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D2_RNA_r2


title: NOD/ShiLtJ, male, Sham-a

description:
Library name: 205
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D4_RNA_r1


title: C57Bl/6J, female, Sham-c

description:
Library name: 203
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D3_RNA_r1


title: C57Bl/6J, female, Blast-b

description:
Library name: 202
Column name in BlastStrainsRPKMs.xlsx


title: ctrl_D3_5_RNA_r1


title: C57Bl/6J, female, Sham-b

description:
Library name: 201
Column name in BlastStrainsRPKMs.xlsx


title: C57Bl/6J, female, Blast-a

description:
Library name: 200
Column name in BlastStrainsRPKMs.xlsx


title: C57Bl/6J, female, Sham-a

description:
Library name: 199
Column name in BlastStrainsRPKMs.xlsx


title: C57Bl/6J, male, Blast-c

description:
Library name: 198
Column name in BlastStrainsRPKMs.xlsx


title: WGBS_SYCP3_NCG15_rep1

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: Whole genome bisulfite sequencing fom iPSC-derived germ cells SYCP3

data_processing:
(SINGLE CELL) Raw data were demultiplexed with the mkfastq command in Cell Ranger (v7.1.0) to generate Fastq files. Trimmed sequence files were mapped to the reference genome for humans (GRCh38) or macaque (Mmul_10) as well as to the mouse (GRCm38) using Cell Ranger mkfastq. Read counts were obtained by using cellranger count.
(SINGLE CELL) Secondary data analyses were performed in Python with Scanpy 1.8.1 or in R (v.4.1.0) with the Seurat (v.4.3.0), SeuratObject (v4.1.3), SeuratWrappers (v0.3.2), tidyverse (v.1.3.2), destiny (v3.10.0), pheatmap (v1.0.12), plot3D (v1.4) and Matrix (v.1.5-1) packages and Excel (Microsoft).
(WGBS) Raw fastq files were demultiplexed with bcl2fastq2 (v.2.20). Barcode and index trimming was performed with Trim Galore (v.0.6.5) as follows: trim_galore --quality 30 --phred33 --illumina --stringency 1 --cores 4 -e 0.1 --fastqc --clip_R1 10 --three_prime_clip_r1 10 --length 20. The trimmed fastq files were then mapped to calJac4 from USCS with Bismark (v.0.22.3) as follows: bismark --parallel 4 --genome_folder $REF --non_directional --score_min L,0,–0.6.
(WGBS) CpG methylation was extracted and analyzed with methylKit (v.1.22.0). Covered CpG loci were included in the analysis. The genome was tiled in 2 kb windows, and DNA methylation levels were summarized with methyKit (v.1.22.0). Data were visualized with R (v.4.1.0).
Assembly: GRCh38/Mmul_10/GRCm38
Supplementary files format and content: h5 cell ranger output files for each sample
Supplementary files format and content: Seurat objects saved as .Robj files

source_name: xrTestis

extract_protocol:
(SINGLE CELL) xrTestis-derived cells were sorted via FACS for expression of AG/VT/PC and collected in CELLOTION. Cell clumps were removed by straining cell suspensions through a 70 µm nylon mesh and then the single-cell suspension was centrifuged at 300 × rcf for 5 min. Cells were resuspended in 0.1% BSA in PBS and counted. All samples had greater than 80% viability as determined by trypan blue staining. Encapsulation was performed using a 10X Genomics Chromium Controller according to the manufacturer’s protocol.
(WGBS) PGCLC aggregates were digested with 400 μl 0.25% trypsin for 15 min. Then, 100 μl FBS was used to stop digestion, and the lysates were pipetted well to obtain a single-cell suspension. The fractions of TFAP2C-eGFP, TFAP2C-eGFP+DDX4-tdTomato and DDX4-tdTomato were sorted for methylome analyses. Cells were collected and lysed in 50 mM Tris (pH 8.0), 10 mM EDTA, 0.5% SDS, and 100 μg/ml proteinase K.
(SINGLE CELL) The Cells were loaded into chromium microfluidic chips with the Chromium Single Cell 3ʼ Reagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer’s protocol. reverse transcription step was performed using a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s protocol.
(SINGLE CELL) Chromium Single Cell 3ʼ Reagent (v3.1 chemistry) was used for library preparation
(WGBS) Crude DNA was used to build a sequencing library according to the protocol of the Pico Methyl-Seq Library Prep Kit (Zymo, #D5455). The libraries were sequenced on the Illumina 2200 platform.

value: xrTestis


title: C57Bl/6J, male, Blast-b

description:
Library name: 196
Column name in BlastStrainsRPKMs.xlsx


title: WGBS_NCG6_VT

description: Whole genome bisulfite sequencing fom iPSC-derived germ cells VT+


title: WGBS_PGCLCs_d5_rep1

description: Whole genome bisulfite sequencing fom iPSC-derived PGCLCs

source_name: PGCLCs

value: PGCLCs


title: WGBS_NCG6_AGVT

description: Whole genome bisulfite sequencing fom iPSC-derived germ cells AGVT+


title: C57Bl/6J, male, Sham-b

description:
Library name: 195
Column name in BlastStrainsRPKMs.xlsx


title: WGBS_PGCLCs_d5_rep2


title: WGBS_NCG6_AG

description: Whole genome bisulfite sequencing fom iPSC-derived germ cells AG+


title: C57Bl/6J, male, Blast-a

description:
Library name: 194
Column name in BlastStrainsRPKMs.xlsx


title: C57Bl/6J, male, Sham-c

description:
Library name: 197
Column name in BlastStrainsRPKMs.xlsx


title: NOD/ShiLtJ, male, Sham-b

description:
Library name: 207
Column name in BlastStrainsRPKMs.xlsx


title: NOD/ShiLtJ, female, Blast-a

description:
Library name: 212
Column name in BlastStrainsRPKMs.xlsx


title: C57Bl/6J, male, Sham-a

description:
Library name: 193
Column name in BlastStrainsRPKMs.xlsx


title: WGBS_NCG11_VT


title: Animal6, SSp, lib2, CYP, ATAC

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

library_source: other

data_processing:
Raw sequencing data from individual libraries were processed and mapped using 10X Genomics cellranger-6.1.2 (10X RNA), 10X Genomics cellranger-arc-2.0.1 (10X Multiome).
Assembly: The reference genome was generated by adding the Sun1-GFP and Projection-TAGs 1-12 to GRCm38. Projection-TAG feature was extended from the 100-nt Projection-TAG sequence by 140-nt on each end, to ensure sequencing reads have at least 10-nt alignment to the Projection-TAGs .
Supplementary files format and content: Gene matrix.rds contains gene-cell counts for all snRNA-seq libraries, and snRNAseq_metadata.csv contains meta data for all snRNA-seq libraries. peak matrix.rds contains peak-cell counts for all snATAC-seq libraries, and snATACseq_metadata.csv contains meta data for all snATAC-seq libraries.

molecule: other

source_name: Primary somatosensory cortex

extract_protocol:
Nuclear extraction for both mice and primates was performed with density gradient centrifugation according to the protocol described previously with modifications to scale down the reaction volume. Samples were moved from -80 ̊C and thawed on ice for 2 minutes. Tissues were transferred to a dounce homogenizer (Millipore Sigma, D8938-1SET) in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, pH 8.0, 5 µg/mL actinomycin, 1% BSA, and 0.08 U/µl RNase inhibitor, 0.01% NP40) on ice. Samples were homogenized for 10 strokes with the loose pestle in a total volume of 1 mL, followed by 10 additional strokes with the tight pestle. The tissue homogenate was then passed through a 50 µm filter and diluted 1:1 with working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 10 mM Tris-HCl, pH 8.0). Nuclei were layered onto an iodixanol gradient after homogenization and ultracentrifuged as described previously. After ultracentrifugation, nuclei were collected between the 30 and 40% iodixanol layers and diluted with resuspension buffer (1xPBS with 1% BSA, and 0.08 U/µl RNase inhibitor). Nuclei are isolated using FACS based on 7-AAD (all nuclei) or 7-AAD and GFP (Projection-TAG+ nuclei). Sorted nuclei are then pooled and diluted to the loading concentration recommneded by the library manuals.
Nuclei were processed according to the manufacturer’s manual of 10X Genomics Chromium Single Cell Gene Expression 3’ V3.1 Assay or 10X Genomics Chromium Single Cell Multiome Assay.
snRNA-seq or snMultiome-seq (bombinatorial RNA and ATAC)

treatment_protocol: Mice were administered an intraperitoneal injection of either cyclophosphamide (Sigma-Aldrich, dissolved and diluted to 40 mg/mL in 0.9% sodium chloride) with a dose of 200 mg/kg or saline (approximately the same volume as CYP). Animals were monitored in their home cage for 30 minutes before perfusion.

value: Primary somatosensory cortex

tag: facs

value: CYP

value: 30 min


title: WGBS_NCG11_AGVT


title: Animal6, SSp, lib1, CYP, ATAC


title: WGBS_NCG11_AG


title: Dox_D3_5_RNA_r1


title: WGBS_SYCP3_NCG15_rep2


title: WGBS_NCG3_VT


title: ctrl_D2_RNA_r1


title: Animal6, MOp, lib1, CYP, ATAC

source_name: Primary motor cortex

value: Primary motor cortex


title: Animal5, SSp, lib1, Saline, ATAC

value: Saline


title: WGBS_NCG3_AG


title: Animal5, MOp, lib1, Saline, ATAC


title: xrTestis_d9_NANOS3KO

description:
iPSC-derived human germ cells, ALI culture 9 days NANOS3-knockout
NANOS3_part1_20210809.rdata

tag: Stage


title: Animal2, SSp, lib1, Saline, ATAC


title: Animal1, SSp, lib1, CYP, ATAC


title: Animal4, MOp, lib1, Saline, RNA

value: Pool 50% GFP+/7AAD+ events and 50% GFP-/7AAD+ events


title: Animal4, SSp, lib1, Saline, RNA


title: xrTestis_d14_DND1KO

description: iPSC-derived human germ cells, ALI culture 14 days DND1-knockout


title: Animal3, SSp, lib1, CYP, RNA


title: xrTestis_d245_human

description: iPSC-derived human germ cells, transplanted 245 days


title: xrTestis_d251_human

description: iPSC-derived human germ cells, transplanted 251 days


title: Animal3, MOp, lib1, CYP, RNA


title: Animal6, SSp, lib2, CYP, RNA


title: xrTestis_d127_human

description: iPSC-derived human germ cells, transplanted 127 days


title: Animal6, MOp, lib2, CYP, ATAC


title: xrTestis_d181_human

description: iPSC-derived human germ cells, transplanted 181 days


title: xrTestis_d180_human

description: iPSC-derived human germ cells, transplanted 180 days


title: WGBS_NCG3_AGVT


title: Animal6, SSp, lib1, CYP, RNA


title: Animal6, MOp, lib2, CYP, RNA


title: xrTestis_c91+d180_human

description: iPSC-derived human germ cells, 2D culture 91 days,  transplanted 180 days


title: xrTestis_d123_human

description: iPSC-derived human germ cells, transplanted 120 days


title: Animal6, MOp, lib1, CYP, RNA


title: Animal2, SSp, lib1, Saline, RNA


title: Animal5, SSp, lib1, Saline, RNA


title: xrTestis_d9_NANOS3WT

description:
iPSC-derived human germ cells, ALI culture 9 days wildtype
NANOS3_part1_20210809.rdata


title: Unaffected Control_F_72_N/A_92_atac

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

institute: Van Andel Research Institute

description: Human prefrontal cortex tissue for this study was obtained NIH NeuroBioBank with approval from the ethics committee of the Van Andel Research Institute (IRB #15025)

data_processing:
ATAC-seq: Trimmed (trim_galore) fastq files were aligned to HG19 using BWA v7.15.
ATAC-seq: Alignments (bam files) were input to macs2 callpeak BAMPE -q 0.1 to determine peaks.
RNA-seq: Alignments (bam files) were converted to .tdf files using  igvtools (V2.3.60) count -z 5 -w 25 -e 250
Assembly: Hg19
Assembly: Illumina Nextera DNA UD Indexes Set C (cat 20027215) (version 1)
Supplementary files format and content: high sensitivity DNA assay

extract_protocol:
Neuronal nuclei were isolated from the human prefrontal cortex using flow cytometry and filtering for an anti-NeuN antibody.
DNA was isolated from the neurons using Zymo DNA concentrator Kit. Library generated using the Nextera XT DNA Library Kit with Tagment Enzyme (TDE1) on 30k nuclei, size selection to remove fragments >1kb
average size 400-500bp
bulk ATAC-seq on neuronal nuclei.

value: Brodman's Area 9 (Right)

value: F

tag: age

tag: symptom onset

tag: brain type

value: Unaffected Control

tag: source

value: UCLA Human Brain and Spinal Fluid Resource Center

tag: hemisphere

value: RT

tag: pmi

value: JC

tag: library prep

value: D

tag: sequencing run


title: Animal5, MOp, lib1, Saline, RNA

tag: tissue

tag: treatment


title: Animal1, SSp, lib1, CYP, RNA


title: xrTestis_c41+d120_human

description: iPSC-derived human germ cells, 2D culture 41 days,  transplanted 120 days


title: Unaffected Control_F_72_N/A_91_atac

tag: cell line

value: Brodman's Area 9 (Left)

tag: Sex

value: LT


title: WT3

city: Hangzhou

first: Zhaofeng

address: No.261, Wunsa Road, Shangcheng District, Hangzhou, Zhejiang, China

institute: Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province

description: control

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

growth_protocol: Hepa1-6 cells were maintained in DMEM supplementred with 10%fetal bovine serum (FBS) under conditions of 37℃ in an atmosphere with 5% CO2.

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

treatment_protocol: Knockout of Matr3 gene using CRISPR/Cas9 technology

tag: cell type

value: Mouse liver cancer cells

tag: genotype

value: WT


title: Unaffected Control_M_61_N/A_90_atac

value: Frozen BA46,9 RT

value: M

value: U. of Miami Brain Endowment Bank

tag: race

value: W


title: Unaffected Control_M_67_N/A_88_atac


title: KO3

description: treatment

value: Matr3 knockout


title: Unaffected Control_F_90_N/A_86_atac


title: Unaffected Control_M_67_N/A_87_atac

value: Frozen BA46,9 LT

tag: cod

value: Coronary Artery Disease


title: KO2

description: treatment


title: KO1

description: treatment


title: Unaffected Control_F_90_N/A_85_atac

value: F

value: Shock; Aortic Stenosis; Left Ventricle Injury; Cardiac Surgery


title: Unaffected Control_M_61_N/A_89_atac

value: Unaffected Control

value: Drowning


title: WT1

description: control


title: PD_F_74_Both_84_atac

value: Both

value: PD

value: RT

value: Respiratory Failure; Pneumonia

value: JC


title: 2D2 Cd4, Spleen, Rep 3

first: Maxwell

last: McDermott

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the sleen of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spleen_3

data_processing:
RNA-seq reads were trimmed using trimmomatic v0.36
Trimmed RNA-Seq reads were mapped to MM10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
read count extraction from BAM files performed using deeptools
Assembly: mm10
Supplementary files format and content: Tab delimited includes raw counts for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted using the RNeasy Micro RNA Isolation Kit (Qiagen). RNA quality and quantity were analyzed on a Nanochip cartridge run on the Agilent 2100 Bioanalyzer system.
RNAseq libraries were prepared using the Illumina TruSeq stranded total RNA kit (Illumina), starting from 100 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol with 15 PCR cycles. The amplified libraries were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized using the high sensitivity DNA screentape on the Agilent Tapestation 2200 system. The libraries were pooled equimolarly, and loaded onto a P2 100 cycle flow cell (run as paired end 50) and run on the Illumina Nextseq 2000 system.

value: Cd4 T Cells

value: 2D2 TCR (TCRMOG)

value: Spleen


title: PD_F_74_Both_83_atac

value: U. of Miami Brain Endowment Bank

value: LT

value: D


title: xrTestis_d120_human

value: xrTestis

tag: Stage


title: 2D2 Cd4, Spleen, Rep 1

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the sleen of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spleen_1


title: PD_M_82_Left_82_atac

value: Frozen BA46,9 RT

value: M

tag: age

value: Left

value: Cardiovascular/Respiratory Arrest

value: W


title: 2D2 Cd4, Spleen, Rep 2

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the sleen of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spleen_2


title: 2D2 Cd4, Spinal Cord, Rep 3

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the spinal cord of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spinal_Cord_3

source_name: Spinal Cord

value: Spinal Cord


title: PD_M_82_Left_81_atac

value: Frozen BA46,9 LT

tag: symptom onset

value: PD


title: 2D2 Cd4, Spinal Cord, Rep 2

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the spinal cord of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spinal_Cord_2


title: 2D2 Cd4, Spinal Cord, Rep 1

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days). Post differentiated cells were transferred into a Rag1-/- host.  At day 14, pth17 were harvested from the spinal cord of  Rag1-/- host mice.  Cells were enriched by FACs sorting for CD4+, Tcrva3.2+, Tcrvb11+ cells.
CD4_Spinal_Cord_1


title: PD_F_80_Left_80_atac

value: F

tag: brain type

value: RT

value: Parkinson's Disease

tag: nucleic acid(ng/ul)

value: C

tag: index id_(i7)


title: 2D2 Cd4, Naive, Rep 1

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells enriched via negative enrichment kit
CD4_Naive_1

source_name: ex vivo

value: Cd4 T Cells

value: 2D2 TCR (TCRMOG)

value: ex vivo


title: PD_F_80_Left_79_atac

tag: source

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: LT

tag: pmi

value: JC


title: 2D2 Cd4, pth17, Rep 1

description:
Naïve Cd4+ T cells isolated from the spleen of 2D2 mice cells.  Cd4+ were enriched via negative enrichment kit, stimulated with aCD3 (0.25ug/ml) and aCD28 (1ug/ml) in the presence of IL6 (20ng/ml), IL1b (20ng/ml), IL23 (20ng/ml), aIL4 (2ug/ml) for 4 days.
CD4_day4_th17_1

source_name: ex vivo pth17 differentiated

tag: tissue

value: ex vivo pth17 differentiated


title: PD_M_82_Left_78_atac

value: Frozen BA46,9 RT

value: M

value: Left

value: Liz

tag: library prep

tag: sequencing run


title: hPGCLCs

description: iPS-derived human PGCLCs

value: xrTestis

value: hPGCLCs


title: WT2

description: control

tag: cell line

value: Mouse liver cancer cells

value: WT


title: PD_M_82_Left_77_atac

value: Frozen BA46,9 LT

tag: Sex

value: PD

value: Cardiovascular/Respiratory Arrest

value: W


title: pTh17, shClns1a, 24hr stimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shClns1a. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then restimulated for another 24 hours, then collected.  Transduced cells were enriched with FACS.

source_name: pTh17 Cells

extract_protocol:
Transduced cells were enriched by FACS sorting. Total RNA was extracted using the RNeasy Micro RNA Isolation Kit (Qiagen). RNA quality and quantity were analyzed on a Nanochip cartridge run on the Agilent 2100 Bioanalyzer system.
RNAseq libraries were prepared using the Illumina TruSeq stranded total RNA kit (Illumina), starting from 100 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol with 15 PCR cycles. The amplified libraries were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized using the high sensitivity DNA screentape on the Agilent Tapestation 2200 system. The libraries were pooled equimolarly, and loaded onto a P2 100 cycle flow cell (run as paired end 50) and run on the Illumina Nextseq 2000 system.

treatment_protocol: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shRenilla or shClns1a. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then collected as non-restimulated, or collected afterrestimulated for 6 or 24h.

tag: cell type

value: pTh17 Cells

tag: genotype

value: Clns1a knockdown

tag: treatment

value: 1ug/ml aCD3/28 and aCD3 (0.25ug/ml) plate bound for 24 hours


title: pTh17, shClns1a, 24hr stimulated, Rep 2


title: PD_M_74_Left_75_atac

value: U. of Miami Brain Endowment Bank

value: LT

tag: cod

value: Severe Aortic Stenosis; Left Ischial Tuberosity and Inferior Pubic Ramus Fractures; Advanced Stage Parkinson's Disease

tag: race

value: C


title: PD_F_74_Both_74_atac

value: Frozen BA46,9 RT

value: F

tag: age

tag: symptom onset

value: Both

value: RT

value: Respiratory Failure; Pneumonia

value: JC


title: pTh17, shClns1a, 24hr stimulated, Rep 1


title: PD_M_74_Left_76_atac

value: M

value: Left

tag: brain type

value: Liz

tag: nucleic acid(ng/ul)


title: PD_F_74_Both_73_atac

value: Frozen BA46,9 LT

value: PD

tag: source

value: W

tag: index id_(i7)


title: pTh17, shRenilla, 24hr stimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shRenilla. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then restimulated for another 24 hours, then collected.  Transduced cells were enriched with FACS.

value: pTh17 Cells

value: WT

value: 1ug/ml aCD3/28 and aCD3 (0.25ug/ml) plate bound for 24 hours


title: pTh17, shRenilla, 24hr stimulated, Rep 2


title: PD_M_79_Right_71_atac

value: Right

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: LT

value: unknown

value: Cardiopulmonary Arrest, Myocardial Infarction

tag: pmi


title: pTh17, shRenilla, 24hr stimulated, Rep 1


title: pTh17, shClns1a, 6hr stimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shClns1a. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then restimulated for another 6 hours, then collected.Transduced cells were enriched with FACS.

value: Clns1a knockdown

value: 1ug/ml aCD3/28 and aCD3 (0.25ug/ml) plate bound for 6 hours


title: pTh17, shClns1a, 6hr stimulated, Rep 2


title: PD_M_79_Right_72_atac

tag: tissue

value: Frozen BA46,9 RT

value: RT

value: w

value: JC

tag: library prep

value: C


title: PD_M_82_Right_60_atac

tag: cell line

value: M

value: PD

value: Pneumonia

value: Liz

value: A

tag: sequencing run


title: pTh17, shRenilla, 6hr stimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shRenilla. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then restimulated for another 6 hours, then collected.Transduced cells were enriched with FACS.

tag: cell type

value: pTh17 Cells

value: WT


title: PD_M_81_Left_63_atac

value: Frozen BA46,9 LT

tag: Sex

value: Left

value: U. of Miami Brain Endowment Bank

value: LT

value: Cancer

value: W


title: pTh17, shRenilla, 6hr stimulated, Rep 2

tag: genotype

tag: treatment

value: 1ug/ml aCD3/28 and aCD3 (0.25ug/ml) plate bound for 6 hours


title: pTh17, shRenilla, 6hr stimulated, Rep 1


title: PD_M_82_Right_59_atac

value: Right

value: unknown

tag: cod

tag: race


title: PD_F_75_Right_57_atac

value: F

tag: age

tag: symptom onset

value: Infection


title: pTh17, shClns1a, Unstimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shClns1a. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then collected without further stimulation.Transduced cells were enriched with FACS.

value: Clns1a knockdown


title: PD_F_75_Right_58_atac

value: Frozen BA46,9 RT

tag: brain type

value: PD

value: RT

tag: nucleic acid(ng/ul)


title: pTh17, shClns1a, Unstimulated, Rep 1

value: pTh17 Cells


title: PD_M_79_Right_56_atac

value: M

tag: source

value: Cardiopulmonary Arrest, Myocardial Infarction

value: w

value: JC

value: A

tag: index id_(i7)


title: pTh17, shClns1a, Unstimulated, Rep 2


title: PD_M_79_Right_55_atac

value: Frozen BA46,9 LT

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: LT

tag: pmi


title: PD_F_85_Left_54_atac

tag: tissue

value: Left

value: Blunt Head Trauma

value: W

value: Liz

tag: library prep

value: C


title: pTh17, shRenilla, Unstimulated, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shRenilla. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 72h. Cells were then collected without further stimulation. Transduced cells were enriched with FACS.

value: WT


title: PD_F_85_Left_53_atac

tag: cell line

value: F

value: PD

tag: sequencing run


title: pTh17, shRenilla, Unstimulated, Rep 1

tag: cell type

value: pTh17 Cells


title: PD_M_69_Left_51_atac

tag: Sex

value: M

value: Aspiration Pneumonia


title: pTh17, Prmt5, Crosslinked Cut and Run, Rep 2

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 3 days.

data_processing:
reads were trimmed using trimmomatic v0.36
Trimmed reads were mapped to MM10 and to Escherichia_coli_K_12_DH10B using Bowtie2 guided by GTF
All duplicates reads were removed via Sambamba from both assemblies
All assembly fragments longer than 500 BP were removed from both assemblies
sequencing depth of spikein DNA from Escherichia_coli_K_12_DH10B was calculated and a scaling factor for each sample was calculated by 10,000/sequencing depth
a scaled bedgraph was created against each sample's calculated scaling factor using bedtools
to create coverage tracks each scaled bedgraph was coonverted into bigwig format via deeptools
Assembly: mm10
Supplementary files format and content: bigwig (narrow peak)
Library strategy: CUT&Run

extract_protocol:
Samples were immobilized to ConA beads and resuspended in ice cold antibody buffer. 1 ug primary antibody or IgG negative control was added into samples followed by incubation at 4°C overnight. On day 2, samples were washed with digitonin buffer, and digested with pAG-MNase. Reaction was stopped by stop buffer containing E.coli spike-in control for sample normalization. Samples were then incubated for 10 min at 37°C to release cleaved chromatin. Supernatant containing released chromatin was collected, and a final concentration of 0.1% SDS and 0.2 μg/μl proteinase K were added into each samples. Incubated samples overnight at 55°C. Purified DNA from supernatant using the CUTANA DNA purification kit and quantified DNA using Qubit fluorometer
DNA library was prepared using CUTANATM CUT&RUN Library Prep Kit (SKU: 14-1001). The libraries were pooled equimolarly, and loaded on theIllumina NovaSeq X Sequencing Systemand run on 1 lane of a NovaSeq X+ 10B 300 Cycle Flowcell.

tag: genotype

tag: c&r antibody

value: Anti-PRMT5 Antibody (Cat.No.07-405)


title: PD_M_69_Left_52_atac

description: Human prefrontal cortex tissue for this study was obtained NIH NeuroBioBank with approval from the ethics committee of the Van Andel Research Institute (IRB #15025)

value: Frozen BA46,9 RT

value: RT

tag: cod

tag: race


title: pTh17, Prmt5, Crosslinked Cut and Run, Rep 1

treatment_protocol: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 3 days.


title: PD_M_81_Left_64_atac

tag: age

tag: symptom onset

value: Cancer


title: PD_F_75_Right_49_atac

value: Frozen BA46,9 LT

value: Right

tag: brain type

value: U. of Miami Brain Endowment Bank

value: Parkinson's Disease

tag: nucleic acid(ng/ul)


title: pTh17, shClns1a, 6hr stimulated, Rep 1

value: Clns1a knockdown

tag: treatment

value: 1ug/ml aCD3/28 and aCD3 (0.25ug/ml) plate bound for 6 hours


title: pTh17, IgG control, Crosslinked Cut and Run, Rep 2

value: Rabbit IgG(Cell Signling Cat. No. 2729)


title: PD_F_75_Right_50_atac

tag: source

tag: hemisphere

value: W

value: Liz

value: C

tag: index id_(i7)


title: PD_M_75_Both_48_atac

tag: tissue

value: Both

value: PD

value: unknown

value: Failure to Thrive

tag: pmi

tag: library prep


title: pTh17, IgG control, Crosslinked Cut and Run, Rep 1

tag: cell type

value: pTh17 Cells

value: WT


title: pTh17, Clns1a, Crosslinked Cut and Run, Rep 2

value: CLNS1A Polyclonal Antibody (thermo, Cat.No. PA5-109555)


title: PD_M_75_Both_47_atac

tag: cell line

value: Frozen BA46,9 LT

tag: Sex

value: M

value: LT

tag: sequencing run


title: pTh17 Cells, ATAC-seq, shRenilla, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shRenilla. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 96hrs, then collected.  Transduced cells were enriched with FACS.

data_processing:
reads were trimmed using trimmomatic v0.36
Trimmed reads were mapped to MM10 using Bowtie2 guided by GTF
Removal of duplicate reads via Sambamba
to create coverage tracks reads were normalzied to reads per kilobase million(rpkm) and reformatted into bigwigs via deeptools
Assembly: mm10
Supplementary files format and content: bigwig (broad peak)

extract_protocol:
Extraction was performed using ATAC-Seq Kit (ActiveMotif, Cat. No 53150). In brief, pTh17 cells were restimluated with plate-bound aCD3 (1ug/ml) and aCD28 (1ug/ml) for 24h followed by enrichment with FACS. Cells were washed once with ice-cold PBS followed by lysis with ice-cold ATAC lysis buffer to get cell nuclei.
library construction was performed using ATAC-Seq Kit (ActiveMotif, Cat. No 53150). In brief, tagmentation buffer was added into cell nuclei and samples were inclubated at 37 ºC for 30 min. Tagmented DNA was purifed with DNA prurification reagents follow by PCR amplification to construct final DNA library.

tag: genotype


title: PD_M_81_Right_43_atac

value: Right

value: U. of Miami Brain Endowment Bank

tag: cod

value: Parkinson's Disease

tag: race

value: B


title: PD_M_72_Right_42_atac

value: Frozen BA46,9 RT

tag: age

tag: symptom onset

value: RT

value: Cardiopulmonary arrest

value: W


title: pTh17 Cells, ATAC-seq, shRenilla, Rep 1


title: pTh17 Cells, ATAC-seq, shRenilla, Rep 2


title: PD_M_91_Right_40_atac

tag: brain type

value: PD

value: Hypotension; Autonomic Dysfunction; Parkinson's Disease

value: Liz

tag: nucleic acid(ng/ul)

value: C


title: pTh17 Cells, ATAC-seq, shClns1a, Rep 3

description: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 and aCD28 and differentiated into pTh17 cells. 24h after activation, cells were transduced with shClns1a. 48h after activation, cells were detached and further cultured in pTh17 cell condition for additional 96hrs, then collected.  Transduced cells were enriched with FACS.

value: pTh17 Cells

value: Clns1a knockdown

tag: treatment


title: PD_M_72_Right_41_atac

value: Frozen BA46,9 LT

tag: source

tag: hemisphere

value: unknown


title: PD_M_91_Right_39_atac

tag: tissue

value: M

value: LT

tag: index id_(i7)


title: pTh17, shRenilla, Unstimulated, Rep 2

value: WT


title: pTh17 Cells, ATAC-seq, shClns1a, Rep 2


title: PD_M_62_Left_38_atac

value: Left

value: U. of Miami Brain Endowment Bank

value: Parkinson's Disease

tag: pmi

tag: library prep


title: PD_M_62_Left_37_atac

tag: cell line

value: B


title: MD4_naïve CD8 T cells_5

city: Aurora

first: Jared

last: Klarquist

state: CO

department: Immunology and Microbiology

institute: University of Colorado, Anschutz

data_processing:
Illumina universal adapters were removed, bases were trimmed if the Phred Score was less than 24, and any reads after trimming that were fewer than 20 base pairs in length were discarded using Cutadapt v4.2 under Python version 3.11.4. Reads were aligned and quantified to the mm10 reference genome using Rsubread v.2.12.3. The quality of the alignments were assessed using PicardTools v2.27.4. Differential gene expression was performed using DESeq2 v1.38.3.
Assembly: mm10
Supplementary files format and content: csv, normalized counts
Supplementary files format and content: csv, log2-fold change MD4 vs wildtype B6, with adjusted p-value from DESeq2 analysis

source_name: spleen

extract_protocol:
RNA was prepared from sorted cells using a PureLink RNA Mini Kit (ThermoFisher). mRNA quality was assessed using NanoDrop (ThermoFisher Scientific) and RNA ScreenTape Analysis on an Agilent 2200 TapeStation (Agilent); all 10 samples had RINe scores >9, indicating negligible RNA degradation.
Universal Plus mRNA-Seq library preparation kit with NuQuant (Tecan) was used with an input of 200ng of total RNA to generate RNA-Seq libraries.

value: spleen

tag: strain

tag: cell type

value: Naive CD8 T cells

value: MD4 BCR Tg

tag: Sex

value: F

value: 73 days/10.4 weeks old


title: MD4_naïve CD8 T cells_2

tag: genotype


title: PD_F_76_Right_35_atac

value: Right

value: PD

tag: cod

tag: race

value: W

value: Liz

value: A

tag: sequencing run


title: MD4_naïve CD8 T cells_1

tag: age


title: B6_naïve CD8 T cells_5

value: Wildtype


title: PD_M_74_Left_34_atac

value: Frozen BA46,9 RT

value: M

tag: symptom onset

tag: brain type

value: RT

value: Severe Aortic Stenosis; Left Ischial Tuberosity and Inferior Pubic Ramus Fractures; Advanced Stage Parkinson's Disease

tag: nucleic acid(ng/ul)


title: PD_F_76_Right_36_atac

tag: source

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: Parkinson's Disease


title: MD4_naïve CD8 T cells_3

tag: tissue

value: spleen

tag: treatment


title: PD_M_81_Right_44_atac

tag: pmi

tag: library prep

value: B

tag: index id_(i7)


title: PD_M_74_Left_33_atac

tag: cell line

value: Frozen BA46,9 LT

value: Left

value: LT


title: MD4_naïve CD8 T cells_4

tag: strain

tag: cell type

value: Naive CD8 T cells

value: MD4 BCR Tg

tag: Sex

value: F

value: 73 days/10.4 weeks old


title: B6_naïve CD8 T cells_3

tag: genotype


title: pTh17, Clns1a, Crosslinked Cut and Run, Rep 1

value: pTh17 Cells

value: WT

tag: c&r antibody

value: CLNS1A Polyclonal Antibody (thermo, Cat.No. PA5-109555)


title: PD_M_82_Left_26_atac

value: Frozen BA46,9 RT

value: M

tag: age

value: PD

tag: cod

value: Cardiovascular/Respiratory Arrest

tag: race

value: W

value: Liz

value: A

tag: sequencing run


title: B6_naïve CD8 T cells_4

value: spleen

value: Wildtype


title: PD_M_82_Left_25_atac

value: Frozen BA46,9 LT

tag: symptom onset

value: Left

tag: brain type

tag: source

value: U. of Miami Brain Endowment Bank

value: LT

tag: nucleic acid(ng/ul)


title: PD_F_80_Left_20_atac

tag: tissue

value: F

tag: hemisphere

value: RT

value: Parkinson's Disease

tag: pmi

value: JC

value: B


title: PD_M_63_Left_21_atac

tag: cell line

value: M

tag: library prep

value: C

tag: index id_(i7)


title: B6_naïve CD8 T cells_2

tag: strain

tag: cell type

value: Naive CD8 T cells

tag: Sex

value: 73 days/10.4 weeks old

tag: treatment


title: B6_naïve CD8 T cells_1

tag: genotype

tag: age


title: pTh17 Cells, ATAC-seq, shClns1a, Rep 1

value: pTh17 Cells

value: Clns1a knockdown


title: PD_F_80_Left_19_atac

value: PD

tag: cod

tag: race

value: W

tag: sequencing run


title: scE14.5_1_seqrep2

data_processing:
Raw paired-end reads were processed using Cell Ranger v.7.0.0 to map reads to the mm10 genome in intron mode. Counts matrices where then filtered and analyzed with Seurat, Monocle3, or scCustomize.
The final processed files contain single cell datasets exactly as they appear for the relevant figures in the manuscript. RDS datafiles can be directly loaded into Seurat.
Assembly: mm10 reference genome

growth_protocol: WT male mice were crossed to WT female mice and resulting progeny were collected at embryonic day post coital 14.5 (E14.5).

extract_protocol:
Both foregut and hindgut were collected from embryos (E14.5), rinsed in 1X PBS, and singularized into individual cells using Accumax and mechanical pipetting. Cells were then turned into scRNA-Seq libraries using standard 10X Genomics 3' scRNA-Seq protocols. Single nuclei were then isolated using 10X Chromium single nuclei isolation kit. 20k nuclei were then used as input into the standard 10X Genomics scRNA-Seq library pipeline.
3' 10X Genomics

value: GI tract, small intestine to colon

value: WT

value: female


title: PD_F_82_Both_16_atac

value: Frozen BA46,9 RT

tag: symptom onset

value: Both

tag: brain type

tag: source

value: U. of Miami Brain Endowment Bank

value: Cerebrovascular Disease

value: Liz


title: PD_F_82_Both_15_atac

tag: tissue

value: Frozen BA46,9 LT

value: F

tag: hemisphere

value: LT

tag: nucleic acid(ng/ul)


title: scE14.5_2

tag: cell line

tag: developmental stage


title: scE14.5_1


title: PD_M_88_Right_14_atac

value: M

value: Right

value: RT

value: Aspiration Pneumonia; Parkinson's Disease

tag: pmi

value: JC

tag: library prep

value: C

tag: index id_(i7)


title: P0_26

description:
Table.S1.txt
Table.S2.csv

data_processing:
Raw paired-end reads were processed using an automated Salmon pipeline, Seq-N-Slide, on New York University’s Ultra Violet computing cluster.
Ensembl stable transcripts were then mapped to gene names using the gencode mouse M28 annotation release and parsed for protein coding genes.
The raw count matrices were further processed using DESeq2 for differential statistics and other custom analyses for visualization.
Assembly: mm10 reference genome
Supplementary files format and content: Table.S1.txt, Tab-deliited filtered counts matrix
Supplementary files format and content: Table.S2.csv, Comma-seperated metadata file that can be loaded into Deseq2

source_name: colon

growth_protocol: Homozygous Piebald male mice were crossed to Ret+/CFP heterozygous female mice and resulting progeny were collected at sample timepoints embryonic day post coital 14.5 (E14.5) or postnatal day 0 (P0).

extract_protocol:
Entire intestine from stomach to anal pore (E14.5) or colon to anal pore (P0) were collected from euthanized animals, rinsed in 1X PBS, and snap frozen in liquid N2. RNA was then extracted and purified.
cDNA and libraries were prepared using Illumina's Truseq kit on an automated Beckman Coulter Biomek SPRIworks platform.

value: colon

tag: cell type

value: Ret+/+ Ednrb+/s

value: male


title: PD_M_63_Right_12_atac

value: Frozen BA46,9 RT

tag: Sex

value: PD

value: unknown

value: Parkinson's Disease; Ischemic Heart Disease

value: W


title: PD_M_88_Right_13_atac

value: Frozen BA46,9 LT

tag: age

value: U. of Miami Brain Endowment Bank


title: PD_F_74_Both_10_atac

value: F

value: Both

tag: cod

value: Respiratory Failure; Pneumonia

value: B


title: P0_13

description:
Table.S1.txt
Table.S2.csv

tag: genotype

value: female


title: P0_21

description:
Table.S1.txt
Table.S2.csv


title: P0_20

description:
Table.S1.txt
Table.S2.csv


title: WT, Activated, Cut&Tag Rep3

city: Iowa City

first: Priya

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

institute: University of Iowa

data_processing:
*library strategy: Cut&Tag
Sequencing adapters were removed from paired‐end reads using Trimmomatic version 0.39. Trimmed reads were aligned to mouse reference genome GRCm38/mm10 using Bowtie 2 version 2.4.1. Following genome alignment, Picard was used to mark PCR duplicates, and samtools version 1.3.1 was used to remove PCR duplicates, discordant pairs, and alignments to the mitochondrial genome. Peak calling was performed using MACS2 version 2.2.7.1, and differential accessibility analyses of MACS2 peaks were performed using the R package DiffBind version 2.10.0. Differentially accessible peaks were annotated to genome regions of interest using the R package ChIPseeker version 1.18.0.
Assembly: mm10 reference genome
Supplementary files format and content: narrow peaks

source_name: Lymph nodes and spleen

extract_protocol:
Nuclei for tagmentation was prepared using the Cut and Tag Kit from Active Motif following the manufacturer's instructions
Cut&Tag libraries were prepared using the Cut&Tag Kit from Active Motif following the manufacturer's instructions

value: Lymph nodes and spleen

value: CD8 T cells

value: WT

tag: treatment

value: TCR activation


title: PD_F_66_Left_5_atac

tag: symptom onset

value: Left

value: LT

value: Respiratory Failure; Parkinson's Disease

tag: race

value: Liz

value: C

tag: sequencing run


title: PD_M_63_Left_22_atac

tag: tissue

value: Frozen BA46,9 RT

value: M

tag: brain type

value: PD

tag: source

value: RT

value: Parkinson's Disease

value: W

value: JC


title: PD_M_79_Left_8_atac

tag: cell line

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: unknown

value: Respiratory Failure

tag: nucleic acid(ng/ul)


title: PD_M_81_Left_4_atac

value: Cancer

tag: pmi

tag: library prep


title: WT, Activated, Cut&Tag Rep1

value: Lymph nodes and spleen

tag: cell type

value: CD8 T cells

value: WT

value: TCR activation


title: PD_F_66_Left_6_atac

tag: Sex

value: F

value: Left

value: Respiratory Failure; Parkinson's Disease

value: Liz

tag: index id_(i7)


title: Tet1/3cDKO, Activated, Cut&Tag Rep3

value: Tet1/3 DKO


title: PD_M_79_Left_7_atac

value: Frozen BA46,9 LT

value: M

tag: age

value: PD

value: LT

tag: cod

value: C


title: Tet1/3cDKO, Activated, Cut&Tag Rep1

tag: genotype

tag: treatment


title: infection in the presence of CPSF6 lacking RRM domain replicate 4

first: Parmit

middle: Kumar

last: Singh

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

data_processing:
Reads were trimmed for U5 LTR and linker sequences; aligned to human genome hg19 to obtained unique integration sites.
Assembly: hg19
Supplementary files format and content: bed formate containing genomic coordinates for integration sites.
Library strategy: Amplicon-seq

source_name: Kidney

extract_protocol:
genomic DNA was isolated from infected cells.
Genomic DNA from infected cells were fragmented by MseI and BglII, ligated to linker to amplyfy virus-host junction by PCR. PCR products were used for Illumina sequencing.

value: Kidney


title: infection in the presence of CPSF6 lacking RRM domain replicate 5


title: WT CD8 T cells, Naive, EM-seq Rep2

data_processing:
*library strategy: EM-seq
Sequencing data quality was assessed using FastQC v0.11.4. Adapters were trimmed from the sequencing reads using Trimmomatic v0.39. Alignment to the GRCm39/mm39 reference genome was performed using Bismark v0.23.1 with options. Deduplication was performed with deduplicate_bismark. Library quality was assessed on the basis of the percentage of reads that aligned to the genome. Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome. Enzymatic methyl conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context. Enzymatic methyl conversion was considered sufficient when this value was less than 3%. Genome coverage was assessed using the bedtools genomecov software v2.25.0. Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. For each library that met these quality metrics, methylation percentages at individual CpG positions in the reference genome were quantified using the Bismark Methylation Extractor.
Assembly: GRCm39/mm39 reference
Supplementary files format and content: .bismark.cov.gz for each file

extract_protocol:
DNA was extracted using the Qiagen Genomic DNA extraction kit
EM-Seq libraries were prepared using the NEBNext Enzymatic Methyl-seq Kit following the manufacturer's instructions

value: No treatment


title: infection in the presence of CPSF6 lacking RRM domain replicate 3


title: infection in the presence of CPSF6 lacking RRM domain replicate 2


title: WT CD8 T cells, Naive, EM-seq Rep1


title: Tet1/3cDKO, Activated, Cut&Tag Rep2


title: Tet1/3-cDKO CD8 T cells, Naive, EM-seq Rep2

value: Tet1/3 cDKO


title: P0_22

description:
Table.S1.txt
Table.S2.csv

value: colon

value: Ret+/+ Ednrb+/s

value: female


title: P0_31

description:
Table.S1.txt
Table.S2.csv

value: male


title: PD_M_63_Right_11_atac

tag: symptom onset

value: Right

value: U. of Miami Brain Endowment Bank

value: unknown

value: Parkinson's Disease; Ischemic Heart Disease

tag: race

value: W


title: No Template Control

city: Oklahoma city

first: Lorin

middle: E

last: Olson

state: OK

department: CVB

institute: OMRF

description:
Library name: NTC
NanoString GeoMX

data_processing:
Data was transferred to the GeoMx DSP instrument for further processing and analysis.
Please note that the data columns in 'Nanostring_all_ROIs_genes_normalized_expression.xlsx' refer to different regions of interest among the 4 samples, which are notated within the document. Additionally, the .RDS object contains the relevant metadata assigned to its corresponding data.
Assembly: Mouse mm10
Supplementary files format and content: Nanostring_joint_e14.5.RDS: Seurat object made from nanostring data
Supplementary files format and content: Nanostring_all_ROIs_genes_normalized_expression.xlsx
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissues were fixed in 10% NBF, embedded in paraffin, and sectioned at 5 μm. For GeoMx WTA profiling, slides were deparaffinized and rehydrated, underwent antigen retrieval and Proteinase K digestion, then were hybridized overnight with UV-photocleavable, barcoded oligonucleotide probes from the Mouse Whole Transcriptome Atlas (WTA) RNA probe set. After stringent washing, slides were incubated with Sox9 (EMD-Millipore) and SYTOX13 (NanoString) to allow for visualization of tissue morphology for ROI selection. Slides were placed in the GeoMx Digital Spatial Profiler instrument and ROIs were selected. These selected areas then underwent barcode cleavage from the hybridized probes, with the barcodes collected into individual wells of the collection plate based on ROI of origination.
PCR was used to uniquely index each ROIs barcodes with specific Illumina i5/i7 dual indexing primers. These library products were then pooled, purified, and assessed for quality. Paired-end sequencing was performed on a NextSeq 2K P1 PE50 (Illumina), targeting the NanoString recommended read depth of 86 million read-pairs (based on ROI summed areas).

tag: tissue

tag: batch