title: Embryonic Anterior Neural Plate Cells: Experimental biol rep 3

city: Swarthmore

first: Bradley

last: Davidson

state: PA

address: 500 College Ave

institute: Swarthmore College

data_processing:
FastQC was used to assess reads: maximum reads of 150 nucleotides; read depth of 45–62 million reads/sample
HTSeq was used to perform gene counts
HiSat2 used to align reads to C. robusta genome
Assembly: ci3
Supplementary files format and content: DESeq2 was used to analyze read counts
Supplementary files format and content: CSV file with baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, Intercept, LFC_condition_X_vs_C

organism: Ciona robusta

source_name: Neuroectoderm

growth_protocol: embryos were developed at 18°C

extract_protocol:
RNA was extracted with Qiagen miRNeasy Mini kit (with DNase Treatment) (Penn Genomics & Sequencing Core)
libraries were prepared using NEB kit for ultra-low RNA (E7760S) following the manufacturers protocols (Azenta)

treatment_protocol: embryos were dissociated in Ca/Mg-free seawater, GFP+ cells FACS collected on a BD1 sorter at Penn Cytomics & Cell Sorting Resource Laboratory

value: Neuroectoderm

value: embryonic anterior neural plate

value: wildtype


title: Embryonic Anterior Neural Plate Cells: Experimental biol rep 2

status: Public on Dec 21 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Embryonic Anterior Neural Plate Cells: Experimental biol rep 1


title: TFP 72 hr, biological rep3

city: Taipei

first: MingYing

last: Lan

address: No.201, Sec. 2, Shipai Rd., Beitou District

department: Department of Otolaryngology-Head and Neck Surgery

country: Taiwan

institute: Taipei Veterans General Hospital, Taipei, Taiwan

description: gene expression after 72 hours TFP treatment in NPC cell line

data_processing:
The original data obtained by high-throughput sequencing (NovaSeq 6000; Illumina) were converted into raw se-quenced reads by CASAVA base calling and stored in FASTQ format.
Read pairs from each sample were aligned to the reference genome (H. sapiens) using the HISAT2 software (v2.1.0)
FeatureCounts v2.0.0 was performed to calculate the read numbers mapped to individual genes
For gene expression, the relative log expression (RLE) normalization was performed us-ing DESeq2 (v1.26.0) with a biological duplicate.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted using clusterProfiler (v3.14.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Map_stat.txt
Supplementary_files_format_and_content: Original_read_count.txt
Supplementary_files_format_and_content: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway files

molecule: total RNA

organism: Homo sapiens

source_name: Nasopharyngeal carcinoma cells

growth_protocol: The NPC cell line was maintained in DMEM with 10% FBS at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NPC cells treated with or without TFP for 72 hours at 37°C

value: Nasopharyngeal carcinoma cells

tag: passage

value: passage at p3-p10

value: TFP


title: T47D_Clone28_DMSO_rep4

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
T47D_Clone28_DMSO_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts file
Library strategy: PRO-seq

growth_protocol: T47D cells (RRID:CVCL_0553) (ATCC) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gemini) and 10ug/ml insulin from bovine pancreas (Sigma, made as a 1000x solution in 1% aqueous glacial acetic acid).

extract_protocol:
Cell permeabilization was performed as previously described (Mahat et al. 2016), with modifications. At the time of harvest, cells were scraped in 10mL ice cold PBS and washed in 5mL buffer W (10mM Tris-HCl pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 0.004U/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)). Cells were permeabilized by incubating with buffer P (10 mM Tris-HCl pH 7.5, KCl 10 mM, 250 mM sucrose , 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40, 0.5 mM DTT, 0.004 units/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)) for 3 minutes on ice. Cells were washed with 10 mL buffer W before being transferred into 1.5mL tubes using wide bore pipette tips. Finally, cells were resuspended in 50μL buffer F (50mM Tris-HCl pH 8, 5mM MgCl2, 0.1mM EDTA, 50% Glycerol, 0.5 mM DTT). Cells were snap frozen in liquid nitrogen and stored at -80°C.
PRO-seq libraries were prepared as previously described (Judd et al. 2020), with modifications. RNA extraction after the run-on reaction was performed with 500μL Trizol LS (Thermo Fisher) followed by 130μL chloroform (Sigma). The equivalent of 1μL of 50μM for each adapter was used. A random eight base unique molecular identifier (UMI) was included at the 5′ end of the adapter ligated to the 3′ end of the nascent RNA. 37°C incubations were performed with rotation with 1.5mL tubes placed in 50mL conical tubes in a hybridization oven. For the reverse transcription reac- tion, RP1 was used at 100μM and dNTP mix was used at 10mM each. Libraries were amplified by PCR for a total of 8 cycles in 100μL reactions with Phusion polymerase (New England Biolabs). No PAGE purification was performed to ensure that our libraries were not biased against short nascent RNA insertions.

treatment_protocol: 4 replicates were performed from cells treated and collected at different times in the same day. 4*10^6 cells per sample were plated in 10cm dishes 1 day before harvest. Cells were treated with DMSO or 100nM dTAG-13 in DMSO for 90 minutes and collected simultaneously.

tag: cell line

value: 0.1% v/v DMSO for 90 minutes


title: T47D_Clone28_DMSO_rep3

description:
T47D_Clone28_DMSO_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: Control_3, biological rep3

value: Control


title: nasopharyngeal carcinoma patients 15

type: RNA

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

country: China

institute: Sun Yat-sen University Cancer Center

description: circRNA expression data from nasopharyngeal carcinoma

hyb_protocol: 1.65 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using R software. Differentially expressed circRNAs with statistical significance between groups were identified through P-value/FDR filtering.
Quantile normalization and subsequent data processing were performed with using R software.

source_name: primary nasopharyngeal carcinoma without posttreatment relapse

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from frozen fresh tissues using the AllPrep DNA/RNA Mini Kit (QIAGEN GmbH, Hilden, Germany)

value: Nasopharyngeal carcinoma


title: nasopharyngeal carcinoma patients 14


title: Embryonic Anterior Neural Plate Cells: Control biol rep 3

value: Dmrt>GFP


title: nasopharyngeal carcinoma patients 13


title: nasopharyngeal carcinoma patients 12


title: T47D_Clone28_DMSO_rep2

description:
T47D_Clone28_DMSO_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: nasopharyngeal carcinoma patients 11


title: Control_2, biological rep2


title: nasopharyngeal carcinoma patients 10


title: T47D_Clone28_DMSO_rep1

description:
T47D_Clone28_DMSO_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: nasopharyngeal carcinoma patients 02

source_name: primary nasopharyngeal carcinoma with posttreatment relapse


title: Control_1, biological rep1


title: nasopharyngeal carcinoma patients 16


title: WT, basal (cka control), rep3

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

data_processing:
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of Cryptococcus neoformans H99 and annotation data were downloaded from the NCBI ftp server
The reads were aligned to the Cryptococcus neoformans H99 genome sequence using Hisat2 v2.2.1 with the Hisat and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30”and “– dta -1”option and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with “-Sb -@ 8”option for converting, and “-@ 20 –m 2000000000” option for sorting and the other parameters set as default
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using “-p 12” option, and also “-B” option to run the Ballgown analysis.
Assembled transcripts were merged to single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase ofexon per Million fragments mapped (FPKM). The FPKM and readcount matrix was generated by R package “isoformswitchanalyzerR” and analyzed by DESeq2.
Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown. Volcano plot was illustrated by using R v4.1.0, with the cutoff (more than two-fold changes with p< 0.05).
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample

organism: Cryptococcus neoformans

growth_protocol: C. neoformans strains grown overnight in YPD medium weretransferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8.

extract_protocol:
The cells were then harvested by centrifugation and lyophilized. Total RNAs were isolated by Easy-BLUE (iNtRON), treated with DNase I (Qiagen), and puriﬁed with RNeasy MiniElute clean up kit (Qiagen) following the manufacturer’s instruction
Cultured samples were prepared independently three times for each strain, the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by Illumina platform.

value: Fungi

value: WT

value: basal


title: WT, basal (cka control), rep2


title: nasopharyngeal carcinoma patients 07


title: WT, basal (cka control), rep1


title: Embryonic Anterior Neural Plate Cells: Control biol rep 2


title: nasopharyngeal carcinoma patients 17


title: Embryonic Anterior Neural Plate Cells: Control biol rep 1


title: nasopharyngeal carcinoma patients 09


title: nasopharyngeal carcinoma patients 08


title: nasopharyngeal carcinoma patients 03


title: CRMCs of miR-183C WT of MS-CKO strain (CRMCs-MS-WT)

status: Public on Dec 20 2023

city: Detroit

first: Shunbin

last: Xu

state: MI

address: 540 E Canfield St, Scott Hall 8133/8137

department: Opthalmology, Visual and Anatomical Sciences

institute: Wayne State University, School of Medicine

data_processing:
Reads were trimmed using Bbduk
Reads were aligned using STAR
Reads were tabulated with htseq-count
Assembly: mm10
Supplementary files format and content: Excel File

organism: Mus musculus

source_name: Purified CRMCs

extract_protocol:
Total RNA was prepared using  the RNeasy (Qiagen, Frederick, MD, USA).
3’ mRNA-Seq libraries were prepared by the Genome Sciences Core (GSC), WSU using the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen, Greenland, NH)88.

value: Purified CRMCs

value: miR-183C WT


title: CRMCs of miR-183C KO mice (CRMCs-KO)

value: miR-183C KO


title: CRMCs of miR-183C WT of KO strain (CRMCs-WT)


title: Myeloid cell of the spleen of miR-183C WT of MS-KO strain (Speen MCs-MS-WT)


title: Myeloid cell of the spleen of miR-183C MS-KO mice (Speen MCs-MS-KO)

value: miR-183C MS-CKO


title: Cornea of miR-183C WT control mouse of the MS-CKO strain-4 (Cornea MS-WT-4)

source_name: Primary cornea tissue

value: Primary cornea tissue


title: Cornea of miR-183C WT control mouse of the MS-CKO strain-5 (Cornea MS-WT-5)


title: Myeloid cell of the spleen of miR-183C WT of KO strain (Speen MCs-WT)


title: Cornea of miR-183C MS-CKO strain-5 (Cornea MS-CKO-5)


title: Cornea of miR-183C MS-CKO strain-3 (Cornea MS-CKO-3)


title: Cornea of miR-183C MS-CKO strain-1 (Cornea MS-CKO-1)


title: Myeloid cell of the spleen of miR-183C KO mice (Speen MCs-KO)


title: CRMCs of miR-183C MS-KO mice (CRMCs-MS-KO)


title: Cornea of miR-183C MS-CKO strain-4 (Cornea MS-CKO-4)


title: Cornea of miR-183C MS-CKO strain-2 (Cornea MS-CKO-2)


title: nasopharyngeal carcinoma patients 04


title: nasopharyngeal carcinoma patients 05


title: nasopharyngeal carcinoma patients 06


title: Cornea of miR-183C WT control mouse of the MS-CKO strain-2 (Cornea MS-WT-2)


title: TG of miR-183C MS-CKO strain-4 (TG MS-CKO-4)

source_name: Primary TG tissue

value: Primary TG tissue


title: TG of miR-183C MS-CKO strain-5 (TG MS-CKO-5)


title: nasopharyngeal carcinoma patients 01


title: Cornea of miR-183C WT control mouse of the MS-CKO strain-1 (Cornea MS-WT-1)


title: TG of miR-183C MS-CKO strain-2 (TG MS-CKO-2)


title: TG of miR-183C MS-CKO strain-1 (TG MS-CKO-1)


title: TG of miR-183C WT control mouse of the MS-CKO strain-4 (TG MS-WT-4)


title: TG of miR-183C WT control mouse of the MS-CKO strain-3 (TG MS-WT-3)


title: Cornea of miR-183C WT control mouse of the MS-CKO strain-3 (Cornea MS-WT-3)


title: TG of miR-183C MS-CKO strain-3 (TG MS-CKO-3)


title: TG of miR-183C WT control mouse of the MS-CKO strain-5 (TG MS-WT-5)


title: Cornea of miR-183C SNS-CKO strain-3 (Cornea SNS-CKO-3)

value: miR-183C SNS-CKO


title: TG of miR-183C WT control mouse of the MS-CKO strain-2 (TG MS-WT-2)


title: TG of miR-183C WT control mouse of the MS-CKO strain-1 (TG MS-WT-1)


title: Cornea of miR-183C SNS-CKO strain-2 (Cornea SNS-CKO-2)


title: TG of miR-183C SNS-CKO strain-2 (TG SNS-CKO-2)


title: Cornea of miR-183C WT control mouse of the SNS-CKO strain-4 (Cornea SNS-WT-4)


title: Cornea of miR-183C SNS-CKO strain-1 (Cornea SNS-CKO-1)


title: TG of miR-183C SNS-CKO strain-3 (TG SNS-CKO-3)


title: TG of miR-183C WT control mouse of the SNS-CKO strain-4 (TG SNS-WT-4)


title: TG of miR-183C WT control mouse of the SNS-CKO strain-2 (TG SNS-WT-2)


title: TG of miR-183C WT control mouse of the SNS-CKO strain-1 (TG SNS-WT-1)


title: TG of miR-183C SNS-CKO strain-1 (TG SNS-CKO-1)


title: Cornea of miR-183C WT control mouse of the SNS-CKO strain-2 (Cornea SNS-WT-2)


title: Cornea of miR-183C WT control mouse of the SNS-CKO strain-3 (Cornea SNS-WT-3)


title: TG of miR-183C WT control mouse of the SNS-CKO strain-3 (TG SNS-WT-3)


title: Cornea of miR-183C WT control mouse of the SNS-CKO strain-1 (Cornea SNS-WT-1)


title: Cornea of miR-183C KO mouse-3 (Cornea KO-3)


title: Cornea of miR-183C WT control mouse-2 (Cornea WT-2)


title: Cornea of miR-183C KO mouse-2 (Cornea KO-2)


title: Cornea of miR-183C WT control mouse-3 (Cornea WT-3)


title: Cornea of miR-183C KO mouse-1 (Cornea KO-1)


title: TG of miR-183C KO mouse-3 (TG KO-3)


title: Cornea of miR-183C WT control mouse-1 (Cornea WT-1)


title: TG of miR-183C KO mouse-1 (TG KO-1)


title: TG of miR-183C WT control mouse-2 (TG WT-2)


title: TG of miR-183C KO mouse-2 (TG KO-2)


title: TG of miR-183C WT control mouse-1 (TG WT-1)


title: P2 Upper first Molar Whole Tooth ATAC-seq

city: Iowa City

first: HUOJUN

last: CAO

state: IA

address: 801 Newton Road

institute: University of Iowa

library_source: genomic

data_processing:
Reads were quality checked using the FastQC tool. Low-quality and adapter sequences were removed using Trimmomatic. Reads were mapped to mm10 with Bowtie2. bigWig files were generated using bamCoverage. narrowPeak files were generated using Genrich with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

source_name: Mouse Upper Molar

extract_protocol:
Embryonic day 11.5 (E11.5) embryos were dissected in ice cold DPBS. The first pharyngeal arches were dissected from embryos and treated with Dispase II. After 20-30 min, the ectoderm were carefully peeled from the mesencyme tissue. For postnatal tissues, P2 incisor or molar were dissected under microscopy. For isolation of Sox2 positive DESC, labial cervical loop (LaCL) region of P2 mouse lower incisors were dissected and kept in ice cold DMEM. Collagenase and Neutral Protease mixture were used to dissociate tissue to single cells. Sox2 positive DESC cells were sorted with FACS.
The improved ATAC-seq protocol (Omni-ATAC) were used to generate ATAC-seq libraries. Quality of cDNA and sequencing libraries were determined using a Bioanalyzer system (Agilent) and real time PCR. The KAPA Library Quantification Kit (Roche) was used for quantification of RNA sequencing libraries.

value: Mouse Upper Molar

tag: developmental stage

value: Postnatal day 2


title: P2 Lower first Molar Whole Tooth ATAC-seq

source_name: Mouse Lower Molar

value: Mouse Lower Molar


title: P2 Lower Incisor Whole Tooth ATAC-seq

source_name: Mouse Lower Incisor

value: Mouse Lower Incisor


title: P2 Lower Incisor Sox2-Positive DESC ATAC-seq rep 1


title: TG of miR-183C WT control mouse-3 (TG WT-3)


title: batchB Sox2-Positive 3

data_processing:
RNA-seq reads were quality checked using the FastQC tool. Low-quality and adapter sequences were removed using Trimmomatic. Expression of transcripts was quantified using Salmon, and estimates of transcript abundance for gene-level analysis were imported and summarized using the tximport package of the R/Bioconductor software suite.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts (gene level summarized with tximport) for each sample

extract_protocol:
Labial cervical loop (LaCL) region of P2 mouse lower incisors were dissected and kept in ice cold DMEM. Collagenase and Neutral Protease mixture were used to dissociate tissue to single cells. Sox2 positive DESC and Sox2 negative cells were sorted with FACS. Batch A and Batch B are experiments performed in two seperated days with different mouses.
The Smart-Seq2 protocol was followed for cDNA preparation, Tn5 Tagmentation, and library preparation for next generation sequencing. Quality of cDNA and sequencing libraries were determined using a Bioanalyzer system (Agilent) and real time PCR. The KAPA Library Quantification Kit (Roche) was used for quantification of RNA sequencing libraries.

tag: batch

value: batchB


title: batchB Sox2-Positive 6


title: batchB Sox2-Negative 4


title: batchB Sox2-Positive 7


title: batchB Sox2-Positive 5


title: batchA Sox2-Positive 6

value: batchA


title: batchA Sox2-Positive 4


title: batchA Sox2-Positive 5


title: E11.5 first pharyngeal arches ectoderm ATAC-seq rep 2

source_name: Mouse first pharyngeal arches ectoderm

value: Mouse first pharyngeal arches ectoderm

value: Embryonic day 11.5


title: E11.5 first pharyngeal arches ectoderm ATAC-seq rep 1


title: batchB Sox2-Negative 3


title: batchB Sox2-Negative 2


title: P2 Lower Incisor Sox2-Positive DESC ATAC-seq rep 2


title: batchB Sox2-Positive 4


title: batchB Sox2-Positive 2


title: batchB Sox2-Positive 1


title: batchA Sox2-Positive 3


title: batchA Sox2-Positive 2


title: batchB Sox2-Negative 1


title: batchA Sox2-Positive 1


title: batchA Sox2-Negative 6


title: batchA Sox2-Negative 5


title: batchA Sox2-Negative 4


title: batchA Sox2-Negative 2


title: batchA Sox2-Negative 3


title: batchA Sox2-Negative 1


title: K14CreTfap2afl/flTfap2bfl/fl 6 month-old 1

city: Charlestown

first: Alexander

last: Marneros

state: MA

address: 13th Street

institute: Massachusetts General Hospital

data_processing:
Raw sequence reads were trimmed to remove possible adapter sequences and low-quality reads using Trimmomatic v.0.36 (PMID: 24695404). The trimmed reads were mapped to the mouse GRCh38 reference genome using the STAR aligner v.2.5.2b (PMID: 23104886). Reads mapping to annotated genes were quantified using featureCounts from the Subread package v.1.5.2 (PMID: 23558742).
Assembly: GRCm38
Supplementary files format and content: counts.txt: Tab-delimited text files include raw read counts

source_name: epidermis

extract_protocol:
Total RNA was isolated with Trizol reagent and then with Zymo Direct-zol RNA Mini Prep Plus and DNase treatment
For RNA-seq library construction, rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA), and loaded to Illumina NovaSeq 6000 system for 150bp paired-end sequencing.

value: epidermis

tag: age


title: K14CreTfap2afl/flTfap2bfl/fl 6 month-old 2


title: kidney_KO control_rep1

city: West Haven

first: Xiaojia

last: Guo

state: Connecticut

address: Rm 7-188, Building 2, 950 Campbell Ave

department: Internal Medicine

institute: Yale University School of Medicine

description: 6 month old mouse with normal kidney function

hyb_protocol: cRNA were hybridized using Clariom S assay. GeneChip™ Hybridization, Wash, and Stain Kit, Cat# 900720 from Applied Biosystems was used. Automated array processing with the Fluidics Station done commercially by Thermofisher Scientific Transcriptome Profiling team.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G, scanned by Thermofisher Scientific Transcriptome Profiling team.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC4.0) Software

label: biotin

organism: Mus

source_name: kidney, Apobec1 KO mouse treated with saline

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). labeled with GeneChip™ WT Terminal Labeling Kit, Applied Biosystems. Commercially done using conveniently packaged target amplification and labeling, array processing and various process control reagents

growth_protocol: C57Bl/6j mice were purchased from Jaxson Lab, Apobec1 KO mice were raised in house and has C57Bl/6j background

extract_protocol: RNAs were extracted from kidneys using Trizol extraction followed by RNeasy kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Mice were treated with cisplatin disolved in saline at 15mg/kg for 3 days. Control groups received saline

tag: Sex

value: male

tag: strain background

value: Apobec1 KO

value: saline

value: kidney


title: kidney_KO+cisplatin_rep3

description: 6 month old mouse with severe acute kidney injury

source_name: kidney, Apobec1 KO mouse treated with cisplatin

value: cisplatin


title: kidney_KO control_rep3


title: K14CreTfap2afl/flTfap2bfl/fl 6 month-old 3


title: kidney_KO+cisplatin_rep2


title: kidney_KO control_rep2


title: kidney_WT+cisplatin_rep3

description: 6 month old mouse with acute kidney injury

source_name: kidney, wild type mouse treated with cisplatin

value: wild type


title: kidney_KO+cisplatin_rep1


title: control-strain specific 6 month-old 2

value: WT


title: control-strain specific 6 month-old 3

value: Wt


title: control-strain specific 6 month-old 1


title: 171342A_A3

city: nantong

first: zhaolian

last: bian

address: No. 60, Middle Qingnian Road

institute: Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University

description: circRNA expression of HCC

hyb_protocol: According to the  Agilent-084217 CapitalBio Technology Human CircRNA Array v2 Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: Adjacent to normal liver tissue 3

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent-084217 CapitalBio Technology Human CircRNA Array v2 microarray, according to manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

tag: tissue type

value: Adjacent to normal liver

tag: gender

tag: molecule subtype

value: circRNA


title: hF3-sgMED12-2-scRNAseq

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: raw counts

library_source: transcriptomic single cell

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

value: human pancreatic cancer organoid

tag: time


title: K14CreTfap2afl/flTfap2bfl/fl 3 week-old 3


title: kidney_WT+cisplatin_rep1


title: 171342A_A5

description: circRNA expression of HCC

source_name: Adjacent to normal liver tissue 5


title: kidney_WT control_rep3

source_name: kidney, wild type mouse treated with saline


title: 171342A_A2

description: circRNA expression of HCC

source_name: Adjacent to normal liver tissue 2


title: kidney_WT+cisplatin_rep2


title: 171342A_T3

description: circRNA expression of HCC

source_name: Hepatocellular carcinoma tissue 3

value: Hepatocellular carcinoma


title: 171342A_T5

description: circRNA expression of HCC

source_name: Hepatocellular carcinoma tissue 5


title: hF3-sgROSA26-scRNAseq

description: raw counts


title: 171342A_A1

description: circRNA expression of HCC

source_name: Adjacent to normal liver tissue 1


title: K14CreTfap2afl/flTfap2bfl/fl 3 week-old 1


title: kidney_WT control_rep1


title: 171342A_T2

description: circRNA expression of HCC

source_name: Hepatocellular carcinoma tissue 2


title: hF3-sgTP63-51e1-scRNAseq

description: raw counts


title: 171342A_T4

description: circRNA expression of HCC

source_name: Hepatocellular carcinoma tissue 4


title: BxPC3-T3M4-sgMED12-2-scRNAseq

description: raw counts

source_name: BxPC3, T3M4

value: human pancreatic cancer cell line

value: BxPC3, T3M4


title: K14CreTfap2afl/fl 3 week-old 3


title: 171342A_T1

description: circRNA expression of HCC

source_name: Hepatocellular carcinoma tissue 1


title: BxPC3-T3M4-sgROSA26-scRNAseq

description: raw counts


title: 1284_2023, high

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Reads were trimmed using Trimgalore (v0.6.7) with default parameters
Reads were aligned to the human reference genome GRCh38 using STAR (v2.7.10a) with default parameters
SAM files were converted to BAM and sorted using sambamba (v2.098.1)
The count matrix was generated with the function featureCounts of the R package Rsubread (v2.8.2) and annotation from ENSEMBL GRCh38.101
Assembly: GRCh38
Supplementary files format and content: Excel file with raw counts

source_name: Colon

growth_protocol: Tumor cells were grown as organoids embedded in basement membrane extract (Cultrex BME Type 2, AMSbio) using tumor organoid medium composed of Advanced DMEM/F12 (Gibco), 10 mM HEPES (Sigma-Aldrich), 1% GlutaMax; 1× B-27, 20 ng ml-1 Human FGF (fibroblast growth factor) basic (all from Gibco); 50 ng ml-1 recombinant human EGF (epidermal growth factor) and recombinant Noggin (100 ng ml-1) (both from Peprotech). The medium was supplemented with 0.2% Normocin (InvivoGen) as an antimicrobial agent.

extract_protocol:
Organoids grown in BME for 6-7 days were harvested using TrypLE and centrifuged at 400 g for 4 min.  Cells were then resuspended in cold tumor organoid medium and sorted into LGR5-, LGR5med and LGR5+ cells (two biological replicates for each sample). RNA was extracted using the Qiagen RNeasy Micro Kit and following the manufacturer’s instructions (Qiagen).
RNA libraries were prepared for sequencing using the kits Illumina® Stranded mRNA Prep, Ligation (20040534) and IDT® for Illumina® RNA UD Indexes Set A, Ligation (20040553), following manufacturer´s instructions and 11 cycles of amplification.

value: Colon

value: PDO7 GS605

value: Colorectal cancer cells

tag: replicate

tag: lrg5 expression

value: high


title: 1285_2023, med

tag: tissue

value: med


title: control-strain specific 3 week-old 2

value: epidermis


title: control-strain specific 3 week-old 3


title: 171342A_A4

description: circRNA expression of HCC

source_name: Adjacent to normal liver tissue 4

value: male


title: 1282_2023, total

tag: cell type

value: total


title: 1283_2023, neg

value: neg


title: K14CreTfap2afl/flTfap2bfl/fl 3 week-old 2

source_name: epidermis

tag: genotype


title: 1280_2023, med


title: S2_GB_LM_PC [FR985_GB]

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

data_processing:
Celseq2: Fastq files were aligned using STAR v2.7.10a with default parameters. 10X: Non-multiplexed files were run with Cellranger v7.1.0 count functionality, multiplexed and fixed RNA profiling samples were run using the Cellranger v7.1.0. multi functionality.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
The number of observed UMIs was converted into transcript counts using Seurat v4 Hao et al, Cell 2021 10.1016/j.cell.2021.04.048
GENCODE human genome release 33
Assembly: Celseq2: matrix files as output by StarSolo, with up to 192 cells per sample. 10X h5 files with counts information and, where available CITE-Seq and multiplexing information

source_name: Bain or brain tumor

extract_protocol: Single-cell RNA sequencing using 10x and Cel-Seq2 was conducted on cell suspensions and after nuclei extraction from fresh frozen sections or formalin-fixed formalin embedded tissues. A part of the single cell analyses was multilexed and analyzed using CITE-Seq.

value: Bain or brain tumor

value: CD45-positive cells

value: postnatal


title: control 3 week-old 3

value: WT


title: 1281_2023, high


title: S2_GB_LM_PC [FR910_GB_Men]


title: S2_GB_LM_PC [FR901_GB]


title: 1279_2023, neg


title: control 3 week-old 1


title: S2_GB_LM_PC [FR607_GB_Men]


title: S2_GB_LM_PC [FR210_CTX]

value: prenatal


title: control 3 week-old 2


title: BxPC3-T3M4-sgTP63-51e1-scRNAseq

description: raw counts


title: Tryptophan benzyl ester-betaxanthin treated  JK1466 animals, Independent Trial 3

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

institute: University of Murcia

description:
Gene expression data from animals treated with 25 uM Tryptophan benzyl ester-betaxanthin
JK-BE3.ga.rma-gene-full.chp Signal

hyb_protocol: 3.75 µg of fragmented and biotinylated ss-cDNA were included in the hybridization mix, using the GenAtlas Hybridization, Wash and Stain kit for WT Array Strips (Affymetrix, P/N 901667) according to the recommendations of the manufacturer. The resulting preparations were hybridized to GeneChip® C. elegans Gene 1.1 ST Array Strip (Affymetrix, 902157) with 26 unique sequences of each transcript. After applying hybridization (spike controls) and labeling tests it was observed that the 20 chips had fulfilled the quality criteria.

scan_protocol: GeneAtlas Microarray System from Affymetrix

data_processing:
After scanning, microarrays data were processed using Affymetrix Expression Command Console (Affymetrix) and all samples were within bounds for hybridization and labeling tests. Three independent RNA samples were employed. Samples from worms treated with food colorants were grouped as “treatment” and worms with no exposition were grouped as “control”. Data analysis was then performed with RMA (Robust Multiarray Average) allowing raw intensity values to be background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: BIOTIN-STREPTAVIDIN

organism: Caenorhabditis elegans

source_name: C. elegans  JK1466 treated with 25 uM Tryptophan benzyl ester-betaxanthin

label_protocol: Ss-cDNA was synthetized from 3.5 ng of each sample using the GeneChip WT Pico Reagent kit (Affymetrix, P/N 703262). The amount and quality of ss-cDNA were checked by Nanodrop and Bioanalyzer. ss-cDNA targets were cleaned up, and after fragmentation and terminal labelling with biotin

growth_protocol: JK1466 worms  were syncronized using the bleaching protocol, from adult worms maintained in standart NGM agar plates at 20 ºC

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions, followed by a purification using  PureLink TM RNA Mini Kit from Invitrogen

treatment_protocol: 16-18 hours after haching L1 larvae were treated with 25 uM of each tryptophan derived-betaxanthin in S. medium for 48 hours at 20 ºC

value: Whole animal

value: 2 days after hacht, L4/young adults


title: K14CreTfap2bfl/fl 3 week-old 3


title: Tryptophan methyl ester-betaxanthin treated  JK1466 animals, Independent Trial 2

description:
Gene expression data from animals treated with 25 uM Tryptophan-methyl ester-betaxanthin
JK-ME2.ga.rma-gene-full.chp Signal

source_name: C. elegans  JK1466 treated with 25 uM Tryptophan methyl ester-betaxanthin


title: Tryptophan methyl ester-betaxanthin treated  JK1466 animals, Independent Trial 3

description:
Gene expression data from animals treated with 25 uM Tryptophan-methyl ester-betaxanthin
JK-ME3_1.ga.rma-gene-full.chp Signal


title: Tryptophan benzyl ester-betaxanthin treated  JK1466 animals, Independent Trial 2

description:
Gene expression data from animals treated with 25 uM Tryptophan benzyl ester-betaxanthin
JK-BE2.ga.rma-gene-full.chp Signal


title: P6_CP2 [P6_CP2_15984_fCP_20pcw]

description:
harmony_integrated_nucseq_all_cells.H5Seurat
immune_combined_with_Braun_Yang_et_al.H5Seurat

value: NeuN-Olig2-negative nuclei


title: P6_CP2 [P6_CP2_FR210_fCP_23pcw]


title: kidney_WT control_rep2

value: wild type

tag: treatment

value: saline

value: kidney


title: K14CreTfap2afl/fl 3 week-old 1


title: P6_CP2 [P6_CP2_15983_hCP_20pcw]


title: Tryptophan benzyl ester-betaxanthin treated  JK1466 animals, Independent Trial 1

description:
Gene expression data from animals treated with 25 uM Tryptophan benzyl ester-betaxanthin
JK-BE1.ga.rma-gene-full.chp Signal


title: K14CreTfap2bfl/fl 3 week-old 2


title: P6_CP2 [P6_CP2_15983_fCP_20pcw]


title: control-strain specific 3 week-old 1


title: P5_CP1 [P5_CP1_17724_fCP_CS21]


title: K14CreTfap2bfl/fl 3 week-old 1


title: BMDM,SIRT7+/+,H37Rv,12h,rep3

city: Shenzhen

first: Fuxiang

address: Nanhai Avenue 3688

institute: shenzhen university

data_processing:
Quality Control.Tool: Cutadapt (V1.9.1). Removal of technical sequences and bases with quality lower than 20.
Read Mapping. Tool: Hisat2 (v2.0.1). Alignment of clean data to reference genome.
Expression Analysis. Tool: HTSeq (v0.6.1). Estimation of gene and isoform expression levels.
Differential Expression Analysis. Tool: DESeq2 Bioconductor package. Utilization of a model based on the negative binomial distribution, with data-driven prior distributions for estimates of dispersion and logarithmic fold changes. Padj <0.05 for differential expression detection.
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RpkM values for each Sample

source_name: bone marrow-derived macrophages

growth_protocol: BMDMs were isolated from Sirt7+/+ and Sirt7-/- mice, Bone marrow cells were cultured for 7 days in DMEM containing 20% L929 cell-conditioned medium, 1 mM sodium pyruvate, 2 mM L-glutamine, and 10% fetal bovine serum. The culture and induction process was carried out at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. Poly(A) mRNA isolation or rRNA removal, mRNA fragmentation and priming, first and second-strand cDNA synthesis, end preparation, adaptor ligation, size selection (~400 bp fragments), PCR amplification, and cleanup. Size: ~400 bp fragments.

treatment_protocol: BMDMs of Sirt7+/+ or Sirt7-/- were uninfected or H37Rv-infected 12h.

value: bone marrow-derived macrophages

value: macrophages


title: Tryptophan methyl ester-betaxanthin treated  JK1466 animals, Independent Trial 1

description:
Gene expression data from animals treated with 25 uM Tryptophan-methyl ester-betaxanthin
JK-ME1.ga.rma-gene-full.chp Signal


title: P5_CP1 [P5_CP1_17708_hCP_CS23]


title: Tryptophan-betaxanthin treated  JK1466 animals, Independent Trial 3

description:
Gene expression data from animals treated with 25 uM Tryptophan-betaxanthin
JK-Tryp3.ga.rma-gene-full.chp Signal

source_name: C. elegans  JK1466 treated with 25 uM Tryptophan-betaxanthin


title: P5_CP1 [P5_CP1_15982_fCP_12pcw]


title: P5_CP1 [P5_CP1_15853_hCP_13pcw]


title: K14CreTfap2afl/fl 3 week-old 2

value: epidermis


title: Tryptophan-betaxanthin treated  JK1466 animals, Independent Trial 1

description:
Gene expression data from animals treated with 25 uM Tryptophan-betaxanthin
JK-Tryp1.ga.rma-gene-full.chp Signal


title: Tryptophan-betaxanthin treated  JK1466 animals, Independent Trial 2

description:
Gene expression data from animals treated with 25 uM Tryptophan-betaxanthin
JK-Tryp2.ga.rma-gene-full.chp Signal


title: BMDM,SIRT7+/+,H37Rv,12h,rep2


title: P5_CP1 [P5_CP1_15895_fCP_15pcw]


title: P5_CP1 [P5_CP1_15665_fCP_9pcw]


title: P4_LM2 [P4_LM2_17724_Par_CS21]


title: P5_CP1 [P5_CP1_17708_fCP_CS23]


title: P4_LM2 [P4_LM2_15982_Par_12pcw]


title: BMDM,SIRT7-/-,H37Rv,12h,rep4


title: BMDM,SIRT7+/+,H37Rv,12h,rep1


title: P4_LM2 [P4_LM2_14572_Par_11pcw]


title: P4_LM2 [P4_LM2_13927_Par_14pcw]


title: BMDM,SIRT7-/-,H37Rv,12h,rep3


title: BMDM,SIRT7-/-,H37Rv,12h,rep2


title: Water treated JK1466 animals, Independent Trial 3

description:
Gene expression data from control (non treated) animals
JK-C3.ga.rma-gene-full.chp Signal

source_name: C. elegans Jk1466 water control


title: P4_LM2 [P4_LM2_15161_Par_CS23]


title: P3_LM1 [P3_LM1_15895_Par_15pcw]


title: hippocampus, Male Het WT rep 2

city: Los Angeles

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2(Galaxy version 2.1.0+galaxy 7)
featureCounts(Galaxy version 2.0.1) was used to counting the CPM. Allow reads to map to multiple featues: Diabled.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampus

extract_protocol:
Hippocampus tissues were isolated from 3-month-old adult WT and NELL-1(+/6R) mice. Total RNA was isolated using Qiagen Rneasy Lipd Tissue Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

value: Male

value: 3-month-old adult


title: P3_LM1 [P3_LM1_14773_Par_17pcw]

value: Bain or brain tumor


title: BMDM,SIRT7-/-,H37Rv,12h,rep1


title: P3_LM1 [P3_LM1_14159_Par_20pcw]


title: hippocampus, Male Het WT rep 3


title: P4_LM2 [P4_LM2_11938_Par_9pcw]


title: Water treated JK1466 animals, Independent Trial 1

description:
Gene expression data from control (non treated) animals
JK-C1_1.ga.rma-gene-full.chp Signal


title: P3_LM1 [P3_LM1_13885_Par_19pcw]


title: Water treated JK1466 animals, Independent Trial 2

description:
Gene expression data from control (non treated) animals
JK-C2_1.ga.rma-gene-full.chp Signal


title: BMDM,SIRT7+/+,control,rep3

value: DMEM


title: P3_LM1 [P3_LM1_13800_Par_17pcw]


title: hippocampus, Male Het [NELL-1(+/6R)] rep 3


title: P2_Par2 [P2_Par2_15895_Par_15pcw]


title: hippocampus, Male Het WT rep 1


title: P3_LM1 [P3_LM1_13103_Par_19pcw]


title: hippocampus, Male Het [NELL-1(+/6R)] rep 2


title: P2_Par2 [P2_Par2_14773_Par_17pcw]


title: BMDM,SIRT7+/+,control,rep2


title: P2_Par2 [P2_Par2_14159_Par_20pcw]


title: P2_Par2 [P2_Par2_13885_Par_19pcw]


title: BMDM,SIRT7+/+,control,rep1


title: BMDM,SIRT7-/-,control,rep3


title: hippocampus, Male Het [NELL-1(+/6R)] rep 1


title: hippocampus, Female Het WT rep 3

value: Female


title: P2_Par2 [P2_Par2_13103_Par_19pcw]


title: BMDM,SIRT7-/-,control,rep2


title: hippocampus, Female Het WT rep 2

value: WT


title: BMDM,SIRT7-/-,control,rep1


title: P1_Par1 [P1_Par1_15982_Par_12pcw]

value: prenatal


title: P1_Par1 [P1_Par1_15161_Par_CS23]


title: hippocampus, Female Het WT rep 1


title: P1_Par1 [P1_Par1_14572_Par_11pcw]


title: hippocampus, Female Het [NELL-1(+/6R)] rep 3


title: P1_Par1 [P1_Par1_13927_Par_14pcw]


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

city: Milano

first: Sara

last: Valsoni

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument and raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Reads quality was controlled with Fastqc v0.11.9, while low quality reads and the adapters were removed using Trim Galore v0.6.6 according to following parameters: --quality 20, --length 25, --paired
Remaining reads were aligned to the murine reference genome GRCm38 using STAR v2.7.6a with default parameters
Gene counts were quantified using the featureCounts function from Subread package v 2.0.1 and Gencode v M25 as gene model
Raw counts were corrected for biases due to different library preparations using the ComBat_seq function from the R/Bioconductor package sva v3.38.0
The differential expression analysis was performed using the R/Bioconductor package DESeq2 v1.30.0
Assembly: GRCm38
Supplementary files format and content: text file with raw counts

source_name: Liver

extract_protocol:
RNA exrtraction by RNeasy® Mini Kit (QIAGEN), following provider indications
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations

value: Liver

value: Hepa 1-6

value: Hepatocyte

value: Mock


title: P1_Par1 [P1_Par1_11938_Par_9pcw]

value: NeuN-Olig2-negative nuclei


title: hippocampus, Female Het [NELL-1(+/6R)] rep 2


title: C4 [C4]

description:
all_cells.H5Seurat
micr_ffpe.H5Seurat

value: postnatal


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

value: ZFP-ETRs against Pcsk9


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: P2_Par2 [P2_Par2_13800_Par_17pcw]


title: T4 [T4]

description:
all_cells.H5Seurat
micr_ffpe.H5Seurat


title: HGC27, RUNX3KO, RUNX3, ChIP, rep1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Basecalls were performed using bcl2fastq.
ChIP-seq experiment were aligned to UCSC human genome (hg19) using bowtie 1.0.1.
Duplicated reads were removed with Picard tools 2.3.0.
bigWig files were generated using HOMER 4.11.1.
Peaks were called using HOMER 4.11.1  findPeaks.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: MEM, 10% fetal bovine serum, 1x penicillin/streptmycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picoruptor (Diagenode).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for Input and ChIP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Tapestation.

value: RUNX3 knock-out

tag: chip antibody


title: S3 [FR890_GB]

description: multimodal_harmony_integrated_controls.RData

value: CD45-positive cells


title: T2 [T2]

description:
all_cells.H5Seurat
micr_ffpe.H5Seurat


title: C3 [C3]

description:
all_cells.H5Seurat
micr_ffpe.H5Seurat


title: S3 [FR721_DM]


title: hippocampus, Female Het [NELL-1(+/6R)] rep 1

value: hippocampus


title: EvoETRs 3 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

tag: cell line

value: EvoETRs 3 against Pcsk9


title: T3 [T3]

description:
all_cells.H5Seurat
micr_ffpe.H5Seurat

tag: developmental stage


title: S3 [FR510_LM_GB]


title: HGC27, RUNX3KO, H3K4me1, ChIP, rep2


title: EvoETRs 3 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: HGC27, wt, RUNX3, ChIP, rep2

value: wildtype


title: S3 [FR510_CTX]

value: Bain or brain tumor


title: S3 [FR250_LM]


title: EvoETRs 6 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

value: EvoETRs 6 against Pcsk9


title: HGC27, RUNX3KO, H3K4me1, ChIP, rep1


title: EvoETRs 6 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: S3 [FR250_CTX]


title: S1_Ctrl_LM_CP_PC [FR850_CP]


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: EvoETRs 8 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

value: EvoETRs 8 against Pcsk9


title: S1_Ctrl_LM_CP_PC [FR742_Men]


title: S1_Ctrl_LM_CP_PC [FR615_CTX]


title: HGC27, wt, H3K4me1, ChIP, rep2


title: HGC27, wt, H3K4me1, ChIP, rep1


title: CAM_FB-CPLX [FR925_LM]


title: HGC27, RUNX3KO, H3K27ac, ChIP, rep2


title: EvoETRs 8 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: S1_Ctrl_LM_CP_PC [FR210_CP]


title: HGC27, wt, H3K4me3, ChIP, rep2


title: S1_Ctrl_LM_CP_PC [FR240_CTX]


title: S1_Ctrl_LM_CP_PC [FR240_Men]


title: HGC27, RUNX3KO, H3K4me3, ChIP, rep2


title: C2C12 cells, YBX3-targeting siRNA, differentiating myoblasts_bio rep 2

city: Haverford

first: Amy

last: Cooke

address: 370 Lancaster Ave

department: Biology

institute: Haverford College

data_processing:
Illumina bcl files were demuliplexed and processed with the standard pipeline v3.4.4 to produce fastq files
Fastq files were mapped using Salmon (https://salmon.readthedocs.io/en/latest/) to the transcriptome defined in Genecode M30 (https://www.gencodegenes.org) which was built version GRCm39 of the mouse genome.
Assembly: GRCm39 / Gencode M30
Supplementary files format and content: raw counts per sample keyed by EnsemblID - gzipped comma separated values

growth_protocol: C2C12 proliferating myoblasts were maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin & 10% L-glutamine

extract_protocol:
Total RNA was extracted using the GeneJet RNA purification kit (Thermo). 1 ug of total RNA was submitted for the construction of sequencing libraries.
High-throughput library prep using the Illumina Stranded mRNA Prep kit following manufacturer's protocols.

treatment_protocol: siRNAs were reverse transfected into proliferating C2C12 myoblasts using lipofectamine RNAiMAX transfection reagent (Thermo) following manufacturer's instruction. 24 hours after siRNA transfection, skeletal muscle differentiation was either not induced (i.e., maintained in standard DMEM) or induced by a media change containing DMEM with 10% horse serum instead of fetal bovine serum. The media included the antibiotics and glutamine.

value: differentiating myoblast

tag: sirna

tag: timepoint


title: C2C12 cells, YBX3-targeting siRNA, differentiating myoblasts_bio rep 3


title: CAM_FB-CPLX [FR882_CP]


title: HGC27, wt, H3K27ac, ChIP, rep2


title: S1_Ctrl_LM_CP_PC [FR127_CP]


title: CAM_FB-CPLX [FR900_LM]


title: CAM_FB-CPLX [FR818_LM]


title: CAM_FB-CPLX [FR793_DM]


title: C2C12 cells, YBX3-targeting siRNA, differentiating myoblasts_bio rep 1


title: CAM_FB-CPLX [FR648_LM]


title: C2C12 cells, YBX3-targeting siRNA, proliferating myoblasts_bio rep 4

value: proliferating myoblast


title: CAM_FB-CPLX [FR484_LM]


title: C2C12 cells, YBX3-targeting siRNA, proliferating myoblasts_bio rep 3


title: S1_Ctrl_LM_CP_PC [FR210_LM]

value: prenatal


title: CAM_FB-CPLX [FR449_LM]


title: C2C12 cells, YBX3-targeting siRNA, proliferating myoblasts_bio rep 2


title: CAM_FB-CPLX [FR898_DM]


title: CAM_FB-CPLX [FR110_LM]


title: MiaTAMs schwann cells rep3

first: Leyi

last: Huang

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a protocol from  Mortazavi A et al., Nat Methods, 2008.We first applied StringTie (version:1.3.0) to the Fragments of each gene after Hisat2 comparison, then normalized with TMM (mean of M values) , and finally calculates the FPKM value for each gene with Perl.
Genome_build: Rnor_6.0.81
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

organism: Rattus norvegicus

source_name: MIA PaCa-2 induced-TAMs co-cultured Rat Schwann cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were conducted with standard Illumina protocols, using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina® (Vazyme, China), Agencourt ® AMPure XP Beads(Beckman, USA),Qubit™ dsDNA HS Assay Kit(Invitrogen, USA) and Agilent High Sensitivity DNA Kit(Agilent, USA).

value: Rat Schwann cells

value: culture with MiaTAMs


title: MiaTAMs schwann cells rep1


title: Botrytis cinerea △BcSpd1 treated for 24h rep2

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

description: Botrytis cinerea △BcSpd1 treated  sample 24h- 2

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: http://ginsengdb.snu.ac.kr/
Assembly: All ginseng genomic sequence data were deposited to the National Agricultural Biotechnology Information Center (NG-0858-000001~NG-0858-009845) (http://nabic.rda.go.kr).
Supplementary files format and content: Excel file includes FPKM values  and counts for each Sample

organism: Panax ginseng

source_name: leaf

growth_protocol: The ginseng were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark.The plants were watered once a week and kept growing for about 2 years.

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

treatment_protocol: The Botrytis cinerea were grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were spray infected with 2.5*105 spores mL-1. The buffer without any spores were sprayed as untreated control (CK). All leaves were harvest at 14hours and 24 hours and frozen at -80℃ for RNA sequencing.

value: leaf

tag: age

value: 2 years old ginseng plant

value: Botrytis cinerea deltaBcSpd1 treated 24h


title: Botrytis cinerea △BcSpd1 treated for 24h rep1

description: Botrytis cinerea △BcSpd1 treated  sample 24h- 1


title: Botrytis cinerea △BcSpd1 treated for 14h rep3

description: Botrytis cinerea △BcSpd1 treated  sample 14h- 3

value: Botrytis cinerea deltaBcSpd1 treated 14h


title: C2C12 cells, non-targeting siRNA control, proliferating myoblasts_bio rep 4

value: siNT


title: Botrytis cinerea △BcSpd1 treated for 24h rep3

description: Botrytis cinerea △BcSpd1 treated  sample 24h- 3


title: C2C12 cells, non-targeting siRNA control, differentiating myoblasts_bio rep 1


title: Botrytis cinerea △BcSpd1 treated for 14h rep2

description: Botrytis cinerea △BcSpd1 treated  sample 14h- 2


title: CK rep2

description: uninfected control samples replicate 2

value: control


title: CAM_FB-CPLX [FR288_LM]

value: CD45-positive cells

value: postnatal


title: Botrytis cinerea △BcSpd1 treated for 14h rep1

description: Botrytis cinerea △BcSpd1 treated  sample 14h- 1

value: wildtype


title: BxTAMs schwann cells rep3

city: Guangzhou

source_name: BxPC-3 induced-TAMs co-cultured Rat Schwann cells

value: culture with BxTAMs


title: CK rep3

description: uninfected control samples replicate 3


title: C2C12 cells, non-targeting siRNA control, proliferating myoblasts_bio rep 3


title: LM_GB [FR549_LM_GB]

value: Bain or brain tumor

value: NeuN-negative nuclei


title: BxTAMs schwann cells rep2


title: CK rep1

description: uninfected control samples replicate 1


title: cKO_scATAC

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

library_source: genomic single cell

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v1.2).
Hashtag processing followed the original recommendations of the ASAP-seq paper (Mimitou et al, Nature Biotech, 2021), using asap_to_kite (https://github.com/caleblareau/asap_to_kite) to process FASTQs files for downstream quantification by the bustools and kite workflows {Melsted et al, Nature Biotech 2021; Booeshagi et al, bioRxiv, 2022}. We used the HTODemux() (Stoeckius et al, Genome Biology, 2018)  function in the Seurat package (v4.0.2) (Hao et al, Cell, 2021) to remove doublets and call hashtag identities.
To enable comparisons across conditions and datasets, we used a common set of Treg-specific open chromatin regions, defined previously (Chowdhary et al., 2023) by supplementing pan-immunocyte OCRs from the ImmGen consortium(Yoshida et al., 2019) with additional peaks from Treg spleen and colon scATAC-seq data in (Chowdhary et al., 2023). To arrive at the final peak set, we also called peaks on the data generated in this study, using Archr v1.0.1(Granja et al., 2021) and MACS2 v2.2.7.1(Zhang et al., 2008) to call fixed-width peaks of 250bp within cell clusters. Any new OCRs not overlapping with the previous peak sets were added to the final merged peak set used for downstream analysis.
scATACseq data analysis was performed using Signac v1.4(Stuart et al., 2021). For quality control, only cells with at least 1x103 fragments per cell (depending on sequencing depth of experiment), greater than 25 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05 were retained for further analysis. Putative doublets identified by ArchR v1.0.1(Granja et al., 2021) and non-Treg, non-Tconv contaminant cells were also removed. We used the latent semantic indexing approach as previously described (Cusanovich et al., 2018; Stuart et al., 2019). Binarized count matrices were normalized using the term frequency-inverse document frequency (TF-IDF) transformation and reduced in dimensionality by singular value decomposition (SVD). As the first component was highly correlated with sequencing depth, SVD components 2-30 were used to generate a shared nearest neighbor (SNN) graph for clustering and as input into UMAP(McInnes et al., 2018) with cosine distance metric for visualization.
Assembly: mm10
Supplementary files format and content: .mtx ATAC counts matrices, peaks.txt files have OCR locations, barcodes.txt files have cell barcodes
Supplementary files format and content: fragments.tsv.gz files have raw ATAC fragments, fragments.tsv.gz.tbi files are index of fragments files
Supplementary files format and content: MetaData.txt files have relevant metadata, including cell population assignment, UMAP coordinates
Supplementary files format and content: Hashtag_Counts.txt files contain raw counts of ASAPseq hashtags by cell barcode for cells included in ATAC counts matrices

extract_protocol:
For scATAC-seq, colonic lamina propria cells were sorted for Tregs (DAPI-CD19-CD8-CD11b-CD4+TRCRb+CD25hi) and activated Tconvs (DAPI-CD19-CD8-CD11b-CD4+TRCRb+CD25loCD44hi). Cells were hashtagged by condition at the time of staining as detailed below.
Nuclei isolation, transposition, GEM generation, and library construction targeting capture of 10000 cells were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics) with modifications to allow sample hashtagging (see below). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 to a final median depth of approximately 20-30,000 paired-end reads per cell. Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v1.2).  To include multiple experimental conditions in the same scATAC run, we hashtagged cells using a modification of the ASAP-seq strategy (Mimitou et al., 2021) for low cell input primary cell samples. Before sorting, cells were hashtagged with mouse TotalSeqA DNA-barcoded hashtag antibodies at the same time as staining with fluorophore-conjugated antibodies (BioLegend). Cells were sorted into RPMI + 5% FCS in DNA Lo-Bind tubes (Eppendorf, cat # 022431021). After spinning down for 5 min at 500g in a refrigerated centrifuge at 4C, cells were resuspended in 100 μl chilled 0.1x Omni Lysis buffer (1x Omni Lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute/IGEPAL, 0.01% Digitonin, 1% BSA in nuclease free water) diluted 1:10 in Wash/Lysis Dilution Buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 1% BSA in nuclease free water), gently mixed by pipetting, and incubated on ice for 6.5 min. Following lysis, 100 μl chilled wash buffer was added and gently mixed by pipetting. Cells were spun down for 5 min at 500g at 4C, all but 5 μl of supernatant was removed, and 45 μl of chilled 1x nuclei buffer (10x Genomics) was added without mixing. After one more centrifugation step at 500g, 4C for 5 min, supernatant was removed, and samples were resuspended in 7ul 1x nuclei buffer for cell counting and input into transposition, barcoding, and library preparation according to the Chromium Next GEM Single Cell ATAC manual (10x Genomics).  Modifications to the original 10X protocol were made as described in the original ASAP-seq publication (Mimitou et al., 2021) and as detailed at https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf. Briefly, 0.5 μl of 1uM BOA bridge oligo was spiked into the barcoding reaction. During GEM incubation, an additional 5 min incubation at 40C was added to the beginning of the protocol. 43.5 instead of 40.5 μl of Elution Solution I was added during silane bead elution to recover 43 μl. 40 μl was used for SPRI clean up as indicated in the protocol, while 3 μl was set aside. During SPRI cleanup, the supernatant was saved. The bead bound fraction was processed as in the protocol, while for the supernatant fraction, 32 μl SPRI was added for 5 min. Beads were collected on a magnet, washed twice with 80% ethanol, and eluted in 42 μl EB. This 42 μl was combined with the 3 μl set aside from the previous step as input into the HTO indexing reaction. HTO Indexing PCR was run with partial P5 and indexed Rpxx primers (https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf) as: 95C 3 min, 12-14 cycles of (95C 20 sec, 60C 30 sec, 72C 20 sec), 72C 5 min. The PCR product was cleaned up with 1.6X SPRI purification for quantification and sequencing alongside ATAC libraries.

value: Colon

value: Treg

value: WT, Foxp3Cre x Rorc fl/fl, Foxp3Cre x Ikzf2 fl/fl, Foxp3Cre x Gata3 fl/fl, Foxp3Cre x cMaf fl/fl

tag: strain

tag: Sex

value: pooled male and female


title: C2C12 cells, non-targeting siRNA control, proliferating myoblasts_bio rep 2

value: proliferating myoblast


title: BxTAMs schwann cells rep1

value: Rat Schwann cells


title: LM_GB [FR549_LM]

description: harmony_integrated_nucseq_all_cells.H5Seurat


title: C2C12 cells, YBX3-targeting siRNA, proliferating myoblasts_bio rep 1


title: MiaTAMs schwann cells rep2

value: culture with MiaTAMs


title: C2C12 cells, non-targeting siRNA control, differentiating myoblasts_bio rep 2

value: differentiating myoblast


title: LM_GB [FR322_LM]


title: Multiplexed Control, VSV-LV, CD8-LV, CD4-LV from donors 2 and 3

city: Langen

first: Christian

middle: J.

last: Buchholz

state: Hessen

address: Paul-Ehrlich-Strasse 51-59

institute: Paul Ehrlich Institut

description: Multiplexed samples

data_processing:
Seven Bridges Bioinformatics Platform Filtering, Alignment, run locally in a server
Use default settings of:
BD Rhapsody™ WTA Analysis Pipeline run
Demultiplexing concatenated samples via sample tag calls  SampleTag01_hs = Control_donor2, SampleTag02_hs=VSV-LV_donor2, SampleTag03_hs=CD8-LV_donor2, SampleTag04_hs=CD4-LV_donor2, SampleTag05_hs=Control_donor3, SampleTag06_hs=VSV-LV_donor3, SampleTag07_hs=CD8-LV_donor3, SampleTag08_hs=CD4-LV_donor3
Guidelines for loading matrices and demultiplexing Guidelines for demultiplexing.txt
Assembly: GRCh38-PhiX-gencodev29 Including the supplementary sequences in  CAR_reference.fasta
Supplementary files format and content: Metrics Summary output
Supplementary files format and content: Gene / cell count matrix

source_name: PBMC

growth_protocol: RPMI medium with 10% FCS, 2 mM glutamine, 0.5% penicillin/streptomycin, 25 mM HEPES

extract_protocol:
Nanowell-based scRNA isolation and library preparation based on manufacturer's instructions (BD Biosciences) for targeted gene amplification
BD Rhapsody, Whole Transcriptome Analysis

treatment_protocol: Pre-activated PBMC inoculated with LVs and cultured for 3 days

tag: days expansion

tag: lv type

value: Multiplexed samples


title: C2C12 cells, non-targeting siRNA control, proliferating myoblasts_bio rep 1

value: siNT


title: LM_FB-CLPLX [FR808_LM]


title: LM_FB-CLPLX [FR496_LM]


title: LM_FB-CLPLX [FR231_LM]


title: PBMC rep2

source_name: MDMs co-cultured Rat Schwann cells

value: untreated


title: LM_FB-CLPLX [FR472_LM]


title: FR210_Par_23pcw [FR210_Par_23pcw]

description:
harmony_integrated_nucseq_all_cells.H5Seurat
immune_combined_with_Braun_Yang_et_al.H5Seurat

value: NeuN-Olig2-negative nuclei

value: prenatal


title: adult-control-mixed [adult-control-mixed]

value: postnatal


title: men [men]

value: CD45-positive cells


title: FR210_LM_23pcw [FR210_LM_23pcw]

value: Bain or brain tumor


title: cp [cp]


title: Rsc96 rep3

source_name: Rat Schwann cells


title: PBMC rep1


title: Rsc96 rep1


title: CD4-LV_Donor3

description: CAR T cells

value: CD4 targeted


title: TEC+G-1

city: Shanghai

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

data_processing:
RNA libraries were constructed using the VAHTS® Universal V6 RNA-seq Library Prep Kit.
Transcriptome sequencing and paired-end reads were obtained on the Novaseq 6000 platform.
The quality of RNA-seq data was estimated using RSeQC (version 2.6.4).
Differentially expressed genes were identified using the DESeq2. P value <0.05 and foldchange >2 or foldchange <0.5 was set as the threshold for selecting significantly differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: table-delimited text file includes raw counts for each Sample

source_name: primary tubular epithlial cells

extract_protocol:
RNA were  extracted using TRIzol
VAHTS® Universal V6 RNA-seq Library Prep Kit

value: primary tubular epithlial cells

value: primary tubular epithelial cells

value: tubular epithelial cells

value: WT

value: co-cultured with macrophages pretreated with LPS/IFN+G-1


title: Rsc96 rep2

value: Rat Schwann cells


title: CD4-LV_Donor2

description: CAR T cells


title: TEC

value: co-cultured with macrophages pretreated with LPS/IFN


title: CD8-LV_Donor3

description: CAR T cells

value: CD8 targeted


title: CD8-LV_Donor2

description: CAR T cells


title: IL4+G-1

source_name: primary BMDMs

value: primary BMDMs

value: macrophage


title: VSV-LV_Donor2

description: CAR T cells

value: Conventional


title: subjectC_unpooled_replicate7

type: genomic

city: Jupiter

first: Anderson

last: Butler

state: Florida

institute: VoLo Voundation

hyb_protocol: Deamination was carried out using EZ-96 DNA Methylation Kit (Zymo Research) according to Illumina’s recommended deamination protocol. Hybridization was carried out according to Illumina standard protocol.

data_processing: Beta values were generated using SeSAMe with package authors recommended settings

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, Cat No. 69504) with RNase treatment option, using RNAse cocktail from Ther-mofisher (AM2286).

treatment_protocol: Whole blood was collected into K2EDTA tubes, then aliquoted into 1.5mL tubes and frozen on dry ice until extraction.

value: male

tag: ethnicity

value: hispanic


title: subjectC_unpooled_replicate8


title: CD8-LV_Donor1

description: CAR T cells


title: PBMC rep3

value: untreated


title: IL4


title: Control_Donor3

description: control


title: subjectC_unpooled_replicate5


title: LPS+G-1


title: Control_Donor2

description: control


title: subjectD_unpooled_replicate3


title: G-1


title: CD4-LV_Donor1

description: CAR T cells


title: subjectD_unpooled_replicate2


title: LPS

value: differentiation+LPS/INF


title: P1_Par1 [P1_Par1_17724_Par_CS21]

value: Bain or brain tumor

value: NeuN-Olig2-negative nuclei

value: prenatal


title: CON-1

value: differentiation


title: Control_Donor1

description: control


title: subjectD_unpooled_replicate1


title: subjectB_unpooled_replicate8


title: subjectB_unpooled_replicate7


title: B cells from blood, scRNA-seq, GEX

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

institute: Technical University of Munich

description:
10x Genomics
Sample_05_Bood_GEX

data_processing:
Cellranger-7.1.0 count pipeline, with the `include introns` option disabled, was used to process FASTQ raw data (GEX and HTO together for each sample), align reads to the mm10 mouse reference genome and perform gene counting. VDJ data was not processed for this study.
Cellranger output files were further processed using the velocyto-0.17.17 run10x pipeline to generate spliced/unspliced matrices (loom files).
Filtered feature-barcode matrices were analyzed using SCANPY-1.9.2. For quality control, cells with more than 15% mitochondrial gene counts were excluded as well as cells with more than 2% hemoglobin gene counts and cells with less than 5% ribosomal gene counts. Cells with less than 200 detected genes and cells with more than 1E4 counts per cell were also removed. Genes detected in less than 3 cells were excluded. 254 variable B cell receptor chain genes detected in the dataset were excluded using the regex `^Ig[hjkl].*[-v]`. Doublet exclusion was performed using scrublet. Gene counts were normalized to 1E4 total counts per cell and variance was stabilized by log1p transformation.
Loom files were analyzed using scvelo-0.2.5 and UniTVelo-0.2.5.2.
Assembly: mm10-2020-A
Supplementary files format and content: Filtered feature-barcode matrices as generated using cellranger-7.1.0 count pipeline.
Supplementary files format and content: Loom files as generated using velocyto-0.17.17 run10x pipeline.

source_name: blood

extract_protocol:
Blood was drawn from the heart shortly after euthanization and collected into PBS with 2 mM EDTA. Inguinal lymph nodes, spleen, thymus and femurs were dissected. Bone marrow was extracted using centrifugation (10000g, 4 °C, 1 min). Lymph nodes, spleens, and thymi were passed through 100-μm cell strainers, followed by centrifugation (400g, 4 °C, 10 min). Spleen, bone marrow and blood samples underwent erythrocyte lysis with BD Pharm Lyse (BD Biosciences). All samples were pre-enriched for B cells using CD19 microbeads (130-121-301, Miltenyi Biotec) and Magnetic Activated Cell Sorting. Organs from two mice were pooled. Single-cell suspensions were incubated with LIVE/DEAD fixable dye (Invitrogen) and mouse Fc Block in PBS for 15 min on ice. Cells were washed with fluorescence-activated cell sorting (FACS) buffer (2% FCS in PBS) and incubated with fluorochrome-conjugated antibodies (1:100) against surface markers for 30 min on ice. Additionally, samples were labeled with TotalSeq-C anti-mouse Hashtags 1-3 and 5-6 (M1/42; 39-F11, Biolegend, 1:100 for all antibodies; HTO) as to the manufacturer's instruction. 12.000 live cells per organ were sorted for CD3-CD11b-F4/80-NK1.1-CD19+ B cells on a FACSAria III (BD Biosciences) into an FCS-coated 96-well plate.
scRNA-seq (GEX), scBCR-seq (VDJ), and cell hashing libraries (HTO) were prepared using the 10x Chromium Single Cell 5' Solution (Chromium Next GEM Single Cell VDJ v1.1 with feature barcoding technology for cell surface protein, 10x Genomics). In brief, sorted cells were transferred to a Chromium Next Gem chip (10x Genomics), and partitioning was performed automatically by Chromium Controller (10x Genomics). Library preparation was performed according to the manufacturer's instructions. For quality control and quantification, a Bioanalyzer 2100 (Agilent Technologies) was used. Cells from individual organs were processed in separate GEM wells, so hashtag antibodies served only as additional control in this dataset (no demultiplexing).

value: B cells

value: blood

value: female

value: 8 weeks

tag: library type

value: GEX


title: B cells from thymus, scRNA-seq, HTO

description:
10x Genomics
Sample_04_THY_HTO

library_source: other

molecule: protein

source_name: thymus

value: thymus

value: HTO


title: B cells from thymus, scRNA-seq, GEX

description:
10x Genomics
Sample_04_THY_GEX


title: VSV-LV_Donor3

description: CAR T cells


title: subjectC_unpooled_replicate6


title: subjectB_unpooled_replicate6


title: subjectB_unpooled_replicate5


title: B cells from bone marrow, scRNA-seq, HTO

description:
10x Genomics
Sample_03_BM_HTO

source_name: bone marrow

value: bone marrow


title: VSV-LV_Donor1

description: CAR T cells

value: Conventional


title: B cells from bone marrow, scRNA-seq, GEX

description:
10x Genomics
Sample_03_BM_GEX


title: subjectD_unpooled_replicate4

value: male


title: B cells from inguinal lymph nodes, scRNA-seq, HTO

description:
10x Genomics
Sample_02_LN_HTO

source_name: lymph node

value: lymph node


title: B cells from blood, scRNA-seq, HTO

description:
10x Genomics
Sample_05_Bood_HTO


title: B cells from inguinal lymph nodes, scRNA-seq, GEX

description:
10x Genomics
Sample_02_LN_GEX


title: subjectC_unpooled_replicate2

value: hispanic


title: S2, Aef1, biol_rep1, ChIP

city: Moscow

first: Aleksey

last: Krasnov

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
Basecalls were performed using bcl2fastq v2.17.
ChIP-Seq reads were filtered using atropos v1.1.31, trimming 3' adapters and low-quality bases, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the dm6 genome by Hisat2 v2.1.1. Only uniquely mapping reads were retained.
BigWig files were generated using bamCoverage 3.5.4. Score represents the normalized (CPM) coverage of DNA fragments at a given genomic coordinate.  CPM – Counts Per Million mapped reads.
Assembly: dm6 (Drosophila melanogaster Release 6)
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine (crosslinking in Drosophila tissues was performed by 0,7% formaldehyde). After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-2000 bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
ChIP-Seq libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina®.


title: S2, CG10543, biol_rep2, ChIP


title: PDDM6

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

institute: Pusan National University

description: 10X genomics

data_processing:
Single cell gene expression data were processed using the 10× Genomics Cell Ranger v5.0.1 and FASTQ files were generated using ‘cellranger mkfastq’. Raw FASTQ files were analysed using ‘cellranger count’. Reads are aligned to the human reference genome (GRCh38, v3.0.0) and gene expression matrix was measured with a unique molecular identifier (UMI) and cell barcode.
Assembly: human reference genome (GRCh38, v3.0.0)

extract_protocol:
PBMCs were separated using SepMate within 30 minutes after being collected.  The insert was added with density gradient medium, and the SepMate tube was filled with an identical amount of blood samples that had been diluted with phosphate buffer saline (PBS) and 2 percent fetal bovine serum (FBS). Then, tubes were then centrifuged at room temperature with 1200 × g for 10 minutes. The top layers were transferred into fresh tubes and twice washed with PBS including 2% FBS. The tubes underwent 120 × g for 10 minutes centrifugation at room temperature.
Libraries for scRNA-seq were generated using the chromium controller according to the 10× chromium Next GEM Single Cell 3’ v3.1 protocol. After mixing cell suspension and loading on Single Cell 3’ v3.1 Gel Beads, cDNA library was amplified and sequenced on Illumina HiSeq platform.

tag: subject status

value: patients with PDDM

value: PBMC


title: S2, CG10543, biol_rep1, ChIP


title: S2, Input


title: S2, Aef1, biol_rep2, ChIP


title: PDDM4

description: 10X genomics


title: subjectC_unpooled_replicate1


title: subjectA_unpooled_replicate8


title: PDDM2

description: 10X genomics


title: PDDM3

description: 10X genomics


title: P4skinK14KCTD1KCTD15DKO [47347P4-2KO]

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

data_processing:
Raw sequence reads were trimmed to remove possible adapter sequences and low-quality reads using Trimmomatic v.0.36 (PMID: 24695404). The trimmed reads were mapped to the mouse GRCh38 reference genome using the STAR aligner v.2.5.2b (PMID: 23104886). Reads mapping to annotated genes were quantified using featureCounts from the Subread package v.1.5.2 (PMID: 23558742).
Assembly: GRCm38
Supplementary files format and content: counts.txt: Tab-delimited text files include raw read counts

source_name: whole skin

extract_protocol:
Total RNA was isolated with Trizol reagent and then with Zymo Direct-zol RNA Mini Prep Plus and DNase treatment
For RNA-seq library construction, rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA), and loaded to Illumina NovaSeq 6000 system for 150bp paired-end sequencing.

tag: tissue

value: whole skin


title: PDDM1

description: 10X genomics

tag: cell type


title: PD10

description: 10X genomics

value: patient with PD without DM


title: subjectA_unpooled_replicate7


title: subjectC_unpooled_replicate4


title: P4skinK14KCTD1KCTD15DKO [47347P4-1KO]

tag: genotype


title: S2, CG9609, biol_rep2, ChIP


title: PD9

description: 10X genomics


title: PD8

description: 10X genomics


title: S2, CG9609, biol_rep1, ChIP


title: subjectA_unpooled_replicate6


title: subjectC_unpooled_replicate3


title: PD7

description: 10X genomics


title: PDDM5

description: 10X genomics


title: P4skinK14KCTD1KCTD15DKO [40972P4KO]


title: P4WTcontrolskin [40972P4WT]

value: WT


title: B cells from spleen, scRNA-seq, GEX

description:
10x Genomics
Sample_01_SPL_GEX

source_name: spleen

value: B cells

value: spleen


title: B cells from spleen, scRNA-seq, HTO

description:
10x Genomics
Sample_01_SPL_HTO

value: female


title: PD4

description: 10X genomics


title: PD5

description: 10X genomics


title: P4WTcontrolskin [47347P4-3WT]


title: PD6

description: 10X genomics


title: subjectB_unpooled_replicate3


title: subjectA_unpooled_replicate5


title: PD2

description: 10X genomics


title: P4WTcontrolskin [47347P4-7WT]


title: healthy control 11

description: 10X genomics

value: healthy control subject


title: PD1

description: 10X genomics


title: subjectB_unpooled_replicate1


title: subjectB_unpooled_replicate2


title: healthy control 9

description: 10X genomics


title: K14KCTD1KCTD15KO [49458]

source_name: epidermis

value: epidermis


title: healthy control 8

description: 10X genomics


title: subjectD_unpooled_replicate8


title: healthy control 7

description: 10X genomics


title: K14KCTD1KCTD15KO [50264]


title: healthy control 10

description: 10X genomics


title: healthy control 6

description: 10X genomics


title: subjectD_unpooled_replicate7


title: subjectB_unpooled_replicate4


title: healthy control 5

description: 10X genomics


title: healthy control 4

description: 10X genomics


title: K14KCTD1KCTD15KO [48198]


title: PD3

description: 10X genomics


title: K14KCTD1KCTD15KO [50053]


title: K14KCTD15KO [49655]


title: healthy control 3

description: 10X genomics


title: healthy control 1

description: 10X genomics


title: subjectD_unpooled_replicate6


title: K14KCTD15KO [49654]


title: subjectA_unpooled_replicate4


title: subjectD_unpooled_replicate5


title: K14KCTD15KO [49656]


title: TS543 PDX mouse biol rep 3

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Microwell-based scRNA-seq, 8-base index read, 26-base read 1, 58-base read 2

data_processing:
Read 1 and read 2 fastq files were generated on basespace. Hashtag barcodes and cell barcode and umi for gene expressions were preprocessed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8).
HTO raw counts were normalized by centered log ratio (CLR) transformation and performed k-means clustering and statistical identification of singlets by fitting a negative binomial model for demultiplexing
Gene expressions matrix were recovered by EmptyDrops algorithm
Assembly: HTO libraries: TotalSeqA hashtag sequence
Assembly: TS543 Transcriptome libraries: GRCh38
Assembly: TS543 PDX mouse: GRCh38 GRCm38
Supplementary files format and content: HTO libraries: Tab-delimited text files that contain the cell barcode and cell hashtag
Supplementary files format and content: Transcriptome libraries: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: Brain tumor tissue resection

growth_protocol:
For PW073 to PW079: TS543 cells were plated at density 1 × 104 viable cells/cm2 and cultured with NeuroCult™ NS-A basal medium supplemented with NeuroCult™ NS-A proliferation supplement, 20 ng/ml EGF, 10 ng/ml bFGF, and 2 µg/ml heparin (Stem Cell Technologies) in a humidified incubator with 5% CO2 at 37°C.
For PLZ019: Mice were bred in house and housed under standard conditions. TS543 cells (100,000 cells in 2 μL, passage 8) were injected in 8-week old female nude mice (CrTac:NCr-Foxn1nu,Taconic)

extract_protocol:
For PW073 to PW079: At the end of culture, neurospheres were collected and dissociated to single cells by pipetting and stained with with TotalSeq™-A hashtag antibodies (BioLegend), then pooled for scRNA-seq.
For PLZ019: Mice were sacrificed for collecting brain tumor tissues 21 post-injection. Freshly resected tumor tissues were kept in ice-cold PBS for transportation prior to dissociation. Mouse brain tumor resections were collected for dissociation using Papain Dissociation System (Worthington) as previously described(Mizrak et al., 2020; Mizrak et al., 2019) with following modifications. Briefly, minced tissue was digested with papain (Worthington, 10 units per sample) in PIPES solution (120 mM NaCl, 5 mM KCl, 20 mM PIPES (Sigma), 0.45% glucose, DNase I (Worthington, 100 units per sample), 1xAntibiotic/Antimycotic (GIBCO), pH adjusted to 7.6) for 30 min at 37°C on gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec, program 37C_ABDK). After digestion, the cell suspension was applied to a MACS SmartStrainer (70 μm, Miltenyi Biotec) and centrifuged at 300xg for 10 minutes at 4°C. The cell pellets were then subjected to red blood cell removal (Red Blood Cell Lysis Solution (10x), Miltenyi Biotec) and debris removal (Debris Removal Solution, Miltenyi Biotec) according to the manufacturer’s instructions.
For PW073 to PW079: mRNA and hashtag molecues were captured using bead-bound oligo dT(30). Captured mRNA and hashtag molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. Cell Hashtag (HTO)-containing fraction and the large cDNA library were separated by SPRI (Beckman Ampure XP beads). Purified large cDNA PCR products were used as the input for Nextera XT reactions to generate sequencing library. Purified Cell Hashtag (HTO)-containing fraction were used as input for PCR amplification using TruSeq DNA D703 primer and P5-SMARTpcr primer to generate the Cell Hashtag library.
For PLZ019: mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
For PW073 to PW079: scRNA-seq with TotalseqA hashtag
For PLZ019: scRNA-seq

treatment_protocol: For PW073 to PW079: When the diameters of neurospheres reached to approximately 50 to 100 μm after about 5 days’ culture, the culture medium of neurospheres were replaced with pre-warmed medium containing RSL3 or corresponding volume of vehicle (DMSO).

value: Brain tumor tissue resection

value: Neurosephere

value: sp/sp

tag: tumor stage

value: 21 days post-injection

tag: background strain


title: TS543 PDX mouse biol rep 4

tag: cell line


title: TS543 PDX mouse biol rep 1


title: subjectA_unpooled_replicate3

value: male


title: healthy control 2

description: 10X genomics


title: Bone marrow stromal cells Pth1rΔNLS rep3

city: changsha

first: Jian xi

last: Zhu

state: -- Select state --

address: XiangYa hospital

department: Department of Orthopaedics

institute: Xiangya Hospital, Central South University

data_processing:
Solexa pipeline 1.8 (Off-Line Base Caller software, version 1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 software.
Using StringTie software to estimate transcript abundance with reference to official database annotation information
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Ballgown.
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM for every gene/ transcript and every sample

source_name: primary cells

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

value: primary cells

value: Bone marrow stromal cells


title: Bone marrow stromal cells Pth1rΔNLS rep2


title: subjectA_unpooled_replicate2

value: hispanic


title: subjectA_unpooled_replicate1


title: subjectD_pooled_replicate8


title: Bone marrow stromal cells Pth1rΔNLS rep1


title: Bone marrow stromal cells WT rep3


title: subjectD_pooled_replicate7


title: CD40KO B cells (Total) Biological Replicate 5

description: CAATGATG

data_processing:
BCL files were demultiplexed using bcl2fastq v2.20.0.422
Fastq files were mapped to the GRCm38 genome using STAR (version 2.7.5b). Transcript and gene definitions were used according to GENCODE version M25.
Final raw count matrix was obtained using the published Drop-seq pipeline (v1.12) to generate sample- and gene-wise UMI tables (Macosko et al, 2015, Cell).
Raw counts of two separate sequencing runs of the same library were merged and non-overlapping genes were dropped. Genes with low expression (defined as < 1 counts per million in at least 4 samples) were removed and differential gene expression analysis was performed using the edgeR package (v3.42.4) in R (v3.1).
PCA analysis was performed using the PCA function of the FactoMineR package (v2.6) on log2 transformed cpm (counts per million)-normalized counts derived from 5 biological replicates of thymic WT_IgM and CD40KO B cells.
Gene set enrichment analysis (GSEA) was performed using unfiltered DESeq2-normalized counts, calculated using the DESeq2 package v1.40.2 (Love et al, 2014, Genome Biol.) using the GSEA 4.3.2 software (Subramanian et al., 2005, PNAS; Mootha et al. 2003, Nature Genetics) in conjunction with MSigDB v2023.1. The interrogated gene sets were derived from the M8 collection of cell type signature gene sets (MSigDB). Analysis was run with Permutation type phenotype and thus applied a false discovery rate (FDR) of 0.25.
Assembly: GRCm38
Supplementary files format and content: Sample annotations in CSV format
Supplementary files format and content: Gene Expression Matrix files for Run1 and Run2 in CSV format

extract_protocol:
Single-cell suspensions of thymi from 5 mice per genotype were incubated with LIVE/DEAD fixable dye (Invitrogen, 1:500) and mouse Fc Block (1:100) in PBS for 15 min on ice. Cells were washed with fluorescence-activated cell sorting (FACS) buffer (2% FCS in PBS) and incubated with fluorochrome-conjugated antibodies (1:300) for 25 min on ice in the dark. For each sample, 2000 cells were sorted into 10 µl TCL Buffer (Qiagen). For WT samples, the sort-gate was set to viable CD3-CD4-CD8a-NK1.1-CD11b-F4/80-CD19+B220+IgM+IgD- cells, representing the thymic B cell population known from other experiments to have the highest Aqp4 expression. For CD40KO samples, the thymic B cell population diversity was strongly diminished, containing virtually no IgM+IgD- cells, requiring us to sort the entire thymic B cell population for comparison, i.e. with the sort gate set to viable CD3-CD4-CD8a-NK1.1-CD11b-F4/80-CD19+B220+ cells.
RNA was isolated from TCL lysate via AmpureXP beads (Beckman Coulter). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016, Sci Rep). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher, #EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 5‘-ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016, Sci Rep), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 65 cycles for the cDNA in read1 and 19 cycles for the barcodes and UMIs in read2.

value: thymus

value: 6-8 weeks


title: CD40KO B cells (Total) Biological Replicate 4

description: TCTATCAG


title: CD40KO B cells (Total) Biological Replicate 3

description: CGAGCCGG


title: Bone marrow stromal cells WT rep2


title: CD40KO B cells (Total) Biological Replicate 1

description: GAACTTAT


title: CD40KO B cells (Total) Biological Replicate 2

description: TGAGTCAG


title: subjectC_pooled_replicate8


title: WT B cells (IgM+, IgD-) Biological Replicate 5

description: GTACAGCT