title: Drosophila_bipectinata_testes_NG_60_60_S14

organism: Drosophila bipectinata

value: testes

tag: sample id


title: Sham

status: Public on Oct 15 2024

type: SRA

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

country: USA

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files

molecule: total RNA

organism: Mus musculus

source_name: ventricular heart tissue

extract_protocol:
Heart tissue was harvest and stored at -80C until processing
10x Genomics platform

tag: tissue

value: ventricular heart tissue

tag: genotype

tag: treatment

value: Vehicle


title: 6T-CEM, ERG, CUT&Tag, rep1

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

country: China

institute: Children’s Hospital of Soochow University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

tag: cell line

tag: cell type

value: T-ALL cells

value: ERG(Proteintech, #14356-1-AP)


title: G7-TH-1-plasma intensity none

city: Stanford

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

description: smart-seq 2

library_source: transcriptomic

data_processing:
raw sequencing files in blc format were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR (v.2.5.3a) GeneCounts function, multi-mapped reads were filtered, and gene expression matrices were generated using SeqMonk. Seurat package was used to perform all downstream analysis.
Assembly: mm10
Supplementary files format and content: counttable (Text file)

source_name: Brain

extract_protocol:
cells were lysed in the lysis buffer and follow the smart-seq2 pipeline to generate cDNA
smart-seq2 in house pipeline

value: Brain

value: isolated cells

value: microglia


title: TAC


title: Drosophila_bipectinata_testes_NG_60_60b_S25

city: Davis

first: Ben

last: Hopkins

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

molecule: polyA RNA

source_name: testes

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

tag: library name

tag: strain information


title: Drosophila_bipectinata_testes_NG_61_61_S91


title: SJ donor 4 PBMC and SJ donor 4 Biopsy (SJ04_PBMC_SJ04_Biopsy) - CSP

city: Woolloongabba

first: Ranjeny

last: Thomas

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute, Translational Research Institute

description:
SJ04_PBMC_Biopsy_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_metadata.csv.gz

data_processing:
Single cell RNA-seq data was processed using the 10x Genomics Cell Ranger Software (v3.0.2). The command “cellranger mkfastq” was used to demultiplex raw BCL files and generate FASTQ files for individual samples. The command “cellranger count” was used to align RNA-Seq reads to the pre-built human reference genome GRCh38 and to filter out low quality cell barcodes and unique molecular identiﬁers (UMI). The resulting single-cell gene count matrices were further processed using the Seurat R package (v3.0.5)
Assembly: human GRCh38
Supplementary files format and content: tsv, csv.gz

source_name: CD45+ cells

extract_protocol:
Salivary gland biopsy were collected from all donors and stored in cryostor. Biopsy was disaggregated using a protocol published by the AMP consortia and CD45+ cells from all thawed disaggregated ST samples were sorted via flow cytometric activated cell sorting. PBMC were collected from each participant and frozen. CD45+ immune cells from all thawed PBMC samples were sorted via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. GEM generation and barcoding, cDNA amplification, cell surface protein and library construction was performed according to the 10X Genomics Chromium User Guide. Sequencing was performed using the Illumina NovaSeq 6000.

value: PBMC and salivary gland


title: SJ donor 10 and SJ donor 11 PBMC (SJ10_SJ11_PBMC) - GEX

description:
SJ10_SJ11_PBMC_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_NormExpresMatrix.csv.gz

extract_protocol:
PBMC were collected from each participant and frozen. CD45+ immune cells from all thawed PBMC samples were sorted via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. GEM generation and barcoding, cDNA amplification, cell surface protein and library construction was performed according to the 10X Genomics Chromium User Guide. Sequencing was performed using the Illumina NovaSeq 6000.

value: PBMC


title: SJ donor 10 and SJ donor 11 PBMC (SJ10_SJ11_PBMC) - CSP


title: G5-TH-1-plasma intensity none

description: smart-seq 2


title: G4-TH-1-plasma intensity none

description: smart-seq 2


title: Drosophila_bipectinata_testes_G_59_59_S13


title: LPS induced and LIPUS treated RAW264.7 cells, repeat 2

first: Juan

last: Yin

address: 80 Tian'e Dang Road

department: Suzhou Key Laboratory of Gut Microecology

institute: The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Assembly: mm10
Supplementary files format and content: excel files include TPM/counts for each Sample
Supplementary files format and content: excel files include all/different mRNAs/genes for each Sample

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol. The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: mouse leukemia cells of monocyte macrophage

value: WT

value: LPS induced and LIPUS treated


title: Drosophila_bipectinata_ag_NG_17_17b_S150

source_name: accessory glands

value: accessory glands


title: Pool of 12-16 of preadapted larvae.

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

description: Coregonus baicalensis Dybowski, 1874

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v. 0.36.
The preprocessed reads were subjected to a de novo assembly procedure the Trinity v.2.13.2. software package
Read count extrraction and normalization were perfomed using the R package EdgeR v4.0.3.
Assembly: de novo assembly
Supplementary files format and content:tab-delimited text file includes normalized FPKM values ??for each sample

organism: Coregonus baicalensis

source_name: Pool of 12-16 of preadapted larvae.

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) from each individual sample (the whole larvae). RNA samples from the same group (12-16 individuals) have been combined into mixtures to obtain four RNA pools.
The library was examined using Qubit and real-time PCR for quantification and size distribution detection. Quantified libraries were pooled in equimolar amounts and sequenced on Illumina NovaSeq 6000 High Throughput Sequencer using a NovaSeq 6000 Reagent Kit v1.5 in 150 bp paired-end reads at Novogen company (China).

value: Pool of 12-16 of preadapted larvae.


title: SJ donor 1 and SJ donor 3 PBMC (SJ01_SJ03_PBMC) - CSP

description:
SJ01_SJ03_PBMC_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_NormExpresMatrix.csv.gz


title: LPS induced RAW264.7 cells, repeat 3

value: LPS induced


title: 6T-CEM, ETV6, CUT&Tag, rep1

value: ETV6(Abclonal, #A1637)


title: Drosophila_kikkawai_testes_NG_90_90c_S12

organism: Drosophila kikkawai

value: testes

value: Brazil D iso-B I-3


title: Drosophila_bipectinata_ag_NG_17_17_S100


title: G3-TH-1-plasma intensity none

description: smart-seq 2


title: ART

value: ventricular heart tissue

value: Artesunate


title: LPS induced and LIPUS treated RAW264.7 cells, repeat 3


title: SJ donor 1 and SJ donor 3 PBMC (SJ01_SJ03_PBMC) - GEX


title: LPS induced RAW264.7 cells, repeat 2


title: G1-TH-1-plasma intensity none

description: smart-seq 2


title: G2-TH-1-plasma intensity none

description: smart-seq 2


title: Drosophila_bipectinata_ag_NG_16_16_S99


title: F23-TH-1-plasma intensity high

description: smart-seq 2


title: SJ donor 10 and SJ donor 11 Biopsy (SJ10_SJ11_Biopsy) - CSP

description:
SJ10_SJ11_Biopsy_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_NormExpresMatrix.csv.gz

extract_protocol:
Salivary gland biopsy were collected from all donors and stored in cryostor. Biopsy was disaggregated using a protocol published by the AMP consortia and CD45+ cells from all thawed disaggregated ST samples were sorted via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. GEM generation and barcoding, cDNA amplification, cell surface protein and library construction was performed according to the 10X Genomics Chromium User Guide. Sequencing was performed using the Illumina NovaSeq 6000.

value: Salivary gland


title: LPS induced RAW264.7 cells, repeat 1


title: transplant-derived, BMDM, Pristane, replicate 3 [RNA-Seq]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
The quality of the fastq files was accessed using FastQC  (v.0.11.8), , FastQ Screen (v.0.13.0), and MultiQC (v.1.8)
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the hg38 human reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a)
Differential gene expression analysis was performed using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Text file containing normalized count matrix
Supplementary files format and content: bigwig files

source_name: Bone marrow

growth_protocol: Bone marrow derived macrophages (BMDMs) were generated by flushing one femur, and BM cells were then placed into culture with BMDM media (DMEM base, 10% FBS, 1x Anti Anti, 1x MEM-NEAA, 1x Sodium Pyruvate, 1x L-glutamine, and 50ng/mL of M-CSF).

extract_protocol:
Harvested cells were pelleted and then lysed in mild lysis buffer (10mM Nacl, 10mM Tris-HSC, 0.5% NP-40, Rnase inhibitor) for 30 minutes. Cells were vortexed for 1 minute and centrifuged at 2000 g for 5 minutes at 4oC. The lysis supernatant, containing the RNA fraction was removed and immediately placed into RLT buffer from the Qiagen RNeasy micro kit and processed following manufacturer's instructions
Ribo-depleted RNA isolation

treatment_protocol: N/A cells were not treated

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophage

tag: strain

value: Pristane


title: Drosophila_bipectinata_ag_G_46_46b_S17


title: Drosophila_bipectinata_ag_NG_16_16b_S149


title: SJ donor 1 and SJ donor 3 Biopsy (SJ01_SJ03_Biopsy) - CSP

description:
SJ01_SJ03_Biopsy_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_NormExpresMatrix.csv.gz


title: LPS induced and LIPUS treated RAW264.7 cells, repeat 1


title: SJ donor 10 and SJ donor 11 Biopsy (SJ10_SJ11_Biopsy) - GEX


title: transplant-derived, BMDM, Pristane, replicate 2 [RNA-Seq]


title: F22-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Drosophila_ficusphila_testes_NG_89_89_S15

organism: Drosophila ficusphila


title: F21-TH-1-plasma intensity high

description: smart-seq 2


title: Drosophila_bipectinata_ag_G_46_46_S97


title: transplant-derived, BMDM, Pristane, replicate 1 [RNA-Seq]


title: PBMCs + CD34+ Tapestri

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

country: Italy

institute: University of Modena and Reggio Emilia

data_processing:
FASTQ files for single-cell DNA libraries were processed through the Tapestri Pipeline V2, for adapter trimming, sequence alignment, barcode correction, cell ﬁnding, and variant calling.
Assembly: hg19
Supplementary files format and content: custom_Tapestri_panel.zip is a folder containing the .bed files of the custom DNA panel employed in the experiment. It can be uploaded into Tapestri pipeline in order to analyze the raw fastq sequencing data.
Supplementary files format and content: MPN_DNA.loom is a file generated from the Tapestri Pipeline that can be further analyzed through Tapestri Insights software to retrieve mutational data at the single-cell level.
Library strategy: scDNA-seq

source_name: Peripheral Blood

extract_protocol:
Frozen PBMC’s were thawed following 10X Genomics “Sample Preparation Demostrated Protocol”. Immunomagnetic selection of CD34+ cell population was then performed by means of “CD34 Microbead kit, human” (Miltenyi Biotec) following the protocol provided by the manufacturer.
100000 cells (a mix of PBMCs and CD34+ cells) were resuspended in cell buffer and loaded in the Tapestri Platform as recommended in manufacturer protocol. Samples were processed using the Tapestri® Single-Cell DNA Sequencing V2 (Mission Bio, San Francisco, California, USA) and the libraries were  sequenced on a NovaSeq 6000 using High Output Kit v2.5 chemistry (Illumina, San Diego, California, USA).

value: Peripheral Blood

value: PBMCs and CD34+ cells


title: SJ donor 1 and SJ donor 3 Biopsy (SJ01_SJ03_Biopsy) - GEX


title: Drosophila_ficusphila_testes_NG_47_47_S88


title: transplant-derived, BMDM, Control, replicate 2 [RNA-Seq]

value: Control


title: F19-TH-1-plasma intensity high

description: smart-seq 2


title: Drosophila_ficusphila_testes_NG_47_47b_S11


title: Kidney_U1152R_pre (761119)

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Adapter sequences were trimmed off from the raw reads using Cutadapt (Martin, 2011) and only reads with minimum 30bp were kept for downstream analysis.  Reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function (Farrell et al, 2021).  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 30 -min-sample 1.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing methylation level per CpG site for each sample

source_name: Blood

extract_protocol:
8ml of blood was drawn into the ACD tube.  After Ficol density gradient centrifugation, PBMCs were separated isolated  and cryopreserved in FCS/DMSO.
Genomic DNA was extracted from PBMCs using phenol-chloroform method (Guha et al, 2018).  500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).  A comprehensive TBS-seq protocol is demonstrated in (Morselli et al, 2021).

value: Blood

value: PBMC

tag: patient id

tag: age

tag: Sex

value: F

tag: race

value: White

tag: hispanic

value: Y

tag: time

value: PreTx

tag: cmv r

value: POS

tag: cmv d

value: NEG

tag: induction

value: ATG


title: Kidney_U1149R_pre (758623)

tag: tissue

value: M

value: N

value: SIMULECT


title: F18-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: transplant-derived, BMDM, Control, replicate 1 [RNA-Seq]

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophage


title: Kidney_U1146R_post (U447-17)

value: Blood

value: Multi

value: PostTx


title: F17-TH-1-plasma intensity high

description: smart-seq 2

value: microglia


title: F15-TH-1-plasma intensity low

description: smart-seq 2


title: primary, BMDM, Pristane, replicate 3 [RNA-Seq]

value: Pristane


title: Drosophila_ficusphila_ag_NG_27_27_S96

value: accessory glands

tag: sample id


title: Drosophila_ficusphila_ag_NG_27_27b_S146


title: F16-TH-1-plasma intensity low

description: smart-seq 2


title: F20-TH-1-plasma intensity high

description: smart-seq 2


title: primary, BMDM, Pristane, replicate 1 [RNA-Seq]

tag: treatment


title: Drosophila_ficusphila_testes_G_41_41_S86

value: testes


title: Drosophila_ficusphila_testes_G_41_41b_S10


title: Kidney_U1136R_pre (755385)

value: PBMC

value: F

value: White

value: Y

value: PreTx

value: NEG

value: POS


title: Kidney_U1148R_post (U456-19)

value: M

value: Asian

value: N

value: ATG


title: transplant-derived, BMDM, Control, replicate 3 [RNA-Seq]

value: Bone marrow

tag: cell line

value: BMDM

value: Bone marrow derived macrophage

value: Control


title: F14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

tag: cell type

value: microglia


title: Kidney_U1136R_post (U415-17)

value: Blood

value: PBMC

value: F

value: PostTx


title: primary, BMDM, Control, replicate 2 [RNA-Seq]


title: F13-TH-1-plasma intensity low

description: smart-seq 2


title: primary, BMDM, Control, replicate 3 [RNA-Seq]


title: Kidney_U1143R_pre (760863)

value: White

value: PreTx

value: NEG


title: Kidney_U1128R_post (U482-19)

value: Other

value: Y

value: POS


title: Drosophila_ficusphila_ag_G_45_45_S93

value: accessory glands

tag: library name


title: Drosophila_ficusphila_ag_G_45_45b_S28

tag: strain information


title: Kidney_U1120R_pre (751421)

value: M

value: ATG


title: primary, BMDM, Control, replicate 1 [RNA-Seq]

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophage

tag: strain

value: Control


title: F11-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: primary, BMDM, Pristane, replicate 2 [RNA-Seq]

value: Pristane


title: Drosophila_kikkawai_testes_NG_90_90b_S24

value: testes

value: Brazil D iso-B I-3


title: transplant-derived, BMDM, Pristane, replicate 2

data_processing:
The quality of the fastq files was accessed using FastQC.
Illumina adapters and low-quality reads were filtered out using BBDuk.
Bowtie2 (v.2.3.4.3) was used to align the sequencing reads to the mm10 reference murine genome.
Samtools (v.1.11) was used to select the mapped reads (samtools view -b -q 30) and sort the bam files.
PCR duplicates were removed usign Picard MarkDuplicates tool.
The normalization ratio for each sample was calculated by dividing the  number of uniquely mapped murine reads of the sample with the lowest number of reads by the number of uniquely mapped murine reads of each sample. These normalizations ratios were used to randomly sub-sample reads to obtain the same number of reads for each sample using using samtools view -s.
Bedtools genomecov was used to create bedgraph files from the bam files
Bigwig files were created using deepTools bamCoverage
Peaks were called using MACS2 (v2.1.2) with  ENCODE recommended parameters.
Bigwig files were created using deepTools bamCoverage
IDR was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R. Average profiles and heatmaps were generated using ngs.plot.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Harvested cells were pelleted and then lysed in mild lysis buffer (10mM Nacl, 10mM Tris-HSC, 0.5% NP-40, Rnase inhibitor) for 30 minutes. Cells were vortexed for 1 minute and centrifuged at 2000 g for 5 minutes at 4oC. The lysis supernatant was removed, then the transposase reaction mix (Transposase enzyme, buffer, and digitonin) was added to the pelleted nuclei and incubated for 30 minutes at 37oC. DNA was then purified and cleaned.
ATAC-seq libraries were prepared by amplifying the DNA fragments using barcoded primers and the NEBNext HF PCR kit. The samples were amplified on a thermocycler for 10-11 cycles depending on amplification efficiency determined using qRT-PCR. Libraries were validated using the Agilent D1000 ScreenTape system.


title: Kidney_U1120R_post (U388-17)

value: Blood

value: PBMC

tag: patient id

value: White

value: PostTx


title: Drosophila_ficusphila_ag_NG_103_103_S27

value: accessory glands


title: F9-TH-1-plasma intensity low

description: smart-seq 2


title: transplant-derived, BMDM, Pristane, replicate 1


title: F10-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_U1119R_pre (750176)

tag: age

value: F

value: Y

value: PreTx

value: POS


title: Drosophila_kikkawai_testes_NG_90_90_S12


title: Kidney_U1119R_post (AR031515)

tag: Sex

value: ATG


title: F7-TH-1-plasma intensity none

description: smart-seq 2


title: transplant-derived, BMDM, Control, replicate 2

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophage

value: Control


title: transplant-derived, BMDM, Control, replicate 1


title: F12-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Kidney_U1118R_post (U376-23)

value: Blood

value: M

tag: race

value: Other

value: NEG


title: F8-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_U1118R_pre (749028)

value: PBMC

tag: hispanic


title: F6-TH-1-plasma intensity none

description: smart-seq 2


title: Drosophila_kikkawai_testes_G_44_44b_S13

value: testes


title: Drosophila_kikkawai_testes_G_44_44_S92


title: Kidney_U1117R_pre (751384)

value: White

value: N

tag: time

value: SIMULECT


title: primary, BMDM, Pristane, replicate 1

value: Pristane


title: primary, BMDM, Control, replicate 2

value: Bone marrow


title: Drosophila_kikkawai_ag_NG_21_21_S79

value: accessory glands

value: Brazil D iso-B I-3


title: primary, BMDM, Pristane, replicate 2

value: BMDM

value: Bone marrow derived macrophage


title: F5-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: F4-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: Kidney_U1117R_post (U387-18)

value: Blood

value: M

value: PostTx

tag: cmv r

value: POS


title: primary, BMDM, Control, replicate 1

value: Control


title: Drosophila_kikkawai_testes_NG_18_18_S94

value: testes


title: Drosophila_kikkawai_ag_NG_21_21b_S3


title: Kidney_U1115R_pre (749961)

value: PBMC

value: F

value: Asian

value: N

value: PreTx

value: NEG

tag: cmv d

value: ATG


title: Drosophila_kikkawai_testes_NG_18_18b_S144

value: Brazil D iso-B I-3


title: Kidney_U1115R_post (U378-17)

tag: induction


title: Drosophila_kikkawai_ag_NG_20_20b_S19

tag: tissue

value: accessory glands


title: F3-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: Kidney_U1112R_pre (747650)

value: Blood

value: Other

value: Y


title: F2-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: Plasma negative microglia from hypothalamus

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (version 3.0.1)
Assembly: mm 10
Supplementary files format and content: feasutes file (.tsv.gz) and matrix files (.mtz)

source_name: brain

extract_protocol:
Microglia were sorted into receiving buffer (1% ultra BSA in PBS + RNAse inhibitor)  and cells were loaded according to the manufacter's instructions (Chromium Single Cell 3’ Reagents kit v3.1 kit)
The library preparation was performed according to the Chromium Single Cell 3’ Reagents kit v3.1 user guide (10x Genomics) according to the manufacturer’s instructions.

value: brain

tag: genotype

value: wild-type


title: E23-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_U1111R_pre (748623)

value: PBMC

value: POS


title: Drosophila_kikkawai_ag_NG_20_20_S96

tag: sample id


title: Drosophila_kikkawai_ag_G_42_42b_S2


title: F1-TH-1-plasma intensity none

description: smart-seq 2

tag: cell line


title: Mitral valve, WT, 1mo, rep1 (n=5 pooled)

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
10× Genomics
1 month WT mitral valve

data_processing:
The scRNA-seq outputs were processed by CellRanger v3.1.0 according to the manufacturer’s instructions.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart mitral valve

extract_protocol:
Dissected mitral valves, including anterior and posterior leaflets, were digested using digestion buffer containing 2 mg/ml Collagenase II, 2 mg/ml Collagenase IV, 0.65 mg/ml Dispase II, 0.1 mg/ml Elastase, and 1 mg/ml HAase I in HBSS. The valves were incubated in digestion buffer at 37°C for 15 minutes × 2. The digestion was then stopped by DMEM+10% FBS on ice. The cell suspensions were filtered using Falcon Test Tube with 35 μm Cell Strainer and centrifuged. The cell pellet was resuspended in 50 μl DMEM+10% FBS for subsequent single-cell RNA sequencing.
Cells were processed using the Chromium Single Cell 3’ v3.1 Kit from 10× Genomics.

tag: cell type

value: Heart valve cells

value: Heart mitral valve

value: 1 month


title: Mitral valve, Fbn1 C1039G/+, 1mo, rep1 (n=3 pooled)

description:
10× Genomics
1 month Fbn1 Het mitral valve


title: E22-TH-1-plasma intensity high

description: smart-seq 2


title: Drosophila_kikkawai_ag_G_42_42_S78

tag: library name


title: Kidney_U1103R_pre (745956)

value: M

value: Black

value: N

value: PreTx

value: NEG


title: Kidney_U1103R_post (U336-22)

value: PostTx

value: ATG


title: Drosophila_takahashii_testes_NG_67_67_S7

organism: Drosophila takahashii

value: testes

tag: strain information


title: E21-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: Bcl11b-KO-ISC-anti-H3K27me3

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
HISAT2 was used to align the sequences to the mouse genome and generate bam files
Deeptools bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files
MACS2 was used for peak calling and to generate bed files from aligned reads
HOMER annotatePeaks.pl was used to annotate the peaks.
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&TAG

source_name: intestine

growth_protocol: Control and Bcl11b-cKO mice (n=3 mice per group) were injected with tamoxifen for 5 days and and mice were euthanized at day 9.

extract_protocol:
Crypt cells were digested with Tryple and Lgr5-GFP+ cells were sorted by FACS; Organoids were digested with Tryple and alive cells were sorted by FACS
The library of ATAC-seq was constructed with TruePrep DNA library Prep Kit V2 for Illumina (Vazyme, TD 202 and TD502). Subsequently, the ATAC-seq library was purified with AMPuro XP beads (Beckman, A63881) and sequenced with Illumina Novaseq 6000; For ChIP-seq, cells were incubated with 12 μg/mL MEA/B-PAT, then genome DNA was fragmented with reaction buffer.DNA was directly used as templet, amplification was performed with 2X KAPA HIFI HotStart polymerase (KAPA, KK2601). The library was purified with 1.4X AMPure beads and sequenced as paired-end with Illumina Novaseq 6000.

value: intestine

tag: strain

value: Intestinal stem cells

value: Bcl11b KO

tag: chip antibody


title: WT-ISC-anti-H3K27me3

value: WT


title: Kidney_U1097R_pre (745609)

value: Blood

value: PBMC

tag: patient id

tag: age

value: White

value: Y

value: POS


title: Bcl11b-KO-ISC-anti-H3K27Ac


title: Drosophila_takahashii_testes_NG_22_22_S94


title: Kidney_643_pre (764902)

tag: Sex

value: M

tag: race


title: Plasma positive microglia from hypothalamus

description: 10x Genomics

value: brain

value: microglia

value: wild-type


title: E19-TH-1-plasma intensity high

description: smart-seq 2


title: WT-ISC-anti-H3K27Ac


title: Drosophila_kikkawai_ag_NG_20_20c_S16

value: accessory glands

value: Brazil D iso-B I-3


title: Drosophila_takahashii_testes_NG_22_22b_S14

value: testes


title: E18-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: Bcl11b-chip-IgG

data_processing:
HISAT2 was used to align the sequences to the mouse genome and generate bam files
Deeptools bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files
MACS2 was used for peak calling and to generate bed files from aligned reads
HOMER annotatePeaks.pl was used to annotate the peaks.
Assembly: mm10
Supplementary files format and content: bigwig files

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the ENR medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, and 500 ng/mL R-spondin1) was added and refreshed every 2 days.

treatment_protocol: Organoids derived from ROSA26-rtTA mice were infected with Bcl11b-Flag-OE lentivirus, Bcl11b-Flag organoids were treated with doxycycline for 5 days to induced the overexpression,  then harvested for the following procedure.

value: intestine

value: Intestinal organoid cells


title: Kidney_1567_post (R10002-8)

value: F

tag: hispanic

tag: time

value: PostTx

value: ATG


title: Bcl11b-chip-IP


title: Drosophila_takahashii_testes_G_54_54_S99


title: E17-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1566_pre (770433)

value: Blood

value: PBMC

value: Other

value: PreTx

tag: cmv r

tag: cmv d


title: Bcl11b-ko-9d-ISC

tag: tissue

value: Intestinal stem cells

value: Bcl11b KO


title: Kidney_1566_post (R10010-8)

value: M

value: Y

value: POS

tag: induction


title: E16-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: Drosophila_takahashii_ag_NG_24_24b_S135

value: accessory glands

tag: sample id


title: Kidney_1564_pre (770535)

value: Asian

value: N


title: E20-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

tag: cell line

value: isolated cells


title: Bcl11b-wt-9d-ISC

value: intestine

tag: cell type

tag: genotype

value: WT


title: Drosophila_takahashii_ag_NG_24_24_S83

tag: library name

tag: strain information


title: Drosophila_takahashii_ag_NG_23_23_S82


title: Wt1F/+CreMx-1;CPSF6-RARG-2

first: Feng

last: Wang

address: 1 Tian Tan Xi Li

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
Bowtie v1.0.1  was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 V2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq V0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq2 V1.20.0  was used for differential gene expression analysis between two samples with  biological replicates.
Assembly: Mus_musculus.GRCm38.89
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Spleen

extract_protocol:
Cells were collected , flash frozen on dry ice, and the total RNA was extracted by using RNA-QuickTM MicroPrep Kit (ZYMO RESEARCH, R1055).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).

treatment_protocol: Cells were isolated from the spleens of Wt1F/+CreMx-1;CPSF6-RARG mice and  CreMx-1;CPSF6-RARG mice and analyzed through RNA-seq .

value: Spleen

value: primary cells

value: leukemia cells


title: E14-TH-1-plasma intensity low

description: smart-seq 2


title: Wt1F/+CreMx-1;CPSF6-RARG-1


title: Drosophila_takahashii_ag_NG_23_23b_S134


title: Kidney_1564_post (R9999-8)

value: Blood

value: PBMC

value: PostTx

value: ATG


title: Drosophila_takahashii_ag_G_4_4_S80


title: Kidney_1567_pre (770867)

value: F

value: White

value: Y

value: PreTx


title: Kidney_1563_pre (770916)

value: Asian

value: POS

value: NEG


title: Drosophila_takahashii_testes_G_54_54b_S18

value: testes


title: CreMx-1;CPSF6-RARG-2


title: Kidney_1563_post (R10012-8)

value: N


title: E11-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: E15-TH-1-plasma intensity low

description: smart-seq 2


title: CreMx-1;CPSF6-RARG-1

value: Spleen

value: primary cells

value: leukemia cells


title: Drosophila_takahashii_ag_G_4_4c_S4

value: accessory glands


title: Kidney_1561_pre (770480)

value: Blood

value: PBMC

value: M

value: ATG


title: Kidney_1559_pre (764794)

value: F

value: Black

value: PreTx

value: SIMULECT


title: E10-TH-1-plasma intensity low

description: smart-seq 2


title: E9-TH-1-plasma intensity low

description: smart-seq 2


title: Colon muscularis propria, GF, 7

city: Chicago

first: Mary

last: Frith

state: Illinois

address: 900 E 57th St

department: Medicine

institute: University of Chicago

data_processing:
Reads were trimmed using Trimmomatic-0.39.
Alignment was performed using STAR 2.7.9a and BAM files were sorted by coordinate.
Samtools (1.14) was used for indexing.
featureCounts from subread package (2.0.1) was used to generate counts using mm39 (.gtf file obtained from Ensembl.org).
The output files from featureCounts were reformatted such that gene identifiers were in a first column, labeled "Geneid", and the raw counts were in a second column, labeled with the sample identifier.
Assembly: mm39
Supplementary files format and content: comma separated values file including raw counts for all samples
Supplementary files format and content: tab delimited text files including raw counts for each sample

source_name: colon muscularis propria, C57Bl/6, WT, adult, female

extract_protocol:
RNeasy Mini Kit from Qiagen (cat # 74104) was used to extract RNA following the manufacturer instructions. For the lysis and homogenation step, Qiagen PowerBead Tubes with Garnet 0.70mm (cat #13123-50) were used with a bead beater for 1 minute at 3450 oscillations/min (GlenMills, Beadbeater-16).
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ based mRNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).

value: colon muscularis propria

value: WT

tag: developmental stage

value: adult

value: female

tag: strain

tag: treatment

value: germ-free


title: Drosophila_takahashii_ag_G_4_4b_S3


title: wild type, stationary, rep4

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

description: stationary phase

data_processing:
Basecalls performed using CASAVA version 1.9
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle version 1.33 (https://github.com/najoshi/sickle), with a quality threshold of 20 (-q 20). Reads shorter than 20nucleotides were removed
Clean reads were aligned to the Legionella longbeachae NSW150 sequence using Bowtie2 (version 2.3.4.3) and only uniquely mapped reads were kept for the counts
Reads count with featureCounts programm (from the Subreads package version 1.6.3). We used --primary option and stranded counts (option -s 1)
Differential analysis between the different conditions was performed with the R package Sartools (version 1.3.0) using DESeq2 methods. The “median” option was used to compute size factors
Assembly: refSeq : GCF_000091785.1, NC_013861.1
Supplementary files format and content: tabular text file with read count (column 2), sequence accession numbers (columns 3, 4), localisation of the features (columns 5, 6, 7), locus_tag of the features (column 8)

organism: Legionella longbeachae NSW150

source_name: L. longbeachae strain NSW150

growth_protocol: Bacteria were streaked onto BCYE plates and grown for three days at 37°C. From these plates, BYE liquid medium was inoculated and bacteria were grown to exponential phase (OD600 2.0-2.5), post-exponential phase (OD600 3.7-4.2) or stationary phase (overnight) and bacterial pellets were snap-frozen before processing for RNAseq.

extract_protocol:
Total RNA was isolated using Qiazol and miRNA Mini kit (Qiagen)
1 ug of total RNA was then used in Illumina’s TruSeq mRNA Library kit

treatment_protocol: not applicable

value: L. longbeachae strain NSW150

value: wild type


title: Kidney_1559_post (R9981-8)

tag: patient id

tag: age

tag: Sex

value: N

value: PostTx

value: POS

value: NEG


title: Colon muscularis propria, 4wC, 5

value: previously GF, FMT at weaning


title: E13-TH-1-plasma intensity low

description: smart-seq 2

extract_protocol:
cells were lysed in the lysis buffer and follow the smart-seq2 pipeline to generate cDNA
smart-seq2 in house pipeline

value: Brain

value: isolated cells

value: microglia


title: E12-TH-1-plasma intensity low

description: smart-seq 2


title: Colon muscularis propria, GF, 5


title: E7-TH-1-plasma intensity none

description: smart-seq 2


title: Colon muscularis propria, GF, 6


title: E8-TH-1-plasma intensity none

description: smart-seq 2


title: wild type, stationary, rep2

description: stationary phase


title: E6-TH-1-plasma intensity none

description: smart-seq 2


title: Colon muscularis propria, 12wC, 5

value: previously GF, FMT as adult


title: wild type, stationary, rep3

description: stationary phase


title: Kidney_1555_pre (765894)

value: Blood

value: PBMC

value: M

tag: race

value: Other

tag: hispanic

value: Y

tag: time

value: PreTx

value: ATG


title: wild type, stationary, rep1

description: stationary phase

value: L. longbeachae strain NSW150

value: wild type


title: Colon muscularis propria, 12wC, 4

tag: tissue

value: colon muscularis propria

value: WT

value: adult

value: female


title: E5-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: wild type, post exponential, rep4

description: post exponential phase


title: Kidney_1553_post (R9950-8)

value: White

value: PostTx

tag: cmv r

value: POS

tag: cmv d

tag: induction


title: E4-TH-1-plasma intensity none

description: smart-seq 2

tag: cell line

value: isolated cells

tag: cell type

value: microglia


title: E3-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_1551_pre (767837)

value: Blood

value: PBMC

value: M

value: Black

value: N

value: NEG


title: Colon muscularis propria, 4wC, 3

tag: genotype

value: previously GF, FMT at weaning


title: wild type, post exponential, rep3

description: post exponential phase

value: L. longbeachae strain NSW150

value: wild type


title: Kidney_1551_post (R9938-8)

value: ATG


title: Kidney_1558_pre (766672)

value: F

value: PreTx


title: Colon muscularis propria, 4wC, 4

value: colon muscularis propria

value: WT

value: adult

value: female


title: Kidney_1550_pre (767803)

value: Asian

value: POS


title: wild type, post exponential, rep1

description: post exponential phase


title: Colon muscularis propria, 12wC, 2

value: previously GF, FMT as adult


title: wild type, exponential, rep4

description: exponential phase


title: E1-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: D23-TH-1-plasma intensity high

description: smart-seq 2


title: Colon muscularis propria, 12wC, 3


title: Kidney_1558_post (R9970-8)

value: Blood

value: PBMC

value: Black

value: N

value: PostTx

value: NEG


title: Colon muscularis propria, 12wC, 1


title: Kidney_1549_pre (766559)

value: M

value: White

value: Y

value: PreTx

value: ATG


title: Kidney_1549_post (R9974-6)


title: D22-TH-1-plasma intensity high

description: smart-seq 2


title: Colon muscularis propria, 4wC, 2

value: colon muscularis propria

value: WT

value: adult

value: female

value: previously GF, FMT at weaning


title: Kidney_1546_post (R9929-1)

value: F

value: POS


title: D21-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: wild type, exponential, rep2

description: exponential phase

value: L. longbeachae strain NSW150

value: wild type


title: wild type, exponential, rep3

description: exponential phase


title: Colon muscularis propria, 4wC, 1


title: wild type, exponential, rep1

description: exponential phase


title: Kidney_1545_pre (765558)

value: Blood

value: PBMC

value: M

value: Other

value: NEG

value: SIMULECT


title: D20-TH-1-plasma intensity high

description: smart-seq 2


title: E2-TH-1-plasma intensity none

description: smart-seq 2


title: wild type, post exponential, rep2

description: post exponential phase


title: Colon muscularis propria, SPF, 7

value: colon muscularis propria

value: WT

value: conventionally raised


title: delta_ctrC, stationary, rep4

description: stationary phase


title: Kidney_1545_post (AR039486)

value: Y

value: PostTx


title: Kidney_1544_post (R9900-8)

value: POS

value: ATG


title: Colon muscularis propria, SPF, 6

value: adult

value: female


title: delta_ctrC, stationary, rep3

description: stationary phase

value: L. longbeachae strain NSW150


title: delta_ctrC, stationary, rep2

description: stationary phase


title: Colon muscularis propria, SPF, 5


title: D17-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Kidney_1541_pre (763205)

value: Blood

value: PBMC

value: M

value: White

value: N

value: PreTx


title: D16-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1543_pre (766944)

value: Other

value: NEG


title: Colon muscularis propria, GF, 3

value: colon muscularis propria

value: WT

value: germ-free


title: delta_ctrC, post exponential, rep4

description: post exponential phase


title: D15-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1538_pre (767911)

value: F

value: Y

value: POS

value: SIMULECT


title: Colon muscularis propria, GF, 2

value: adult

value: female


title: D14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Kidney_1539_pre (767365)

value: Blood

value: PBMC

value: White

value: ATG


title: Colon muscularis propria, GF, 1


title: delta_ctrC, post exponential, rep3

description: post exponential phase

value: L. longbeachae strain NSW150


title: D19-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1538_post (R9958-8)

value: PostTx

value: NEG


title: Kidney_1535_pre (767726)

value: M

value: PreTx


title: delta_ctrC, post exponential, rep2

description: post exponential phase


title: D13-TH-1-plasma intensity low

description: smart-seq 2


title: Colon muscularis propria, SPF, 4

value: colon muscularis propria

value: WT

value: conventionally raised


title: delta_ctrC, post exponential, rep1

description: post exponential phase


title: D12-TH-1-plasma intensity low

description: smart-seq 2


title: D18-TH-1-plasma intensity high

description: smart-seq 2


title: Colon muscularis propria, SPF, 3

value: adult


title: delta_ctrC, stationary, rep1

description: stationary phase


title: Kidney_1534_pre (768490)

value: Black

value: N

value: POS

value: SIMULECT


title: Colon muscularis propria, GF, 4

value: female

value: germ-free


title: D11-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Colon muscularis propria, SPF, 2


title: D10-TH-1-plasma intensity low

description: smart-seq 2


title: delta_ctrC, exponential, rep3

description: exponential phase

value: L. longbeachae strain NSW150


title: Kidney_1533_pre (766862)

value: Blood

value: PBMC

value: Asian

value: NEG

value: ATG


title: delta_ctrC, exponential, rep2

description: exponential phase


title: D9-TH-1-plasma intensity low

description: smart-seq 2


title: Colon muscularis propria, SPF, 1

value: colon muscularis propria

value: WT

value: conventionally raised


title: delta_ctrC, exponential, rep1

description: exponential phase


title: Kidney_1531_pre (767019)

value: M

value: White

value: N

value: PreTx


title: hLMR-NC_rescue_3

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The FASTQ read files were first trimmed and cleaned using fastp/0.23.2 and assessed for quality using FastQC/0.11.8.
The reads were then aligned using HISAT2/2.2.1.0 with an index created using the GRCm38.p6 genome.
The trimmed reads were aligned with default settings of HISAT2/2.2.1.0 and quantified using featureCounts (subread/2.0) with mouse GENCODE vm24.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: Liver

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Liver


title: D8-TH-1-plasma intensity none

description: smart-seq 2

data_processing:
raw sequencing files in blc format were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR (v.2.5.3a) GeneCounts function, multi-mapped reads were filtered, and gene expression matrices were generated using SeqMonk. Seurat package was used to perform all downstream analysis.
Assembly: mm10
Supplementary files format and content: counttable (Text file)

value: Brain


title: Long Covid 19

city: Edmonton

first: Hussain

last: Syed

state: Alberta

address: 116 Street and 85th Ave

country: Canada

institute: University of Alberta

data_processing:
Kallisto pseudoalignment and bias correction was used for fragment alignment to the human cDNA database (GRCh38)
Fastq files were trimmed prior to Kallisto pseudoalignment using Fastqc
Assembly: GRCh38
Supplementary files format and content: Tab-delemited counts files
Supplementary files format and content: Tab-delemited TPM files

source_name: whole blood

extract_protocol:
Whole blood cell RNA was extracted using PAXgene Blood RNA Kit, Qiagen.
100 ng RNA was used to make libraries using TruSeq RNA Library Prep Kit v2.

value: whole blood

value: No

tag: sample id


title: hLMR-NC_rescue_4


title: Kidney_1529_pre (765559)

value: F

value: Y

value: POS


title: D7-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells

value: microglia


title: hLMR-NC_rescue_2


title: delta_ctrC, exponential, rep4

description: exponential phase

value: L. longbeachae strain NSW150


title: Kidney_1528_pre (767370)

value: Blood

value: PBMC

value: ATG


title: hLMR-NC_rescue_1


title: Long Covid 18


title: D6-TH-1-plasma intensity none

description: smart-seq 2


title: Long Covid 17


title: D5-TH-1-plasma intensity none

description: smart-seq 2


title: D4-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_1526_pre (767311)

value: M

value: Black

value: NEG


title: mLMR-NC_knockdown_4


title: mLMR-NC_knockdown_3


title: Kidney_1527_post (R9937-8)

value: Asian

value: N

value: PostTx


title: Long Covid 16

value: whole blood


title: Kidney_1532_pre (766567)

value: PreTx


title: D3-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: Kidney_1526_post (R9932-8)


title: Long Covid 15

value: No


title: Long Covid 14


title: Kidney_1524_pre (766308)

value: White

value: Y

value: POS


title: D2-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells

value: microglia


title: mLMR-NC_knockdown_1

value: Liver


title: mLMR-NC_knockdown_2


title: Long Covid 13


title: Kidney_1523_pre (766943)

value: Blood

value: PBMC

value: Other

value: ATG


title: Long Covid 12


title: LMR-NC_control_4


title: C23-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1521_pre (763866)

value: M

value: NEG


title: D1-TH-1-plasma intensity none

description: smart-seq 2


title: LMR-NC_control_3


title: Long Covid 11


title: C22-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1517_pre (764694)


title: LMR-NC_control_2


title: Long Covid 10


title: Kidney_1517_post (R9820-8)

value: PostTx


title: LMR-NC_control_1


title: C21-TH-1-plasma intensity high

description: smart-seq 2


title: C20-TH-1-plasma intensity high

description: smart-seq 2


title: Long Covid 8

value: whole blood


title: Kidney_1516_pre (765156)

value: N

value: PreTx


title: Long Covid 9

value: No


title: Long Covid 7


title: hLMR3_rescue_3


title: hLMR3_rescue_2


title: C18-TH-1-plasma intensity high

description: smart-seq 2

value: Brain


title: Kidney_1513_pre (764752)

value: F

value: Islander

value: Y


title: Long Covid 6


title: Kidney_1511_pre (763946)

value: POS

value: SIMULECT


title: C17-TH-1-plasma intensity high

description: smart-seq 2

value: isolated cells

value: microglia


title: hLMR3_rescue_1

value: Liver


title: C16-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1511_post (R9824-8)

value: Blood

value: PBMC

value: Other


title: mLMR3_knockdown_4


title: Long Covid 4


title: hLMR3_rescue_4


title: C15-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1510_pre (763565)

value: ATG


title: Kidney_1507_pre (761304)

value: M

value: White

value: NEG


title: mLMR3_knockdown_3


title: mLMR3_knockdown_2


title: C14-TH-1-plasma intensity low

description: smart-seq 2


title: C19-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1512_pre (763915)

value: N

value: PreTx


title: Long Covid 2

value: whole blood

value: No


title: Kidney_1505_pre (756689)

value: Y


title: mLMR3_knockdown_1


title: Kidney_1505_post (R9743-8)

value: PostTx

value: POS


title: Long Covid 1


title: C13-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells


title: C12-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: Kidney_1501_pre (756760)

value: Blood

value: SIMULECT


title: Long Covid 5


title: Healthy Control 16


title: LMR3_control_3

value: Liver


title: C11-TH-1-plasma intensity low

description: smart-seq 2


title: Healthy Control 17


title: C10-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1501_post (R9735-8)

value: PBMC

value: Other


title: LMR3_control_2


title: Healthy Control 15


title: Long Covid 3


title: Kidney_1496_pre (755235)

value: M

value: White


title: C9-TH-1-plasma intensity low

description: smart-seq 2


title: LMR3_control_1


title: Healthy Control 14


title: Kidney_1496_post (AR034739)

value: N

value: NEG


title: hLMR2_rescue_4


title: Healthy Control 13

value: whole blood


title: Kidney_1494_pre (753559)

value: F

value: Black

value: PreTx

value: ATG


title: C7-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: hLMR2_rescue_3


title: Healthy Control 12

value: No


title: Kidney_1494_post (R9696-8)

value: PostTx

value: POS


title: C6-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells

value: microglia


title: Healthy Control 11


title: Kidney_1492_pre (753718)

value: Blood

value: PBMC

value: SIMULECT


title: C5-TH-1-plasma intensity none

description: smart-seq 2


title: Healthy Control 10


title: Healthy Control 9


title: C4-TH-1-plasma intensity none

description: smart-seq 2


title: mLMR2_knockdown_4

value: Liver


title: Kidney_1492_post (R9718-6)

value: M

value: Other

value: N


title: Kidney_1489_pre (753984)

value: White

value: Y

value: NEG


title: C3-TH-1-plasma intensity none

description: smart-seq 2


title: mLMR2_knockdown_3


title: Healthy Control 8

value: whole blood


title: C2-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: Kidney_1489_post (R9690-8)


title: mLMR2_knockdown_2


title: C8-TH-1-plasma intensity none

description: smart-seq 2


title: Healthy Control 7

value: No


title: Kidney_1484_pre (751946)

value: PreTx


title: mLMR2_knockdown_1


title: hLMR2_rescue_2


title: Healthy Control 6


title: Kidney_1484_post (R9653-8)

value: PostTx


title: B23-TH-1-plasma intensity high

description: smart-seq 2

value: isolated cells


title: LMR2_control_4


title: Healthy Control 5


title: Kidney_1482_pre (749997)

value: F

value: POS


title: Healthy Control 4


title: B22-TH-1-plasma intensity high

description: smart-seq 2

value: microglia


title: hLMR2_rescue_1


title: Kidney_1482_post (R9619-8)

value: Blood

value: PBMC

value: SIMULECT


title: B21-TH-1-plasma intensity high

description: smart-seq 2


title: Healthy Control 3


title: LMR2_control_2

value: Liver


title: LMR2_control_1


title: B20-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1481_post (R9657-8)

value: M

value: Other


title: B19-TH-1-plasma intensity high

description: smart-seq 2


title: Healthy Control 2


title: C1-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_1481_pre (751166)

value: Y


title: Healthy Control 1


title: B18-TH-1-plasma intensity high

description: smart-seq 2


title: hLMR1_rescue_3


title: LMR2_control_3


title: B17-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1480_post (R9617-8)

value: Black

value: N


title: ABO/HLA#3

type: RNA

city: Seoul

first: Minsun

last: Jung

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: Expression of isolated transcripts was assayed using nCounter SPRINT syetem (NanoString Technologies, Seattle, WA, USA).

data_processing: Data preprocessing and quality control followed the standard protocols provided by the manufacturer using nSolver software ver 4.0, NanoStringQCPro ver. 1.14.0, and NanoStringNorm ver. 1.2.1 (NanoString Technologies). Gene counts were normalized using the geometric mean of internal reference genes, and gene expression was log-2 transformed.

source_name: Kidney allograft biopsy

extract_protocol: RNA was extracted from formalin-fixed, paraffin-embedded tissues. One hundred nanograms of RNA from each biopsy were added to the NanoString codeset in hybridization buffer and incubated at 65℃ for 16 h.

value: Kidney allograft biopsy (FFPE)

tag: sample type

value: ABO incompatible and HLA incompatible kidney transplantation with antibody-mediated rejection


title: hLMR1_rescue_2

tag: strain


title: Kidney_1476_pre (748583)

value: White

value: PreTx


title: B16-TH-1-plasma intensity low

institute: Stanford University

description: smart-seq 2

source_name: Brain

value: Brain

value: isolated cells


title: hLMR1_rescue_1

tag: treatment


title: Kidney_1476_post (R9597-8)

tag: patient id

value: PostTx

value: POS


title: B15-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: ABO/HLA#2


title: mLMR1_knockdown_4


title: ABO/HLA#1


title: mLMR1_knockdown_3


title: Kidney_1464_post (R9527-8)

value: Blood

value: PBMC

tag: age

value: NEG


title: NR#3

value: ABO incompatible kidney transplantation without antibody-mediated rejection


title: Kidney_1480_pre (749046)

tag: Sex

value: M

value: SIMULECT


title: Kidney_1457_pre (757911)

value: F

tag: race

value: Other

value: Y

value: ATG


title: hLMR1_rescue_4

value: Liver


title: B13-TH-1-plasma intensity low

description: smart-seq 2


title: mLMR1_knockdown_2


title: B12-TH-1-plasma intensity low

description: smart-seq 2


title: NR#1

value: Kidney allograft biopsy (FFPE)


title: mLMR1_knockdown_1


title: Kidney_1455_pre (R9454-8)

value: White

tag: hispanic

value: N

value: PreTx


title: Kidney_1455_post (R9517-8)

tag: time

value: PostTx


title: LMR1_control_4

tag: tissue


title: ABO#3

value: ABO incompatible kidney transplantation with antibody-mediated rejection


title: B10-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: B11-TH-1-plasma intensity low

description: smart-seq 2


title: B9-TH-1-plasma intensity low

description: smart-seq 2


title: LMR1_control_2


title: Kidney_1438_pre (R9089-8)

value: Blood

value: PBMC

tag: cmv r

value: POS


title: B14-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_1437_pre (R9073-8)

value: M

tag: cmv d

value: SIMULECT


title: Kidney_1438_post (R9284-8)

tag: induction


title: B8-TH-1-plasma intensity none

description: smart-seq 2

tag: cell line


title: ABO#1


title: NR#2

value: ABO incompatible kidney transplantation without antibody-mediated rejection


title: LMR1_control_3


title: B7-TH-1-plasma intensity none

description: smart-seq 2

tag: cell type


title: Case#2

value: ABO incompatible and HLA incompatible kidney transplantation with probably antibody-mediated rejection


title: Homo2, snRNA-seq

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

institute: the First affiliated hospital of Sun Yat-sen University

data_processing:
snRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline
Gene expression matrix was created by using Seurat pipeline.
Assembly: mm10
Supplementary files format and content: CellRanger files

growth_protocol: C57BL/6N WDR4 mutated knock-in (mKI) mice with NM_021322.2 c.664G>T mutation were generated using CRISPR-Cas9 system by Biocytogen Co., Ltd.  Mice were grown under SPF condition.

extract_protocol:
Cell nuclei were isolated the from brain tissues using Shbio Cell Nuclear Isolation Kit (Shbio, #52009–10).
The nuclei suspension was then processed with Chromium Next GEM Chip G Single Cell Kit (10X Genomics) and Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics) for cDNA library construction according to manufacturer's protocol. snRNA-seq was performed on the Illumina system with paired-end program

treatment_protocol: Two months old wild type and WDR4 homozygous mutated mice were sacrified and the brain of mice were isolated for snRNA-seq.

value: brain

tag: genotype

value: WDR4 mKI


title: Kidney_1430_pre (R8999-8)

value: F

value: White


title: Kidney_1430_post (R9257-8)

value: N


title: Homo1, snRNA-seq


title: B5-TH-1-plasma intensity none

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

description: smart-seq 2


title: Case#1-1

value: Kidney allograft biopsy (FFPE)

value: ABO incompatible kidney transplantation with probably antibody-mediated rejection


title: WT2, snRNA-seq

value: wild type


title: Case#1-2

value: ABO incompatible kidney transplantation with borderline T-cell mediated rejection


title: C1L

city: Wuhan

first: Shuang

last: Lu

address: East Lake Road 185

department: State Key Laboratory of Virology/Institute of Medical Virology/Department of Infectious Diseases

institute: School of Basic Medical Sciences/Renmin Hospital, Wuhan University

data_processing:
The raw data were filtered according to the following criteria: 1) Cutadapt is used to remove the adaptor sequence at the 3' end, and the removed part has at least a 10-bp overlap (AGATCGGAAG) with known ligation, allowing a 20% base mismatch; 2) the reads are removed if their average quality score is lower than Q20.
Then, the filtered reads are mapped to the reference genomes using the Bowtie2 tool (http://bowtie-bio.sourceforge.net/index.shtml).
According to the sequence alignment results, the expression level of each gene was calculated, and the expression level was normalized by Fragments Per Kilo bases Per Million Fragments (FPKM). DESeq (version 1.18.0) was used to identify the differentially expressed genes (DEGs).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000009045.1/)
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

organism: Bacillus subtilis

source_name: Bacillus subtilis spores

growth_protocol: The freshly prepared spores were centrifuged and resuspended in 100 mM L-alanine buffered by 50 mM Tris-HCl.

extract_protocol:
Total RNA from Bacillus strains was isolated with TRIzol reagent (Invitrogen, USA).
The ribosomal RNA was removed using the Ribo-Zero rRNA removal kit (Illumina, CA, USA, MRZB12424). The RNA was then fragmented to 200-300 bp, followed by random primers and reverse transcriptase to synthesize the first strand of cDNA, and then the second strand of cDNA. The library size was then measured using an Agilent 2100 Bioanalyzer and the cDNA was sequenced on the Illumina HiSeq 3000.

treatment_protocol: Spores were mock treated or treated with L-alanine

tag: agent

value: L-alanine treatment


title: Kidney_1429_pre (R9000-8)

value: Blood

value: PreTx

value: NEG


title: B4-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: ABO#2

tag: sample type

value: ABO incompatible kidney transplantation with antibody-mediated rejection


title: Kidney_1428_pre (R9159-8)

value: PBMC

value: SIMULECT


title: C2

tag: strain

value: mock treatment


title: WT1, snRNA-seq

value: brain


title: B3-TH-1-plasma intensity none

description: smart-seq 2


title: C1


title: LMR1_control_1

tag: treatment

value: Liver


title: B2-TH-1-plasma intensity none

description: smart-seq 2


title: M2L


title: Kidney_1423_pre (R8961-8)

tag: patient id

value: M

value: Black

value: N

value: POS


title: Batch3_Sample25_MPL_Stroma

city: Oxford

first: Antonio

last: Rodriguez-Romera

address: John Radcliffe Hospital, Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

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

source_name: bone marrow

extract_protocol:
We sequenced single cell transcriptomes of freshly collected mononuclear cells, LK (HSPCs), CD41+ and CD45- Lin- Ter119- CD71low/-stromal cells from MF (MPLW515L) mice or healthy controls transplanted with HSCs transduced with GFP only.
Library were prepared according to the manufacter’s instructions (single cell 3’ v3 or 3.1 protocol, 10x Genomics).

value: bone marrow

tag: age

value: 8-9 weeks


title: Batch3_Sample24_GFP_Stroma


title: C2L

value: wild type

value: L-alanine treatment


title: Kidney_1428_post (R9271-8)

value: Blood

tag: Sex

value: F

value: White

value: PostTx

value: NEG


title: B1-TH-1-plasma intensity none

city: Stanford

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: B6-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_1437_post (R9290-8)

value: PBMC

tag: race

value: Y

value: SIMULECT


title: Kidney_1423_post (R9268-8)

value: M

value: Black

tag: hispanic

value: N


title: Kidney_1417_pre (R8908-8)

value: Other

tag: time

value: PreTx

value: POS


title: M2

value: wild type

value: mock treatment


title: A22-TH-1-plasma intensity high

description: smart-seq 2

tag: tissue


title: A23-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1417_post (R9216-8)

value: Blood

value: F

tag: cmv r


title: Batch3_Sample22_GFP_CD41

value: CD41+ Cells

value: bone marrow

value: 8-9 weeks


title: Batch3_Sample21_MPL_CD41


title: A21-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: A20-TH-1-plasma intensity high

description: smart-seq 2


title: CD38KO, rep 3

city: Boston

first: Morgane

last: h

state: MA

address: 3 Blackfan Street

department: Rheumatology

institute: BIDMC

data_processing:
Samples were sequenced on an Illumina NextSeq500 run with single-end 75-bp reads
Data analyses were performed using the VIPER pipeline by the Dana Farber Cancer Institute Core
Assembly: hg19
Supplementary files format and content: bg and bw

source_name: Jurkat

extract_protocol:
Total RNA was extracted from Jurkat Control and Jurkat CD38KO cells using the RNeasy mini kit (Quiagen, #74104) according to manufacturer's instructions.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits according to the manufacturer’s protocols.

value: Jurkat

value: T cell


title: Batch3_Sample20_MPL_LK

value: LK Cells


title: M1


title: Batch3_Sample19_GFP_LK


title: Batch3_Sample18_MPL_MNC

value: Total Mononuclear Cells


title: CD38KO, rep 2


title: Kidney_1415_post (R9196-8)

data_processing:
Adapter sequences were trimmed off from the raw reads using Cutadapt (Martin, 2011) and only reads with minimum 30bp were kept for downstream analysis.  Reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function (Farrell et al, 2021).  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 30 -min-sample 1.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing methylation level per CpG site for each sample

value: PBMC

value: M

value: Other

value: Y

value: PostTx

tag: cmv d

value: NEG

value: SIMULECT


title: A19-TH-1-plasma intensity high

description: smart-seq 2


title: Batch3_Sample23_GFP_Stroma


title: CD38KO, rep 1


title: M1L

value: wild type

value: L-alanine treatment


title: A18-TH-1-plasma intensity high

description: smart-seq 2


title: Kidney_1410_post (R9172-8)

value: Blood

value: Asian

value: N

value: POS

tag: induction


title: WT, rep 3

tag: cell line

value: Jurkat

value: WT


title: Kidney_1410_pre (R8805-8)

tag: cell type

value: PreTx


title: Batch3_Sample17_GFP_MNC

value: Total Mononuclear Cells

value: bone marrow

value: 8-9 weeks


title: WT, rep 2

value: T cell

tag: genotype


title: A17-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Kidney_1400_pre (R8779-8)

value: PBMC

value: F

value: Unknown

value: NEG

value: ATG


title: Kidney_1415_pre (R8893-8)

value: Blood

value: M

value: Other

value: Y

value: SIMULECT


title: A16-TH-1-plasma intensity low

description: smart-seq 2


title: WT, rep 1

value: Jurkat

value: WT


title: A15-TH-1-plasma intensity low

description: smart-seq 2


title: Batch2_Sample11_MPL_MNC

value: Total Mononuclear Cells

value: bone marrow

value: 8-9 weeks


title: Kidney_1354_pre (R8609-8)

value: Black

value: N

value: PreTx

value: POS


title: A14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: SLE3 high CD38

data_processing:
atropos Adapter trimming
bowtie2 alignmanet
Peak-calling macs2
QC with FastQC
Grey-listing, blacklisting, and chrM removal
Assembly: hg19
Supplementary files format and content: ATAC-seq comparing CD4CD38low vs CD4CD38high T cells from healthy donors and SLE

source_name: T cell

extract_protocol: omniATAC

treatment_protocol: sorted by FACS ARIA and frozen in bambanker

value: T cell


title: Batch2_Sample10_GFP_MNC


title: Kidney_1245_post (AR018833)

extract_protocol:
8ml of blood was drawn into the ACD tube.  After Ficol density gradient centrifugation, PBMCs were separated isolated  and cryopreserved in FCS/DMSO.
Genomic DNA was extracted from PBMCs using phenol-chloroform method (Guha et al, 2018).  500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).  A comprehensive TBS-seq protocol is demonstrated in (Morselli et al, 2021).

value: Blood

value: PBMC

value: F

value: White

value: PostTx

value: UNK


title: Batch2_Sample15_MPL_Stroma


title: SLE2 low CD38


title: Kidney_1354_post (R8920-10)

value: SIMULECT


title: A12-TH-1-plasma intensity low

description: smart-seq 2


title: Kidney_U1111R_post (U486-6_S24)

data_processing:
Reads were aligned to reference genome GRCh38 using STAR using default parameters (Dobin et al, 2013).   A gene count table was generated using featurecount (Liao et al, 2013).  Gene count matrix was first normalized and DEGs were identified using R package DEseq2 (Love et al, 2014).  Genes with adjusted p value < 0.05 and at least 2-fold difference between CMV serostatus were considered differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
8ml of blood was drawn into the ACD tube.  After Ficol density gradient centrifugation, PBMCs were separated isolated  and cryopreserved in FCS/DMSO.
mRNA libraries were constructed using KAPA RNA HyperPrep Kit following the manufacture’s instruction (Cat# KK8540).  RNA was sheared and primed with oligos for cDNA synthesis.  After adapter ligation and PCR amplified, the final library was quantified and accessed quality with TapeStation.

value: NEG

tag: atg

value: Y

tag: simulect


title: SLE2 high CD38


title: A13-TH-1-plasma intensity low

description: smart-seq 2


title: Batch2_Sample9_MPL_LK

value: LK Cells

value: bone marrow

tag: strain

value: 8-9 weeks


title: Batch2_Sample8_GFP_LK


title: Batch3_Sample16_GFP_MNC

value: Total Mononuclear Cells


title: A11-TH-1-plasma intensity low

description: smart-seq 2

value: Brain


title: Kidney_U1143R_post (U462-6_S18)

value: POS

value: N


title: Batch1_Sample7_GFP_LK


title: SLE1 low CD38

value: T cell


title: Kidney_U1148R_post (U456-6_S30)

value: Blood

value: M


title: SLE3 low CD38


title: SLE1 high CD38


title: Batch1_Sample6_MPL_LK


title: HC3 low CD38


title: Batch1_Sample5_MPL_CD41

value: CD41+ Cells


title: Kidney_U1146R_post (U447-10_S66)

value: PBMC

value: F


title: A9-TH-1-plasma intensity low

description: smart-seq 2

value: isolated cells

value: microglia


title: Kidney_U1132R_post (U416-6_S70)

value: PostTx


title: A8-TH-1-plasma intensity none

description: smart-seq 2


title: A7-TH-1-plasma intensity none

description: smart-seq 2


title: Batch1_Sample3_GFP_Stroma


title: HC2 low CD38


title: HC3 high CD38


title: Kidney_U1123R_post (U391-6_S42)

value: Y


title: Batch1_Sample1_GFP_MNC


title: A10-TH-1-plasma intensity low

description: smart-seq 2


title: A5-TH-1-plasma intensity none

description: smart-seq 2


title: HC1 high CD38


title: HC2 high CD38


title: A4-TH-1-plasma intensity none

description: smart-seq 2


title: HC1 low CD38


title: Kidney_U1124R_post (U410-9_S40)

value: NEG


title: A3-TH-1-plasma intensity none

description: smart-seq 2


title: Kidney_1558_post (R9970-6_S2)


title: A6-TH-1-plasma intensity none

description: smart-seq 2


title: AM3_2

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
Raw sequencing reads were quality-checked using FastQC and were subsequently trimmed using Trim Galore. Following this, the reads were aligned to the human genome sequence hg38, employing the R packages Rbowtie2 and Rsamtools. Differential analysis of count data was performed using the R package DeSeq2. Transcripts exhibiting |log2 fold change| > 1 and q < 0.01 (FDR-adjusted P-values) were identified as differentially expressed genes (DEGs). Cluster analysis was conducted using the R packages pvclust and dendextend. To determine the cell type, the R package clustifyr was employed against the scRNA-seq human cortex database. Cellular deconvolution was carried out using BrainDeconvShiny with the assistance of dtangle and the NG database. Heatmaps were constructed using R package ComplexHeatmap.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw count for each sample

source_name: iPSC-derived astrocyte

growth_protocol:
NPCs were thawed in completed neural maintenance medium (NMM) (containing 50% DMEM/F12 with glutamine, 50% Neurobasal medium, 1X B27 supplement, 1X N2 supplement, 1% Penicillin/Streptomycin, 1% GlutaMax (all purchased from Gibco), non-essential amino-acids (Sigma), completed with 10 ng/mL recombinant human epidermal growth factor, and 10 ng/mL basic fibroblast growth factor) supplemented with Rhock-inhibitor at a final concentration of 10 µM and plated into poly-L-ornithine/laminin-coated dishes. On the next day, the medium was changed to completed NMM. The cell culture medium was changed every two days. Thawed NPC lines were propagated for the next passage (with a density of 100.000 cells/cm2) and seeded into Matrigel-coated dishes for astrocyte differentiation at day 10, upon reaching confluence again, (with a cell-density of 50.000/cm2).
LSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into poly-L-ornithine/laminin-coated plates at a density of 50.000 cells/cm2 and maintained in GPC expansion medium (containing DMEM/F12 Glutamax, 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF) and 10 ng/ml basic fibroblast growth factor (FGF2)) for 2 weeks. The medium was changed every two days. At day 24, cells were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. The medium was changed every two days. At day 36, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement, and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
SSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. Medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell-dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 24, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
TUSP method of Astrocyte differentiation and treatment: The NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in the astrocyte induction medium (ScienceCell’s astrocyte growth medium supplemented with 2% FBS) for 4 weeks. The medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 42, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was serum-free astrocyte growth medium containing 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging. On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM A42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq and cellular media for IL-6 analysis were collected 72 hours after the treatment.

extract_protocol: The cellular pellet samples were used to isolate total RNA with TRI Reagent (Merck, USA) and RapidOutput DNA removal kit (ThermoFisher Scientific, USA). A Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA) were used to analyse the isolated RNA for quantity and quality, respectively. Complementary DNA (cDNA) libraries were synthesized using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, UK). The concentration and quality of cDNA libraries were assessed using a Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA). The cDNA samples were then diluted to 4 nM and sequenced on the Illumina NextSeq® platform with NextSeq® 500/550 High Output Kit v2.5 (150 cycles) (Illumina, USA), generating 75 bp pair-end reads, and on the Illumina NovaSeq® 6000 platform with NovaSeq® S4 300 kit (Illumina, USA), generating 150 bp pair-end reads.

treatment_protocol: On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM AB42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq were collected 72 hours after the treatment.

tag: differentiation protocol

value: TUSP method

value: iPSC-derived astrocyte

value: control, healthy

tag: treatment

value: non-treated

tag: donor

value: healthy, 35-years old, female


title: Kidney_U1112R_post (U356-6_S26)

tag: patient id

tag: age

tag: Sex

value: POS

value: N


title: A2-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: Batch1_Sample4_MPL_Stroma

value: bone marrow

value: 8-9 weeks


title: MPPG/M, Pristane, replicate 2 [lupus_MPP3_2]

first: Andrew

last: Goodspeed

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl mouse transcriptome (GRCm38.p6, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Assembly: GRCm38
Supplementary files format and content: Text file containing STAR gene count values

source_name: Bone Marrow

extract_protocol:
Sorted cells were pelleted and then RNA was isolated via the Qiagen RNeasy micro kit
Ribo-depleted RNA was isolated

treatment_protocol: N/A cells were processed immediately after sorting

value: Bone Marrow

value: MPPG/M

value: Pristane


title: AM3_1


title: MPPG/M, Pristane, replicate 1 [lupus_MPP3_1]


title: Kidney_U1136R_post (U415-6_S22)

source_name: Blood

value: Blood

value: PBMC

value: F

tag: time


title: A1-TH-1-plasma intensity none

description: smart-seq 2

tag: tissue

value: isolated cells

value: microglia


title: Kidney_1547_post (R9957-6_S56)

value: M

value: PostTx

value: NEG

value: Y


title: Batch1_Sample2_MPL_MNC

value: Total Mononuclear Cells


title: Kidney_1534_post (R9968-7_S6)

value: POS

value: N


title: MPPG/M, Pristane, replicate 3 [lupus_MPP3_3]


title: Kidney_1535_post (R9953-7_S74)


title: AM1_2

value: LSFP method

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated

value: healthy, 35-years old, female


title: Plasma-positive microglia-4

data_processing:
raw sequencing files were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR, multi-mapped reads were filtered, and gene counts were made using HTSEQ.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM counts for each sample

extract_protocol:
RNA was harvested using RNeasy Plus Micro kit
Smart-seq2 protocol

value: Brain

value: cell isolated from brain

value: wild-typte


title: AM1_1


title: Kidney_1553_post (R9950-6_S64)

value: Blood

value: PBMC


title: BM Mon, Pristane, replicate 2 [lupus_monocyte_2]

value: Bone Marrow

value: BM Mon

value: Pristane


title: Plasma-positive microglia-3

value: microglia


title: AM2_2

value: SSFP method


title: BM Mon, Pristane, replicate 1 [lupus_monocyte_1]


title: SLAM, Pristane, replicate 3 [lupus_HSC_3]

value: SLAM


title: Plasma-positive microglia-2


title: Kidney_1551_post (R9938-6_S28)

value: M

value: PostTx

value: POS

value: NEG

value: Y

value: N


title: AM2_1

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated

value: healthy, 35-years old, female


title: Kidney_1527_post (R9937-6_S58)

value: Blood

value: PBMC


title: Plasma-positive microglia-1

value: Brain

value: cell isolated from brain

value: wild-typte


title: SLAM, Pristane, replicate 2 [lupus_HSC_2]

value: Bone Marrow

value: Pristane


title: AI3_2

value: TUSP method


title: Kidney_1536_post (R9931-6_S36)

value: M

value: PostTx

value: UNK


title: BM Mon, Pristane, replicate 3 [lupus_monocyte_3]

value: BM Mon


title: GMP, Pristane, replicate 3 [lupus_GMP_3]

value: GMP


title: Plasma-negative microglia-3

value: microglia


title: SLAM, Pristane, replicate 1 [lupus_HSC_1]

value: SLAM


title: Kidney_1528_post (R9924-6_S60)

value: F

value: POS

value: Y

value: N


title: AI1_2

value: LSFP method

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated

value: healthy, 35-years old, female


title: AI3_1

value: TUSP method


title: Plasma-negative microglia-4

value: Brain

value: cell isolated from brain

value: wild-typte


title: Kidney_1546_post (R9927-6_S54)

value: Blood

value: PBMC

value: PostTx


title: Kidney_1523_post (R9917-6_S71)

value: M


title: GMP, Pristane, replicate 2 [lupus_GMP_2]

value: Bone Marrow

value: GMP

value: Pristane


title: Kidney_1541_post (R9908-6_S20)

value: NEG

value: Y

value: N


title: Plasma-negative microglia-1

value: microglia


title: AI2_2

value: SSFP method

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated


title: AI1_1

value: LSFP method

value: healthy, 35-years old, female


title: GMP, Pristane, replicate 1 [lupus_GMP_1]


title: MPPG/M, Control, replicate 3 [control_MPP3_3]

value: MPPG/M

value: Control


title: TY84_S11

city: Olsztyn

first: Dawid

last: Tobolski

state: Warmińsko-mazurskie

address: Kazimierza Jaroszyka

department: Department of Large Animal Diseases and Clinic

country: Poland

institute: Institute of Veterinary Medicine, Warsaw University of Life Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: EquCab 3.0
Supplementary files format and content: Cell Ranger software output files H5

organism: Equus caballus

source_name: endometrium

extract_protocol:
Endometrial biopsies were collected from the base of the uterine horn of pregnant pony mares on days 33 (n=5) and 42 (n=5) post-ovulation, following confirmation of normally progressing pregnancies. Samples were digested to obtain suspensions of single cells according to De Mestre et al. (2010).Cell viability was determined using Trypan blue solution 0.4%. Endometrial cell suspensions were immediately processed for scRNA-seq with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) according to the manufacturer's instructions. An input of 10,000 cells per preparation were used. Libraries were sequenced at a depth of approximately 35,000 paired-end reads per cell on an Illumina NovaSeq6000 (Illumina, San Diego, CA, USA).
Library was generated according to the manufacter’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1;Dual Index; 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: endometrium


title: AI2_1


title: Kidney_1543_post (R9899-6_S10)

first: Fei-Man

last: Hsu

address: 610 Charles E Young Dr S

institute: UCLA

value: Blood

value: PBMC

value: M

value: PostTx

value: POS


title: MPPG/M, Control, replicate 2 [control_MPP3_2]

city: Aurora

value: Bone Marrow


title: Kidney_1522_post (R9868-6_S12)

value: F

value: NEG

value: Y

value: N


title: TY70_S8

description: 10x Genomics


title: AE3_2

value: TUSP method

value: iPSC-derived astrocyte

value: control, healthy


title: MPPG/M, Control, replicate 1 [control_MPP3_1]


title: TY66_S6

description: 10x Genomics


title: AE3_1

value: non-treated

value: healthy, 35-years old, female


title: Plasma-negative microglia-2

value: Brain

value: cell isolated from brain

value: microglia

value: wild-typte


title: Kidney_1515_post (R9852-6_S50)

value: Blood

value: PBMC

value: M

value: UNK


title: AE2

value: SSFP method


title: BM Mon, Control, replicate 3 [control_monocyte_3]

value: Bone Marrow

value: BM Mon

value: Control


title: Kidney_1511_post (R9824-6_S32)

value: F

value: PostTx

value: POS

value: N

value: Y


title: TY06_S3

description: 10x Genomics

value: endometrium


title: TY05_S2

description: 10x Genomics


title: BM Mon, Control, replicate 2 [control_monocyte_2]


title: AE1_1

value: LSFP method

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated

value: healthy, 35-years old, female


title: TY68_S7

description: 10x Genomics


title: SLAM, Control, replicate 3 [control_HSC_3]

value: SLAM


title: F94520

city: Vancouver

first: Marco

last: Marra

state: BC

address: 570 W 7th Ave

institute: Canada's Michael Smith Genome Sciences Centre

description:
23239-OCT-2_Per-Site-Unphased-Methylation, 23239-OCT-2_Per-Read-Unphased-Methylation, 23239-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 23239-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 23239-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 23239-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

data_processing:
Per-site and per-read unphased methylation data detected from nanopore sequencing raw signals using nanopolish. Phased methylation data were obtained using NanoMethPhase.
Assembly: GRCh38
Supplementary files format and content: Phased and Unphased CpG methylation data in tsv.gz format.
Library strategy: NanoMethPhase

extract_protocol:
Frozen tissue sections were immersed in 420 μL of RLT Plus buffer (QIAGEN) containing tris(2-carboxyethyl)phosphine (a reducing agent; TCEP) and a unique sample tracking DNA plasmid, and gently agitated overnight at room temperature. Lysates were transferred from 2 mL tubes to wells of a 1.2 mL plate (Thermo Scientific, AB1127) to which was added 400 mL of 5x bind buffer (80 mL beads in 320 mL isopropyl alcohol). Following a 5 minute incubation at room temperature lysates were cleared on a Magnum FLX magnet place (Alpaqua Inc) for 6 minutes and the protein-containing supernatant removed. The beads, with bound nucleic acids, were washed by pipetting 10 times in wash buffer and returned to the magnet. Beads were washed three times in 70% ethanol then dried for 10 minutes. 40 mL nuclease-free water was added to the dried beads and returned to the magnet. The eluted total nucleic acids were transferred to a 96-well storage plate and aliquots taken for quantification using Invitrogen Qubit 4 Fluorometer (Thermo Fisher Q33226)  For samples with concentrations below 166 ng/µL or in volumes greater than 30 µL, 5000 ng of Total Nucleic Acid (TNA) was transferred to a 1.5 mL DNase/RNase free tube and concentrated without heat on the Savant SpeedVac Plus (SC210A) to a maximum volume of 30 µL. This 5000 ng sample in 30 µL was topped up with 10 µL of Qiagen Buffer EB (Cat.19086). The samples were then run on the SAGE Science Blue Pippin instrument using the High Pass Plus Cassette (BPPLUS 10) with a maximum of 4 samples per run. The start range was selected at 15,000 base pairs and the end range was selected at 150,000 base pairs yielding a targeted size of 82,500 base pairs. Following the run completion, each sample was eluted in 80 µL and each sample elution well was then washed with 80 µL of 10 mM Tris, 1mM EDTA containing 0.1% Tween to maximize sample recovery. The total volume of 160µL was then concentrated without heat to 50 µL using the SpeedVac Plus. Each sample was then quantified using the Invitrogen Qubit 4 Fluorometer (Q33226) and normalized to 2000 ng in 47.5 µL for PromethION genome sequencing.
Library construction and sequencing followed the Oxford Nanopore Technologies Genomic DNA by Ligation (SQK-LSK110) protocol. DNA libraries starting with 2 µg of sample per library. No shearing was performed. The NEBUltra-II kit, (New England Biolabs, Ipswich, MA, USA, cat. no. E7646A) was used for end-repair and A-tailing. NEBNext quick ligase (E6056S) was used to ligate the Oxford Nanopore sequencing adapter. A final size selection of 0.4:1 ratio beads:library (PCRClean – DX Aline Biosciences L/N 06180316) was done to select against smaller molecules. These library preparation steps were performed on Hamilton Nimbus96 liquid handlers. An example deck layout, in this case for the bead purification step, is shown in Extended Data Figure 1c. DNA libraries were loaded in R9.4.1 pore flow cells on PromethION 24 instrument running software version 19.06.9 (MinKNOW GUI v4.0.23). Sequencing was carried out for 72 hours. DNase I (Invitrogen cat no. AM2222) nuclease flush was performed after 24-48 hours by reloading the flow cell with the same library mix.


title: Kidney_1517_post (R9820-6_S52)

city: Los Angeles

value: Blood

value: PBMC

value: M

value: NEG


title: Kidney_1521_post (R9822-6_S16)


title: AE1_2


title: GSCs, shMDH2_63_IP02

city: Pittsburgh

first: Jeremy

last: Rich

state: PA

address: 5115 Centre Ave

department: Hillman Cancer Center

institute: University of Pittsburgh Medical Center

data_processing:
MeRIP-seq reads were aligned to human genome hg38 by using the Hisat2 with reference annotation from NCBI. To minimize the rate of false positives, only uniquely mapped and without-duplication reads were selected by samtools. Then, the reads were extended to a length of 200 nt in the 5’-to-3’ direction, accounting for the length of RNA fragments, to calculate the reads coverage along the genome by MACS2.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: 738 GSC

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (Roche) to deplete DNA contamination.
PolyA RNA was purified using a GenElute mRNA Miniprep Kit (Sigma-Aldrich) as per the manufacturer's instructions and fragmented using an RNA fragmentation kit (Ambion). Note that 200 μg of fragmented RNA was incubated with 3 μg anti-m6A (Synaptic Systems, Cat# 202 003) in RIP buffer (150 mmol/L NaCl, 10 mmol/L Tris, and 0.1% NP-40) for 2 hours at 4°C, followed by addition of washed protein A/G magnetic beads (Millipore) and incubation at 4°C for a further 2 hours. Beads were washed 6 times in RIP buffer and incubated with 50 μL immunoprecipitation buffer containing 0.5 mg/mL m6AMP (Sigma-Aldrich) to elute RNA. Immunoprecipitated RNA was extracted with phenol/chloroform, and RNA samples were sent for next-generation sequencing.

value: 738 GSC

value: Glioblastoma stem cells


title: GSCs, shMDH2_63_IP01


title: Kidney_1505_post (R9743-6_S34)

value: PostTx


title: Kidney_1508_post (R9748-6_S38)

value: F

value: POS


title: F94519

description:
40168-OCT-1_Per-Site-Unphased-Methylation, 40168-OCT-1_Per-Read-Unphased-Methylation, 40168-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 40168-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 40168-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 40168-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SLAM, Control, replicate 1 [control_HSC_1]

value: Bone Marrow

value: Control


title: GSCs, shMDH2_63_in02


title: GSCs, shMDH2_63_in01


title: F94516

description:
41813-OCT-1_Per-Site-Unphased-Methylation, 41813-OCT-1_Per-Read-Unphased-Methylation, 41813-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 41813-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 41813-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 41813-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SLAM, Control, replicate 2 [control_HSC_2]


title: GMP, Control, replicate 3 [control_GMP_3]

value: GMP


title: Kidney_1468_post (R9741-6_S8)

value: Y

value: N


title: BM Mon, Control, replicate 1 [control_monocyte_1]

value: BM Mon


title: GMP, Control, replicate 2 [control_GMP_2]


title: Kidney_1512_post (R9811-6_S68)


title: GMP, Control, replicate 1 [control_GMP_1]


title: GSCs, shMDH2_03_IP02


title: Kidney_1501_post (R9735-6_S48)