title: doxee17_d16dox_Rep1

description: Library name: doxee17_d16dox_Rep1

value: H1 hESC

value: hematopoietic progenitor cells


title: doxee17_d12dox_Rep1

status: Public on Mar 26 2026

type: SRA

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: doxee17_d12dox_Rep1

library_source: transcriptomic

data_processing:
Trim Galore! (v 0.6.5) was used to trim the adaptor sequences with a quality threshold of 20. Alignment was performed with STAR aligner . All samples passed the quality control requirements with > 50% of reads uniquely mapping (>20M uniquely mapped reads for each library). Gene level read counts were obtained using Salmon for all libraries.
Assembly: hg38
Supplementary files format and content: tab-delimited file with raw counts from all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: hematopoietic

growth_protocol: H1 hESCs were differentiated into HPCs.

extract_protocol:
200,000hESC-HPCs were collected and RNA extraction was performed with the RNeasy mini kit (QIAGEN).
PolyA-tailed mRNA was selected with beads from 300ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs)

tag: tissue

value: hematopoietic

tag: cell line

tag: cell type

tag: time

tag: treatment

value: DOX

tag: batch


title: doxee17_d12dox_Rep2

description: Library name: doxee17_d12dox_Rep2


title: 23366-15_ATAC

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description:
Library name: 23366-15_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI

library_source: other

data_processing:
The nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2/) was used to process ATAC-Seq data (Ewels et al., 2020). Following the initial analysis with the nf-core/atacseq pipeline, further explorations into the data were carried out using customized bioinformatics tools including differential analysis and motif analysis. First, FastQC (Andrews, 2010) was used to produce quality metrics. Then adapter trimming was performed with Trim Galore, a comprehensive wrapper combining Cutadapt and FastQC, for the refinement of FastQ files (Andrews, 2010; Martin, 2011). We used default settings to identify and remove adapter sequences to streamline preprocessing steps without manual intervention.
Hisat2 was used to align sequencing data (Kim et al., 2015). Trimmed ATAC-Seq reads were aligned against the MorexV3 reference genome with the addition of Bln1 (Bln1 was not annotated in the original MorexV3 release) (Mascher et al., 2021). The output was transmitted into Samtools (Li and Durbin, 2009), which was then converted into a compressed BAM file, filtering out secondary alignments, and leveraging multiple threads for efficiency. After alignment, reads were filtered using a combination of SAMtools, BEDTools, BAMTools, and Pysam (https://github.com/pysam-developers/pysam) to ensure high-quality alignments for downstream analysis (Li and Durbin, 2009; Quinlan and Hall, 2010; Barnett et al., 2011). SAMtools and BEDTools were used to remove reads mapping to blacklisted genomic regions, as well as reads marked as duplicates, non-primary alignments, unmapped reads, and those mapping to multiple genomic locations. BAMTools handled the exclusion of reads with excessive mismatches (more than four), soft-clipped alignments, large insert sizes (>2 kb), and provided additional quality control. Pysam was employed to filter out inter-chromosomal paired-end reads, those with improper FR orientation, and to remove both reads from any pair where a single read failed the criteria.
MACS2 was applied to identify regions with narrow peaks or broad peaks (Zhang et al., 2008). Then, deepTools (Ramírez et al., 2014) was used to convert filtered BAM files into BigWig format, employing Counts Per Million (CPM) as the default normalization method to prepare the data for such comparative analyses and further bioinformatics processing.
After obtaining the count matrix where each row is a consensus peak region and each column is a sample, we implemented a differential analysis to compute statistically significant differential peaks between pairwise comparisons through DESeq2 (Love et al., 2014). A minimal pre-filtering step was performed to keep only rows that had at least 10 reads total. After differential tests were been applied to each peak, p-values were calculated and adjusted to control false positives via  multiple testing. This filtering threshold was automatically determined to maximize detection power (i.e., maximize the number of differential peaks detected) at a specified false discovery rate (FDR). Tables were generated to report the peak annotation, and statistics and p adjusted and fold change for each pairwise comparison.
Assembly: Barley (Mascher 2021) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary files format and content: Aligned Next-Generation Sequencing reads in BAM format

molecule: other

organism: Hordeum vulgare

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: The wild-type progenitor, CI 16151 (Mla6, Bln1), was developed by the introgression of Mla6 into the Manchuria background (Moseman 1972) [10.2135/cropsci1972.0011183X001200050038x] and maintained by single seed descent. CI 16151 derived mutants [m18982 (mla6, Bln1); m19089 (Mla6, bln1); m19028 (mla6, bln1)] were generated via fast-neutrons (4 Gy Nf) as described in Meng et al. (2009) [10.1104/pp.108.129031] and Xi et al. (2009) [https://doi.org/10.1105/tpc.109.066167] and further characterized by  Chapman et al. 2021 [10.1093/genetics/iyaa026] and Velásquez-Zapata et al. (2024) [https://doi.org/10.1016/j.isci.2024.111013]. Seven-day old barley (Hordeum vulgare) first leaves were grown in 20 × 30-cm trays using sterilized potting mix (Sunshine Mix #1, Sungrow) in a climate-controlled greenhouse (16 h supplemental light, 20-22 C).

extract_protocol:
Nuclei were prepared by REquest Genomics (Athens, GA, USA). Barley tissue was chopped on ice using a razor blade for ~2 minutes in 600 μL of pre-chilled Nuclei Isolation Buffer (NIB) [https://doi.org/10.1186/1746-4811-9-31]. The chopped tissue was filtered through a 40-μm cell strainer and then subjected to centrifugation at 500 rcf for 5 minutes at 4C. The supernatant was removed and the pellet was resuspended in 500 μL of NIB. The sample was filtered again using a 20-μm cell strainer and then loaded onto the surface of 1 mL of a 35% Percoll buffer, prepared by mixing 35% Percoll with 65% NIB wash buffer. The nuclei centrifuged at 500 rcf for 10 minutes at 4C. The supernatant was carefully removed, and the pellets were washed in 100 μL of 1X TAPS buffer (5X TAPS buffer:  50mM TAPS-NaOH, pH8.0; 25mM MgCl2) [https://doi.org/10.1093/nar/gkw1179].
ATAC-seq libraries were prepared by REquest Genomics (Athens, GA, USA). Nuclei were reconstituted in 30 μL of 2.5X TAPS buffer. A total of 5 μL of nuclei were diluted tenfold and stained with DAPI (Sigma Cat. D9542) to evaluate the quality and abundance using a hemocytometer. A total of 50,000 nuclei were use for library preparation. The Tn5 assembly and library preparation procedures were conducted following previously established methods [https://doi.org/10.1093/nar/gkw1179].

treatment_protocol: Trays were blocked by biological replicate and plant genotype with seedling rows randomly assigned to one of four harvest timepoints (0, 16, 20, and 32 HAI). First leaf seedlings were inoculated with Blumeria hordei (Bh) isolate 5874 (AVRa6) and immediately transferred to a growth chamber (16 h light / 8 dark, 18 C). One gram of pooled tissue was collected for each timepoint and flash frozen in liquid nitrogen. Four biological replicates were collected for each genotype / timepoint combination; two replicates on August 25/26, 2023 and two replicates on September 29/30, 2023 and processed for ATAC-Seq protocols.

value: Barley infected first leaf (PO:0007094)

tag: plant genotype

value: CI 16151 (resistant progenitor)

tag: fungal isolate

value: Bh isolate 5874 (AVRa6)

tag: time point

value: 20 HAI

tag: replication

value: Rep # 1


title: doxee17_d20ut_Rep2

description: Library name: doxee17_d20ut_Rep2

value: UT


title: doxee17_d14dox_Rep1

description: Library name: doxee17_d14dox_Rep1


title: 23366-14_ATAC

description:
Library name: 23366-14_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI

value: m18982 (susceptible mla6 mutant)

value: 0 HAI


title: RNAseq of CUL_17R

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

description: Library name: CUL_17R

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software.
Cleaned data were aligned to human reference genome (GRCh38 release 106 version) by STAR software (v 2.7.10).
RNA expression quantification with RSEM (v 1.3.3) for further quantification were calculated by rsem-calculate-expression.
Assembly: GRCh38 release 106 version
Supplementary files format and content: TissueRNAseq_count.csv is a CSV file that records the count for each sample.
Supplementary files format and content: TissueRNAseq_tpm.csv is a CSV file that records the tpm for each sample.

molecule: total RNA

source_name: NPC tumor tissue

extract_protocol:
We extracted RNA from tissue samples using the AllPrep DNA/RNA Micro Kit (QIAGEN GmbH).
Sequencing libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations.

value: NPC tumor tissue

tag: microbial subtype


title: RNAseq of CUL_18R

description: Library name: CUL_18R


title: 23366-13_ATAC

description:
Library name: 23366-13_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI

value: 16 HAI


title: 23366-12_ATAC

description:
Library name: 23366-12_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI

value: 32 HAI


title: RNAseq of CUL_16R

description: Library name: CUL_16R


title: liver piz vehicle 3

city: Saint Louis

first: Paul

last: Cliften

state: MO

address: 4444 Forest Park Avenue

department: Genetics

institute: Washington University School of Medicine

description:
Library name: piz_pbs_15
sample.piz_pbs_15

data_processing:
BATCH1: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read
BATCH2: Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software
BATCH1&2: RNA-seq reads were aligned with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
BATCH1&2: Differential expression analysis was performed with EdgeR
Assembly: Ensembl release 101 top-level assembly (GRCm38)
Supplementary files format and content: SR003713-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts
Supplementary files format and content: mgi3302-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts

organism: Mus musculus

source_name: liver

growth_protocol: Three month old male mice were maintained on 12-hour dark/light cycles with ad libitum access to standard rodent chow and water

extract_protocol:
Described in Kulkarni et al., PPAR Research, 2021
Described in Kulkarni et al., PPAR Research, 2021

treatment_protocol: Mice were treated with intraperitoneal injection of sterile PBS, TNFa (2 hours), DMSO or tunicamycin (24-hours).

value: liver

tag: genotype

value: PiZ

value: vehicle (PBS)


title: liver wildtype tnfa 4

description:
Library name: dz_tnfa_10
sample.dz_tnfa_10

value: wildtype

value: TNFa


title: RNAseq of CUL_15R

description: Library name: CUL_15R


title: liver wildtype tnfa 2

description:
Library name: dz_tnfa_8
sample.dz_tnfa_8


title: 23366-16_ATAC

description:
Library name: 23366-16_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: m19089 (resistant bln1 mutant)


title: RNAseq of CUL_19R

description: Library name: CUL_19R


title: liver wildtype tnfa 1

description:
Library name: dz_tnfa_7
sample.dz_tnfa_7


title: 23366-11_ATAC

description:
Library name: 23366-11_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI

value: Barley infected first leaf (PO:0007094)


title: liver wildtype vehicle 6

description:
Library name: dz_pbs_6
sample.dz_pbs_6


title: liver wildtype vehicle 5

description:
Library name: dz_pbs_5
sample.dz_pbs_5


title: 23366-10_ATAC

description:
Library name: 23366-10_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI


title: RNAseq of CUL_13R

description: Library name: CUL_13R


title: doxee17_d18ut_Rep2

description: Library name: doxee17_d18ut_Rep2

value: hematopoietic

value: H1 hESC

value: hematopoietic progenitor cells


title: RNAseq of CUL_14R

description: Library name: CUL_14R


title: 23366-09_ATAC

description:
Library name: 23366-09_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI

value: Bh isolate 5874 (AVRa6)

value: Rep # 1


title: liver wildtype vehicle 4

description:
Library name: dz_pbs_4
sample.dz_pbs_4


title: doxee17_d18ut_Rep1

description: Library name: doxee17_d18ut_Rep1

value: UT


title: doxee17_d16ut_Rep2

description: Library name: doxee17_d16ut_Rep2


title: liver wildtype vehicle 2

description:
Library name: dz_pbs_2
sample.dz_pbs_2


title: liver wildtype vehicle 1

description:
Library name: dz_pbs_1
sample.dz_pbs_1


title: liver wildtype vehicle 3

description:
Library name: dz_pbs_3
sample.dz_pbs_3


title: 23366-08_ATAC

description:
Library name: 23366-08_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI

value: 20 HAI


title: RNAseq of CUL_11R

description: Library name: CUL_11R

value: NPC tumor tissue


title: doxee17_d20ut_Rep1

description: Library name: doxee17_d20ut_Rep1


title: 23366-06_ATAC

description:
Library name: 23366-06_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI


title: RNAseq of CUL_9R

description: Library name: CUL_9R


title: doxee17_d16ut_Rep1

description: Library name: doxee17_d16ut_Rep1


title: doxee17_d14ut_Rep2

description: Library name: doxee17_d14ut_Rep2


title: 23366-07_ATAC

description:
Library name: 23366-07_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI

value: m18982 (susceptible mla6 mutant)

value: 16 HAI


title: RNAseq of CUL_8R

description: Library name: CUL_8R


title: doxee17_d12ut_Rep2

description: Library name: doxee17_d12ut_Rep2


title: SP_AKI_kidney5

city: Nanjing

first: Mengqing

last: Ma

state: Jiangsu

address: 68 Changle Road

institute: Nanjing First Hospital, Nanjing Medical University

description:
Library name: Sample 20
RNA sequencing of kidney tissue from SP-AKI mouse

data_processing:
Raw reads were filtered using Cutadapt to remove adapter sequences, reads containing polyA/polyG tails, reads with more than 5% unknown nucleotides, and low-quality reads with more than 20% bases with Q ≤ 20.
Clean reads were assessed for quality using FastQC.
Clean reads were aligned to the mouse reference genome using HISAT2.
Mapped reads were assembled and quantified using StringTie, and gene expression levels were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Differentially expressed genes between groups were identified using DESeq2 with a false discovery rate (FDR) < 0.05 and |fold change| ≥ 2.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: Processed data files include gene expression matrices calculated as FPKM values for lung and kidney tissues (fpkm_expression_lung.txt and fpkm_expression_kidney.txt).
Supplementary files format and content: Each file contains gene identifiers in the first column and FPKM expression values for each sample in subsequent columns.

source_name: kidney

growth_protocol: Male C57BL/6 mice were maintained under specific pathogen-free (SPF) conditions with a 12-h light/dark cycle and free access to food and water. Lung and kidney tissues were collected from control mice and mice with severe pneumonia–associated acute kidney injury (SP-AKI).

extract_protocol:
Total RNA was extracted from lung and kidney tissues using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA quantity and quality were assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit. Only RNA samples with RIN > 7.0 were used for library construction.
mRNA was purified from total RNA using oligo(dT) magnetic beads and fragmented into short fragments. First-strand cDNA was synthesized using reverse transcriptase, followed by second-strand cDNA synthesis. After end repair and A-tailing, sequencing adapters were ligated to the fragments. The ligated products were amplified by PCR and purified to construct sequencing libraries with an average insert size of approximately 300 bp. Paired-end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were divided into control and SP-AKI groups (n=5 per group). The SP-AKI model was established by intratracheal instillation of Pseudomonas aeruginosa suspension (50 μL 1×10⁸ CFU); control mice received 50 μL sterile saline. At 24 hours post-inoculation, lung and kidney tissues were collected for RNA sequencing analysis.

value: kidney

value: wild type


title: 23366-05_ATAC

description:
Library name: 23366-05_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI

value: 0 HAI


title: RNAseq of CUL_10R

description: Library name: CUL_10R


title: SP_AKI_kidney4

description:
Library name: Sample 19
RNA sequencing of kidney tissue from SP-AKI mouse

value: severe pneumonia–associated acute kidney injury


title: 23366-04_ATAC

description:
Library name: 23366-04_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI

value: CI 16151 (resistant progenitor)

value: 32 HAI


title: RNAseq of CUL_12R

description: Library name: CUL_12R


title: 23366-03_ATAC

description:
Library name: 23366-03_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI

value: Barley infected first leaf (PO:0007094)


title: SP_AKI_kidney2

description:
Library name: Sample 17
RNA sequencing of kidney tissue from SP-AKI mouse


title: doxee17_d10_Rep1

description: Library name: doxee17_d10_Rep1

value: hematopoietic


title: 23366-02_ATAC

description:
Library name: 23366-02_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI


title: doxee17_d14ut_Rep1

description: Library name: doxee17_d14ut_Rep1

value: H1 hESC


title: SP_AKI_kidney1

description:
Library name: Sample 16
RNA sequencing of kidney tissue from SP-AKI mouse


title: RNAseq of CUL_4R

description: Library name: CUL_4R


title: Su(var)3-9 St7-8, RNA-seq, rep2

city: Freiburg im Breisgau

first: Derek

last: Atkinson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute for immunobiology and epigenetics

description: Library name: SuVar39-G_2

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakePipes-v2.8.1. RNA-seq was processed using the mRNA-seq and noncoding-RNA-seq workflow (–trim option).  Differentially expressed genes and repeats were called using DESeq2
Assembly: dm6
Supplementary files format and content: counts.tsv

organism: Drosophila melanogaster

source_name: embryo St7-8

growth_protocol: Drosophila stocks used in this study were cultivated on corn flour molasses food (per liter: 12 g agar, 18 g dry yeast, 10 g soy powder, 22 g molasses, 80 g malt extract, 80 g corn flour, 6.25 ml propionic acid, 2.4 g nipagin) at 20 °C, 70% relative humidity and 12h light / 12h dark cycle.

extract_protocol:
Cages of flies with apple juice agar plates were set up and maintained at 25°C for 24-48h. Flies were allowed to lay eggs for one hour, and embryos were aged for another two hours at 25°C.  NC14 Hand-sorted embryos were flash-frozen and stored in batches of 50 per sample.
libraries were prepared using the Illumina TruSeq Stranded Total RNA kit, following the manufacturer’s instructions.

value: embryo St7-8


title: doxee17_d12ut_Rep1

description: Library name: doxee17_d12ut_Rep1

value: hematopoietic progenitor cells


title: 23366-01_ATAC

description:
Library name: 23366-01_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI

value: Bh isolate 5874 (AVRa6)

value: Rep # 1


title: control_kidney4

description:
Library name: Sample 14
RNA sequencing of kidney tissue from control mouse

value: control


title: Su(var)3-9 St7-8, RNA-seq, rep1

description: Library name: SuVar39-G_1


title: SP_AKI_kidney3

description:
Library name: Sample 18
RNA sequencing of kidney tissue from SP-AKI mouse


title: control_kidney5

description:
Library name: Sample 15
RNA sequencing of kidney tissue from control mouse


title: P. salmonis, control, replicate 3

city: Santiago

first: Veronica

last: Cambiazo

address: Av. El Libano 5524

country: Chile

institute: Instituto de Nutrición y Tecnología de los Alimentos (INTA)

data_processing:
Low quality reads and Illumina adapters were eliminated using BBduk software
Filtered reads were mapped using the STAR RNA-Seq alignment tool to P. salmonis CGR02 (NCBI accession N° GCF_001534725.1) assembly and S. salar (NCBI accession Nº GCA_905237065.2)
Reads that failed to map to any gene or mapped to multiple genes were removed before transcript analysis
Gene quantification was generated using the quantMode option available at STAR program
Assembly: S. salar GCA_905237065.2; P. salmonis CGR02 GCF_001534725.1
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Piscirickettsia salmonis

source_name: bacterial cells

growth_protocol: P. salmonis strain CGR02 (GCA_001534725.1) was grown at 18 °C with agitation on Nutrient Piscirickettsia Broth (NPB; 30 gr/L Tryptic Soy Broth, 256.6 mM NaCl, 8.25 mM L-Cystein, 37µM FeCl3). SHK-1 cells were grown in Leibovitz's medium supplemented with 5% of fetal bovine serum (FBS) and without antibiotics. For infection experiments, bacteria were recovered from Nutrient Piscirickettsia Agar (NPA) plates and used to inoculate NPB. Cultures were incubated in a shaking incubator at 140 rpm and 18 °C for 3 days (exponentially growing bacteria) or 7 days (stationary state bacteria) before harvesting for infection experiments or RNA purification.

extract_protocol:
The pellets were suspended in 1.0 mL of TRIzol Reagent (Invitrogen), and total RNA was purified according to manufacturer`s instructions.
The libraries were generated using TruSeq Stranded Total RNA Library Prep (Illumina), with rRNA removal.

value: bacterial cells

tag: strain


title: Su(var)3-9 NC14, RNA-seq, rep2

description: Library name: SuVar39-NC14_2

source_name: embryo NC14

value: embryo NC14


title: P. salmonis, control, replicate 2


title: doxee17_d10_Rep2

description: Library name: doxee17_d10_Rep2

value: UT


title: RNAseq of CUL_3R

description: Library name: CUL_3R

value: NPC tumor tissue


title: RNAseq of CUL_2R

description: Library name: CUL_2R


title: RNAseq of CUL_5R

description: Library name: CUL_5R


title: RNAseq of CUL_1R

description: Library name: CUL_1R


title: control_kidney3

description:
Library name: Sample 13
RNA sequencing of kidney tissue from control mouse

value: kidney

value: wild type


title: P. salmonis, control, replicate 1


title: control_kidney2

description:
Library name: Sample 12
RNA sequencing of kidney tissue from control mouse


title: Su(var)3-9 NC14, RNA-seq, rep1

description: Library name: SuVar39-NC14_1


title: RNAseq of CUL_6R

description: Library name: CUL_6R


title: DNMT1_KO_rep_4_RNA_seq

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description:
Library name: DNMT1_KO_rep_4_RNA_seq
HCT116 with knocked out DNMT1

data_processing:
RNA-seq fastq files were quality checked using FastQC (v0.11.4) and reads were trimmed using TrimGalore (v0.4.1) and default settings. Reads were then mapped to the genome (hg38) using bowtie2 for paired end data (2.3.1, settings: -N1 -L 20 --no-unal -- no-mixed -- no-discordant -X 1000) (Langmead & Salzberg, 2012). Low mapping quality reads were removed using samtools (settings: -bq10). The bam file was then converted into bed using bedtools and CPM values calculated. BigWig files were then generated using the ucsc toolset, for visualisation in the genome browser. FeatureCounts (settings: -T 4 -t exon -p, from subread package) was then used to count how many reads align to each gene. For a summary of RNA-seq alignment statistics, see Supplementary Table 10.
Assembly: hg38
Supplementary files format and content: Processed data files provided are tab-delimited files containing counts for genes derived from the featureCounts software. Columns are Geneid, Chr, Start, End, Strand, Length, count

source_name: HCT116 DNMT1 KO

growth_protocol: HCT116 and DNMT1 KO cells were gifts from B. Vogelstein (Rhee et al., 2000). Cells were cultured in McCoy’s 5A (Gibco) supplemented with 10% Fetal Calf Serum (Life Technologies) and penicillin–streptomycin antibiotics at 140 and 400 μg/ml, respectively at 37°C with 5% CO2. Cell lines were routinely tested for mycoplasma contamination. DNMT1 KO genotype was confirmed by western blot and sequencing.

extract_protocol:
RNA extraction was performed from snap-frozen cell pellets using RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s instructions. Quantity and quality of RNA samples were assessed using the Nanodrop spectrophotometer (Nanodrop ND-1000, Thermo Scientific) and Qubit fluorometer (Invitrogen).
Size distribution of RNA fragments and the RNA integrity number (RIN) value were determined by using Agilent 2100 BioAnalyzer with the RNA nano chip. RNA samples for whole genome sequencing were sent to Edinburgh Genomics for library preparation and sequence data generation. Library preparation was performed using the TruSeq stranded mRNA-seq library kit. The libraries were then sequenced on NovaSeq with 50bp paired end (PE) reads and aiming for 50M reads per sample.

value: HCT116 DNMT1 KO

value: colorectal cancer cell line

value: DNMT1 KO


title: RSBD-3

city: Qingdao

first: Peng

last: Chen

address: 308 Ningxia road, Qingdao

institute: Qingdao University

description:
Library name: Sample9
LPS+RSBD-treated mouse lung, replicate 3

data_processing:
Raw sequencing data were processed as follows: (1) Adapter trimming and low-quality read filtering using fastp (v0.23.2) with parameters: --qualified_quality_phred 20 --unqualified_percent_limit 50 --length_required 36. (2) Clean reads aligned to mouse reference genome mm10 (GRCm38) using HISAT2 (v2.2.1) with default parameters. (3) Gene-level read counts quantified with StringTie (v2.2.0) using Ensembl vM25 annotation. (4) Raw counts imported into R. (5) Differential expression analysis performed using DESeq2 (v1.38.3) with thresholds |log2FC| > 1 and padj < 0.05. (6) TPM values were also generated by StringTie for normalization.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for all 9 samples. Rows represent genes (Ensembl gene IDs), columns represent individual samples.
Supplementary files format and content: Tab-delimited text file containing TPM-normalized gene expression values for all 9 samples. Rows represent genes (Ensembl gene IDs), columns represent individual samples.

source_name: lung

growth_protocol: Male C57BL/6 mice (6–8 weeks old) were housed under specific pathogen-free conditions with a 12 h light/dark cycle, controlled temperature (22 ± 2°C) and humidity (50–60%), and had free access to standard chow and water.

extract_protocol:
Strand-specific RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).
Briefly, mRNA was enriched from total RNA, fragmented, and reverse-transcribed into double-stranded cDNA. After end repair, adapter ligation, and PCR amplification, libraries were sequenced on an Illumina NovaSeq 6000 platform (150 bp paired-end).

treatment_protocol: Mice were anesthetized with 1.25% tribromoethanol (20 mL/kg, i.p.) and received intratracheal instillation of lipopolysaccharide (LPS, 2 mg/kg) or sterile saline. Twenty-four hours later, mice were treated daily by oral gavage with Renshen Baidu Powder (RSBD) decoction or vehicle for five consecutive days. Lung tissues were collected on day 5 post-LPS.

value: lung

tag: Sex

value: male


title: Su140 St7-8, RNA-seq, rep2

description: Library name: Su140-G_2


title: control_kidney1

description:
Library name: Sample 11
RNA sequencing of kidney tissue from control mouse


title: DNMT1_KO_rep_3_RNA_seq

description:
Library name: DNMT1_KO_rep_3_RNA_seq
HCT116 with knocked out DNMT1


title: Su140 St7-8, RNA-seq, rep1

description: Library name: Su140-G_1


title: RSBD-2

description:
Library name: Sample8
LPS+RSBD-treated mouse lung, replicate 2


title: SP_AKI_lung5

description:
Library name: Sample 10
RNA sequencing of lung tissue from SP-AKI mouse

value: severe pneumonia–associated acute kidney injury


title: LPS-3

description:
Library name: Sample6
PS-treated mouse lung, replicate 3


title: RSBD-1

description:
Library name: Sample7
LPS+RSBD-treated mouse lung, replicate 1


title: DNMT1_KO_rep_1_RNA_seq

description:
Library name: DNMT1_KO_rep_1_RNA_seq
HCT116 with knocked out DNMT1


title: SP_AKI_lung4

description:
Library name: Sample 9
RNA sequencing of lung tissue from SP-AKI mouse


title: DNMT1_KO_rep_2_RNA_seq

description:
Library name: DNMT1_KO_rep_2_RNA_seq
HCT116 with knocked out DNMT1


title: Su140 NC14, RNA-seq, rep1

description: Library name: Su140-NC14_1


title: LPS-2

description:
Library name: Sample5
PS-treated mouse lung, replicate 2


title: LPS-1

description:
Library name: Sample4
PS-treated mouse lung, replicate 1


title: Su140 NC14, RNA-seq, rep2

description: Library name: Su140-NC14_2


title: Su113 St7-8, RNA-seq, rep2

description: Library name: Su113-G_2

value: embryo St7-8


title: SP_AKI_lung3

description:
Library name: Sample 8
RNA sequencing of lung tissue from SP-AKI mouse


title: HCT116_rep_9_RNA-seq

description:
Library name: HCT116_rep_9_RNA_seq
HCT116 cells

value: WT


title: Su113 St7-8, RNA-seq, rep1

description: Library name: Su113-G_1


title: control-3

description:
Library name: Sample3
Control mouse lung, replicate 3


title: SP_AKI_lung1

description:
Library name: Sample 6
RNA sequencing of lung tissue from SP-AKI mouse


title: HCT116_rep_7_RNA-seq

description:
Library name: HCT116_rep_7_RNA_seq
HCT116 cells


title: control-2

description:
Library name: Sample2
Control mouse lung, replicate 2


title: SP_AKI_lung2

description:
Library name: Sample 7
RNA sequencing of lung tissue from SP-AKI mouse


title: Su113 NC14, RNA-seq, rep1

description: Library name: Su113-NC14_1


title: HCT116_rep_3_RNA-seq

description:
Library name: HCT116_rep_3_RNA_seq
HCT116 cells


title: control_lung5

description:
Library name: Sample 5
RNA sequencing of lung tissue from control mouse


title: control-1

description:
Library name: Sample1
Control mouse lung, replicate 1


title: RNAseq of CUL_7R

description: Library name: CUL_7R


title: control_lung4

description:
Library name: Sample 4
RNA sequencing of lung tissue from control mouse


title: HCT116_rep_2_RNA-seq

description:
Library name: HCT116_rep_2_RNA_seq
HCT116 cells


title: HCT116_rep_8_RNA-seq

description:
Library name: HCT116_rep_8_RNA_seq
HCT116 cells


title: control_lung3

description:
Library name: Sample 3
RNA sequencing of lung tissue from control mouse


title: CTL_10_mERRBS

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

description: Library name: CTL_10_mERRBS

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt
Reads were aligned against a bisulfite-converted human genome using Bismark with Bowtie2
Downstream analysis  was performed on MethylSig using beta-binomial regression (FDR less than 0.1) with a minimum cutoff of 25% methylation difference to identify Differential Methylated Cytosines (DMCs). Differentially Methylated Regions (DMRs) were identified by first summarizing the methylation status of the genomic regions into 25-bp tiles and then identifying regions with an absolute methylation difference more than 25% and an FDR less than 0.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files with CpGs for each sample. mERRBS gives us base pair resolution info of the sequenced DNA (chr position of the detected base,  first column), the chromosome of the detected base (second column), the position of the detected base on the specific chromosome (third column),sequencing info was assessed from which strand (forward, reverse, fourth column), read coverage (fifth column), frequency of methylated cytosine (sixth column), frequency of unmethylated cytosine (last column).

molecule: genomic DNA

source_name: Unsorted Bone Marrow cells

extract_protocol:
DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). 100ng of high quality genomic DNA were digested with 200U of methylation-insensitive endonuclease enzyme MspI (New England Biolabs, NEB),end repaired, A-tailed and ligated to RNA TruSeq Illumina indexed adapters (Illumina, RS-122-2001). Library fragments were gel isolated from a 1.8% agarose gel (Low range Ultra aga-rose, Biorad) using Qiaquick Gel Extraction kit and bisulfite converted using EZ DNA Methylation kit (Zymo Research). Products were amplified by PCR and final libraries were purified using AMPure XP beads (Agencort).
mERRBS libraries were prepared for sequencing using manufacturer’s recommended protocol for 50bp stranded single-end read runs (Illumina San Diego, CA)

value: Unsorted Bone Marrow cells

tag: cytogenetics

tag: age

tag: mutations

tag: disease

value: Healthy


title: Su113 NC14, RNA-seq, rep2

description: Library name: Su113-NC14_2


title: wm4h St7-8, RNA-seq, rep1

description: Library name: wm4h-G_1


title: HCT116_rep_1_RNA-seq

description:
Library name: HCT116_rep_1_RNA_seq
HCT116 cells

tag: cell line


title: wm4h NC14, RNA-seq, rep2

description: Library name: wm4h-NC14_2

tag: cell type


title: CTL_8_mERRBS

description: Library name: CTL_8_mERRBS

tag: tissue


title: control_lung2

description:
Library name: Sample 2
RNA sequencing of lung tissue from control mouse

tag: treatment

value: control


title: control_lung1

description:
Library name: Sample 1
RNA sequencing of lung tissue from control mouse


title: nkMN_12_mERRBS

description: Library name: nkMN_12_mERRBS

value: AML


title: TCR of CD4 T Cells with TET2 KO cultured in vitro at day3 or day6 after 30 cycles of stimulations

city: Omaha

first: Javeed

last: Iqbal

state: Nebraska

address: 601 S 42nd St

institute: University of Nebraska Medical Center

description:
Library name: Late_TCR
TCR
Pooled TCR sequence of four samples incduing TET2KO stimulation30 day3, TET2KO stimulation30 day6.

data_processing:
The CellRanger Single-Cell software suite (v.5.0.1; 10xGenomics) was used to process the raw sequencing data through demultiplexing, alignment to CellRanger GRCh38 reference genome, barcode processing, and read counting.
Assembly: GRCh38
Supplementary files format and content: Processed data format and content: Processed data are provided as 10x Genomics feature-barcode matrices generated using Cell Ranger (v5.0.1). For each library, the filtered gene-barcode matrix is supplied in sparse matrix format, including: matrix.mtx.gz (sparse UMI count matrix), barcodes.tsv.gz (cell barcode identifiers), and features.tsv.gz (gene identifiers and feature types).

molecule: protein

source_name: Blood

growth_protocol: CRISPER modified human CD4+ T cells were cultured in X-VIVO 15 serum-free hematopoietic cell Medium (Lonza, Inc) with FBS (10%),  IL-2 (200 IU/ml), Penicillin(100units/ml), and Streptomycin (100μg/ml) and stimulated using anti-CD3/anti-CD28-conjugated beads (Thermo Fisher Scientific Inc) every 10 days.  Cells were used for the scRNAseq after 4, 9, and 30 cycles of stimulation.

extract_protocol:
WT and TET2-/- CD4+ T cells were prepared as a single-cell suspension. Cells were tagged with TotalSeq- anti-Human hashtag oligos (DNA barcodes), washed, pooled, and loaded on the 10x Genomics Chromium platform according to the manufacturer’s protocol. > Day 200 TET2-/- cells were processed in a separate run using the same workflow.
WT and TET2-/- cells collected at days 40 and 90 were labeled with different DNA barcodes using TotalSeq anti-Human Hashtag 1, 2,3, and 4. Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell platform and 10x Genomics TCR V(D)J libraries were constructed using the Chromium Next GEM Single Cell V(D)J v1.1 chemistry kit following the manufacturer’s instructions. Libraries sequenced on an Illumina Novaseq6000 (PE101). Cells cultured longer (>200 days were) at day 3 or day 6 after added anti-CD3/anti-CD28 beads were processed in a separate run with the same workflow.

value: Blood

value: CD4+ T cells

value: TET2 knockout

tag: library type

value: TCR


title: wm4h NC14, RNA-seq, rep1

description: Library name: wm4h-NC14_1

value: embryo NC14


title: GEX  of CD4 T Cells with TET2 KO cultured in vitro at day3 or day6 after 30 cycles of stimulations

description:
Library name: Late_mRNA
polyA RNA
Pooled RNA of four samples incduing TET2KO stimulation30 day3, TET2KO stimulation30 day6.

library_source: transcriptomic single cell

value: mRNA


title: Hashtag of CD4 T Cells with TET2 KO cultured in vitro at day3 or day6 after 30 cycles of stimulations

description:
Library name: Late_HTO
Hashtag-derived oligonucleotide (HTO)
Pooled Hashtag of four samples incduing TET2KO stimulation30 day3, TET2KO stimulation30 day6. Their barcodes are respectively GTCAACTCTTTAGCG and TGATGGCCTATTGGG.

value: HTO

tag: hto

value: TotalSeq A Human Universal Hashtag


title: Sample 2 (LP T. cruzi infected)

city: Silver Spring

first: Erica

last: Silberstein

state: MD

address: 10903 New Hampshire Ave

department: DETTD

institute: CBER-FDA

description:
Library name: SAMN54986973_scRNAseq_BD_Rhapsody
Lamina propria cells were isolated from the colon of three pooled naive C57BL/6 mice. Single-cell RNA-seq libraries were prepared using the BD Rhapsody platform, capturing transcriptomes of individual immune and non-immune cells. The processed data is provided as a Seurat .rds object containing filtered and normalized single-cell expression data. Downstream analysis included intercellular communication inference using CellChat.

data_processing:
1) Raw FASTQ files were quality-checked using FastQC. 2) Sequencing reads were aligned to the mouse (GRCm39) and T. cruzi (ASM371945v1.61) reference genomes using the BD Rhapsody pipeline. 3) Cell barcodes and UMIs were extracted and filtered to remove low-quality or doublet cells. 4) Count matrices were generated for each cell, representing gene expression levels. 5) Data were imported into Seurat for normalization, scaling, and clustering.
Assembly: Mouse reference genome GRCm39 (accession number GCF_000001635.27); T. cruzi reference genome ASM371945v1.61 (accession number GCA_003719455).
Supplementary files format and content: Processed data are provided as Seurat .rds files. Each file contains filtered and normalized single-cell expression data, including cell metadata, gene expression matrices, and results of dimensionality reduction and clustering.
Supplementary files format and content: Seurat .rds files are compatible with R and Seurat package version 4.4. They include all data required to reproduce downstream analyses of cellular heterogeneity and host responses during Trypanosoma cruzi infection.

source_name: colon

growth_protocol: Lamina propria cells were isolated from the colon of three pooled naive C57BL/6 mice. No in vitro culture was performed; cells were immediately processed for single-cell RNA-seq.

extract_protocol:
Lamina propria cells were extracted from colon tissue using enzymatic digestion and mechanical dissociation. Cells were filtered to obtain a single-cell suspension suitable for single-cell RNA-seq.
Single-cell RNA-seq libraries were prepared using the BD Rhapsody platform. Individual cells were captured in microwells, barcoded, and reverse-transcribed to generate cDNA libraries for sequencing.

treatment_protocol: Samples were from naïve and T. cruzi infected mice at 110 dpi

value: colon

value: lamina propria cells

value: Infected with T. cruzi

tag: batch


title: nkMN_11_mERRBS

description: Library name: nkMN_11_mERRBS

value: MDS


title: Sample 1 (LP Naive)

description:
Library name: SAMN54986944_scRNAseq_BD_Rhapsody
Lamina propria cells were isolated from the colon of three pooled naive C57BL/6 mice. Single-cell RNA-seq libraries were prepared using the BD Rhapsody platform, capturing transcriptomes of individual immune and non-immune cells. The processed data is provided as a Seurat .rds object containing filtered and normalized single-cell expression data. Downstream analysis included intercellular communication inference using CellChat.

value: Control


title: Su140 NC14, HiC, rep6

description: Library name: HiC_Su140_st5_rep6

data_processing:
Raw sequencing data were processed using the nf-core/hic pipeline (v2.0.0)
Assembly: dm6
Supplementary files format and content: mcool

source_name: NC14 embryos

extract_protocol:
For each genotype, six biological replicates of 100 hand-staged NC14 embryos were analyzed.
Libraries were prepared directly on beads using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645S and #E6440 or equivalents), with adapter ligation performed on-bead. Prior to PCR amplification (12–13 cycles), ligated DNA fragments were released by heating.

value: NC14 embryos


title: TCR of of WT or TET2 KO CD4 T Cells  cultured in vitro for 4 cycles or 9 cycles of stimulations (pool of 4 samples)

description:
Library name: Early_TCR
TCR
Pooled TCR sequence of four samples incduing TET2KO stimulation4, WTstimulation4, TET2KO stimulation9, and WTstimulation9.

value: WT and TET2 knockout


title: Su140 NC14, HiC, rep5

description: Library name: HiC_Su140_st5_rep5


title: wm4h St7-8, RNA-seq, rep2

description: Library name: wm4h-G_2

value: embryo St7-8


title: Su140 NC14, HiC, rep4

description: Library name: HiC_Su140_st5_rep4


title: Hashtag of WT or TET2 KO CD4 T Cells  cultured in vitro for 4 cycles or 9 cycles of stimulations (pool of 4 samples)

description:
Library name: Early_HTO
Hashtag-derived oligonucleotide (HTO)
Pooled Hashtag of four samples incduing TET2KO stimulation4, WTstimulation4, TET2KO stimulation9, and WTstimulation9. Their barcodes are respectively GTCAACTCTTTAGCG, TGATGGCCTATTGGG, TTCCGCCTCTCTTTG, AGTAAGTTCAGCGTA


title: SCA1fl; NG2-cre, 4, female

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

department: Neuroscience

institute: Yale University

description:
Library name: FICre6354
10x Genomics

data_processing:
CellRanger v8.0.1
Preprocessing quality control including doublet detection using Scrublet
Normalization and square root transformation
BBKNN batch correction
Cell type annotation
Assembly: mm10
Supplementary files format and content: h5ad

molecule: nuclear RNA

source_name: cerebellum

extract_protocol:
Nuclei isolation from frozen tissue followed a previously established protocol. Cerebellar hemispheres from four animals (two males and two females) per genotype (SCA1fl/+ and SCA1fl/+; NG2-cre/+) were collected at 30 weeks. Briefly, frozen tissues were gently homogenized using Dounce homogenizer in 2 mL of ice-cold Nuclei EZ Prep buffer (Sigma; NUC101-1KT) with a large clearance pestle A, followed by a small clearance pestle B, each for 25 strokes. The homogenized tissue was then incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Following incubation, the homogenates were centrifuged at 500xg for five minutes at 4°C. The resulting nuclear pellets were resuspended in 4 mL of cold EZ Prep buffer, incubated on ice for five minutes, and centrifuged again at 500xg for five minutes at 4°C. The nuclei were then washed in 4 mL of Nuclei Suspension Buffer (NSB), containing 1x PBS, 0.01% BSA, and 0.1% RNase inhibitor (Clontech/Takara; 2313B). The final washing step was followed by centrifugation at 500xg for five minutes at 4°C. The purified nuclei were resuspended in 1 mL of NSB, filtered through a 40 μm cell strainer (Fisher Scientific; 22-363-547), and quantified using a Countess III FL Cell Counter (Thermo Fisher Scientific; AMQAF2000) with trypan blue. Single-nucleus suspensions were then diluted to approximately 1000 nuclei per μL in NSB for library preparation.
Libraries were prepared from diluted single-nucleus suspensions using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v.3.1 at the Yale Center for Genome Analysis (YCGA). Briefly, 10,000 cells per sample were mixed with RT Master Mix, loaded onto the Single Cell A Chip, and combined with approximately 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead contained primers with the following components: an Illumina R1 sequence (read 1 sequencing primer), a 16-nucleotide barcode, a 12-nucleotide unique molecular identifier (UMI), and a 30-nucleotide poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the released primers mixed with the cell lysate and Master Mix, enabling the generation of barcoded, full-length cDNA from poly-adenylated mRNA after incubation. Silane magnetic beads were then used to excess biochemical reagents from the post-GEM reaction mixture. Next, full-length, barcoded cDNA underwent PCR amplification to generate sufficient material for library construction. Enzymatic fragmentation and size selection were performed to optimize the cDNA amplicon size before library construction. During library construction, P5 and P7 adapters, a sample index, and R2 (read 2 primer sequence) were added via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. Sequencing was performed using the NovaSeq6000 at the YCGA. Sample concentrations were normalized to 1.2 nM and loaded onto an Illumina NovaSeq S4 flow cell at a concentration yielding 20,000 to 50,000 passing filter clusters per cell per sample. Paired-end sequencing was conducted on an Illumina NovaSeq6000 instrument following Illumina protocols and 10x sequencing specifications. The 8 bp index was read during an additional sequencing cycle that automatically followed the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster. To monitor quality in real time, a positive control (a prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3%. Signal intensities were converted to individual base calls during the run using the system’s Real-Time Analysis (RTA) software. Base calls were transferred from the machine’s dedicated personal computer to the Yale high-performance computing cluster via a 1-gigabit network mount for downstream analysis.

value: cerebellum

value: female

value: SCA1 fl/+; NG2-cre


title: Su140 NC14, HiC, rep3

description: Library name: HiC_Su140_st5_rep3


title: SCA1fl; NG2-cre, 3, male

description:
Library name: FICre4432
10x Genomics

value: male


title: GEX of WT or TET2 KO CD4 T Cells  cultured in vitro for  4 cycles or 9 cycles of stimulations (pool of 4 samples)

description:
Library name: Early_mRNA
polyA RNA
Pooled RNA of four samples incduing TET2KO stimulation4, WTstimulation4, TET2KO stimulation9, and WTstimulation9.

value: Blood

value: CD4+ T cells


title: CTL_1_mERRBS

source_name: Unsorted Bone Marrow Cells

value: Not Found


title: CTL_3_mERRBS


title: SCA1fl; NG2-cre, 1, female

description:
Library name: FICre2510
10x Genomics


title: CTL_2_mERRBS


title: Su140 NC14, HiC, rep1

description: Library name: HiC_Su140_st5_rep1


title: Mon7_3_mERRBS

value: IDH2 c.419G>A, p.Arg140Gln   DNMT3A c.2645G>A, p.Arg882His


title: CTL_4_mERRBS

description: Library name: CTL_4_mERRBS

value: Unsorted Bone Marrow cells

value: Healthy


title: Su140 NC14, HiC, rep2

description: Library name: HiC_Su140_st5_rep2


title: wm4h NC14, HiC, rep6

description: Library name: HiC_wm4h_st5_rep6


title: nkMN_6_mERRBS

description: Library name: nkMN_6_mERRBS

value: AML


title: SCA1fl, 4, female

description:
Library name: FI6355
10x Genomics

value: SCA1 fl/+


title: nkMN_3_mERRBS

description: Library name: nkMN_3_mERRBS

value: MDS


title: Mon7_2_mERRBS


title: Mon7_1_mERRBS

value: CSF3R c.2245C>T, p.Gln749*   ASXL1 c.1534C>T, p.Gln512*   SRSF2 c.284C>G, p.Pro95Arg  NBN c.37G>A, p.Asp13Asn   LIG4 c.2465C>T, p.Ser822Leu


title: nkMN_5_mERRBS

description: Library name: nkMN_5_mERRBS


title: SCA1fl; NG2-cre, 2, male

description:
Library name: FICre4430
10x Genomics


title: SCA1fl, 3, male

description:
Library name: FI4433
10x Genomics


title: wm4h NC14, HiC, rep5

description: Library name: HiC_wm4h_st5_rep5

value: NC14 embryos


title: SCA1fl, 2, male

description:
Library name: FI4431
10x Genomics


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep3

city: Bethesda

first: Mark

middle: R

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

description: Library name: WT_UNT3_arc_gex

data_processing:
Paired end sequencing was completed on a NovaSeq6000. Samples were processed using the count method from CellRanger (v5.0.1, introns included and refdata-gex-GRCh38-2020-A annotation file) and CellRanger-atac (v2.0.0, refdata-cellranger-arc-GRCh38-2020-A-2.0.0 annotation file) tool packages for RNA and ATAC respectively.
Assembly: GRCh38
Supplementary files format and content: Cell ranger output files per sample: filtered_feature_bc_matrix.h5,  atac_cut_sites.bigwig, atac_fragments.tsv.gz

source_name: human iPSC-derived microglia

growth_protocol: Differentiation protocol: iPSCs were cultured in E8 media without ROCK for at least 2 days before beginning the differentiation as described (25). On the first day of the differentiation, 10,000 cells were plated per well in 96-well V-bottom shapes ultra-low attachment plates (Sunoko) in Embryoid body medium (EBM) containing E8 media, 10 mM ROCK inhibitor, 50 ng/ml BMP-4, 20 ng/mL SCF,and  50 ng/mL VEGF-121. Next day, 80 μM of media was replaced with 100 μM of EBM without ROCK inhibitor. Culture EBs for additional 2 days, with EBM medium change every day.  On day 4, 20-24 EBs were transferred to 1 well of a 6-well plate and 3 mL of Microglia progenitor media (MPM) containing X-VIVO 15 Lonza media, 2 mM GlutaMax, 55 mM beta-Mercaptoethanol, 100 ng/mL M-CSF and 25 ng/mL IL-3 was added. After adherence of EBs in a non-coated cell culture dish for 3-4 days, media was changed every other day for fresh MPM. Large amounts of microglia progenitor cells usually appeared on day 12-day 18. Microglia progenitor cells were collected by centrifugation and 0.6-0.7 million cells per 1well of the non-coated 6-well plate were seeded for the final differentiation in Microglia maturation media (MMM) containing Advanced RPMI, 2 mM GlutaMax, 100 ng/mL IL-34 and 10 ng/mL GM-CSF. Cells were further differentiated for additional 10 days with full MMM media changes every other day.

extract_protocol:
Differentiated iPSc-derived microglia cells were washed with 1x PBS, Accutase solution was added to each well and cells were incubated at RT for 10 min. Next, cells were collected in 1xPBS by centrifugation, 300g, 5min and washed once with 1xPBS + 0.04% BSA. 100 μl of chilled Lysis Buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl, 1% BSA, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin) were added to 500,000 cells, cells were resuspended 10 times, and incubated on ice for 5 min. Next, 1 ml of chilled Wash Buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl, 1% BSA, 0.1% Tween-20) was added to the lysed cells and mixture was pipetted 5 times. Nuclei were precipitated at 500g for 5 min at 4°C. Nuclei were washed in the Wash  Buffer for a total of 3 washes.
20,000 nuclei/sample were processed according to  Chromium next GEM Single cell Multiome ATAC+Gene Expression user guide (CG000338 Rev E). Chromium Single Cell Multiome  Gene Expression and ATAC libraries were sequenced using standard Illumina® paired-end sequencing with P5 and P7 primers.

treatment_protocol: Fully differentiated iMicroglia were treated with 25 ng/mL IFN-γ for 24 hours.

value: human iPSC-derived microglia

value: LRRK2 +/+

value: untreated


title: dicMN_5_RNAseq

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt
Reads were aligned against hg19 build of the human genome using STAR
Counts were generated using STAR
DESeq2 was used for differential expression analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts generated for each Sample.

extract_protocol:
RNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). Libraries were prepared from 500ng of RNA using Oligo-dT and standard Illumina TruSeq® Stranded mRNA Library Prep kit following manufacturer’s instructions (Illumina San Diego, CA).
RNA-seq libraries were sequenced on Illumina HiSeq2500® using manufacturer’s recommended protocol for 150 bp stranded paired-end read runs (Illumina San Diego, CA).


title: dicMN_4_RNAseq

value: Not Available


title: HC21 - mPCLS_Spn - Spn

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description: Library name: HC21

data_processing:
FASTQ reads were mapped on human (Ensembl GRCh38 v110) or mouse (Ensembl GRCm39 v110) genome with software HISAT2 (V2.2.1)
Gene quantification was obtained with summarizeOverlaps() method from R package GenomicAlignments.
Assembly: GRCh38 or GRCm39 from Ensembl v110
Supplementary files format and content: All processed files are tables in TSV format (Tab Separated Values);hs_counts.tsv contains read count matrix of human libraries;mm_counts.tsv contains read count matrix of mouse libraries; metadata.tsv contains a table of library metadata.

source_name: Lung - in vivo

growth_protocol: PCLS generation in DMEM/F12

extract_protocol:
NucleoSpin RNA XS kit (Macherey-Nagel) for murine & human PCLS or trizol extraction for murine or human in vivo samples
Illumina TruSeqHT Stranded mRNA protocol except for mIV, mPCLS & hPCLS, RNA exome-seq human in vivo samples

treatment_protocol: Untreated or A/Netherlands/602/2009 (H1N1) for 48h or Spn (ATCC: (Klein) Chester 6303, serotype 3 for 24h

value: Lung - in vivo

value: Spn

tag: specimen id

tag: specimen sex

value: Female

tag: specimen age


title: SCA1fl, 1, female

description:
Library name: FI2505
10x Genomics

value: cerebellum

value: female

tag: genotype


title: HC20 - mPCLS_Spn - mock

description: Library name: HC20

value: mock


title: wm4h NC14, HiC, rep4

description: Library name: HiC_wm4h_st5_rep4


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep2

description: Library name: WT_UNT2_arc_gex


title: wm4h NC14, HiC, rep3

description: Library name: HiC_wm4h_st5_rep3


title: wm4h NC14, HiC, rep2

description: Library name: HiC_wm4h_st5_rep2


title: dicMN_3_RNAseq


title: dicMN_2_RNAseq

value: GGPS1 (R74H); ANKS1B (T247I)


title: wm4h NC14, HiC, rep1

description: Library name: HiC_wm4h_st5_rep1


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep3

description: Library name: WT_UNT3_arc_atac

library_source: genomic single cell


title: HC19 - mPCLS_Spn - Spn

description: Library name: HC19


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep2

description: Library name: WT_UNT2_arc_atac


title: dicMN_1_RNAseq


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep1

description: Library name: WT_UNT1_arc_gex


title: CTL_3_RNAseq

value: Not Found


title: CTL_2_RNAseq


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep3

description: Library name: WT_IFN3_arc_gex

value: interferon-ɣ exposed


title: HC18 - mPCLS_Spn - mock

description: Library name: HC18


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, control, rep1

description: Library name: WT_UNT1_arc_atac


title: HC08 - mIV - Spn

description: Library name: HC08

value: mIV


title: HC09 - mIV - Spn

description: Library name: HC09


title: WT NC14, H3K9me2, ChIP, rep2

description: Library name: Jasper_wt_2

data_processing:
Sequencing reads were aligned to a combined dm6 reference genome using the DNA-mapping workflow from snakePipes v2.8.1, with adapter trimming and mapping quality filtering (MAPQ ≥ 3). Bowtie2 alignment parameters were customized: --local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700. Additional flags included --trim, --properPairs, and --dedup.
Assembly: dm6
Supplementary files format and content: BigWig

extract_protocol:
Cages of flies with apple juice agar plates were set up and maintained at 25°C for 24-48h. Flies were allowed to lay eggs for one hour, and embryos were aged for another two hours at 25°C.  NC14 Hand-sorted embryos were flash-frozen and stored in batches of 50 per sample. ChiP-Seq was performed according to the standard protocol using the Low Cell ChIP Kit (Active Motif #53086), and DNA was obtained.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645) and NEBNext® Multiplex Oligos for Illumina® (NEB #E7600).

tag: chip antibody

value: V5 (Life technologies, 377500)


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep2

description: Library name: WT_IFN2_arc_gex


title: Jasper NC14, H3K9me2, ChIP, rep2

description: Library name: Jasper_Su140_2


title: CTL_1_RNAseq


title: HC17 - mPCLS_Spn - Spn

description: Library name: HC17


title: nkMN_7_mERRBS

description: Library name: nkMN_7_mERRBS

value: Unsorted Bone Marrow cells

value: MDS


title: HC16 - mPCLS_Spn - mock

description: Library name: HC16


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep3

description: Library name: WT_IFN3_arc_atac

value: human iPSC-derived microglia


title: WT NC14, Jasper, ChIP, rep1

description: Library name: Jasper_wt_1

value: NC14 embryos


title: WT NC14, IgG, ChIP, rep1

description: Library name: IgG_1


title: Su140 NC14, H3K36me3, CUT&Tag

description: Library name: Su140_H3K36me3

data_processing:
Sequencing reads were aligned to a combined dm6 and lambda phage reference genome using the DNA-mapping workflow from snakePipes v2.8.1, with adapter trimming and mapping quality filtering (MAPQ ≥ 3). Bowtie2 alignment parameters were customized: --local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700. Additional flags included --trim, --properPairs, and --dedup.
Assembly: dm6
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Cages of flies with apple juice agar plates were set up and maintained at 25°C for 24-48h. Flies were allowed to lay eggs for one hour, and embryos were aged for another two hours at 25°C.  NC14 Hand-sorted embryos were flash-frozen and stored in batches of 50 per sample.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645) and NEBNext® Multiplex Oligos for Illumina® (NEB #E7600).


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep1

description: Library name: WT_IFN1_arc_gex

value: LRRK2 +/+


title: TauPS2APP;Ptpn6Het -4

city: South San Francisco

first: Xingyue

middle: Monica

last: Ge

address: 1 DNA Way

institute: Genentech

description: Library name: LIB6227675

data_processing:
CellRanger 7.1.0 was run to process raw FASTQ files and generate UMI counts per cell and gene, using alignment to GRCm38 genome. The outputs from CellRanger were used to run CellBender 0.3.0.2 in order to remove ambient RNA contamination.89 The Bioconductor packages scater90 and scran91 were used to perform QC steps. perCellQCMetrics() function was used to filter out low-quality cells (either due to low UMI counts, low genes detected, or high percent mitochondrial UMI), and normalization was performed by calling librarySizeFactors() followed by logNormCounts(). Cells were annotated first by using the label transfer framework using the SingleR package and using our previous study as a referened in Lee et al. (doi 10.1016/j.celrep.2021.110158)   Further data analyses including dimensional reduction and pseudobulk analysis were performed on Partek Flow platform (Partek Flow, version 2.7, https://www.partek.com/partek-flow/). Seuret-based tSNE coordinates were calculated to finalize annotation of cell types. Microglia, oligodendrocytes and astrocytes were subclustered and each subcluster was interpreted based on its marker gene set.
Assembly: GRCm38
Supplementary files format and content: .tab (gene count), .zip (count matrix), .rds (summarized experiment object)

source_name: Hippocampus

extract_protocol:
Live single cell suspensions from mouse hippocampus and fimbria were prepared using the same methods detailed in Lee et al.(doi 10.1016/j.celrep.2021.110158). Mice were perfused with ice-cold PBS and 5 µg/ml Actinomycin D was added during digestion with Neural Tissue Dissociation Kit (Miltenyi) at 37℃. Live single cells were collected by FACS with BD FacsAria Fusion sorters. Cell viability was >70%. Single cell suspensions were adjusted to 2,000 cells/µl.
Libraries were prepared with Chromium Next GEM Automated Single Cell 3’ Reagent Kit v.3.1 and Chromium Connect (10X Genomics) following manufacturer’s instructions. Libraries were quantified by Qubit dsDNA HS assay kit (ThermoFisher) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies), and sequencing was performed with NovaSeq6000 (Illumina).

value: Hippocampus

value: multiple brain cell types


title: Mon7_3_RNAseq

value: IDH2 c.419G>A, p.Arg140Gln   DNMT3A c.2645G>A, p.Arg882His


title: adult ventricle, tcf21 cKO, 3dps, replica 3

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

country: Lithuania

institute: Vilnius University

description: Library name: S3_tcf21_cKO_3

data_processing:
Raw reads quality was investigated using FASTQC (v0.11.9) and reads were quality trimmed using trim_galore (0.6.10).
Reads were mapped to Danio rerio reference genome using hisat2 (2.1.0). Gene expression was evaluated using stringtie (v2.1.1). Count aggregation was performed using tximport package from the Bioconductor.
Assembly: GRCz11
Supplementary files format and content: Tab delimited table containing FPKM and TPM values per sample (generated using stringtie) and tab delimited file with raw read counts for all samples (generated using tximport package).

organism: Danio rerio

source_name: ventricle

growth_protocol: Adult zebrafish (Danio rerio) were maintained at standard husbandry conditions with 14-hour light and 10-hour dark cycle at 28⁰C.

extract_protocol:
RNA from 2-3 ventricles per sample was extracted using TRI reagent (Sigma-Aldrich, T9424) and treated with DNaseI (Thermo Scientific, 89836) according to the manufacturer’s recommendations.
mRNA purification, library preparation, and sequencing were carried out following standard Illumina protocols by Novogene Co., Ltd. (Cambridge, UK).

treatment_protocol: Individual fish were placed in 100 mL of 5 μM 4-Hydroxytamoxifen solution three times for 24 h in the dark, allowing them to recover for 24 h at normal husbandry conditions between each treatment. After the last treatment, fish were left for a week to recover before further procedures. 12 days post-first treatment, uninjured hearts were harvested, and the rest of the fish hearts were injured with liquid-nitrogen-cooled cryoprobe or exposed without injury for sham control.

value: ventricle

tag: developmental stage

value: adult

tag: time

value: 3 dps


title: Mon7_1_RNAseq

tag: cytogenetics

value: CSF3R c.2245C>T, p.Gln749*   ASXL1 c.1534C>T, p.Gln512*   SRSF2 c.284C>G, p.Pro95Arg  NBN c.37G>A, p.Asp13Asn   LIG4 c.2465C>T, p.Ser822Leu

tag: age


title: adult ventricle, tcf21 cKO, 3dps, replica 2

description: Library name: S3_tcf21_cKO_2


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout, control, rep3

description: Library name: KO_UNT3_arc_gex

value: LRRK2 -/-

value: untreated


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep2

description: Library name: WT_IFN2_arc_atac

value: interferon-ɣ exposed


title: Su140 NC14, H3K27Ac, CUT&Tag, rep2

description: Library name: Su140_H3K27Ac_2

value: H3K27Ac (ActiveMotive, 39034)


title: WT NC14, IgG, ChIP, rep2

description: Library name: IgG_2


title: Jasper NC14, H3K9me2, ChIP, rep1

description: Library name: Jasper_Su140_1

value: V5 (Life technologies, 377500)


title: Mon7_2_RNAseq

tag: mutations


title: adult ventricle, tcf21 cKO, 3dpci, replica 3

description: Library name: C3_tcf21_cKO_3

value: 3 dpci


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, control, rep3

description: Library name: KO_UNT3_arc_atac

tag: cell line


title: wm4h NC14, H3K36me3, CUT&Tag

description: Library name: wm4h_H3K36me3

tag: cell type


title: wm4h NC14, H3K27Ac, CUT&Tag, rep2

description: Library name: wm4h_H3K27Ac_2


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout, control, rep2

description: Library name: KO_UNT2_arc_gex

tag: tissue


title: TauPS2APP;Ptpn6Het -3

description: Library name: LIB6227674


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 wildtype, interferon-ɣ exposed, rep1

description: Library name: WT_IFN1_arc_atac

tag: treatment


title: Su140 NC14, H3K4me1, CUT&Tag, rep2

description: Library name: Su140_H3K4me1_2


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, control, rep2

description: Library name: KO_UNT2_arc_atac


title: TauPS2APP;Ptpn6WT -4

description: Library name: LIB6227670


title: HC07 - mIV - Spn

description: Library name: HC07

value: Lung - in vivo

value: Spn

value: Female

value: mIV


title: TauPS2APP;Ptpn6cKO -4

description: Library name: LIB6227669

value: Hippocampus


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout,control, rep1

description: Library name: KO_UNT1_arc_gex

value: human iPSC-derived microglia


title: adult ventricle, tcf21 cKO, 3dpci, replica 1

description: Library name: C3_tcf21_cKO_1


title: adult ventricle, tcf21 cKO, day0, replica 3

description: Library name: D0_tcf21_cKO_3

value: Day 0 (no injury)


title: Su140 NC14, H3K4me1, CUT&Tag, rep1

description: Library name: Su140_H3K4me1_1

value: NC14 embryos


title: TauPS2APP;Ptpn6cKO -6

description: Library name: LIB6227673

value: multiple brain cell types


title: TauPS2APP;Ptpn6WT -5

description: Library name: LIB6227672


title: Su140 NC14, H3K27Ac, CUT&Tag, rep1

description: Library name: Su140_H3K27Ac_1


title: TauPS2APP;Ptpn6cKO -5

description: Library name: LIB6227671


title: TauPS2APP;Ptpn6WT -3

description: Library name: LIB6227668


title: adult ventricle, tcf21 cKO, 3dps, replica 1

description: Library name: S3_tcf21_cKO_1

value: ventricle

value: adult

value: 3 dps


title: adult ventricle, tcf21 cKO, 3dpci, replica 2

description: Library name: C3_tcf21_cKO_2


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep3

description: Library name: KO_IFN3_arc_atac

value: LRRK2 -/-


title: TauPS2APP;Ptpn6Het -2

description: Library name: LIB6227667


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep3

description: Library name: KO_IFN3_arc_gex

value: interferon-ɣ exposed


title: wm4h NC14, H3K4me1, CUT&Tag, rep1

description: Library name: wm4h_H3K4me1_1


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, control, rep1

description: Library name: KO_UNT1_arc_atac

value: untreated


title: adult ventricle, tcf21 cKO, day0, replica 2

description: Library name: D0_tcf21_cKO_2


title: TauPS2APP;Ptpn6Het -1

description: Library name: LIB6227666


title: wm4h NC14, H3K27Ac, CUT&Tag, rep1

description: Library name: wm4h_H3K27Ac_1

value: H3K27Ac (ActiveMotive, 39034)


title: adult ventricle, tcf21-floxed (WT), 3dps, replica 3

description: Library name: S3_tcf21_WT_3


title: TauPS2APP;Ptpn6cKO -3

description: Library name: LIB6227665


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep2

description: Library name: KO_IFN2_arc_atac


title: Su140 NC14, H3K9me3, CUT&Tag, rep2

description: Library name: Su140_H3K9me3_2


title: Su(var)3-9 NC14, H3K9me3, CUT&Tag, rep2

description: Library name: SuVar39_H3K9me3_2


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep2

description: Library name: KO_IFN2_arc_gex


title: TauPS2APP;Ptpn6cKO -2

description: Library name: LIB6227663


title: adult ventricle, tcf21 cKO, day0, replica 1

description: Library name: D0_tcf21_cKO_1


title: TauPS2APP;Ptpn6WT -2

description: Library name: LIB6227664


title: Su(var)3-9 NC14, H3K9me3, CUT&Tag, rep1

description: Library name: SuVar39_H3K9me3_1


title: Su140 NC14, H3K9me3, CUT&Tag, rep1

description: Library name: Su140_H3K9me3_1


title: multiome GEX-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep1

description: Library name: KO_IFN1_arc_gex


title: TauPS2APP;Ptpn6cKO -1

description: Library name: LIB6227661


title: adult ventricle, tcf21-floxed (WT), 3dps, replica 2

description: Library name: S3_tcf21_WT_2


title: wm4h NC14, H3K9me3, CUT&Tag, rep1

description: Library name: wm4h_H3K9me3_1


title: wm4h NC14, H3K4me1, CUT&Tag, rep2

description: Library name: wm4h_H3K4me1_2


title: Control -3

description: Library name: LIB5452285

value: Control


title: adult ventricle, tcf21-floxed (WT), 3dps, replica 1

description: Library name: S3_tcf21_WT_1


title: adult ventricle, tcf21-floxed (WT), 3dpci, replica 3

description: Library name: C3_tcf21_WT_3

value: 3 dpci


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, Input

description: Library name: InputIFN

data_processing:
ENCODE4 transcription factor ChIP-seq pipeline was utilized to map sequence reads to human reference GRCh38, identify signals, and peaks calling.The Irreproducible Discovery Rate (IDR) was used to evaluate consistency of ChIP-seq experiments with replicates and to create the optimal set of more sensitive peaks. The signal coverages at nucleotide resolution are reported as signal p-values and fold change over control at each position.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak, as fold-over control at each position, and as a p-value to reject the null hypothesis that the signal at that location is present in the control (except for Input samples)

extract_protocol:
iPSC-derived microglia (iMGL) were seeded at 4 × 10⁶ cells/ml in 10 cm dishes, crosslinked with 1% formaldehyde for 10 min at RT, and quenched with 10X glycine for 5 min. Cells were washed with cold PBS, scraped in PBS + protease inhibitors, and nuclei were isolated. Chromatin was digested with micrococcal nuclease at 37 °C for 20 min and briefly sonicated to yield 150–900 bp fragments. Immunoprecipitation was performed overnight at 4 °C with IgG, or STAT1 antibodies. Complexes were captured using Protein G magnetic beads (2 h, 4 °C), washed with low/high salt buffers, and eluted. Crosslinks were reversed with 5 M NaCl and proteinase K at 65 °C for 2 h. DNA was purified via spin columns.
ChIP DNA libraries were prepared using the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina,IP‑102‑1001) following end-repair, A-tailing, and adapter ligation steps, followed by PCR amplification and size selection. Final libraries were purified, quantified, and quality-checked before sequencing on an Illumina platform.


title: wm4h NC14, H3K9me3, CUT&Tag, rep2

description: Library name: wm4h_H3K9me3_2


title: multiome ATAC-seq, human iPSC-derived microglia, LRRK2 knockout, interferon-ɣ exposed, rep1

description: Library name: KO_IFN1_arc_atac


title: adult ventricle, tcf21-floxed (WT), 3dpci, replica 1

description: Library name: C3_tcf21_WT_1


title: Su(var)3-9 NC14, H3K9me2, CUT&Tag, rep2

description: Library name: SuVar39_H3K9me2_2


title: adult ventricle, tcf21-floxed (WT), 3dpci, replica 2

description: Library name: C3_tcf21_WT_2


title: TauPS2APP;Ptpn6WT -1

description: Library name: LIB6227662


title: adult ventricle, tcf21-floxed (WT), day0, replica 2

description: Library name: D0_tcf21_WT_2


title: ChIP-Seq, human iPSC-derived microglia, control, Input

description: Library name: InputPBS


title: adult ventricle, tcf21-floxed (WT), day0, replica 3

description: Library name: D0_tcf21_WT_3


title: Ptpn6cKO -3

description: Library name: LIB5452284


title: ChIP-Seq, human iPSC-derived microglia, untreated, control,  STAT1 antibody, ChIP, rep3

description: Library name: STAT1PBS3

value: STAT1 (Cell Signaling Technology, Cat # 9172)


title: ChIP-Seq, human iPSC-derived microglia, untreated, control,  STAT1 antibody, ChIP, rep2

description: Library name: STAT1PBS2


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, STAT1 antibody, ChIP, rep3

description: Library name: STAT1IFN3


title: Su(var)3-9 NC14, H3K9me2, CUT&Tag, rep1

description: Library name: SuVar39_H3K9me2_1


title: CTL_13_RNAseq

description: Library name: CTL_13_RNAseq

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt
Reads were aligned against hg19 build of the human genome using STAR
Counts were generated using STAR
DESeq2 was used for differential expression analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts generated for each Sample

extract_protocol:
RNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). Libraries were prepared from 500ng of RNA using Oligo-dT and standard Illumina TruSeq® Stranded mRNA Library Prep kit following manufacturer’s instructions (Illumina San Diego, CA).
RNA-seq libraries were sequenced on Illumina system using manufacturer’s recommended protocol for 150 bp stranded paired-end read runs (Illumina San Diego, CA).

value: Unsorted Bone Marrow cells

value: Not found

tag: disease

value: Healthy


title: Su140 NC14, H3K9me2, CUT&Tag, rep2

description: Library name: Su140_H3K9me2_2


title: adult ventricle, tcf21-floxed (WT), day0, replica 1

description: Library name: D0_tcf21_WT_1


title: Control -2

description: Library name: LIB5452283

value: Hippocampus


title: Ptpn6cKO -1

description: Library name: LIB5452280


title: Su140 NC14, H3K9me2, CUT&Tag, rep1

description: Library name: Su140_H3K9me2_1


title: CTL_12_RNAseq

description: Library name: CTL_12_RNAseq


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, STAT1 antibody, ChIP, rep2

description: Library name: STAT1IFN2

value: human iPSC-derived microglia


title: 933000320697720

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description: Library name: 933000320697720

data_processing:
Expression levels were quantified directly from FASTQ files using kallisto v0.48. Transcript sequences from GRCr8 RefSeq were used as reference. Isoform-level counts were summed per gene to get gene expression counts.
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

organism: Rattus norvegicus

source_name: Rostromedial tegmental nucleus

growth_protocol: Outbred laboratory rats

extract_protocol:
Unknown
Unknown

value: Rostromedial tegmental nucleus


title: wm4h NC14, H3K9me2, CUT&Tag, rep2

description: Library name: wm4h_H3K9me2_2

value: NC14 embryos


title: 933000320697708

description: Library name: 933000320697708


title: ChIP-Seq, human iPSC-derived microglia, untreated, control,  STAT1 antibody, ChIP, rep1

description: Library name: STAT1PBS1


title: Cortex Ctrl Stroke

city: Palo Alto

first: Karen

last: Bradshaw

address: 1201 Welch Road

institute: Stanford University

description:
Library name: K_07
10x Genomics

data_processing:
The Cell Ranger (v.6.0.0) analysis pipeline was employed to align sequencing reads to the mm10-GRCh38 hybrid reference genome and quantify barcodes and unique molecular identifiers (UMIs). Reads mapping to introns were excluded. Cells with a high mitochondrial content (>20%) relative to endogenous RNAs were removed in Seurat. Cells were also removed if they expressed fewer than 100 unique genes. After filtering, the following cell counts remained: blood: 7,486 (control diet sham), 5,722 (control diet stroke), 7,519 (high-fat diet sham), and 6,710 (high-fat diet stroke); brain: 5,477 (control diet sham), 11,068 (control diet stroke), 5,236 (high-fat diet sham), and 12,026 (high-fat diet stroke). Genes not detected in any cell were removed from subsequent analysis.
Mitochondrial and cell cycle gene regression was performed to ensure that clustering reflects true cell type identities. Principal component analysis was performed on the 2000 most variable genes of the dataset followed by UMAP clustering using the Seurat R Package (v. 4.3.0.1) on the first 20 principal components.
Identification of significant clusters was performed via the standard FindClusters()algorithm in the Seurat package with a resolution parameter of 0.4 for PBMCs and 0.6 for brain. The cell type of each significant cluster was identified using marker genes generated by the Seurat function FindAllMarkers(). Major cell types were identified using formerly established cell markers in the literature (McManaman et al. 2013, Cho et al. 2017; Qian et al. 2017, Tillander et al. 2017; Heden et al. 2023, (Gropler et al. 2009; van Harmelen et al. 2007; Chen et al. 2015; VandeKopple et al. 2019; Maier et al. 2017; van Dierendonck et al. 2020; de la Rosa Rodriguez et al. 2021; Pulido et al. 2011; Dejgaard and Presley 2019; Zhang et al. 2024; Kiss and Nilsson 2014; Chen and Farese 2005; Chitraju et al. 2019; Chen 2006; Chitraju et al. 2017; Castoldi et al. 2020; Yen et al. 2008; Uchańska et al. 2024, CellMarker.2.0). One PBMC cluster was removed as identified contaminating red blood cells and three brain clusters were removed as unidentifiable clusters. The UMAPs within each cluster and condition were generated using ggplot2 (v. 3.4.4). Cell counts were found once the clusters were subset by condition.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: sensory cortex; infarct core

extract_protocol:
Brain tissue was dissociated with the Miltenyi neural dissociation kit following the manufacturer’s instructions, with minor adjustments to optimize the isolation of endothelial and immune cells. In brief, 4–5 mice per treatment group were anesthetized with ketamine/xylazine solution and perfused with 15mL ice cold phosphate buffered saline (PBS) following cardiac blood collection. The stroke core and peri-infarct cortex, defined as ~2mm surrounding the visible lesion, were dissected and pooled by condition, minced, and digested using the neural dissociation kit (Miltenyi, 130–092-628). Brain homogenates were further diluted in Dulbecco’s PBS (dPBS) and filtered through a 100 µm strainer. The filtered homogenate was then centrifuged (300 g for 10 minutes) and the pellets were resuspended in 0.9 M sucrose in dPBS followed by centrifugation for 20 minutes at 850 g at 4 °C to separate the myelin. Cell pellets were resuspended in FACS buffer (1% BSA in PBS with 2 mM EDTA) and blocked for 5 min on ice with Fc block (CD16/CD32, BD 553141), followed by staining for 10 minutes with anti-CD31-PE/TR594 (1:200, BD 563616) and anti-CD45-PE/Cy7 (1:200, BD 103114) antibodies. Dead cells were excluded by staining with SYTOX Blue Dead Cell Stain (1:5,000, Thermo Fisher Scientific S34857).
Reagents of the Chromium Single Cell 3’ GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer’s protocol. Cells and master mix solution were adjusted to target 10,000 cells per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using the Chromium Single Cell 3’ Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. Illumina sequencing of the resulting libraries was performed by Novogene (https://en.novogene.com/) on an Illumina NovaSeq S4 (Illumina). Base calling, demultiplexing, and generation of FastQ files were conducted by Novogene.

treatment_protocol: Mice had ad libitum access to water and a 60% kcal fat diet (no. d12492; Research Diets, Inc., New Brunswick, NJ) or a normal 18% kcal fat diet (no. 2018SX; Harlan Laboratories, Indianapolis, IN) for 6 weeks before undergoing dMCAO or sham surgery.

value: sensory cortex; infarct core

tag: strain

value: dMCAO Surgery; control diet for 6 weeks


title: Gamma  neurons,Adult,rep4

city: Rehovot

first: Oren

last: Schuldiner

address: 234 Herzl Street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: gamma_adult_J_5_S31

data_processing:
Two sequencing runs of RNA were combined, yielding a mean of 22.5 million reads (single-read sequencing) and a minimum of 10 million reads per sample. The reads were aligned with STAR (DOI: 10.1093/bioinformatics/bts635) v2.5.2 to the reference genome of Drosophila melanogaster (DM6, UCSC). Gene annotations were obtained from FlyBase.org (Dmel r6.46). Gene expression levels were quantified using STAR.
Assembly: DM6
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

source_name: Brain

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places while adult refers to 3-5 days post eclosion.

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 GFP+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Libraries were prepared based on the smart-seq2 protocol (Picelli et al., 2014). Briefly, Reverse transcription was performed using Oligo-dT primers, followed by PCR.The amplified cDNA underwent library generation using Nextera XT (Illumina)

value: Brain

value: Gamma neurons

tag: time point

value: Adult


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, STAT1 antibody, ChIP, rep1

description: Library name: STAT1IFN1

value: interferon-ɣ exposed


title: Ptpn6cKO -2

description: Library name: LIB5452282

value: multiple brain cell types


title: Control -1

description: Library name: LIB5452281

value: Control


title: 933000320697542

description: Library name: 933000320697542


title: ChIP-Seq, human iPSC-derived microglia, untreated, control, without antibody, ChIP, rep1

description: Library name: ControlPBS1

value: untreated


title: wm4h NC14, H3K9me2, CUT&Tag, rep1

description: Library name: wm4h_H3K9me2_1


title: Gamma  neurons,Adult,rep5

description: Library name: gamma_adult_k_5_S55


title: Cortex HFD Stroke

description:
Library name: K_08
10x Genomics

value: dMCAO Surgery; High fat diet for 6 weeks


title: 933000320697540

description: Library name: 933000320697540


title: Cortex HFD Sham

description:
Library name: K_06
10x Genomics

value: Sham Surgery; High fat diet for 6 weeks


title: Gamma  neurons,Adult,rep3

description: Library name: gamma_adult_J_4_S42


title: PBMC HFD Stroke

description:
Library name: K_04
10x Genomics

source_name: PBMC

value: PBMC


title: ChIP-Seq, human iPSC-derived microglia, untreated, control, without antibody, ChIP, rep3

description: Library name: ControlPBS3


title: PBMC Ctrl Stroke

description:
Library name: K_03
10x Genomics


title: ChIP-Seq, human iPSC-derived microglia, untreated, control, without antibody, ChIP, rep2

description: Library name: ControlPBS2


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, without antibody, ChIP, rep3

description: Library name: ControlIFN3


title: 933000320697543

description: Library name: 933000320697543


title: Gamma  neurons, 30 hours after pupa formation,rep5

description: Library name: gamma30H_5_S60

value: 30 hours after pupa formation


title: Gamma  neurons,Adult,rep2

description: Library name: gamma_adult_J_2_S18


title: PBMC Ctrl Sham

description:
Library name: K_01
10x Genomics

value: Sham Surgery; control diet for 6 weeks


title: PBMC HFD Sham

description:
Library name: K_02
10x Genomics


title: 933000320697539

description: Library name: 933000320697539


title: Gamma  neurons, 30 hours after pupa formation,rep4

description: Library name: gamma30E_4_S37


title: Gamma  neurons, 30 hours after pupa formation,rep2

description: Library name: gamma30E_2_S13


title: Cortex Ctrl Sham

description:
Library name: K_05
10x Genomics


title: 933000320624964

description: Library name: 933000320624964


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, without antibody, ChIP, rep2

description: Library name: ControlIFN2

value: human iPSC-derived microglia


title: 933000320624968

description: Library name: 933000320624968

value: Rostromedial tegmental nucleus


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, male, rep4

description: Library name: SN32koIFNm4_arc_atac

data_processing:
Paired-end sequencing was performed on a NovaSeq 6000. Samples were processed using the cellranger count pipeline (v7.1.0) for gene expression data, including intronic reads, with the reference genome refdata-gex-mm10-2020-A. For ATAC-seq data, the cellranger-atac count pipeline (v2.0.0) was used with the refdata-cellranger-arc-mm10-2020-A-2.0.0 reference package.
Assembly: mm10
Supplementary files format and content: Cell ranger output files per sample: filtered_feature_bc_matrix.h5,  atac_cut_sites.bigwig, atac_fragments.tsv.gz

source_name: substantia nigra

extract_protocol:
After 24 hours, striatum and substantia nigra were collected for nuclei purification using 10x Genomics single-cell nuclei isolation kit (PN-1000494)
20, 000 nuclei/sample were processed according to  Chromium next GEM Single cell Multiome ATAC+Gene Expression user guide (CG000338 Rev E). Chromium Single Cell Multiome  Gene Expression and ATAC libraries were sequenced using standard Illumina® paired-end sequencing with P5 and P7 primers.

treatment_protocol: C57Bl/6J WT and LRRK2 knockout mice (3 months old) received bilateral stereotaxic injections of mouse IFN-γ (20 ng/site) or PBS into the striatum and substantia nigra. Tissues were collected 24 hours post-injection.

value: substantia nigra

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

tag: Sex

value: male

value: recombinant mouse IFN-γ injected


title: hp58_hIV - hIV - mock

description: Library name: hp58_hIV

value: Lung - in vivo

value: mock

tag: specimen id

tag: specimen sex

value: Male

tag: batch

value: hIV


title: 933000320625027

description: Library name: 933000320625027


title: 933000320697537

description: Library name: 933000320697537


title: 933000320624895

description: Library name: 933000320624895


title: ChIP-Seq, human iPSC-derived microglia, IFN-γ treatment, without antibody, ChIP, rep1

description: Library name: ControlIFN1

tag: chip antibody

value: interferon-ɣ exposed


title: 933000320624887

description: Library name: 933000320624887


title: Gamma  neurons, 30 hours after pupa formation,rep3

description: Library name: gamma30E_3_S36

value: Brain

value: Gamma neurons


title: hp57_hIV - hIV - mock

description: Library name: hp57_hIV

value: Female

tag: specimen age


title: Gamma  neurons,Adult,rep1

description: Library name: gamma_adult_J_1_S7

value: Adult


title: HC35 - hPCLS - IAV

description: Library name: HC35

source_name: Lung - pcls

value: Lung - pcls

value: IAV

value: hPCLS


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout IFN-γ injected, male, rep4

description: Library name: SN32koIFNm4_arc_gex

tag: genotype


title: HC36 - hPCLS - Spn

description: Library name: HC36

value: Spn


title: HC34 - hPCLS - mock

description: Library name: HC34


title: Gamma neurons, 27 hours after pupa formation,rep3

description: Library name: gamma27J_4_S38

value: 27 hours after pupa formation


title: Gamma  neurons, 30 hours after pupa formation,rep1

description: Library name: gamma30D_1_S12

value: 30 hours after pupa formation


title: hp59_hIV - hIV - mock

description: Library name: hp59_hIV


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, female, rep3

description: Library name: SN31koIFNf4_arc_gex

value: substantia nigra

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

value: female


title: 933000320624881

description: Library name: 933000320624881

value: Rostromedial tegmental nucleus


title: Gamma neurons, 27 hours after pupa formation,rep2

description: Library name: gamma27H_2_S14


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype,IFN-γ injected, male, rep4

description: Library name: SN30wtIFNm5_arc_atac

value: C57Bl/6J (WT; Jax)

value: male

value: recombinant mouse IFN-γ injected


title: hp58_mock - hPCLS - mock

description: Library name: hp58_mock

value: mock

value: Male


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, male, rep4

description: Library name: SN30wtIFNm5_arc_gex


title: hp58_Spn - hPCLS - Spn

description: Library name: hp58_Spn


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, female, rep3

description: Library name: SN31koIFNf4_arc_atac


title: Gamma neurons, 27 hours after pupa formation,rep4

description: Library name: gamma27J_5_S59

value: Brain

value: Gamma neurons


title: Gamma neurons, 24 hours after pupa formation,rep5

description: Library name: gamma24E_4_S39

value: 24 hours after pupa formation


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, female, rep3

description: Library name: SN29wtIFNf4_arc_gex


title: hp58_IAV - hPCLS - IAV

description: Library name: hp58_IAV

value: Lung - pcls

value: IAV


title: 933000320524354

description: Library name: 933000320524354


title: 933000320524357

description: Library name: 933000320524357


title: 933000320524337

description: Library name: 933000320524337


title: Gamma neurons, 24 hours after pupa formation,rep3

description: Library name: gamma24C_5_S58


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, control, male, rep4

description: Library name: SN28koPBSm2_arc_gex

value: PBS injected


title: 933000320624747

description: Library name: 933000320624747


title: 933000320524192

description: Library name: 933000320524192


title: HC29 - hPCLS - IAV

description: Library name: HC29

value: Female

value: hPCLS


title: Gamma neurons, 24 hours after pupa formation,rep2

description: Library name: gamma24A_2_S15


title: 933000320500408

description: Library name: 933000320500408


title: HC28 - hPCLS - mock

description: Library name: HC28


title: 933000320500240

description:
Library name: 933000320500240
removed: not genotyped


title: Gamma neurons, 24 hours after pupa formation,rep1

description: Library name: gamma24A_1_S10


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, female, rep3

description: Library name: SN29wtIFNf4_arc_atac

value: substantia nigra


title: Gamma neurons, 21 hours after pupa formation,rep5

description: Library name: gamma21G_6_S33

value: 21 hours after pupa formation


title: HC27 - hPCLS - Spn

description: Library name: HC27

value: Spn


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, control, female, rep3

description: Library name: SN27koPBSf2_arc_atac

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

value: female


title: HC30 - hPCLS - Spn

description: Library name: HC30


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, control, female, rep3

description: Library name: SN27koPBSf2_arc_gex


title: HC26 - hPCLS - IAV

description: Library name: HC26


title: 933000320500166

description: Library name: 933000320500166

value: Rostromedial tegmental nucleus


title: Gamma neurons, 21 hours after pupa formation,rep3

description: Library name: gamma21B_4_S40


title: Gamma neurons, 24 hours after pupa formation,rep4

description: Library name: gamma24D_7_S34


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, control, male, rep4

description: Library name: SN26wtPBSm2_arc_atac

value: C57Bl/6J (WT; Jax)

value: male


title: 933000320499909

description: Library name: 933000320499909


title: 933000320500161

description: Library name: 933000320500161


title: HC25 - hPCLS - mock

description: Library name: HC25

value: mock

value: Male


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, control, male, rep4

description: Library name: SN26wtPBSm2_arc_gex


title: Gamma neurons, 21 hours after pupa formation,rep2

description: Library name: gamma21A_2_S16

value: Brain

value: Gamma neurons


title: HC24 - hPCLS - Spn

description: Library name: HC24

value: Lung - pcls


title: 933000320499908

description: Library name: 933000320499908


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, control, female, rep3

description: Library name: SN25wtPBSf2_arc_gex


title: HC23 - hPCLS - IAV

description: Library name: HC23

value: IAV


title: Gamma neurons, 21 hours after pupa formation,rep4

description: Library name: gamma21C_5_S57


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, control, male, rep4

description: Library name: SN28koPBSm2_arc_atac

value: PBS injected


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, control, female, rep3

description: Library name: SN25wtPBSf2_arc_atac


title: Gamma neurons,18 hours after pupa formation,rep5

description: Library name: gamma18F_6_S32

value: 18 hours after pupa formation


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, male, rep2

description: Library name: SN24koIFNm3_arc_gex

value: recombinant mouse IFN-γ injected


title: 933000320499902

description: Library name: 933000320499902


title: 933000320499907

description: Library name: 933000320499907


title: Gamma neurons,18 hours after pupa formation,rep4

description: Library name: gamma18F_5_S56


title: RH4, sh4, P7F1-Turbo, Rep2

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

data_processing:
Trimmed with fastp toolkit, aligned with STAR RNA, Normalization by DEseq2
Assembly: GRch38 Ver 106
Supplementary files format and content: Normalized counts

source_name: Cell Line

growth_protocol: Cells were grown in RPMI + 10%FBS at 37C and 5% CO2. All cells were grown in the presense of doxycycline to induce shRNA expression

extract_protocol:
Qiagen RNEasy
Library was prepared using Kapa stranded mRNA seq Kit

value: Cell Line

value: Rhabdomyosarcoma


title: HC22 - hPCLS - mock

description: Library name: HC22

value: Female

value: hPCLS


title: 933000320499746

description: Library name: 933000320499746


title: RH4, sh4, P7F1-Turbo, Rep3


title: Gamma neurons, 21 hours after pupa formation,rep1

description: Library name: gamma21A_1_S9

value: 21 hours after pupa formation


title: RH4, sh4, P7F1-Turbo, Rep1


title: Gamma neurons,18 hours after pupa formation,rep3

description: Library name: gamma18E_4_S41


title: 933000320499722

description: Library name: 933000320499722

value: Rostromedial tegmental nucleus


title: 933000320188753

description: Library name: 933000320188753


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, female, rep1

description: Library name: SN23koIFNf3_arc_gex

value: substantia nigra

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

value: female


title: RH4, sh4, P3I-Turbo, Rep3


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, female, rep1

description: Library name: SN23koIFNf3_arc_atac


title: 933000320188691

description: Library name: 933000320188691


title: Alpha-beta neurons,Adult,rep5

description: Library name: ab_adult_k_5_S49

value: Alpha-beta neurons

value: Adult


title: Gamma neurons,18 hours after pupa formation,rep2

description: Library name: gamma18E_2_S17

value: Brain

value: Gamma neurons


title: Gamma neurons,18 hours after pupa formation,rep1

description: Library name: gamma18B_1_S8


title: 933000320188599

description: Library name: 933000320188599


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, male, rep2

description: Library name: SN22wtIFNm3_arc_gex

value: C57Bl/6J (WT; Jax)

value: male


title: RH4, sh4, P3I-Turbo, Rep2


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, IFN-γ injected, male, rep2

description: Library name: SN24koIFNm3_arc_atac