title: Blood_Het

description: 10X Genomics

source_name: Blood

extract_protocol:
Blood
Blood: N=4 non-sister female mice at GD10.5 were processed per group (WT and Het). After terminal anesthesia by pentobarbital, maximum peripheral whole blood (~2 mL) was collected via cardiac puncture. Biological replicates from each group were then pooled together and an equal volume of 1X DPBS without magnesium or calcium was added to the whole blood. The diluted whole blood was layered onto Ficoll-Paque PREMIUM 1.084 (2 parts blood to 3 parts Ficoll in volume). The gradient was spun at 400 x g for 30 min with the brakes off at room temperature (RT). Plasma was removed and the layer containing peripheral blood mononuclear cell (PBMC) was collected and transferred to a new tube. The remaining Ficoll layer was removed, and the RBC/granulocyte pellet was suspended in 1X RBC Lysis Buffer in a 1:10 ratio. The solution was gently inverted a few times, incubated at RT for 15 minutes, then spun at 300 x g for 5 minutes with brakes on low at RT. The supernatant with lysed RBC fragments was removed. The pellet was washed with a volume of DPBS equal to the amount of RBC Lysis Buffer used and spun at 350 x g with brakes on low for 5 minutes at RT. Wash was repeated, the supernatant was removed, and the resulting pellet of granulocytes was resuspended in 1 mL DPBS with 2% FBS and set on ice. Separately, the volume of collected PBMC was estimated and 4X that volume of DPBS was added to the PBMC fraction. The sample was gently triturated with a serological pipet, then spun at 400 x g for 10 minutes with brakes on low at RT. RBC lysis buffer was added to the pellet as above and the resulting pellet was washed twice with DPBS. Final PBMC pellet was resuspended in 1 mL DPBS with 2% FBS, combined with granulocyte suspension, and visually inspected with a hemocytometer under a microscope for cell counting.
Placenta: After dissection of the maternal decidua, N=3 decidua from non-sibling placenta at GD10.5 were processed per group (WT and Het decidua from WT and F1 placenta). Single nuclei suspension was prepared from frozen tissue with slight modifications to the method described by Marsh and Blelloch 2020 (Marsh and Blelloch 2020). In brief, 1 mL prechilled Nuclei EZ lysis buffer was added to each flash-frozen decidua sample, which was then minced finely with dissection scissors. A wide bore pipet was used to transfer pooled minced tissue into a glass dounce homogenizer. Tissue was lysed with 20 strokes of the loose pestle followed by 20 strokes of the tight pestle. The homogenate was transferred to a new tube and an additional 3 mL of prechilled Nuclei EZ Lysis Buffer was added. The sample was incubated on ice for 5 min and was resuspended a few times throughout. The lysate was filtered through a 70 µM filter and spun at 500 x g for 5 min at 4°C in a centrifuge with a swinging bucket rotor. The supernatant was removed, and the pellet was resuspended with 2 mL Nuclei EZ Lysis Buffer and incubated for an additional 5 min on ice. The sample was spun at 500 x g for 5 min at 4°C and the supernatant was removed. 1 mL Nuclei Wash Buffer (DPBS without magnesium and calcium, 2% BSA, and 0.2U Protector RNase inhibitor was layered onto the pellet and the sample was incubated on ice for 5 min without mixing or resuspending in order to promote buffer exchange. An additional 2 mL Nuclei Wash Buffer was used to resuspend, and the sample was spun at 500 x g for 5 min at 4°C. The lysate was removed, and this wash step was repeated. Finally, the pellet was resuspended in 1.5 mL Nuclei Wash Buffer, filtered through a 70 µM filter, and visually inspected with a hemocytometer under a microscope for cell counting.
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: Blood

value: PBMC; granulocytes

value: 5HT1A-R+/- (heterozygous)


title: Blood_WT

status: Public on Nov 29 2022

type: SRA

city: New York

first: Miklos

last: Toth

address: 525 E. 68th St Whitney Pavilion Floor 5

country: USA

institute: Weill Cornell Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Blood: Raw sequencing data was processed using the CellRanger v5.0.0 pipeline.
Placenta: Raw sequencing data was processed using the CellRanger v6.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: Swiss Webster wild type

tag: Sex

value: Female

tag: gestational day


title: WT_CUTRUN_IgG

city: Hirosaki

first: Rika

last: Kanezaki

address: 5 Zaifucho

country: Japan

institute: Hirosaki University Graduate School of Medicine

library_source: genomic

data_processing:
library strategy: CUT&RUN
For ChIP-seq data,sequence reads were aligned to genome by Bowtie2 (ver 2.2.2) with option -N1. For CUT&RUN-seq data, reads were aligned according to the method by Skene and Heinikoff (Nature Protocols 2018 13, 1006-1019). For RNA-seq data, sequence reads were aligned to genome using STAR (ver 2.6.1d). Aligned reads were counted by RSEM (ver 1.3.1). The count data normalized using the DESeq2 package (ver 1.32.0).
Duplicated reads of ChIP-seq and CUT&RUN-seq were removed by Picard (ver. 2.18).
The BAM files of ChIP-seq and CUT&RUN data were converted to bigWig coverage files using bamCoverage command of deepTools (ver 3.1.3). Read coverages were normalized to Read per genomic content (RPGC). For the GATA1 and GATA2 ChIP-seq data, peak call was performed using HOMER (ver 4.11)  with default settings.
Genome_build: hg19 (ChIP-seq, CUT&RUN-seq), hg38 (RNA-seq)
Supplementary_files_format_and_content: bigWig files normalized in reads per genomic content (RPGC) and bed files.

molecule: genomic DNA

organism: Homo sapiens

source_name: K562, wild type

growth_protocol: K562 cells were cultured with RPMI1640 (Sigma-Aldrich) containing 10% heat inactivated fetal bovine serum (FBS) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Chromatin samples were extracted using SimpleChIP Enzymatic Chromatin IP Kit (CST) according to the protocol. For ChIP reactions, Dynabeads anti-rabbit IgG (Thermo Fisher Scientific) was used to reduce noise instead of the Protein G magnetic beads included in the kit. CUT&RUN assay was performed using CUT&RUN Assay Kit (CST), and samples were purified using Monarch PCR & DNA Cleanup Kit (NEB). total RNA was extracted using the RNeasy plus mini kit (Qiagen).
ChIP-seq and CUT&RUN libraries were prepared using KAPA HyperPrep Kit (KAPA Biosystems). Total RNA was purified by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and RNA-seq library was prepared by KAPA RNA Hyper prep kit (KAPA Biosystems).

tag: cell line

value: wild

tag: chip and cut&run antibody

value: normal IgG (CST, 66362)


title: 8_TAM_Mm_2

city: Leiden

first: Ralf

last: Boland

address: Einsteinweg 55

department: IBL-ASH-CO

country: Netherlands

institute: Leiden University

library_source: transcriptomic

data_processing:
Filtered reads were mapped to the zebrafish version GRzv11 using Salmon v.0.14.1
Data were analyzed in DESeq2 (86) following a linear model taking into account possible gene expression differences from the embryo parents, drug treatments, infections, and its interaction (design: ~genotype + treatment + infection + treatment:infection). Statistical significance was defined by s-value ≤ 0.005 using apeglm. S-values are aggregate statistics that have been recently proposed as an alternative to adjusted p-value and false discovery rate (FDR), calculating the probability of getting the sign of an effect wrong in biological contexts.
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample

organism: Danio rerio

source_name: zebrafish embryo infected with 200CFU of M. marinum with Tamoxifen treatment, 2 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were kept in egg water (60µg/ml Instant Ocean sea salts) at 28.5°C.

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
3µg was used to create RNAseq libraries using the Illumina TruSeq strand-specific mRNA polyA preparation kit (Illumina, San Diego, US). The resulting RNAseq library was sequenced for at least 10 million reads per sample using an Illumina HiSeq2500 with a read length of 1 × 50 nucleotides (Baseclear, Leiden, The Netherlands).

treatment_protocol: Zebrafish embryos from four independent crosses were manually dechorionated at 24 hpf and at 30 hpf they were micro-injected into the blood island with 200  CFU of M. marinum strain M bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. Embryos were treated with 0.02% ethyl 3-aminobenzoate methanesulfonate (Tricaine, SIGMA-ALDRICH) for anesthesia before bacterial injections and RNA extraction. Embryos were incubated with the specified drug treatment (10uM Tamoxifen, 10uM Amiodarone, or same v/v DMSO). At 4 days post fertilization (2 days post infection), total RNA from pools of 10 embryos for treatment group was isolated using QIAzol® Reagent (Qiagen).

tag: blood island injection

value: M. marinum, M strain 200 cfu

tag: developmental stage rna isolation

value: 2 dpi

tag: parental strain

value: B

tag: description


title: Brain microglia : PLX_21

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.vM15 database .
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Mus musculus (GRCm38)
Supplementary_files_format_and_content: RSEM expected counts

molecule: polyA RNA

source_name: Brain microglia

growth_protocol: Microglia cells from adult young or old mice were isolated and cultured using immunomagnetic separation (Miltenyi Biotec, Germany). Mice were perfused via the left ventricle with 60 mL of cold saline and collected in Hanks' balanced salt solution (HBSS) buffer without calcium/magnesium (#14175-05; Life Technologies). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit-P (#130-092-628; Miltenyi Biotec). The gentleMACS™ Dissociator with Heaters (#130-096-427; Miltenyi Biotec) was used for mechanical dissociation steps during 30 minutes at 37ºC. The digested tissue was filtered (70µm) with HBSS buffer with calcium and magnesium (#14025-050; Life Technologies) and prepared for myelin removal process (Myelin Removal Beads II, #130-096-733; Miltenyi Biotec). Then, cells were magnetically labeled with CD11b microbeads (#130-093-634; Miltenyi Biotec) diluted in PBS supplemented with 0.5% BSA for 15 minutes in the dark in the refrigerator (2−8 °C).  CD11b+ cells were collected using magnetic field columns (Miltenyi Biotec). Cell suspensions (35 l) were then plated in complete medium consisting of DMEM medium (#10569010; Gibco-BRL) supplemented with 10% fetal bovine serum (FBS; Gibco-BRL) and containing 40U/mL penicillin/40μg/mL streptomycin (#15140122; Gibco-BRL) added as a drop in the middle of each well of a Poly-L-Lysine (#P4832; Sigma) pre-coated 8-well plate (µ-Slide 8 Well, IBIDI #80826). Cells were incubated for 30 minutes at 37 °C and then 250 µL of complete medium were carefully added to each well. 24 hours later, we replaced 50% of complete medium, and we did a full medium change at day 5. The cells were maintained at 37 °C in a humidified atmosphere of 5% CO2 for 7 DIV.

extract_protocol:
RNA was extracted from samples of FACS-sorted microglia with PureLink™ RNA Micro Kit (#12183016, Invitrogen) following manufacturer indications with minor modifications. RNA was precipitated with 70% ethanol overnight at -20°C. To avoid genomic DNA contamination a DNAse step was performed. RNA quantity and purity were assessed with the High Sensitivity RNA ScreenTape® (Agilent 2200 TapeStation system).
RNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (#RS-122-2101/2, Illumina) according to the manufacturer's protocol. Briefly, from 2.4 to 147 ng of total RNA were used for poly(A)-mRNA selection using streptavidin-coated magnetic beads and were subsequently fragmented to approximately 300bp. cDNA was synthesized using SuperScript II reverse transcriptase (#18064-014, Invitrogen) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP. Double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. All purification steps were performed with AMPure XP beads and eluted in 20 µl EB. Library amplification was performed by PCR on selected fragments using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (#KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Libraries were sequenced Single Reads, 50nts on the Illumina HiSeq 2500.

treatment_protocol: For microglia depletion, mice received the CSF1R inhibitor PLX5622 (Plexxikon Inc, Berkeley USA) following previously reported protocols (Otxoa-de-Amezaga et al., 2019). The inhibitor was mixed into AIN-76A standard chow at 1200 ppm (Brogaarden, Denmark). Treatment controls received AIN-76A chow devoid of the drug for the same period. Both diets were given in parallel in groups of 5 animals per cage. Mice received the diet ad libitum. In as much as possible, we blinded the treatment, e.g for evaluation of behavioral data.

tag: group

value: O-re

tag: strain

value: female

value: Microglia cells


title: Brain microglia : Young (14C)

description: 14C.tsv:  (polyA RNA)

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.vM15 database .
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: RSEM expected counts

growth_protocol: Mice were anesthetized with isoflurane and euthanized by cervical dislocation. The brain was carefully collected, in order not to damage the tissue, and immersed in Hanks’ Balanced Salt solution w/o ions (HBSS w/o Ca2+ and Mg2+; #14175-053, Thermo Fisher Scientific) on ice. The forebrain was dissected with a scalpel, discarding the cerebellum and the olfactory bulbs, and minced in small pieces. The Neural Tissue Dissociation Kit - P (NTDK, #130-092-628, Miltenyi Biotec) based on the enzymatic dissociation with papain was used to homogenize the tissue. Mechanical dissociation was performed with the gentleMACS™ Octo Dissociator (#130-096-427, Miltenyi Biotec: 1x m_Brain_1 program and 1x ABDK_37C program by Miltenyi) with the tissue immersed in the buffers and enzymes from the NTDK kit, according to manufacturer instructions. The tissue was then filtered through a 70 mm cell strainer (#352350, Falcon) previously humidified with HBSS with Ca2+ and Mg2+ (#14025-092, Thermo Fisher Scientific). Then, cells were separated from myelin by an immunomagnetic separation method. Brain cells were incubated with Myelin Removal Beads II (#130-096-733, Miltenyi Biotec) and then passed through LS Columns (#130-042-401, Miltenyi Biotec) held onto the OctoMACS Separator (#130-091-051, Miltenyi Biotec) and to the MACS® MultiStand (#130-042-303, Miltenyi Biotec). Unspecific binding of antibodies was blocked by previous incubation for 10 min with anti CD16/CD32 (Fc block, clone 2.4G2; #55314, BD Pharmingen) in Fluorescence Activated Cell Sorting (FACS) buffer at 4 °C. LViakrome 405 Fixable Viability Dye (#C36614, Beckman Coulter) was used to determine the viability of cells. Cells were incubated during 30 minutes at 4°C with the following primary antibodies: CD11b (clone M1/70, AF647, #557686, BD Pharmingen), CD45 (clone 30-F11, Brilliant Violet 786, #564225, BD Horizon). After washing once with phosphate buffered saline (PBS), cells were stained with BODIPY (4,4-difluoro-3a,4adiaza-s-indacene, Molecular Probes BODIPY 493/503, #D3922, Life Technologies) diluted 1:1,000 during 15min at RT. After washing with FACS Stain Buffer (#554656, BD Biosciences), the cells were sorted in a FACSAriaII SORP sorter (BD Biosciences). Microglial cells were collected in sterile DPBS (#14190-094, Thermo Fisher Scientific), centrifuged, and resuspended in lysis buffer (from PureLink™ RNA Micro Kit #12183016, Invitrogen) supplemented with 10% β-mercaptoethanol and finally snap-frozen in dry ice.

extract_protocol:
RNA was extracted from samples of FACS-sorted microglia with PureLink™ RNA Micro Kit (#12183016, Invitrogen) following manufacturer indications with minor modifications. RNA was precipitated with 70% ethanol overnight at -20°C. To avoid genomic DNA contamination a DNAse step was performed. RNA quantity and purity were assessed with the High Sensitivity RNA ScreenTape® (Agilent 2200 TapeStation system).
Library Preparation - custom SMARTseq2 (NEBnext) (low input/non-stranded),

treatment_protocol: No drug treatment. We compared microglia of adult young (3-4 month) male mice with microglia of  old (21-22 month) male mice in the C57BL/6 background obtained from Janvier (Lyon, France)

value: Young


title: Brain microglia : PLX_20


title: Brain microglia : PLX_7


title: Brain microglia : PLX_11


title: Brain microglia : PLX_8


title: Brain microglia : PLX_18

value: O


title: Brain microglia : PLX_10


title: Brain microglia : PLX_9


title: Brain microglia : PLX_19


title: Brain microglia : PLX_16


title: F1_Maternal

description: 10X Genomics

source_name: Placenta

extract_protocol:
Placenta
Blood: N=4 non-sister female mice at GD10.5 were processed per group (WT and Het). After terminal anesthesia by pentobarbital, maximum peripheral whole blood (~2 mL) was collected via cardiac puncture. Biological replicates from each group were then pooled together and an equal volume of 1X DPBS without magnesium or calcium was added to the whole blood. The diluted whole blood was layered onto Ficoll-Paque PREMIUM 1.084 (2 parts blood to 3 parts Ficoll in volume). The gradient was spun at 400 x g for 30 min with the brakes off at room temperature (RT). Plasma was removed and the layer containing peripheral blood mononuclear cell (PBMC) was collected and transferred to a new tube. The remaining Ficoll layer was removed, and the RBC/granulocyte pellet was suspended in 1X RBC Lysis Buffer in a 1:10 ratio. The solution was gently inverted a few times, incubated at RT for 15 minutes, then spun at 300 x g for 5 minutes with brakes on low at RT. The supernatant with lysed RBC fragments was removed. The pellet was washed with a volume of DPBS equal to the amount of RBC Lysis Buffer used and spun at 350 x g with brakes on low for 5 minutes at RT. Wash was repeated, the supernatant was removed, and the resulting pellet of granulocytes was resuspended in 1 mL DPBS with 2% FBS and set on ice. Separately, the volume of collected PBMC was estimated and 4X that volume of DPBS was added to the PBMC fraction. The sample was gently triturated with a serological pipet, then spun at 400 x g for 10 minutes with brakes on low at RT. RBC lysis buffer was added to the pellet as above and the resulting pellet was washed twice with DPBS. Final PBMC pellet was resuspended in 1 mL DPBS with 2% FBS, combined with granulocyte suspension, and visually inspected with a hemocytometer under a microscope for cell counting.
Placenta: After dissection of the maternal decidua, N=3 decidua from non-sibling placenta at GD10.5 were processed per group (WT and Het decidua from WT and F1 placenta). Single nuclei suspension was prepared from frozen tissue with slight modifications to the method described by Marsh and Blelloch 2020 (Marsh and Blelloch 2020). In brief, 1 mL prechilled Nuclei EZ lysis buffer was added to each flash-frozen decidua sample, which was then minced finely with dissection scissors. A wide bore pipet was used to transfer pooled minced tissue into a glass dounce homogenizer. Tissue was lysed with 20 strokes of the loose pestle followed by 20 strokes of the tight pestle. The homogenate was transferred to a new tube and an additional 3 mL of prechilled Nuclei EZ Lysis Buffer was added. The sample was incubated on ice for 5 min and was resuspended a few times throughout. The lysate was filtered through a 70 µM filter and spun at 500 x g for 5 min at 4°C in a centrifuge with a swinging bucket rotor. The supernatant was removed, and the pellet was resuspended with 2 mL Nuclei EZ Lysis Buffer and incubated for an additional 5 min on ice. The sample was spun at 500 x g for 5 min at 4°C and the supernatant was removed. 1 mL Nuclei Wash Buffer (DPBS without magnesium and calcium, 2% BSA, and 0.2U Protector RNase inhibitor was layered onto the pellet and the sample was incubated on ice for 5 min without mixing or resuspending in order to promote buffer exchange. An additional 2 mL Nuclei Wash Buffer was used to resuspend, and the sample was spun at 500 x g for 5 min at 4°C. The lysate was removed, and this wash step was repeated. Finally, the pellet was resuspended in 1.5 mL Nuclei Wash Buffer, filtered through a 70 µM filter, and visually inspected with a hemocytometer under a microscope for cell counting.
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: Placenta

value: Decidual cells; immune cells


title: Brain microglia : PLX_6


title: Brain microglia : PLX_17


title: Brain microglia : PLX_12

value: Y


title: Brain microglia : PLX_24

value: Y-re


title: Brain microglia : PLX_3


title: Brain microglia : PLX_15


title: Brain microglia : PLX_2


title: Brain microglia : PLX_4


title: A498 STING WT shCtrl RNA Rep1

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were filtered for adaptor contamination using cutadapt and filtered with the fastx-toolkit such that at least 90% of bases of each read had a quality score > 20.
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments.
Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon, and differential expression was detected using DESeq2.
Pathway enrichment analysis was performed by using the GSEA software and Hallmark signatures.
Genome_build: hg19
Supplementary_files_format_and_content: sf files are gene-level expression data (TPM) generated by salmon quant.
Supplementary_files_format_and_content: Tab-delimited txt is a matrix of per-gene TPMs for all samples.
Supplementary_files_format_and_content: The xlsx contains all differentially expressed genes as determined by DESeq2 across all shSTING samples versus shCtrl.

source_name: A498, STING, shCtl

growth_protocol: Human renal cell carcinoma cell lines 786-O, A498, ACHN, Caki-1, RCC4, RCC10, RXF-393, UMRC2 and UMRC6, human immortalized kidney cell lines HEK293, HEK293T and HKC-8, human cervical adenocarcinoma cell line HeLa, human umbilical vein cell line EA.hy926, and human glioblastoma cell line U87-MG were cultured in DMEM medium supplemented with 10% FBS. Human Ewing sarcoma cell line A673 and human benign prostatic hyperplasia cell line BPH-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. All cell culture media were supplemented with 100 units of penicillin and 100 mg/mL streptomycin unless otherwise stated.

extract_protocol:
Total RNA from triplicate samples of A498 cells infected with shScr or shSTING was extracted with RNeasy mini kit (Qiagen, 74104).
Library preparation and sequencing were performed by GENEWIZ as paired-end 150-bp reads.

treatment_protocol: Cell transfection was performed using lipofectamine 3000 or polyethylenimine (PEI), as described previously. Packaging of lentiviral shRNA or cDNA expressing viruses, as well as subsequent infection of various cell lines were performed according to the protocols described previously. Following viral infection, cells were maintained in the presence of hydromycin (200 μg/mL) or puromycin (2 μg/mL), depending on the viral vector used to infect cells.

value: clear cell renal cell carcinoma (ccRCC) cells

tag: treatment

value: shCtrl

value: WT


title: Brain microglia : PLX_13


title: A498 STING KD sh45 RNA Rep3

source_name: A498, STING, sh45

value: STING knockdown


title: Brain microglia : PLX_1


title: A498 STING KD sh45 RNA Rep2


title: Brain microglia : PLX_14


title: A498 STING WT shCtrl RNA Rep3


title: A498 STING KD sh45 RNA Rep1


title: Brain microglia : PLX_23


title: A498 STING KD sh29 RNA Rep1

source_name: A498, STING, sh29


title: A498 STING KD sh29 RNA Rep2


title: mouse_ striatum_WT_NT gRNA 2

status: Public on Nov 15 2022

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
RNAseq reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i) (Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the mouse genome assembly (mm10) with STAR (v2.4.0i)
Read counts for all genes annotated in GENCODE (vM20) were calculated using the read summarization program featureCounts (v1.5.3) (Liao et al., 2014).
Batch correction was completed with Combat-seq
Differential expression was completed by DESeq2 (v1.5.3)
Assembly: mm10

source_name: WT

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a KAPA Hyperprep total RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were treated with AAV9 viral vectors encoding Cas13d/NT or Cas13d/CAGEX at 2 months of age.

tag: time

value: 10 months of age


title: mouse_ striatum_WT _CAGEX gRNA 5


title: A498 STING KD sh29 RNA Rep3


title: mouse_ striatum_WT _CAGEX gRNA 4


title: mouse_ striatum_HD_NT gRNA 5

source_name: HD

value: HD


title: mouse_ striatum_HD_NT gRNA 4


title: mouse_ striatum_WT_NT gRNA 3


title: mouse_ striatum_HD_CAGEX gRNA 5


title: mouse_ striatum_WT _CAGEX gRNA 3


title: mouse_ striatum_WT_NT gRNA 4


title: A498 STING WT shCtrl RNA Rep2


title: Brain microglia : PLX_22


title: mouse_ striatum_HD_CAGEX gRNA 4


title: mouse_ striatum_WT_NT gRNA 1


title: mouse_ striatum_HD_NT gRNA 2


title: mouse_ striatum _WT_CAGEX gRNA 1


title: mouse_ striatum_WT _CAGEX gRNA 2


title: mouse_ striatum_HD_NT gRNA 3


title: mouse_ striatum_HD_CAGEX gRNA 2


title: mouse_ striatum_HD_NT gRNA 1


title: mouse_ striatum_HD_CAGEX gRNA 3


title: THP-1 cells, LAA treatment, replicate 3

status: Public on Nov 12 2022

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

data_processing:
Raw reads were filtered to remove low quality (Qscore ≤ 5 for > 50% of bases) reads, reads containing adaptors, and reads containing > 10% undetermined bases.
Filtered reads were aligned to reference genome with HISAT2; multi mapped reads were filtered out.
Mapped reads were counted with samtools.
Differential gene expression was determined using DESeq2 with default options.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file gene_count.txt contains raw count data for all samples.
Supplementary files format and content: Tab-delimited text file gene_fpkm.txt contains FPKM-normalized count data for all samples.

growth_protocol: MOLM-13 and THP-1 human acute myeloid leukemia cell lines were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Cells were homogenized with QIAshredder (Qiagen 79654), then total RNA was extracted using RNeasy Plus Mini kits (Qiagen 74136), both following the manufacturer protocols.
1µg total RNA was used as input for library construction. Libraries were then generated from polyA-selected RNA using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB E7530).

treatment_protocol: Cells were treated with 250µM L-ascorbic acid (LAA; Sigma A4544; dissolved in PBS), 1µM Olaparib (Olap; SelleckChem S1060; dissolved in DMSO), the combination thereof, or vehicle control (PBS + DMSO) for 72hr.

value: acute myeloid leukemia

value: L-ascorbic acid (LAA, 250uM)

tag: time point


title: THP-1 cells, LAA + Olap treatment, replicate 2

value: LAA + Olap


title: THP-1 cells, Olaparib treatment, replicate 2

value: Olaparib (Olap, 1uM)


title: THP-1 cells, Olaparib treatment, replicate 3


title: THP-1 cells, Olaparib treatment, replicate 1


title: THP-1 cells, LAA + Olap treatment, replicate 1


title: THP-1 cells, LAA + Olap treatment, replicate 3


title: THP-1 cells, vehicle treatment, replicate 3

value: Vehicle


title: THP-1 cells, vehicle treatment, replicate 1


title: THP-1 cells, LAA treatment, replicate 2


title: MOLM-13 cells, LAA + Olap treatment, replicate 3


title: MOLM-13 cells, LAA + Olap treatment, replicate 2


title: MOLM-13 cells, Olaparib treatment, replicate 1


title: MOLM-13 cells, Olaparib treatment, replicate 2


title: MOLM-13 cells, Olaparib treatment, replicate 3


title: MOLM-13 cells, LAA treatment, replicate 3


title: MOLM-13 cells, LAA treatment, replicate 2


title: mouse_ striatum_HD_CAGEX gRNA 1


title: MOLM-13 cells, LAA treatment, replicate 1


title: Terminal secondary transplant, Tet2 knockdown, ASC-treated, mouse #28

data_processing:
Reads were filtered to remove low quality, adaptor-containing, or high undetermined base-count reads.
Reads mapped using splice-aware STAR aligner.
Counts generated using featureCounts.
DESeq2 was used to test for differential expression.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file counts_raw.txt contains raw count data for all samples.
Supplementary files format and content: Tab-delimited text file counts_fpkm.txt contains FPKM-normalized count data for all samples.

source_name: spleen

growth_protocol: cKit+ cells isolated from bone marrow of C57BL/6J mice were transduced with an AE9a+ retrovirus containing a doxycycline (DOX) inducible hairpin targeting Tet2. 50,000 AE9a+ and 500,000 support wild-type bone marrow cells were transplanted into lethally irradiated 6-8wk old C57BL/6J mice fed a DOX diet to generate a primary leukemia. When mice developed a leukemia and became moribund, splenic AE9a+ tumor cells were harvested and 50,000 cells retransplanted with 500,000 support bone marrow to generate a secondary leukemia.

extract_protocol:
Cells were homogenized with QIAshredder (Qiagen 79654), then total RNA was extracted using RNeasy Plus Mini kits (Qiagen 74136), both following the manufacturer protocols.
Oligo-dT beads (Life Technologies) were used to enrich for mRNA, from which libraries were made using NEXTflex RNA-seq Kit, following manufacturer instructions.

treatment_protocol: Secondary-transplant mice were divided into 3 cohorts: sustained Tet2 knockdown (+DOX, PBS), Tet2 restoration (-DOX, PBS), or ascorbate treatment (+DOX, ASC). Splenic AE9a+ tumor cells from moribund mice were harvested for RNA-sequencing.

tag: transplant type

value: secondary

value: spleen

value: AE9a+ leukemic cell

value: RTA shTet2

value: Tet2 knockdown, ASC treatment


title: MOLM-13 cells, vehicle treatment, replicate 3


title: MOLM-13 cells, vehicle treatment, replicate 2


title: Terminal secondary transplant, Tet2 restored, PBS-treated, mouse #21

tag: tissue

value: Tet2 restoration, PBS


title: Terminal secondary transplant, Tet2 restored, PBS-treated, mouse #23

tag: cell type


title: MOLM-13 cells, vehicle treatment, replicate 1


title: Terminal secondary transplant, Tet2 knockdown, PBS-treated, mouse #19

tag: genotype

value: Tet2 knockdown, PBS


title: THP-1 cells, LAA treatment, replicate 1


title: MOLM-13 cells, LAA + Olap treatment, replicate 1


title: Terminal secondary transplant, Tet2 knockdown, PBS-treated, mouse #16


title: Terminal primary transplant, Tet2 knockdown, mouse #12

value: primary

value: Tet2 knockdown


title: THP-1 cells, vehicle treatment, replicate 2


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) late stage biological replicate 3

status: Public on Oct 21 2022

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

description:
Raw data associated with this sample contains only scRNA-seq data.
Processed data associated with this sample contains both scRNA-seq and scATAC-seq data.

data_processing: Data generated using the 10X Multiome platform were processed using 10X’s cellranger-arc toolkit in Linux per the manufacturer’s instructions. This included (1) an ATAC matrix computer step of barcode processing, read trimming, read alignment, duplicate marking, peak calling, and peak-barcode matrix generation using either the mm10 mouse or GRCh38 human reference genome; (2) a gene expression (GEX) Matrix Computer step of read trimming, genome alignment, transcriptome alignment, UMI correction, and UMI counting; and joint cell calling. Downstream secondary analysis for ATAC and GEX included dimensionality reduction, clustering, peak annotation, transcription factor analysis, differential expression analysis, differential accessibility analysis, and feature linkage as described above using the Seurat, Signac, and ArchR toolkits.

source_name: endogenous breast tumors

extract_protocol:
Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturer's protocol. Cells were counted and re-suspended for further processing.
Multiome was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines. Nuclei isolation was pursued as for scATAC-seq sequencing using 0.1x lysis buffer with 3-minute incubation.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: endogenous breast tumors

value: all cells (unsorted)

value: black 6


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) late stage biological replicate 2


title: R07B-5, vestimentum_WGBS

status: Public on Nov 06 2022

city: Montreal

first: Maeva

last: Perez

state: Qc

address: 1375 Avenue Thérèse-Lavoie-Roux

country: Canada

institute: Université de Montréal

description: bisulfitetotal_all_genome_C_report.txt.gz

data_processing:
Step1: Decontamination. Genomic ONT reads were mapped onto the mitochondrial (Accession: KJ872501) and symbiont (Accession: LDXT01) references with minimap2 (v2.17) and extracted with bbmap (v38.86) filterbyname.sh.
Step2: Nuclear reads were mapped onto the reference genome (Accession: NP49301) with minimap2
Step3: Methylation calling with Nanopolish (v0.13.2). The raw electric signatures (or squiggles) were fetched and aligned back onto their respective mapped reads. Then, the likelihoods of each CpG-containing 6-mer given a 5-base alphabet (with A, T, G, C and M for methylated cytosines) were  calculated and CpG call groups (i.e. sequences containing one or multiple CpG motifs within 10bp of each other) were considered methylated if their log-likelihood of being methylated was twice that of being unmethylated (LLR>2).
Step4: Per-CpG normalisation: We generated a bed file of all CpGs using seqkit (v0.15.0) locate function and mapped to it the respective methylation call coverages and frequencies with bedtools (v2.29.2) map function.
Assembly: JAODUO01
Supplementary files format and content: tab-delimited text file of methylation call coverage and frequency for all CpGs. The file includes contig_id, start position (the first base on the chromosome is 0), end position (non-inclusive), methylation call coverage (number of reads for which methylation could be assessed), methylation frequency (methylated reads / total reads assessed)
Supplementary files format and content: UCSC Genome Browser bigWig format file of genome-wide CpG methylation frequency : contig_id, start coordinate, stop coordinate, and methylation level (#methylated reads/ total reads called for methylation). Minimum methylation call coverage threshold=10X.

organism: Ridgeia piscesae

source_name: vestimentum

extract_protocol:
Phenol-chloroform followed by ethanol precipitation
A whole-genome shotgun library was prepared by Novogene (Beijing, China) for sequencing on the Oxford Technologies Nanopore (ONT) PromethION platform

value: vestimentum


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) early stage biological replicate 3


title: mouse breast (non-cancer) multiome (scRNA-seq + scATAC-seq) biological replicate 1


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) early stage biological replicate 1


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) early stage biological replicate 2


title: mouse breast (non-cancer) multiome (scRNA-seq + scATAC-seq) biological replicate 2


title: mouse breast (non-cancer) multiome (scRNA-seq + scATAC-seq) biological replicate 3


title: human breast cancer multiome (scRNA-seq + scATAC-seq) biological replicate 3

description:
Raw data associated with this sample contains both scRNA-seq and scATAC-seq data.
Processed data associated with this sample contains both scRNA-seq and scATAC-seq data.

source_name: breast tumor

value: breast tumor


title: human breast cancer multiome (scRNA-seq + scATAC-seq) biological replicate 2


title: human breast cancer multiome (scRNA-seq + scATAC-seq) biological replicate 1


title: Terminal secondary transplant, Tet2 knockdown, ASC-treated, mouse #30


title: murine splenic immune cells, WT STm infected, TNFa-neutralizing antibody [T2_antiTNF]

status: Public on Oct 20 2022

first: Yuan

last: Xue

address: 318 Campus Drive

description:
201221_10X_velocyto_all.h5ad
harmony.sam_T_C_treatment.200119.sam_full.210505.h5ad
ABCT_SAM_momac.220828_review.h5ad

data_processing:
Raw sequencing data were demultiplexed by SFGF to yield fastqs reads. Paired-end reads were mapped to Mus musculus genome reference GRCm38 using 10X cellranger (version 3.1.0) with parameters “--expect-cells=10000 --chemistry=auto”. Spliced and unspliced read counts were estimated by velocyto (v 0.17.17) in “run10x” mode. We performed downstream preprocessing and analyses on the UMI count matrices estimated by cellranger. To eliminate low-quality cells, we kept cells that had more than 500 detected genes and 1000 UMI read counts. We removed any stressed cells that had greater than 5% of total UMI counts that mapped to the mitochondrial genome. In total, we identified 22512 cells (WT + DsteE STm-infected mice) and 9892 cells (WT STm-infected mice treated with isotype control and anti-TNF antibodies) for downstream analysis. UMI counts were normalized for sequencing coverage such that each cell has a total number of counts equal to the median library size of all cells, yielding counts per median (CPM). The normalized CPM were added with a pseudocount of 1 and log2 transformed. Scanpy package (v 1.6.0) was used to perform data preprocessing and data transformation. RNA velocity was inferred using scVelo (v 0.2.2) with default parameters in “dynamical” mode.
The SAM algorithm (version 0.8.5) was run with default parameters. SAM outputs gene weights, principal component (PC) coordinates, a nearest-neighbor graph, and 2D UMAP projections used for visualization, on which the processed gene expression data can be also overlaid. We used the Leiden algorithm (version 0.8.4) to determine the number of clusters in the entire immune population and inferred the immune cell type based on the approach proposed by panglaoDB.
Assembly: GRCm38
processed data files format and content:
sam_full.210505.h5ad - Processed 10X chromium v3.1 scRNA-seq data of splenocyte isolate. Contains samples collected from mouse infected by WT STm and dSTeE STm. Shown in Figure 1A-C. Shown in Figure S2A-B.
sam_full_velocyto.210505.h5ad - Contains same set of cells in "sam_full.210505.h5ad". Dataset is pre-processed with velocyto to yield RNA-velocity prediction.
sam_myeloidSubset.210505.h5ad - Myeloid sub-population derived from "sam_full.210505.h5ad".
sam_monocyteSubset.210505.h5ad - Monocyte macrophage sub-population derived from "sam_myeloidSubset.210505.h5ad". Shown in Figure 1D-G, Figure 2A-D, Figure S3A-C.
sam_monocyte_velocyto.210505.h5ad - Monocyte macrophage sub-population, same set of cells as in "sam_monocyteSubset.210505.h5ad". Dataset is pre-processed with velocyto to yield RNA-velocity prediction. Shown in Figure 2G.
sam_macrophageSubset_AB.210919.h5ad - Macrophage sub-population derived from "sam_monocyteSubset.210505.h5ad". Shown in Figure 3A-H.
harmony.sam_T_C_treatment.200119.sam_full.210505.h5ad - Processed 10X chromium v3.1 scRNA-seq data of splenocyte isolate. Contains samples collected from mouse treated with isotype control antibody or anti-TNFa antibody and then infected by WT STm. Data was aligned to "sam_full.210505.h5ad" using python implentation of harmony method.
ABCT_SAM_momac.220828_review.h5ad - Derived from "sam_macrophageSubset_AB.210919.h5ad" and "harmony.sam_T_C_treatment.200119.sam_full.210505.h5ad". Contains samples collected from mouse infected by WT STm and dSTeE STm and from mouse treated with control antibody or anti-TNFa antibody. Both datasets have been subset to contain only the macrophage sub-population. "fig3_cell_type" and "fig3_leiden" have been updated to show cluster labels that are consistent with "sam_macrophageSubset_AB.210505.h5ad", which are the labels shown in Figure 6. "cell_type" and "leiden" reflect the original cluster labels generated by the analysis.
201221_10X_velocyto_all.h5ad - This h5ad includes raw count values and velocyto estimate for all samples, including cells isolated from 4 x WT STm infected mice ("A"), 4 x dSTeE STm infected mice ("B"), 2 x isotype control antibody treated and WT STm infected mice ("C"), and 2 x anti-TNFa antibody treated and WT STm infected mice ("T").

growth_protocol: Salmonella enterica serovar Typhimurium strain SL1344 was utilized in this study. SL1344 DsteE and SL1344 Tomato were generated as described previously. For all mouse infections, S. Typhimurium strains were maintained aerobically on LB agar supplemented with 200 μg/mL streptomycin, + 40 μg/mL kanamycin, and grown aerobically to stationary phase overnight at 37 °C with broth aeration. Bacterial cultures were spun down and washed with sterile phosphate-buffered saline (PBS) before suspension in PBS for infection.

extract_protocol:
All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS.  Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller.
Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3’ GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell.
10X Genomics 3' GEX v3.1 kit.

treatment_protocol: Mice were allocated to control and experimental groups randomly, sample sizes were chosen based on previous experience to obtain reproducible results and the investigators were not blinded. Mice were inoculated intraperitoneally (i.p.) with 1-2 x 103 CFU S. Typhimurium SL1344 WT or DsteE in 200 mL PBS. For TNF neutralization, infected mice were injected i.p. with either 500 μg anti-TNF monoclonal Ab, clone MP6-XT22 (Biolegend), or isotype control Ab in sterile PBS in 400 μL total volume before scRNA-sequencing or analysis 4 days later. Mice were euthanized at the indicated time points post-inoculation by CO2 asphyxiation followed by cervical dislocation as the secondary method of euthanasia. Organs were collected, weighted, and either homogenized in PBS for CFU enumeration, used to make single cell suspension for flow cytometric analysis, or prepared for microscopy examinations.

value: immune cells

value: WT STm infected + TNFa-neutralizing antibody


title: murine splenic immune cells, WT STm infected, TNFa-neutralizing antibody [T1_antiTNF]


title: murine splenic immune cells, dSTeE STm infected, no antibody [B4_dSTeE]

description:
201221_10X_velocyto_all.h5ad
sam_full_velocyto.210505.h5ad
sam_monocyte_velocyto.210505.h5ad
sam_monocyteSubset.210505.h5ad
harmony.sam_T_C_treatment.200119.sam_full.210505.h5ad
sam_full.210505.h5ad
sam_myeloidSubset.210505.h5ad
sam_macrophageSubset_AB.210919.h5ad
ABCT_SAM_momac.220828_review.h5ad

value: dSTeE STm infected


title: murine splenic immune cells, WT STm infected, isotype control antibody [C2_CtrlAb]

value: WT STm infected + isotype control antibody


title: Terminal secondary transplant, Tet2 knockdown, PBS-treated, mouse #17

value: secondary

value: spleen


title: murine splenic immune cells, dSTeE STm infected, no antibody [B2_dSTeE]


title: murine splenic immune cells, dSTeE STm infected, no antibody [B1_dSTeE]


title: murine splenic immune cells, WT STm infected, no antibody [A3_WT]

value: WT STm infected


title: mouse breast cancer multiome (scRNA-seq + scATAC-seq) late stage biological replicate 1


title: murine splenic immune cells, WT STm infected, no antibody [A4_WT]


title: murine splenic immune cells, WT STm infected, no antibody [A2_WT]


title: murine splenic immune cells, WT STm infected, no antibody [A1_WT]


title: HDF-B - untreated - rep 2

city: Freiburg

first: Eyleen

last: Corrales

address: Breisacherstr. 153

department: Medizinische Fakultät

country: Germany

institute: Institut für Medizinische Bioinformatik und Systemmedizin

data_processing:
Adapter trimming and quality filtering of reads was performed with Trimmomatic, with parameters HEADCROP:3 TRAILING:20 MINLEN:35
Reads were mapped to the Ensembl GRCh37 reference genome with the STAR aligner, with parameters --twopassMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5
Non-uniquely mapped reads were discarded.
Genes that failed to achieve a minimum of one count-per-million (CPM) in at least two of the samples were filtered out as unexpressed.
Assembly: GRCh37
Supplementary files format and content: raw counts

source_name: dermal fibroblasts

growth_protocol: The cell lines were maintained at 37°C in a humidified atmosphere of 5 % CO2 using RPMI-1640 medium supplemented with 10 % FCS, 1 % L-glutamine, and 1 % penicillin-streptomycin.

extract_protocol:
Cell pellets were collected by scrapping. Total RNA was isolated using the Universal RNA Purification Kit (Roboklon).
Libraries were prepared using standard Illumina protocols.

treatment_protocol: Pharmacological inhibition was performed with 2 µM of vemurafenib (PLX4032), or an analog volume of vehicle (0.2 % of DMSO) as control, during 4 h, 8 h, 18 h (for HDF), or 24 h (for MaMel).

value: human dermal fibroblasts

value: juvenile foreskin

tag: gender

value: male

value: BRAF wild-type

value: untreated


title: HDF-B - untreated - rep 1


title: HDF-A - untreated - rep 2


title: Mouse, DMSO, H3K27ac (Hi-CHIP)

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the mouse reference genome (mm10) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_allValidPairs (txt file output from HiC-Pro)
Supplementary files format and content: *.intra.loop_counts.bedpe (bedpe file output from hichipper)
Supplementary files format and content: *.anchors.bed (anchor used by hichipper)
Library strategy: HiChIP

source_name: T-ALL cell line

growth_protocol: 1x10E7 mouse T-ALL cells were washed in serum free medium and crosslinked for 10 minutes in 1% formaldehyde solution. Glycine (125 mM) was used to quench the crosslinking reaction.

extract_protocol:
DNA was then purified with DNA Clean and Concentrate 5 columns (D4013; Zymo), and PCR amplification was performed. DNA was purified and sequenced by BGISeq500, using a 50-bp paired-end library.
Paired-end HiChIP

treatment_protocol: Chromatin was incubated with 7.5 µg of H3K27ac antibody overnight at 4°C. The next day, 60 µL of protein G magnetic beads was used to isolate antibody-bound chromatin.

value: T-ALL cell line

value: DMSO

tag: chip antibody

value: H3K27ac Antibody (abcam; ab4729)


title: Mouse, DEX, H3K27ac (Hi-CHIP)

tag: cell line

value: Dexamethasone


title: HS360-Day20-rep1 [scATAC-seq]

status: Public on Oct 13 2022

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
Cell Ranger ATAC version 1.2.0 was used to preprocess scATAC-seq raw sequencing data into fastq files
Single cell accessibility counts for the cells were generated from reads using the ‘cellranger-atac count’ pipeline.
Down stream analysis was perfomed using R programming languages and the R package ArchR v.1.0.1
Genome_build: refdata-cellranger-atac-GRCh38-1.2.0
Supplementary_files_format_and_content: Output from cellranger ATAC: Per-barcode fragment counts & metrics, Barcoded and aligned fragment file, Filtered peak barcode matrix in hdf5 format

source_name: HS360, day 20, past stage III maturation

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol:
Cells were harvested using Accutase. Nuclei isolation was done according to the 10x Genomics protocol CG000169 (Rev D) using 2 minutes of incubation in lysis buffer diluted to 0.1x and 0.5x for Day 0 and Day 20 cells, respectively. Nuclei were counted and processed on the 10x Chromium controller (10x Genomics) using Next GEM Chip H Single Cell Kit (10x Genomics). The targeted nuclei recovery was 5,000 nuclei per sample.
Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10 x Genomics) and Chromium i7 Multiplex Kit N Set A (10x Genomics) were used to generate scATAC-seq libraries.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected.

tag: source cell line/type

value: Human embryonic stem cells HS360

value: Day 20

tag: tissue/cell type

value: maturated NPCs


title: murine splenic immune cells, WT STm infected, isotype control antibody [C1_CtrlAb]

value: immune cells


title: murine splenic immune cells, dSTeE STm infected, no antibody [B3_dSTeE]

value: dSTeE STm infected


title: Experiment 2, Xmoo1 line, 3dpi, replicate 1, for single-cell RNA-seq

status: Public on Oct 11 2022

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
all_timepoints.rds
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
Dropseq including second strand synthesis

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Assembly: Homo sapiens hg38
Assembly: HSV-1 GFP truncated corrected
Supplementary files format and content: fasta file
Supplementary files format and content: gtf file
Supplementary files format and content: Seurat R object

source_name: Brain organoid

growth_protocol: Cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013, doi: 10.1038/nature12517),

extract_protocol:
For single-cell RNA-sequencing, single cell suspensions were generated by enzymatic digestion of organoids, and then fixed using methanol (Alles et al. 2017, doi: 10.1186/s12915-017-0383-5)
Single-cell RNA-seq libraries were generated using an extended Dropseq protocol containing a second-strand synthesis step (Wyler et al. 2021, doi: 10.1016/j.isci.2021.102151)

treatment_protocol: Organoids were infected using Herpes simplex virus 1, strain 17 containing a GFP gene controlled by an MCMV promoter (Snijder et al. 2012, doi: 10.1038/msb.2012.9)

value: Brain organoid

tag: hsv-1 infection

value: yes

tag: sampling timepoint

tag: rna population

value: polyA+ RNA


title: Experiment 2, Xmoo1 line, 3dpi + ACV, replicate 2, for single-cell RNA-seq

description:
all_timepoints.rds
HSV1GFPtrunc_corr.gtf.gz
HSV1GFPtrunc_corr.gtf.gz
Dropseq including second strand synthesis

value: ACV


title: HS360-Day0-rep1 [scATAC-seq]

source_name: HS360, day 0, hESCs undifferentiated

value: Day 0

value: hESCs


title: Experiment 2, Xmoo1 line, 3dpi + ACV, replicate 1, for single-cell RNA-seq


title: SC cells-RAD21_rep3-ChIP-seq

status: Public on Oct 15 2022

city: Tianjin

first: Mulin Jun

last: Li

state: Tianjin

address: No.22, Qixiangtai Road, Hepin

department: Basic Medical Research Center

country: China

institute: Tianjin Medical University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.13 with "-q 5 -l 32 -k 2".
Unmapped reads, low quality mapped reads and PCR duplicates were discarded by picard.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: SC

extract_protocol:
For ChIP-seq, ChIP assays were performed as previously described (Li et al., 2017c) with modifications. Briefly, for each sample, ~1 × 107 SC cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 10 min at room temperature and quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice with ice-cold lysis buffer (20 mM Tris-HCl pH 7.5 [ThermoFisher, 15567027], 2 mM EDTA [ThermoFisher, 15575020], 1% Triton X-100 [Sigma-Aldrich, T8787], 0.1% SDS [ThermoFisher, 15525017], 0.1% Sodium Deoxycholate [Sigma-Aldrich, D6750], and 1× Protease Inhibitors [ThermoFisher, 78425]) for 10 min with slow rotations at 4 °C. The nuclear lysates were sonicated to obtain DNA fragments of 200~500 bp using a Biorupter system (Diagenode, B01060001) by high energy, with a working time of 30 s and a resting time of 30 s, 30 cycles, until the solutions turned clear.
After removing insoluble debris, the lysates were separately incubated with specific antibodies against Rabbit IgG (CST, 7074), ZBTB3 (Novus Biologicals, NBP1-82079), CTCF (Abcam, ab128873), RAD21 (Abcam, ab992), H3K4me1 (CST, 5326), H3K4me3 (CST, 9751), or H3K27ac (Abcam, ab4729), and then purified by protein A-agarose beads (Millipore, 16-157). The beads were washed 4 times by TE buffer (10 mM Tris-HCl pH 8.0 [ThermoFisher, 15568025], and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% Sodium Deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction. ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions, and then sequenced on a HiSeq X Ten platform (Illumina). For data analysis, the sequences with adaptor and low quality were trimmed for all 150-bp pair-end reads. The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (Li and Durbin, 2009). All the samples were separately processed, and the unique mapped reads were kept. The peaks were called by MACS2 (v2.1.1) (Zhang et al., 2008) using IgG as control. The results were analyzed and visualized in IGV (v2.8.6) (Thorvaldsdottir et al., 2013).

value: SC

value: Human peripheral blood monocyte-derived SC cells

value: Rabbit polyclonal to RAD21 (Abcam, ab992)


title: SC cells-ZBTB3_rep2-ChIP-seq

value: Rabbit polyclonal to ZBTB3 (Novus Biologicals, Cat#NBP1-82079)


title: SC cells-ZBTB3_rep3-ChIP-seq


title: SC cells-RAD21_rep2-ChIP-seq


title: Experiment 2, Xmoo1 line, 1dpi, replicate 2, for single-cell RNA-seq


title: Experiment 2, Xmoo1 line, 1dpi, replicate 1, for single-cell RNA-seq


title: Experiment 2, Xmoo1 line, ctrl, replicate 2, for single-cell RNA-seq

description:
CTRL.rds
all_timepoints.rds
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
Dropseq including second strand synthesis

value: no


title: Experiment 2, Xmoo1 line, 3dpi, replicate 2, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi + ACV, replicate 2, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 2, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi + ACV, replicate 1, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 1, for single-cell RNA-seq


title: HDF-A - untreated - rep 1

value: human dermal fibroblasts

value: juvenile foreskin

value: male

value: BRAF wild-type

value: untreated


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 1dpi, replicate 2, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 2, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), 1dpi, replicate 1, for single-cell RNA-seq


title: Experiment 2, iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 1, for single-cell RNA-seq


title: PEM22, timepoint 5, scTCR

status: Public on Oct 07 2022

city: New Haven

first: Tai

last: Michaels

state: CT

address: P.O. Box 208011, 300 Cedar Street

department: Immunobiology

institute: Yale School of Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger pipeline (10X Genomics)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood T cells

extract_protocol:
Peripheral blood mononuclear cells were isolated with density gradient centrifugation with Ficoll-Paque
scRNA-seq and scTCR-seq libraries were prepared using 10X Genomics Chromium Single-Cell 5’ and Chromium Single Cell V(D)J kits following the manufacturer’s instructions.

treatment_protocol: Patients were administered 200mg of pembrolizumab every 3 weeks for the duration of treatment (≤2 years)

tag: patient

tag: timepoint

value: F

tag: library type

value: scTCR

tag: mmrd group

value: epiR

value: Peripheral blood T cells


title: PEM23, timepoint 5, scTCR

value: mutR


title: PEM23, timepoint 1, scTCR


title: PEM21, timepoint 1, scTCR


title: PEM10, timepoint 1, scRNA

source_name: Peripheral blood mononuclear cells

value: scRNA

value: NR

value: Peripheral blood mononuclear cells


title: PEM9, timepoint 5, scRNA


title: PEM9, timepoint 3, scRNA


title: PEM20, timepoint 5, scTCR


title: Experiment 2, Xmoo1 line, ctrl, replicate 1, for single-cell RNA-seq

value: Brain organoid

tag: treatment

value: polyA+ RNA


title: PEM20, timepoint 1, scTCR


title: PEM9, timepoint 1, scRNA


title: PEM19, timepoint 5, scTCR


title: PEM19, timepoint 1, scTCR


title: PEM18, timepoint 5, scTCR


title: PEM8, timepoint 5, scRNA


title: RPTEC_3D_D67_rep2

city: Atlanta

first: Shuichi

last: Takayama

state: GA

address: 950 Atlantic Dr NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description: Day 67 organoid rep2

data_processing:
FASTQ files provided by Emory Integrated Genomics Core were first downloaded to Georgia Tech’s high-performance computing cluster called Partnership for an Advanced Computing Environment (PACE). Quality control was then performed using FastQC.
Upon passing quality requirements, the reads were aligned using STAR version 2.7.10a. A custom Python script was written to generate a gene count matrix.
Genes with less than 0.5 CPM in at least 3 samples were eliminated. Differential gene expression analysis was conducted using the EdgeR package in R. PCA analysis was performed to examine the samples for possible outliers prior to further analysis. The counts were normalized based on library size using the default TMM method from EdgeR. A comparison was run between the two groups through GLM, and LRT to identified statistically significant differential expressions. The cutoff for significance was set at under an alpha value of 0.05 for the adjusted p-value, and the log2 fold change of ±1.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: RPTEC organoid

growth_protocol: 2D RPTEC cells were grown in 6-well plates until 95% confluence was achieved. RPTEC organoids were grown in hanging drop culture. Organoids were seeded with 3000 cells, 2.5% fetal bovine serum (FBS), 110-130 ug/mL Matrigel, and 0.24% Methylcellulose. 2D cells and organoids were maintained in renal epithelial cell basal media (ATCC) supplemented with 0.5% fetal bovine serum (FBS), 10 nM triiodothyronine, 10 ng/mL epidermal growth factor (EGF), 100 ng/mL hydrocortisone hemisuccinate, 5 ug/mL insulin, 1.0 µM epinipherine, 5 µg/mL transferrin, 2.4 mM L-glutamine, and 1% penicillin-streptomycin (pen-strep).

extract_protocol:
Cells/organoids were lysed in RLT buffer, then processed for RNA extraction, or flash frozen, and stored in -80oC until future extraction. RNA was isolated using the Quick-RNA Microprep Kit (Zymo Research)
The cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio). The final sequencing library was made using the Nextera XT kit (Illumina). The library construction used Nextera XT chemistry which tagmented 200pg of DNA and added adapters in one step. The fragmented and tagged DNA was then PCR amplified for 12 cycles to incorporate dual-indexing sequencing adapters to generate the final library. A combination of both concentration and library size patterning was used as QC metrics to determine the success of the assay. The UV Qubit fluorometer quantitation step determined the concentration of the library. The Bio/Fragment Analyzer trace revealed the size distribution and concentration of the final sequencing library. Based on these three parameters we assigned library scores to each library. Libraries with a pass score were then used for sequencing in NextSeq 550.

treatment_protocol: The 2D cells and organoids did not undergo any treatment protocols.

value: renal proximal tubule epithelial cell organoids

tag: culture method

tag: time point

value: Day 67


title: PEM8, timepoint 3, scRNA

tag: cell type


title: RPTEC_3D_D67_rep3

description: Day 67 organoid rep3

tag: tissue


title: PEM8, timepoint 1, scRNA

tag: gender


title: RPTEC_3D_D67_rep1

description: Day 67 organoid rep1


title: PEM7, timepoint 5, scRNA


title: PEM18, timepoint 1, scTCR


title: PEM17, timepoint 1, scTCR


title: PEM7, timepoint 1, scRNA


title: PEM17, timepoint 5, scTCR


title: PEM6, timepoint 5, scRNA


title: PEM6, timepoint 3, scRNA


title: PEM16, timepoint 1, scTCR


title: PEM7, timepoint 3, scRNA


title: PEM16, timepoint 5, scTCR


title: PEM15, timepoint 5, scTCR


title: PEM14, timepoint 1, scTCR


title: PEM6, timepoint 1, scRNA


title: PEM13, timepoint 5, scTCR


title: PEM15, timepoint 1, scTCR


title: PEM14, timepoint 5, scTCR


title: PEM5, timepoint 3, scRNA


title: PEM5, timepoint 5, scRNA


title: PEM5, timepoint 1, scRNA


title: PEM3, timepoint 3, scRNA


title: PEM13, timepoint 1, scTCR


title: PEM3, timepoint 5, scRNA


title: PEM2, timepoint 5, scRNA


title: PEM2, timepoint 3, scRNA


title: PEM12, timepoint 5, scTCR


title: PEM12, timepoint 1, scTCR


title: PEM11, timepoint 3, scTCR


title: PEM11, timepoint 5, scTCR


title: PEM3, timepoint 1, scRNA


title: PEM1, timepoint 3, scRNA


title: PEM12, timepoint 3, scTCR


title: PEM11, timepoint 1, scTCR


title: PEM2, timepoint 1, scRNA


title: PEM1, timepoint 1, scRNA


title: PEM9, timepoint 1, scTCR


title: PEM9, timepoint 3, scTCR


title: PEM10, timepoint 5, scTCR


title: PEM9, timepoint 5, scTCR


title: PEM10, timepoint 1, scTCR


title: PEM10, timepoint 3, scTCR


title: PEM8, timepoint 5, scTCR


title: PEM8, timepoint 1, scTCR


title: PEM7, timepoint 3, scTCR


title: PEM8, timepoint 3, scTCR


title: PEM7, timepoint 1, scTCR


title: PEM7, timepoint 5, scTCR


title: PEM6, timepoint 5, scTCR


title: PEM6, timepoint 3, scTCR


title: PEM6, timepoint 1, scTCR


title: PEM5, timepoint 3, scTCR


title: PEM3, timepoint 5, scTCR


title: PEM3, timepoint 3, scTCR


title: PEM5, timepoint 1, scTCR


title: PEM3, timepoint 1, scTCR


title: PEM23, timepoint 1, scRNA


title: PEM1, timepoint 1, scTCR


title: PEM2, timepoint 3, scTCR


title: PEM23, timepoint 5, scRNA


title: PEM2, timepoint 5, scTCR


title: PEM20, timepoint 5, scRNA


title: PEM2, timepoint 1, scTCR


title: PEM1, timepoint 3, scTCR


title: PEM19, timepoint 1, scRNA


title: PEM22, timepoint 5, scRNA


title: PEM18, timepoint 1, scRNA


title: PEM20, timepoint 1, scRNA


title: PEM17, timepoint 5, scRNA


title: PEM18, timepoint 5, scRNA


title: PEM17, timepoint 1, scRNA


title: PEM5, timepoint 5, scTCR


title: PEM16, timepoint 5, scRNA


title: PEM15, timepoint 1, scRNA


title: PEM14, timepoint 5, scRNA


title: PEM14, timepoint 1, scRNA


title: PEM16, timepoint 1, scRNA


title: PEM21, timepoint 1, scRNA


title: PEM15, timepoint 5, scRNA


title: PEM12, timepoint 5, scRNA


title: PEM13, timepoint 5, scRNA


title: PEM19, timepoint 5, scRNA


title: PEM12, timepoint 1, scRNA


title: PEM11, timepoint 3, scRNA


title: PEM11, timepoint 1, scRNA


title: PEM10, timepoint 5, scRNA


title: PEM10, timepoint 3, scRNA


title: SCC08_1e-3_F_L1_tcb_rec

status: Public on Oct 06 2022

city: Boston

first: Arpiar

last: Saunders

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
SCC08
single-cell RNA profiling using 3' counting

data_processing:
Sequencing was performed on either an Illumina MiSeq, NextSeq 500 or NovaSeq6000
Sequencing Reads were aligned against a custom genome containing the GRCm38.81 mouse build; the rabies virus genome (SAD-B19-dG-EGFP) and AAV elements using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows)
Viral barcodes (VBCs) were amplified from sequenced EGFP mRNAs. Raw VBC sequences ascertained from viral genomes or scRNA-seq data (RM) were collapsed (RB) using custom algorithms. UMIs were used count/collapse VBC sequences within the context of a cell (XC)
Assembly: GRCm38.81 + custom genomes for SAD-B19-dG-EGFP and AAV elements
Supplementary files format and content: digital gene expression

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L1_tcb_rec]

extract_protocol:
Saunders and Macosko et al. 2018 Cell
10x Genomics 3' RNA (v2 or v3 chemistry) & this study (for viral barcode processing/sequencing)
10x Genomics 3' RNA & this study (for viral barcode processing/sequencing)

treatment_protocol: Cells were dissociated from in vitro synaptic cultures, FACS to enrich for those cells infected by rabies virus and scRNA-seq libraries were generated using 10x Genomic v2 or v3 platforms

tag: strain


title: CCEx11_B19_1_dense_S_tcb_rec

description:
CCEx11
single-cell RNA profiling using 3' counting

source_name: Cortex Culture + FACS for starter cells (mCherry+/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_S_tcb_rec]


title: SCC08_1e-3_F_L2_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L2_tcb_rec]


title: SCC08_1e-3_B_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_B_tcb_rec]


title: SCC08_1e-3_A_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_A_tcb_rec]


title: SCC08_1e-3_E_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well E. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_E_tcb_rec]


title: CCEx11_B19_1_dense_P_tcb_rec

source_name: Cortex Culture + FACS for presynaptic cells (mCherry-/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_P_tcb_rec]


title: SCC08_1e-2_B_L3_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L3_tcb_rec]


title: CCEx11_B19_1_dense_P

source_name: Cortex Culture + FACS for presynaptic cells (mCherry-/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_P]


title: PEM13, timepoint 1, scRNA


title: SCC08_1e-2_B_L2_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L2_tcb_rec]


title: CCEx11_B19_1_dense_S

source_name: Cortex Culture + FACS for starter cells (mCherry+/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_S]


title: CCEx16_B19_noRG_1in100x_L3

description:
CCEx16
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 3. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CCEx16_B19_noRG_1in100x_L3]


title: SCC08_1e-2_B_L1_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L1_tcb_rec]


title: SCC08_1e-2_A_L3_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L3_tcb_rec]


title: PEM12, timepoint 3, scRNA


title: CEx16_B19_noRG_1in100x_L2

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CEx16_B19_noRG_1in100x_L2]


title: SCC08_1e-2_A_L2_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L2_tcb_rec]


title: CCEx16_B19_noRG_1in100x_L1

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CCEx16_B19_noRG_1in100x_L1]


title: SCC08_1e-2_A_L1_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L1_tcb_rec]


title: PEM11, timepoint 5, scRNA

source_name: Peripheral blood mononuclear cells


title: SCC08_1e-3_D_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well D. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_D_tcb_rec]


title: CCEx16_B19_noRG_1in10x_L2

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx16_B19_noRG_1in10x_L2]


title: CCEx16_B19_noRG_1in10x_L1

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx16_B19_noRG_1in10x_L1]


title: SCC07_1e-3_F_tcb_rec

description:
SCC07
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 7, Well F. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_F_tcb_rec]


title: SCC08_1e-3_C_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 8, Well C. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_C_tcb_rec]


title: CCEx16_B19_noRG_1x_L1

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx16_B19_noRG_1x_L1]


title: SCC07_1e-3_D_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well D. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_D_tcb_rec]


title: SCC08_1e-3_F_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L2]


title: SCC07_1e-3_A_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_A_tcb_rec]


title: CCEx15_B19_noRG_1x_L1

description:
CCEx15
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 15, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx15_B19_noRG_1x_L1]


title: SCC07_1e-3_B_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_B_tcb_rec]


title: SCC07_1e-3_C_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_C_tcb_rec]


title: CCEx12_B19_noRG_1in10x_L1

description:
CCEx12
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 12, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx12_B19_noRG_1in10x_L1]


title: SCC08_1e-3_F_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L1]


title: SCC07_1e-2_C_L3_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L3_tcb_rec]


title: SCC07_1e-2_C_L2_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L2_tcb_rec]


title: SCC07_1e-2_C_L1_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L1_tcb_rec]


title: SCC08_1e-3_C

source_name: Striatal-Cortex Co-Culture Experiment 8, Well C. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_C]


title: SCC08_1e-3_B

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_B]


title: SCC08_1e-3_D

source_name: Striatal-Cortex Co-Culture Experiment 8, Well D. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_D]


title: SCC07_1e-2_B_L3_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L3_tcb_rec]


title: SCC08_1e-3_E

source_name: Striatal-Cortex Co-Culture Experiment 8, Well E. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_E]


title: SCC07_1e-3_E_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well E. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_E_tcb_rec]


title: SCC07_1e-2_B_L1_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L1_tcb_rec]


title: CCEx16_B19_noRG_1x_L2

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx16_B19_noRG_1x_L2]


title: SCC08_1e-2_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L2]


title: SCC08_1e-3_A

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_A]


title: SCC07_1e-2_B_L2_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L2_tcb_rec]


title: SCC08_1e-2_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L1]


title: SCC08_1e-2_B_L3

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L3]


title: SCC06_1e-4_B_tcb_rec

description:
SCC06
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_B_tcb_rec]


title: SCC06_1e-4_C_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 6, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_C_tcb_rec]


title: SCC08_1e-2_A_L3

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L3]


title: SCC08_1e-2_A_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L2]


title: SCC07_1e-2_C_L4_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L4_tcb_rec]


title: SCC06_1e-3_B_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_B_tcb_rec]


title: SCC06_1e-2_A_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC06_1e-2_A_tcb_rec]


title: SCC07_1e-3_E

source_name: Striatal-Cortex Co-Culture Experiment 7, Well E. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_E]


title: SCC06_1e-3_A_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_A_tcb_rec]


title: SCC07_1e-3_D

source_name: Striatal-Cortex Co-Culture Experiment 7, Well D. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_D]


title: SCC07_1e-2_B_L4_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L4_tcb_rec]


title: SCC07_1e-2_C_L3

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L3]


title: SCC07_1e-2_C_L2

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L2]


title: SCC07_1e-2_C_L1

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L1]


title: SCC07_1e-3_B

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_B]


title: SCC07_1e-2_C_L4

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L4]


title: SCC07_1e-2_B_L4

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L4]


title: SCC07_1e-2_B_L3

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L3]


title: SCC06_1e-4_C

source_name: Striatal-Cortex Co-Culture Experiment 6, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_C]


title: SCC07_1e-2_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L1]


title: SCC06_1e-4_B

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_B]


title: SCC06_1e-3_B

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_B]


title: SCC06_1e-2_A

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC06_1e-2_A]


title: SCC08_control_B_L5

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 5. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC06_1e-4_A_tcb_rec

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_A_tcb_rec]


title: SCC06_1e-3_A

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_A]


title: SCC07_1e-2_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L2]


title: SCC08_control_B_L3

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 3. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_1e-3_F

source_name: Striatal-Cortex Co-Culture Experiment 7, Well F. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_F]


title: SCC08_control_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_control_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 2. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_1e-2_A_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L1]


title: SCC08_control_A_L3

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 3. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_control_B_L4

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_control_A_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 2. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_control_A_L4

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_control_A_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_1e-3_C

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_C]


title: SCC07_1e-3_A

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_A]


title: SCC08_AAV_control_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 2. Control Cells (Infected by AAVs only)


title: SCC08_AAV_control_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 1. Control Cells (Infected by AAVs only)


title: SCC07_control_B_L5

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 5. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_control_B_L3

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 3. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC08_AAV_control_A_L2

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 2. Control Cells (Infected by AAVs only)


title: SCC08_AAV_control_A_L1

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 1. Control Cells (Infected by AAVs only)


title: SCC06_1e-4_A

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_A]


title: SCC07_control_B_L4

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_control_A_L4

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_control_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_control_A_L3

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 3. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_AAV_control_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 1. Control Cells (Infected by AAVs only)


title: SCC07_control_A_L1

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_control_A_L2

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 2. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC06_control_B_L4

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_AAV_control_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 2. Control Cells (Infected by AAVs only)


title: SCC06_control_B_L3

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B, Library 3, Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC07_AAV_control_A_L2

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 2. Control Cells (Infected by AAVs only)


title: SCC06_control_B_L1

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC )


title: SCC06_control_B_L2

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B, Library 2. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC06_control_A_L4

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A, Library 4. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC )


title: SCC06_control_A_L3

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A, Library 3. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: SCC06_control_A_L1

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A, Library 1. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: MT2247_OP50 rep1

status: Public on Oct 04 2022

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 2*150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads.
Differential expression analysis of two conditions/groups (four biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value.The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Assembly: Caenorhabditis elegans WBcel235
Supplementary files format and content: xlsx files include RPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: WT worms or egl-44(MT2247) mutants were maintained on nematode growth media (NGM) and fed with E. coli OP50 at 20°C

extract_protocol:
Bacteria were removed and worms were natural precipitation by M9 buffer , flash frozen on dry ice, and RNA was harvested using Trizol reagent.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The young adult wt worms were exposed to either P. aeruginosa PA14 or E. coli OP50 at 25°C. The young adult egl-44(MT2247) mutants maintained on NGM and fed with E. coli OP50 at 25°C. The animals were harvested after 24 hours.

tag: genotype

tag: developmental stage

value: Adult worms


title: MT2247_OP50 rep3


title: MT2247_OP50 rep2