title: Placenta, Female, Benzene, rep1 [B5L1]


title: SubjectID 5002002, LS skin, BL

status: Public on Jun 21 2023

type: SRA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

description: column "sam99" in counts.matrix

library_source: transcriptomic

data_processing:
Libraries prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Nova 6000 with pair-end 100 cycles. Our sequencing depth ranged 50M reads, Image analysis and bases calling was conducted in real-time by the lllumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: counts.matrix (tab delimited gene expression data of each sample)

molecule: total RNA

organism: Homo sapiens

source_name: Skin

extract_protocol: Total RNA was extracted from skin biopsies by the Qiagen miRNeasy Mini Kit (Valencia, CA, USA). DNA was removed with on-column DNase digestion by the Qiagen RNase-free DNase Set. The RNA yield and quality were determined with NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA),

tag: condition

value: psoriatic plaques

tag: individual

tag: treatment

value: Guselkumab

tag: timepoint

value: BL

tag: tissue

value: LS


title: Tag7A6_Tag01

city: Munich

first: Peter

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU Hospital, Institute for Stroke and Dementia Research

library_source: transcriptomic single cell

data_processing:
Fastq files were quality-controlled with FastQC and reads were then aligned using rnaSTAR to the GRCm38 (mm10) genome with addition of ERCC spike-in sequences. To obtain single cell gene expression matrices reads were counted with rnaSTAR using parameter “quantMode GeneCounts” and unstranded argument.
Assembly: mm10
Supplementary files format and content: Tab-separated counts per cell and cell metadata

organism: Mus musculus

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).

treatment_protocol: Lysophosphatidylcholine (LPC) injections were administered at the age of 16-18 weeks. A solution of 1% LPC (L4129, Sigma) in PBS was mixed with Monastral blue (274011, SigmaAldrich) at a concentration of 0.03% to aid with visualization of the lesion during tissue processing. Mice were anaesthetized with an intraperitoneal injection of MMF solution (0.5 mg medetomidin/kg (body weight), 5.0 mg midazolam/kg (body weight) and 0.05 mg fentanyl/kg (body weight)). Then, head fur was removed, the eyes were treated with bepanthene cream (1578847, Bayer) and a small incision in the skin was performed to expose the skull. The mouse was positioned into a stereotactic injection apparatus and a small hole was drilled at the following injection coordinates (from bregma): X, ± 1.0 mm; Y, −0.1 mm). A glass capillary containing the LPC–monastral blue solution was then lowered to Z: −1.30 mm from bregma, and 1 µL was injected at a rate of 100 nL/minute. Two minutes after the delivery of LPC, the capillary was slowly retracted. The mouse was then injected with 0.05 mg buprenorphin/kg (body weight), and the skin was sutured. Anesthesia was terminated by a subcutaneous injection of AFN solution, containing 2.5 mg/kg (body weight) atipamezol, 1.2 mg/kg (body weight) naloxon and 0.5 mg/kg (body weight) flumazenil.

tag: cell type

value: CD11b+ cells

tag: strain

tag: age


title: SubjectID 5002002, NL skin, BL

description: column "sam98" in counts.matrix

value: NL


title: Placenta, Male, Benzene, rep1 [B5L2]

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

data_processing:
Base calling was conducted using HiSeq Control Software (placenta) or NovaSeq Control Software (decidua), converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36 (Placenta) or BBDUK from BBMap package v.38.90 (Decidua)
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR aligner v.2.5.2b
Read count extraction was performed using Subread package v.1.5.2 (Placenta) or HTSeq-count v.2.0.1 (Decidua)
Read count normalization was performed using DESeq2 package (Placenta) or edgeR (Decidua)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Placenta

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 Placental RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols. RNA libraries for Decidua RNA-seq were prepared using Lexogen QuantSeq 3' mRNA-Seq FWD with UDI 12 nt (Unique Dual Indexing) kit according to manufacturer's protocols.

treatment_protocol: C57B/l6 mice were exposed to 50ppm benzene for 5 hours a day from E0.5 to E17.5. Tissues were collected on E17.5

value: Placenta

tag: Sex

value: Male

value: Benzene

tag: mother


title: Tag7A5_Tag01


title: BTC3_OligosPROM_BL_2

city: Edinburgh

first: Giada

last: Forte

address: Peter Guthrie Tait Road

country: United Kingdom

institute: The University of Edinburgh

library_source: genomic

data_processing:
For all samples data were analysed using the capC-MAP software (v1.3.1), which first checks reads for adaptor sequence, removing this using cutadapt (v1.11). An in silico restriction enzyme digestion was performed, breaking reads at the DpnII cutting sequence (GATC). The resulting read fragments were mapped to the mouse genome (mm9 build) using bowtie (v1.1.1). Aligned reads were filtered for PCR duplicates, and checked against the set of "target" restriction enzyme fragments for which oligonucleotide probes were designed. Only read pairs which identified a ligation event between a target and a (uniquely identifiable) "reporter" (i.e. non-target) fragment were retained. CaptureC interaction profiles were obtained for each target and sliding window binning and smoothing applied (using a window of 6kbp and a bin width of 3kbp). Replicate data sets were compared, checked for consistence, and then combined to produce the final interaction profiles.
Assembly: mm9
Supplementary files format and content: Files with name captured_bin_3000_6000_RPM_TARGET_TREATMENT.bdg are bedgraph files containing CaptureC interaction profiles from the specified target oligo; data have been binned using a bin width of 3000bp and a sliding window of 6000bp, and units are reads per million.
Supplementary files format and content: Files with name captured_rawpileup_TARGET_TREATMENT.bdg are bedgraph files containing CaptureC interaction profiles from the specified target oligo; data have been mapped to DpnII restricion enzyme fragments, with no binning or normalisation.
Supplementary files format and content: File capture_oligo_panel.xlsx is an excel spreadsheet containing details of the capture oligos used in these NG CaptureC experiments.
Supplementary files format and content: Files targetPositions_mm9_DpnIIfrag_poolCTCF.bed and targetPositions_mm9_DpnIIfrag_poolPROM.bed are BED format files containing the locations of the DpnII restriction enzyme fragments targetted by the two pools of oligos, using mm9 reference genome coordinates.
Library strategy: Next generation Capture-C

molecule: genomic DNA

growth_protocol: Pax6-HIGH cells (also known as β-TC3 cells) were isolated from a mouse insulinoma and were cultured in Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin-Streptomycin at 37°C in 5% CO2. No cell authentication was performed, and the sex of the cell line is not known

extract_protocol: Cells were further lysed by re-suspension in water, and then in 0.5% SDS at 62°C for 10 min Each replicate was split between three tubes, re-suspend in 800 μL 1x DpnII buffer (NEB) with 1.6% TritonX100, and digested with 3 sequential additions of 750 units DpnII enzyme at 37°C 1200rpm over 24 hours. Samples were heat inactivated at 65°C for 20 min, and 3 samples from each replicate combined into 7 ml with 1xT4 DNA Ligase Buffer (NEB), with 1% TritonX100, and 12,000 units of T4 DNA ligase at 16°C overnight. Samples were treated with Protinease K at 65°C overnight and RNase A/T1 (ThermoFisher) at 37°C for 1 hour, before a standard Phenol Chloroform/Chloroform extraction and ethanol precipitation was performed. Complete digestion and ligation was assessed by gel electrophoresis. Purified 3C DNA from each sample was sonicated to 200-400 bp with a Soniprep 150 probe sonicator at 4°C, and purified with a standard Ampure XP Bead protocol (Beckman Coulter) using a 1/1.5 DNA to bead ratio. Two Illumina sequencing libraries were prepared per capture pool replicate, with 6 μg of starting DNA in each, and generated using NebNext DNA Library Prep Kit (NEB), with samples indexed with unique barcodes using NebNext Multiplex Oligos for Illumina (NEB). Two separate capture pools were designed to the following Pax6 locus elements: CTCF/Cohesin binding sites, known and predicted enhancer clusters, and the multiple promoters of three genes in the locus Pax6, Elp4 and Rcn1. Capture oligos were designed to each end of the targeted DpnII fragments as described by in (Davies, 2016), and each synthesised as a separate 4 nM reaction, with a 5'-Biotin label on a 120 bp Ultramer (IDT). All capture oligos from each of the two capture pools were mixed at equimolar amounts and pooled to a final concentration of 13 pmol in a volume of 4.5 μL per sequence capture. Libraries where sized and quality controlled on a D1000 Tapestation tape (Agilent). NG Capture-C sequence capture was performed using SeqCap EZ HE-Oligo Kit A or B (dependent on the multiplex barcode) and SeqCap EZ Accessory Kit (Nimblegen) as described in (Davies, 2016), using each of the two capture pools, with 1.5-2 μg 3C library DNA per hybridisation reaction. Each hybridisation reaction was performed on a thermocycler at 47°C and incubated for between 66 and 72 hours. Each hybridisation reaction was then bound to streptavidin beads from SeqCap EZ Pure Capture Bead Kit and washed with SeqCap EZ Hybridization and Wash Kit (Nimblegen), following the manufacture's protocol. Hybridization reactions were split into two and libraries re-amplified using Post LM-PCR oligos (Nimblegen) and Q5 High-Fidelity DNA polymerase (NEB) directly from the beads, and then the DNA was purified using Ampure XP Bead 1/1.8 DNA to bead ratio. A second hybridisation reaction was performed as above on the re-amplifed 3C libraries with two reactions pooled together (~1 μg in each) and incubated for 22-24 hours. Washed and re-amplified double captured libraries where sized and quality controlled on a D1000 Tapestation tape (Agilent), and paired-end sequenced on an Illumina NovaSeq 6000.

treatment_protocol: To relieve topological stress, cells at 80-90% confluency were trypsinized to a single cell suspension; 1×10^6 cells where treated with 250 µM of bleomycin (Caymen Chemical) for 15 min in PBS (or in a mock treatment of PBS alone), centrifuged to remove bleomycin, and washed with PBS. Samples were processed via a standard protocol for genomic DNA preparation from a Pure link genomic DNA extraction kit (Invitrogen). Two replicates of cells where processed for each oligo pool, fixed with 2% formaldehyde, and lysed for 15 min with standard 3C lysis buffer before snap freezing at -80°C.

tag: cell line

value: insulinoma

value: bleomycin


title: Tag7A4_Tag01


title: Tag7A8_Tag01


title: 4T1-control tumor, alum treated, bio rep 4 [4T1-control_alum_4.2]

city: Cambridge

first: K Dane

last: Wittrup

state: MA

department: Biological Engineering, Chemical Engineering, Koch Institute of Integrative Cancer Research

institute: Massachusetts Institute of Technology

description:
75-nt kit
4T1-control_alum_4.2

data_processing:
Data preprocessing and count matrix construction were performed using the Smart-seq2 Multi-Sample v2.2.0 Pipeline (RRID:SCR_018920) on Terra
Assembly: GENCODE mouse (M21) reference genome
Supplementary files format and content: Metadata spreadsheet containing sample information
Supplementary files format and content: Count matrix containing counts each sample
Supplementary files format and content: Gene metadata spreadsheet

molecule: polyA RNA

source_name: tumor

extract_protocol:
Total RNA was extracted using RNAeasy plus mini kit
RNA-sequencing was performed by the BioMicro Center at MIT using a modified version of the SCRB-seq protocol (https://www.biorxiv.org/content/10.1101/003236v1)

treatment_protocol: Balb/c mice were inoculated with 1e6 CT26 or 5e5 4T1, 4T1-CAT, or 4T1-control cells subcutaneously on their flank on day 0. 4T1-CAT and 4T1-control cells are 4T1 cells engineered to express catalase (CAT) and GFP or GFP alone respectively in a doxycyline (DOX) inducible fashion. On day 4, mice with 4T1-CAT or 4T1-control tumors were started on a DOX-containing diet to induce gene expression. On day 6, mice were treated intratumorally with 20 ug CAT-ABP + 100 ug alum or alum along. Tumors were harvested on day 8  and processed for RNA extraction.

value: tumor

value: alum

tag: technical replicate


title: 4T1-control tumor, alum treated, bio rep 3 [4T1-control_alum_3.2]

description:
75-nt kit
4T1-control_alum_3.2


title: Tag7A2_Tag01


title: SubjectID 5007001, LS skin, BL

description: column "sam102" in counts.matrix


title: 4T1-control tumor, alum treated, bio rep 5 [4T1-control_alum_5.2]

description:
75-nt kit
4T1-control_alum_5.2


title: SubjectID 5002001, LS skin, BL

description: column "sam96" in counts.matrix

value: Secukinumab


title: SubjectID 5002001, LS skin, W16

description: column "sam97" in counts.matrix


title: BTC3_OligosCTCF_BL_2


title: Tag7A9_Tag01


title: Tag7A7_Tag01


title: BTC3_OligosCTCF_BL_1


title: Tag7A11_Tag01


title: 4T1-control tumor, alum treated, bio rep 1 [4T1-control_alum_1.2]

description:
75-nt kit
4T1-control_alum_1.2


title: SubjectID 5002001, NL skin, BL

description: column "sam95" in counts.matrix


title: SubjectID 4012002, LS skin, BL

description: column "sam93" in counts.matrix


title: BTC3_OligosPROM_WT_2

value: mock


title: Tag7A1_Tag01


title: SubjectID 5002002, LS skin, W16

description: column "sam100" in counts.matrix


title: 4T1-CAT tumor, alum treated, bio rep 4 [4T1-CAT_alum_4.2]

description:
75-nt kit
4T1-CAT_alum_4.2


title: SubjectID 4012002, NL skin, BL

description: column "sam92" in counts.matrix


title: BTC3_OligosPROM_BL_1


title: Tag6H9_Tag01


title: 4T1-CAT tumor, alum treated, bio rep 3 [4T1-CAT_alum_3.2]

description:
75-nt kit
4T1-CAT_alum_3.2


title: 4T1-control tumor, alum treated, bio rep 2 [4T1-control_alum_2.2]

description:
75-nt kit
4T1-control_alum_2.2


title: SubjectID 4012001, LS skin, W16

description: column "sam91" in counts.matrix


title: BTC3_OligosCTCF_WT_2


title: Tag6H8_Tag01


title: Tag7A10_Tag01


title: SubjectID 4012001, LS skin, BL

description: column "sam90" in counts.matrix


title: 4T1-CAT tumor, alum treated, bio rep 5 [4T1-CAT_alum_5.2]

description:
75-nt kit
4T1-CAT_alum_5.2


title: BTC3_OligosPROM_AA_2

growth_protocol: Pax6-HIGH cells (also known as β-TC3 cells) were isolated from a mouse insulinoma and were cultured in Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin-Streptomycin at 37°C in 5% CO2. No cell authentication was performed, and the sex of the cell line is not known.

treatment_protocol: To block transcription, cells were plated in a 6 cm dish and, once at ~80-90%, treated with alpha amanitin (Sigma A2263-1MG) for 7 hours at 100 µM or with mock treatment (PBS alone). Two replicates of cells where processed for each oligo pool, fixed with 2% formaldehyde, and lysed for 15 min with standard 3C lysis buffer before snap freezing at -80°C.

value: alpha amanitin


title: 4T1-CAT tumor, alum treated, bio rep 1 [4T1-CAT_alum_1.2]

description:
75-nt kit
4T1-CAT_alum_1.2


title: Tag6H6_Tag01


title: BTC3_OligosCTCF_WT_1


title: Tag6H7_Tag01


title: SubjectID 4012001, NL skin, BL

description: column "sam89" in counts.matrix


title: 4T1-CAT tumor, alum treated, bio rep 2 [4T1-CAT_alum_2.2]

description:
75-nt kit
4T1-CAT_alum_2.2


title: BTC3_OligosPROM_AA_1


title: BTC3_OligosPROM_WT_1


title: SubjectID 4011005, LS skin, BL

description: column "sam87" in counts.matrix


title: BTC3_OligosCTCF_AA_2


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 5 [4T1-CAT_CAT_5.2]

description:
75-nt kit
4T1-CAT_CAT_5.2

value: CAT alum


title: SubjectID 4011005, NL skin, BL

description: column "sam86" in counts.matrix

value: psoriatic plaques


title: BTC3_OligosCTCF_AA_1


title: Tag6H4_Tag01


title: SubjectID 4011004, LS skin, W16

description: column "sam85" in counts.matrix


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 3 [4T1-CAT_CAT_3.2]

description:
75-nt kit
4T1-CAT_CAT_3.2


title: BTC3_OligosPROM_WT_2


title: SubjectID 4011004, LS skin, BL

description: column "sam84" in counts.matrix


title: Tag6H3_Tag01


title: Tag6H2_Tag01


title: SubjectID 4011004, NL skin, BL

description: column "sam83" in counts.matrix


title: BTC3_OligosPROM_WT_1


title: BTC3_OligosCTCF_WT_2


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 1 [4T1-CAT_CAT_1.2]

description:
75-nt kit
4T1-CAT_CAT_1.2


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 2 [4T1-CAT_CAT_2.2]

description:
75-nt kit
4T1-CAT_CAT_2.2


title: SubjectID 4011003, LS skin, BL

description: column "sam81" in counts.matrix

value: Guselkumab


title: Tag6H10_Tag01


title: Tag6H5_Tag01


title: 4T1 WT tumor, alum treated, bio rep 5 [4T1WT_alum_5.2]

description:
75-nt kit
4T1WT_alum_5.2


title: SubjectID 4011003, NL skin, BL

description: column "sam80" in counts.matrix

value: BL


title: Tag6G9_Tag01


title: BTC3_OligosCTCF_WT_1


title: Tag6G7_Tag01


title: 4T1 WT tumor, alum treated, bio rep 3 [4T1WT_alum_3.2]

description:
75-nt kit
4T1WT_alum_3.2


title: SubjectID 4011002, LS skin, W16

description: column "sam79" in counts.matrix

value: LS


title: 4T1 WT tumor, alum treated, bio rep 2 [4T1WT_alum_2.2]

description:
75-nt kit
4T1WT_alum_2.2


title: SubjectID 4011003, LS skin, W16

description: column "sam82" in counts.matrix


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 4 [4T1-CAT_CAT_4.2]

description:
75-nt kit
4T1-CAT_CAT_4.2


title: SubjectID 4011002, LS skin, BL

description: column "sam78" in counts.matrix


title: 4T1 WT tumor, alum treated, bio rep 1 [4T1WT_alum_1.2]

description:
75-nt kit
4T1WT_alum_1.2


title: Tag6G3_Tag01

value: CD11b+ cells


title: SubjectID 4011002, NL skin, BL

description: column "sam77" in counts.matrix

value: NL


title: KO_ZHX1 _3

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
First, cutadapt (V1.18) was used to remove adaptor sequences, low-quality bases and reads shorter than 50 bases.
Next, the trimmed clean data were mapped to the mouse reference genome (GENCODE GRCm38, release M19) using HISAT2 (V2.1.0) with the parameters “--rna-strandness RF --dta-cufflinks --no-discordant”.
After that, gene expression levels were quantified as FPKM by stringtie (V1.3.4d) with the parameter “-e --rf”.
Differences in expression were determined using Deseq2 with default parameters
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include count for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: mESC-derived CP cell

tag: genotype


title: Ctrl_3

value: control


title: KO_ZHX1 _2


title: KO_ZHX1 _1


title: Ctrl_2


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 6 [4T1WT_CAT_6.2]

description:
75-nt kit
4T1WT_CAT_6.2


title: 4T1 WT tumor, alum treated, bio rep 4 [4T1WT_alum_4.2]

description:
75-nt kit
4T1WT_alum_4.2


title: Tag6G2_Tag01


title: Tag6G5_Tag01


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 5 [4T1WT_CAT_5.2]

description:
75-nt kit
4T1WT_CAT_5.2


title: SubjectID 4011001, LS skin, BL

description: column "sam75" in counts.matrix


title: Tag6G12_Tag01


title: KO,input,ChIP

data_processing:
PolII ChIP-seq data were first filtered using cutadapt (V1.18) to remove adaptor sequences, low-quality bases and reads shorter than 50 bases.
After quality control, the clean data were mapped to the mouse reference genome (GENCODE GRCm38, release M19) by bowtie2 (V2.3.5.1) with the following parameters: -N 1 -X 2000 -q -t -L 25 --no-mixed --no-discordant.
Next, the read counts were normalized to RPKM (reads per kilobase per million) in 100-bp bins for downstream analysis.  ChIP-seq clean reads (ZHX1,Hnrn) were mapped to the mouse reference genome (mm10) using the bwa (V 0.7.12-r1039) mem command with default parameters.
Then, the unmapped reads and PCR duplicates were removed, and the remaining read counts were normalized to RPKM on genome 100-bp bins for downstream analysis.
The PolII and histone modification ChIP-seq signals were visualized using the Integrative Genomics Viewer (IGV) browser (V2.4.10) and deepTools suite (V3.3.0).
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak (except for lnput sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris)
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: SubjectID 4011001, NL skin, BL

description: column "sam74" in counts.matrix


title: KO,Hnrn,ChIP


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 4 [4T1WT_CAT_4.2]

description:
75-nt kit
4T1WT_CAT_4.2


title: Tag6G11_Tag01


title: Ctrl,input,ChIP


title: Tag6G10_Tag01


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 2 [4T1WT_CAT_2.2]

description:
75-nt kit
4T1WT_CAT_2.2


title: Tag6G1_Tag01


title: SubjectID 4011001, LS skin, W16

description: column "sam76" in counts.matrix


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 3 [4T1WT_CAT_3.2]

description:
75-nt kit
4T1WT_CAT_3.2


title: Tag6G4_Tag01


title: SubjectID 4009003, NL skin, BL

description: column "sam71" in counts.matrix


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 1 [4T1WT_CAT_1.2]

description:
75-nt kit
4T1WT_CAT_1.2


title: Ctrl,Hnrn,ChIP


title: Tag6F9_Tag01


title: CT26 WT tumor, alum treated, bio rep 5 [CT26WT_alum_5.2]

description:
75-nt kit
CT26WT_alum_5.2


title: SubjectID 4009002, LS skin, W16

description: column "sam70" in counts.matrix


title: Tag6F8_Tag01


title: Ctrl_1


title: Ctrl,ZHX1,ChIP


title: SubjectID 4009002, LS skin, BL

description: column "sam69" in counts.matrix


title: bystander_both_pool_3

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

data_processing:
The CEL-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10) and gene counting.
Each condition had 3 replicates; 4 samples were excluded due to low coverage -
Data was normalized to a size factor, data was log2 transformed, minimum threshold of 3 was set and replicate samples were averaged (after exclusion of 4 samples as mention above)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample

growth_protocol: J744.1 (4x[10^5] cells/well) were plated 24h prior infection in non-tissue culture treated six–well plates supplemented with DMEM containing 10% FBS and 5% sodium pyruvate

extract_protocol:
Cells were harvested 5 hours post infection by a PBS wash followed by incubation of 15 min with ice-cold EDTA (5mM) and analyzed by flow cytometry (BD FACS Aria III) under continuous cooling at 4°C. Bystanders and infected cells were sorted into 1.7ml low–bind tubes containing 25μl of lysis buffer (0.1% Triton in RNase-free water), placed immediately on dry ice and stored in minus 80.
Bulk samples were processed for libraries generation according to the Cel-seq protocol (Hashimshony et al., 2016)
library strategy: CEL-seq

treatment_protocol: SPI-2 media-grown S.T.m cultures of WT or ∆ssaV strains were opsonized with 20% mouse serum for 30 min and washed with PBS. J744.1 were left uninfected or infected with WT, ∆ssaV and a 1:1 mixture of WT and ∆ssaV at MOIs of 1:1 and spun down for 5 min at 400g to synchronize internalization. After 30 min, cells were washed with media containing 50 μg/ml gentamicin to remove S.Tm that were not internalized. Fresh media containing 50 μg/ml gentamicin was then added back to the cells for the duration of infection

tag: infected with

value: WT+{delta}ssaV

tag: single/pool

value: pool

tag: infected/bystanders

value: bystander

tag: replicate


title: Tag6F5_Tag01


title: SubjectID 4009002, NL skin, BL

description: column "sam68" in counts.matrix

tag: condition


title: bystander_both_pool_2


title: Tag6F4_Tag01


title: SubjectID 4009001, LS skin, W16

description: column "sam67" in counts.matrix

tag: individual


title: CT26 WT tumor, alum treated, bio rep 4 [CT26WT_alum_4.2]

description:
75-nt kit
CT26WT_alum_4.2

value: tumor

tag: treatment

value: alum


title: Tag6F3_Tag01


title: SubjectID 4009003, LS skin, W16

description: column "sam73" in counts.matrix

tag: timepoint


title: CT26 WT tumor, alum treated, bio rep 2 [CT26WT_alum_2.2]

description:
75-nt kit
CT26WT_alum_2.2

tag: tissue


title: bystander_both_pool_1


title: SubjectID 4009001, LS skin, BL

description: column "sam66" in counts.matrix


title: CT26 WT tumor, alum treated, bio rep 1 [CT26WT_alum_1.2]

description:
75-nt kit
CT26WT_alum_1.2


title: Tag6F2_Tag01

tag: cell type


title: CT26 WT tumor, alum treated, bio rep 3 [CT26WT_alum_3.2]

description:
75-nt kit
CT26WT_alum_3.2


title: Tag6F12_Tag01

tag: strain


title: bystander_ssav_single_2

value: {delta}ssaV

value: single


title: SubjectID 4009001, NL skin, BL

description: column "sam65" in counts.matrix


title: bystander_ssav_single_3


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 6 [CT26WT_CAT_6.2]

description:
75-nt kit
CT26WT_CAT_6.2

value: CAT alum


title: SubjectID 4008004, LS skin, W16

description: column "sam64" in counts.matrix

value: psoriatic plaques

value: Secukinumab


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 5 [CT26WT_CAT_5.2]

description:
75-nt kit
CT26WT_CAT_5.2


title: bystander_ssav_single_1


title: Tag6F11_Tag01

tag: age


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 4 [CT26WT_CAT_4.2]

description:
75-nt kit
CT26WT_CAT_4.2


title: bystander_wt_single_3

value: WT


title: Tag6F10_Tag01


title: SubjectID 4008004, NL skin, BL

description: column "sam62" in counts.matrix

value: BL


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 3 [CT26WT_CAT_3.2]

description:
75-nt kit
CT26WT_CAT_3.2


title: bystander_wt_single_2


title: SubjectID 4008003, LS skin, W16

description: column "sam61" in counts.matrix

value: LS


title: Tag6F1_Tag01

value: CD11b+ cells


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 2 [CT26WT_CAT_2.2]

description:
75-nt kit
CT26WT_CAT_2.2


title: Tag6E9_Tag01


title: Tag6E8_Tag01


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 1 [CT26WT_CAT_1.2]

description:
75-nt kit
CT26WT_CAT_1.2


title: inf_ssav_pool_2

value: infected


title: Tag6E7_Tag01


title: SubjectID 4008003, NL skin, BL

description: column "sam59" in counts.matrix

value: NL


title: 4T1-control tumor, alum treated, bio rep 5 [4T1-control_alum_5.1]

description:
75-nt kit
4T1-control_alum_5.1


title: SubjectID 4008002, LS skin, W16

description: column "sam58" in counts.matrix

value: Guselkumab


title: Tag6E6_Tag01


title: 4T1-control tumor, alum treated, bio rep 6 [4T1-control_alum_6.1]

description:
75-nt kit
4T1-control_alum_6.1


title: inf_ssav_pool_1


title: inf_ssav_pool_3


title: 4T1-control tumor, alum treated, bio rep 4 [4T1-control_alum_4.1]

description:
75-nt kit
4T1-control_alum_4.1


title: inf_ssav_single_3


title: SubjectID 4008002, LS skin, BL

description: column "sam57" in counts.matrix


title: Tag6E5_Tag01


title: SubjectID 4008002, NL skin, BL

description: column "sam56" in counts.matrix


title: 4T1-control tumor, alum treated, bio rep 3 [4T1-control_alum_3.1]

description:
75-nt kit
4T1-control_alum_3.1


title: Tag6E4_Tag01


title: SubjectID 4008001, LS skin, BL

description: column "sam55" in counts.matrix


title: SubjectID 4008004, LS skin, BL

description: column "sam63" in counts.matrix


title: bystander_wt_single_1


title: SubjectID 4008003, LS skin, BL

description: column "sam60" in counts.matrix


title: 4T1-control tumor, alum treated, bio rep 2 [4T1-control_alum_2.1]

description:
75-nt kit
4T1-control_alum_2.1


title: Tag6E3_Tag01


title: 4T1-control tumor, alum treated, bio rep 1 [4T1-control_alum_1.1]

description:
75-nt kit
4T1-control_alum_1.1


title: SubjectID 4008001, NL skin, BL

description: column "sam54" in counts.matrix


title: inf_wt_pool_3


title: Tag6E2_Tag01


title: SubjectID 4007002, LS skin, W16

description: column "sam53" in counts.matrix


title: inf_wt_pool_2


title: 4T1-CAT tumor, alum treated, bio rep 5 [4T1-CAT_alum_5.1]

description:
75-nt kit
4T1-CAT_alum_5.1


title: 4T1-CAT tumor, alum treated, bio rep 4 [4T1-CAT_alum_4.1]

description:
75-nt kit
4T1-CAT_alum_4.1


title: SubjectID 4007002, LS skin, BL

description: column "sam52" in counts.matrix


title: Tag6E11_Tag01


title: Tag6E10_Tag01


title: 4T1-CAT tumor, alum treated, bio rep 3 [4T1-CAT_alum_3.1]

description:
75-nt kit
4T1-CAT_alum_3.1


title: Tag6E12_Tag01


title: 4T1-CAT tumor, alum treated, bio rep 2 [4T1-CAT_alum_2.1]

description:
75-nt kit
4T1-CAT_alum_2.1


title: inf_wt_single_3


title: inf_ssav_single_2


title: SubjectID 4007001, LS skin, W16

description: column "sam50" in counts.matrix


title: inf_wt_single_2


title: SubjectID 4007001, LS skin, BL

description: column "sam49" in counts.matrix


title: Tag6D8_Tag01


title: SubjectID 4007002, NL skin, BL

description: column "sam51" in counts.matrix


title: inf_ssav_single_1


title: 4T1-CAT tumor, alum treated, bio rep 1 [4T1-CAT_alum_1.1]

description:
75-nt kit
4T1-CAT_alum_1.1


title: inf_wt_single_1


title: SubjectID 4007001, NL skin, BL

description: column "sam48" in counts.matrix


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 5 [4T1-CAT_CAT_5.1]

description:
75-nt kit
4T1-CAT_CAT_5.1


title: Tag6D7_Tag01


title: SubjectID 4006005, LS skin, W16

description: column "sam47" in counts.matrix


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 4 [4T1-CAT_CAT_4.1]

description:
75-nt kit
4T1-CAT_CAT_4.1


title: lncMGC_KO, TGF-ß, rep2 [ChIP-seq]

city: Duarte

first: Zhuo

last: Chen

address: 1500 E. Durate Rd.

institute: City of Hope

data_processing:
Raw reads were aligned to mouse genome mm10 using BWA Version 0.7.5a-r405.
Bedgraph file for each sample were generated using the aligned paired reads and scaled to 50 million total paired-reads using R.
Assembly: mm10
Supplementary files format and content: bedGraph file containing scaled coverage for each sample

source_name: kidney mesangial cells

growth_protocol: Roswell Park Memorial Institute medium 1640 medium supplemented with 10% fetal bovine serum at 37C 5%CO2.

extract_protocol:
Qiagen's RNA extraction kit.
ChIP-seq libraries were prepared with a Kapa DNA HyperPrep Kit (Kapa, Cat KK 8700) according to the manufacturer's protocol. 5-10 ng of immunoprecipitated DNA was underwent end-repaired, A tailing and adaptor ligation. PCR was rune for 10 cycles of PCR was performed to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity DNA Kit and quantified with Qubit

treatment_protocol: 10 ng/ml  TGF-β (R&D Systems) for 24 hours

value: kidney mesangial cells

value: lncMGC knockout

tag: chip antibody

value: H3k27ac (Abcam, ab4729)


title: inf_wt_pool_1

value: pool


title: Tag6D6_Tag01


title: SubjectID 4006005, LS skin, BL

description: column "sam46" in counts.matrix


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 3 [4T1-CAT_CAT_3.1]

description:
75-nt kit
4T1-CAT_CAT_3.1

value: tumor


title: Tag6D3_Tag01


title: Tag6E1_Tag01


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 2 [4T1-CAT_CAT_2.1]

description:
75-nt kit
4T1-CAT_CAT_2.1


title: lncMGC_KO, SD, rep2 [ChIP-seq]


title: 4T1-CAT tumor, CAT-ABP + alum treated, bio rep 1 [4T1-CAT_CAT_1.1]

description:
75-nt kit
4T1-CAT_CAT_1.1


title: lncMGC_KO, SD, rep1 [ChIP-seq]


title: WT, TGF-ß, rep2 [ChIP-seq]


title: Tag6D12_Tag01


title: 4T1 WT tumor, alum treated, bio rep 5 [4T1WT_alum_5.1]

description:
75-nt kit
4T1WT_alum_5.1

value: alum


title: Tag6D11_Tag01


title: WT, TGF-ß, rep1 [ChIP-seq]


title: SubjectID 4006004, NL skin, BL

description: column "sam43" in counts.matrix


title: 4T1 WT tumor, alum treated, bio rep 4 [4T1WT_alum_4.1]

description:
75-nt kit
4T1WT_alum_4.1


title: Tag6D1_Tag01


title: SubjectID 4006002, LS skin, BL

description: column "sam41" in counts.matrix


title: WT, SD, rep2 [ChIP-seq]


title: 4T1 WT tumor, alum treated, bio rep 3 [4T1WT_alum_3.1]

description:
75-nt kit
4T1WT_alum_3.1


title: WT, SD, rep1 [ChIP-seq]


title: SubjectID 4006002, NL skin, BL

description: column "sam40" in counts.matrix


title: lncMGC_KO, TGF-ß, rep1 [ChIP-seq]


title: Tag6C9_Tag01


title: Tag6C7_Tag01


title: SubjectID 4006005, NL skin, BL

description: column "sam45" in counts.matrix


title: SubjectID 4006001, LS skin, W16

description: column "sam39" in counts.matrix


title: 4T1 WT tumor, alum treated, bio rep 1 [4T1WT_alum_1.1]

description:
75-nt kit
4T1WT_alum_1.1


title: astrocyte, ethanol, TRAP, 18_6

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

data_processing:
Fastq files were assembled from the base call files using bcl2f
The fastq files were trimmed with Trimmomatic
Sequence files were aligned with STAR aligner. The reference genome was Mus musculus GRCm38, downloaded with annotations from Ensembl.
SAM files were converted to BAM format using samtools
Assembly: GRCm38/mm10
Supplementary files format and content: tab separated file, read-counts per gene

source_name: cortex

growth_protocol: Primary mouse astrocyte cultures were created as previously described (Zhang et al., 2021; Goeke et al., 2022) using an equal number of transgenic male and female postnatal day (PD) 0 cortices. As the successfully isolation and culturing of astrocytes is time-sensitive, the presence of the Aldh1l1-EGFP/Rpl10a transgene was detected using the Nightsea DFP-1 fluorescent protein flashlight and glasses in the dissected brain with subsequent confirmation by qPCR for eGFP. In addition, sex determination was based on the ano-genital distance and confirmed by qPCR for Sry as previously described (). Astrocyte cultures were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fisher Scientific, 11885092), with10% Fetal Bovine Serum (Atlanta Biologicals, S12450), 1000 U/mL penicillin-streptomycin (pen-strep, Thermo Fisher Scientific, 15140122) in a humidified incubator at 37° C under at 5% CO2/95 % air atmosphere for 14 d to reach confluence. Astrocytes were subcultured onto 100 mm dishes at a density of 2.5x106 cells/dish.

extract_protocol:
TRAP was carried out on 6 control and 6 ethanol treated 100 mm dishes as previously described (Heiman et al., 2014) with modifications (Sanz et al., 2009). Briefly, homogenization buffer (HB) was used as described in Sanz et al, with heparin omitted. Lysed cells in HB were centrifuged at 10,000 g for 10 min. at 4° C to remove insoluble debris and the supernatant used for all subsequent steps. Input samples were saved from the supernatant equivalent to 5% of the initial HB volume. 50 mg of two GFP antibodies (bioreactor supernatant, clones 19C8 & 19F7 from the Memorial Sloan-Kettering Institute Monoclonal Antibody Facility) were added to each sample for 4h at 4° C under gentle end-over-end rotation. Samples were transferred to tubes containing 200 mL Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific; 88803; lot VF298063) and incubated overnight at 4° C with end-over-end rotation. The following day, beads were washed in high-salt buffer as described in Sanz et al, and RNA was isolated from the beads and input samples using TRIzol (Thermo Fisher Scientific, 15596018) and the Direct-zol RNA Microprep Kit (Zymo Research, R2062).
RNA libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit according to the manufacturer's protocol

treatment_protocol: After 6 d, serum containing medium was replaced with serum-free medium for 24 h followed by 50 mM ethanol treatment in serum-free medium or control serum-free medium. To limit the effect of ethanol evaporation on culture conditions, dishes were place in sealed chambers containing a 5% CO2/95 % air atmosphere with an open dish with either 50 mM ethanol or water as previously described (Goeke et al., 2018). After 24h in the 50mM ethanol or control medium, medium was removed and adherent astrocyte cells were processed for the TRAP procedure.

value: cortex

value: primary culture

value: astrocyte

value: ethanol

tag: fraction

value: TRAP (translating RNA)


title: Tag6D2_Tag01


title: SubjectID 4006004, LS skin, BL

description: column "sam44" in counts.matrix

value: psoriatic plaques

value: BL


title: Tag6C6_Tag01

value: CD11b+ cells


title: 4T1 WT tumor, alum treated, bio rep 2 [4T1WT_alum_2.1]

description:
75-nt kit
4T1WT_alum_2.1

tag: cell line


title: SubjectID 4006001, LS skin, BL

description: column "sam38" in counts.matrix

value: Secukinumab

value: LS


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 5 [4T1WT_CAT_5.1]

description:
75-nt kit
4T1WT_CAT_5.1

value: CAT alum

tag: technical replicate


title: SubjectID 4006002, LS skin, W16

description: column "sam42" in counts.matrix

value: Guselkumab


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 6 [4T1WT_CAT_6.1]

description:
75-nt kit
4T1WT_CAT_6.1


title: Tag6C4_Tag01


title: SubjectID 4005003, LS skin, W16

description: column "sam36" in counts.matrix


title: Tag6C3_Tag01


title: SubjectID 4006001, NL skin, BL

description: column "sam37" in counts.matrix

value: NL


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 4 [4T1WT_CAT_4.1]

description:
75-nt kit
4T1WT_CAT_4.1


title: astrocyte, ethanol, TRAP, 16_4

tag: genotype


title: Tag6C2_Tag01


title: astrocyte, ethanol, TRAP, 14_2


title: astrocyte, ethanol, TRAP, 17_5


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 3 [4T1WT_CAT_3.1]

description:
75-nt kit
4T1WT_CAT_3.1


title: SubjectID 4005003, LS skin, BL

description: column "sam35" in counts.matrix


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 2 [4T1WT_CAT_2.1]

description:
75-nt kit
4T1WT_CAT_2.1


title: SubjectID 4005003, NL skin, BL

description: column "sam34" in counts.matrix


title: Tag6C12_Tag01


title: astrocyte, ethanol, TRAP, 13_1


title: astrocyte, control, TRAP, 24_6

value: control


title: Tag6C10_Tag01


title: SubjectID 4005002, LS skin, W16

description: column "sam33" in counts.matrix


title: 4T1 WT tumor, CAT-ABP + alum treated, bio rep 1 [4T1WT_CAT_1.1]

description:
75-nt kit
4T1WT_CAT_1.1


title: SubjectID 4005002, LS skin, BL

description: column "sam32" in counts.matrix


title: CT26 WT tumor, alum treated, bio rep 5 [CT26WT_alum_5.1]

description:
75-nt kit
CT26WT_alum_5.1


title: Tag6B9_Tag01


title: astrocyte, control, TRAP, 22_4


title: astrocyte, control, TRAP, 23_5


title: CT26 WT tumor, alum treated, bio rep 4 [CT26WT_alum_4.1]

description:
75-nt kit
CT26WT_alum_4.1


title: SubjectID 4005002, NL skin, BL

description: column "sam31" in counts.matrix


title: SubjectID 4005001, LS skin, W16

description: column "sam30" in counts.matrix


title: astrocyte, ethanol, TRAP, 15_3


title: CT26 WT tumor, alum treated, bio rep 3 [CT26WT_alum_3.1]

description:
75-nt kit
CT26WT_alum_3.1


title: astrocyte, control, TRAP, 21_3


title: Tag6C1_Tag01


title: CT26 WT tumor, alum treated, bio rep 1 [CT26WT_alum_1.1]

description:
75-nt kit
CT26WT_alum_1.1


title: Tag6B6_Tag01


title: CT26 WT tumor, alum treated, bio rep 2 [CT26WT_alum_2.1]

description:
75-nt kit
CT26WT_alum_2.1


title: SubjectID 4005001, LS skin, BL

description: column "sam29" in counts.matrix


title: Tag6B7_Tag01


title: astrocyte, control, TRAP, 20_2


title: astrocyte, ethanol, input, 18_6

value: input


title: astrocyte, control, TRAP, 19_1


title: Tag6B8_Tag01


title: Tag6B4_Tag01


title: SubjectID 4003003, LS skin, W16

description: column "sam27" in counts.matrix


title: Tag6B2_Tag01


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 6 [CT26WT_CAT_6.1]

description:
75-nt kit
CT26WT_CAT_6.1

value: tumor


title: astrocyte, ethanol, input, 17_5


title: SubjectID 4003003, LS skin, BL

description: column "sam26" in counts.matrix


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 5 [CT26WT_CAT_5.1]

description:
75-nt kit
CT26WT_CAT_5.1


title: astrocyte, ethanol, input, 16_4


title: Tag6B12_Tag01


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 4 [CT26WT_CAT_4.1]

description:
75-nt kit
CT26WT_CAT_4.1


title: Tag6B11_Tag01


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 3 [CT26WT_CAT_3.1]

description:
75-nt kit
CT26WT_CAT_3.1


title: SubjectID 4003003, NL skin, BL

description: column "sam25" in counts.matrix


title: SubjectID 4003002, LS skin, W16

description: column "sam24" in counts.matrix


title: astrocyte, control, input, 24_6


title: Tag6B10_Tag01


title: astrocyte, control, input, 23_5


title: SubjectID 4003002, NL skin, BL

description: column "sam22" in counts.matrix


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 2 [CT26WT_CAT_2.1]

description:
75-nt kit
CT26WT_CAT_2.1


title: astrocyte, control, input, 22_4


title: SubjectID 4005001, NL skin, BL

description: column "sam28" in counts.matrix


title: SubjectID 4003001, LS skin, W16

description: column "sam21" in counts.matrix


title: wildtype control [G5.2]

city: Houston TX

first: Hua

last: Wang

state: TX

address: 6565 MD Anderson

institute: MD Anderson Cancer Center

data_processing:
Illumina RTA v2.4.11 software was used for basecalling and bcl2fastq v2.17.14 was used for generating fastq files.
Sequenced reads were trimmed for adaptor sequence and low quality, then mapped to mm10 whole genome using STAR v2.6.1a with parameters with default settings.
Reads mapped to annotated genes were counted and aggregated using HTSeq_count v0.6.1.
Differential gene expression was analyzed using R package DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene count values for each gene.

source_name: Pancreas

extract_protocol:
Pancreas were removed, RNA was harvested using Trizol reagent with pooled three mice pancreas, and  100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the KAPA Stranded mRNA-Seq Kit

value: Pancreas

value: 4 month

value: WT


title: Tag6A8_Tag01


title: CT26 WT tumor, CAT-ABP + alum treated, bio rep 1 [CT26WT_CAT_1.1]

description:
75-nt kit
CT26WT_CAT_1.1


title: SubjectID 4003001, LS skin, BL

description: column "sam20" in counts.matrix


title: SubjectID 4003001, NL skin, BL

description: column "sam19" in counts.matrix


title: wildtype control [G5.1]


title: Tag6A6_Tag01


title: DEN5d replicate 1, Multiome snATACseq

city: La jolla

first: Chiara

last: Nicoletti

state: CA

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Reads were then aligned to the mouse genome mm10/GRCm38 using CellRanger (v3.1.0). Doublets presence for each replicate was inferred with Scrublet (v0.2.1) (Wolock et al., 2019) within Python (v3.8). Filtered barcode and count matrices produced by CellRanger were used for downstream analyses in R (v3.6.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tibialis anterior and gastrocnemius

extract_protocol: Samples were processed as previously described in (Liu et al., 2015), and sorted by fluorescence activated cell sorting (FACS) to remove cell debris, doublets and dead cells. 100,000 live cells/sample were sorted and used for downstream processing with the 10X Genomics 3’ v3 kit for single-cell gene expression. 12,000 cells were used for library preparation, a little over the 10,000 suggested by the 10X protocol, in order to reach a higher capture rate. Libraries were constructed per manufacturer’s instructions and sequenced using Illumina’s NextSeq platform.

treatment_protocol: For each time-point post denervation (namely, 2, 5 and 15 days p.d., as well as the non-denervated control (abbreviated as Non-DEN in all figures and tables), 1 wild-type male C5Bl6/N mice at 3 months of age was used for each of the two biological replicates. After sciatic nerve transection, we collected two muscles downstream to the sciatic nerve, the tibialis anterior (TA) and gastrocnemius (GA) muscles.

value: Skeletal muscle-residents cells

value: Tibialis anterior and gastrocnemius

value: 12 weeks old


title: DEN5d replicate 1, snATACseq

description: 10x Genomics


title: Tag6A3_Tag01


title: HPK1 TG [G1.3]

value: 4  month


title: SubjectID 4002002, LS skin, W16

description: column "sam18" in counts.matrix

value: psoriatic plaques


title: HPK1 TG [G1.2]


title: SubjectID 4002002, LS skin, BL

description: column "sam17" in counts.matrix

value: BL


title: Non-DEN, replicate 2, scRNAseq

description: 10x Genomics


title: Tag6A12_Tag01

value: CD11b+ cells


title: SubjectID 4002002, NL skin, BL

description: column "sam16" in counts.matrix


title: Non-DEN, replicate 1, scRNAseq

description: 10x Genomics


title: Tag6B1_Tag01


title: SubjectID 4002001, LS skin, W16

description: column "sam15" in counts.matrix

value: Secukinumab

value: LS


title: M46/Ras/B group [G6.2]

value: 9 month


title: M46/ Ras/B group [G6.1]


title: Tag6A11_Tag01


title: Tag1H9_Tag01


title: SubjectID 4002001, LS skin, BL

description: column "sam14" in counts.matrix


title: Tag1H8_Tag01


title: DEN2d, replicate 2, scRNAseq

description: 10x Genomics


title: Non-DEN, replicate 1, snATACseq

description: 10x Genomics


title: Tag6A2_Tag01


title: SubjectID 3002004, LS skin, BL

description: column "sam11" in counts.matrix


title: Ras/B control group [G4.1]

value: 15 month

value: Ras/B


title: Tag1H7_Tag01


title: Tag1H6_Tag01


title: 5C+IFG2

city: St. Louis

last: Shen

address: 660 S Euclid Ave

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: primed ASC 5

growth_protocol: ASCs with or without pretreatment were cultured in alpha MEM containing in 2% EV-free FBS for 48 hours

extract_protocol:
ASC total RNA were isolated with TRIzol reagent and RNeasy Mini Spin Column. EV RNA was isolated with a SeraMir Exosome RNA Column Purification Kit
Five microliters of each RNA sample was used as input into a TruSeq Small RNA library Preparation kit (Illumina) per manufacturer’s instruction.

treatment_protocol: ASCs were pre-treated with interferon gamma for 24 hour in alpha MEM containing 2% EV-free FBS for 24 hours

value: NGL

value: adipose

value: adult

tag: molecule subtype

value: extracellular vesicle miRNA


title: DEN15d, replicate 2, scRNAseq

description: 10x Genomics


title: SubjectID 4002001, NL skin, BL

description: column "sam13" in counts.matrix

value: NL


title: 5C

source_name: naïve ASC 5


title: DEN2d, replicate 1, scRNAseq

description: 10x Genomics

value: Skeletal muscle-residents cells


title: Tag1H5_Tag01


title: DEN5d, replicate 2, scRNAseq

description: 10x Genomics

value: Tibialis anterior and gastrocnemius


title: Tag1H4_Tag01


title: SubjectID 3002003, LS skin, BL

description: column "sam8" in counts.matrix


title: 4C+IFG2

source_name: primed ASC 4


title: DEN15d, replicate 1, scRNAseq

description: 10x Genomics

value: 12 weeks old


title: 4C

source_name: naïve ASC 4


title: Tag1H3_Tag01


title: HPK1 TG [G1.1]

value: Pancreas

value: 4 month


title: Ras/B control group [G4.2]


title: 3C+IFG2

source_name: primed ASC 3


title: SubjectID 3002003, NL skin, BL

description: column "sam7" in counts.matrix

value: psoriatic plaques

value: BL


title: ESCs, Wild Type, RNAseq, rep1

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description:
Counts_all_samples.xlsx
ESCs_rep1

data_processing:
For RNAseq samples, Quality Control (QC) was performed at the FASTQ raw data file for each sample using the FASTQC software. FASTQ files were aligned to mm10 mouse genome using HISAT2 . Counts were defined using HTSeq htseq-count command with the “intersection non-empty” option. The count files were used as input for DESeq2.
Assembly: mm10
Supplementary files format and content: Regarding RNAseq analysis, the file Counts_all_samples.xlsx contains all the counts per gene for all the samples. The csv files contain the results from  DESeq2 analysis

source_name: Embryonic Stem Cells

growth_protocol: MEFs and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, Cat. No. D6429) supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS), Penicillin/Streptomycin (100 ug/ml; Thermo Fischer Scientific, Cat. No. 15140122), 2 mM GlutaMAX (Gibco, Cat. No. 35-050-061) and 0.1 mM Non-Essential Amino Acids 100X (Gibco, Cat. No. 11140050), at 37°C and 5% CO2. Bruce4 ESCs were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378)

extract_protocol:
Extraction was performed with NucleoSpin RNA extraction kit-MN (740955.50), according to the manufacturer’s protocols
Libraries for RNAseq were constructed with TruSEQ v2 kit according to manufacturer’s protocols

value: Embryonic Stem Cells


title: Tag1H2_Tag01

value: CD11b+ cells


title: MEFs, Wild Type, RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_rep2

source_name: Mouse Embryonic Fibroblasts

value: Mouse Embryonic Fibroblasts


title: SubjectID 3002004, NL skin, BL

description: column "sam10" in counts.matrix

value: Secukinumab


title: 3C

source_name: naïve ASC 3


title: SubjectID 3002002, LS skin, BL

description: column "sam5" in counts.matrix

value: Guselkumab

value: LS


title: Tag1H12_Tag01


title: MEFs, Wild Type, RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_rep1


title: SubjectID 3002003, LS skin, W16

description: column "sam9" in counts.matrix


title: SubjectID 3002002, LS skin, W16

description: column "sam6" in counts.matrix


title: 2C+IFG1

source_name: primed ASC 2

value: NGL

value: adipose


title: Tag1H1_Tag01


title: 1+2C

source_name: naïve ASC 1

value: adult

value: extracellular vesicle miRNA


title: SubjectID 3002001, LS skin, W16

description: column "sam3" in counts.matrix

source_name: Skin


title: Tag1G9_Tag01


title: SubjectID 3002002, NL skin, BL

description: column "sam4" in counts.matrix

value: NL


title: ESCs, Wild Type, RNAseq, rep2

description:
Counts_all_samples.xlsx
ESCs_rep2


title: inf_BMDMs 33 CEL-seq

data_processing:
The CEL-Seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for single cells demultiplexing, alignment to mm10 genome and UMI counts
Overall we sequences 3264 cells, with 136,173 mean reads per cells, 14,929 median UMI count per cell and 3835 median genes per cell
Cells with low coverage (less than 3000 UMIs) and high percent of mitochondrial genes (more than 10%) were removed from downstream analysis
Data was normalized to cell size factors. Size factors were calculated using ‘computeSumFactors’ function of R library ‘scran’ and data normalization was performed using the ‘normalize’ function of R library ‘scater’
Data was log2 transformed with pseudo-count of 1
Assembly: mm10
Supplementary files format and content: Text files include UMI counts table for each gene in each cell in the sample

source_name: BMDMs

growth_protocol: BMDMs (8x[10^5] cells/well) were plated in non-tissue culture treated six–well plates supplemented with DMEM containing 20% FBS and 25 ng/ml rmM-CSF

extract_protocol:
Cells were harvested 20 hours post infection by a PBS wash followed by incubation of 10 min with ice-cold EDTA (5mM) and analyzed by flow cytometry (BD FACS Aria III) under continuous cooling at 4°C. Infected single cells were sorted into twin.tec® PCR plate 384 LoBind® containing 1.2μl of Cel-seq Lysis buffer per each well, placed immediately on dry ice and stored in minus 80.
Single cells were processed for libraries generation according to the Cel-seq protocol (Hashimshony et al., 2016)

treatment_protocol: LB-grown cultures of WT or each of 24 MIB-tagged SPI-2 mutant strains were pooled into one tube and opsonized with 20% mouse serum for 30 min and washed with PBS. BMDMs were infected with the pool of SPI-2 mutants at MOIs of 2:1 and spun down for 5 min at 400g to synchronize internalization. After 30 min, cells were washed with media containing 50 μg/ml gentamicin to remove S.Tm that were not internalized. Fresh media containing 50 μg/ml gentamicin was then added back to the cells for the duration of infection

tag: time post infection

value: 20 hours post infection


title: SubjectID 3002001, NL skin, BL

description: column "sam1" in counts.matrix


title: 5E+IFG2

source_name: primed extracellular vesicles 1


title: Tag1G7_Tag01


title: Tag1G6_Tag01


title: Tag1G5_Tag01


title: 5E

source_name: naive extracellular vesicles 5


title: inf_BMDMs 31 CEL-seq


title: 5E+IFG1

source_name: primed extracellular vesicles 5


title: inf_BMDMs 30 CEL-seq


title: Tag1G4_Tag01


title: inf_BMDMs 29 CEL-seq


title: Salt stress in self rooted seedlings (96h) [ZS14]

city: Baoding

first: ding

last: yuan

address: lekainan

institute: Hebei Agricultural University

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/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 read 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 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 <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes wasimplemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologie (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways
Fusion gene is refers to the two genes of all or part of the sequences performfusion ,results of the chimeric gene, usually caused by reasons such as chromosome translocation and problem.We used star-fusion(1.2.0) software analysis and detection of fusion genes. Fusion gene list were filtered with star-fusion by standard filter method and other parameters(--annotate; -examine_coding_effect; --FusionInspector inspect; --denovo_reconstruct; --min_junction_reads 1 ; --min_sum_frags 2)
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.

organism: Solanum lycopersicum

source_name: Leaves

extract_protocol:
Trizol RNA
RNA libraries were prepared for sequencing using standard Illumina protocolsA total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: agent

value: Salt stress

value: Self rooted seedling

tag: time point


title: Tag1G3_Tag01


title: Salt stress in self rooted seedlings (48h) [ZS12]


title: inf_BMDMs 34 CEL-seq


title: inf_BMDMs 28 CEL-seq


title: Salt stress in self rooted seedlings (96h) [ZS13]


title: 4E+IFG2

source_name: primed extracellular vesicles 4


title: Salt stress in self rooted seedlings (48h) [ZS11]


title: inf_BMDMs 32 CEL-seq


title: inf_BMDMs 27 CEL-seq


title: Salt stress in self rooted seedlings (96h) [ZS15]


title: 3E

source_name: naive extracellular vesicles 3


title: Tag1G12_Tag01


title: Salt stress in self rooted seedlings (48h) [ZS10]


title: inf_BMDMs 26 CEL-seq


title: 2E+IFG1

source_name: primed extracellular vesicles 2


title: Tag1G11_Tag01


title: Salt stress in self rooted seedlings (24h) [ZS9]


title: 1+2E

source_name: naive extracellular vesicles 1


title: Tag1G10_Tag01


title: inf_BMDMs 25 CEL-seq


title: 4E

source_name: naive extracellular vesicles 4


title: inf_BMDMs 24 CEL-seq


title: Salt stress in self rooted seedlings (24h) [ZS8]


title: 2E

source_name: naive extracellular vesicles 2


title: Salt stress in self rooted seedlings (24h) [ZS7]


title: Tag1G1_Tag01


title: Tag1G2_Tag01


title: 3E+IFG1+2

source_name: primed extracellular vesicles 3


title: Tag1F9_Tag01


title: Decidua, Control, rep1 [B1_Decidua_S4_L001]

source_name: Decidua

value: Decidua

tag: Sex

value: Control

tag: mother


title: inf_BMDMs 23 CEL-seq


title: inf_BMDMs 22 CEL-seq


title: Salt stress in self rooted seedlings (12h) [ZS6]


title: Tag1F8_Tag01


title: Salt stress in self rooted seedlings (12h) [ZS4]


title: inf_BMDMs 21 CEL-seq


title: inf_BMDMs 20 CEL-seq


title: Decidua, Benzene, rep1 [B2_Decidua_S85_L002]

tag: treatment

value: Benzene


title: Tag1F5_Tag01


title: Tag1F7_Tag01


title: Decidua, Benzene, rep2 [B3_Decidua_S6_L001]


title: Salt stress in self rooted seedlings (12h) [ZS5]


title: inf_BMDMs 19 CEL-seq


title: Tag1F4_Tag01


title: Salt stress in self rooted seedlings (6h) [ZS3]


title: inf_BMDMs 18 CEL-seq


title: Salt stress in self rooted seedlings (6h) [ZS2]


title: Tag1F3_Tag01


title: C3H,DDC_Refed,week24

city: Guangzhou

first: Hui

last: Liu

address: Xinzao Road No.1

institute: Guangzhou Medical University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Liver tissue

extract_protocol:
After collecting 200mg of fresh liver tissue,remove the unwanted attachment tissue,properly drain the residual blood and other liquids, cut the tissue into 1~2mm3 size fragments in a Petri dish,and quickly transfer the fragments to the cryopreservation tube and snap freeze in liquid nitrogen for 5 min,after which it can be transferred to an ultra-low temperature freezer or liquid nitrogen for preservation. At 4 °C, nuclear suspension preparation is performed with sucrose density gradient centrifugation,using a 2 ml specification Dounce homogenizer for extraction,and all reagents need to be pre-cooled.
Library was performed according to the manufacter’s instructions (single cell 3’ protocol and 10x Genomics). This technology samples a pool of ~750000 barcodes to separately index each cell’s transcriptome. It does so by partitioning thousands of cells into nanoliter-scale Gel Bead-In[1]EMulsions (GEMs), where all generated cDNA share a common 10x Barcode. Upon dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly[1]adenylated mRNA. After incubation, the GEMs are broken and the pooled fractions are recovered. Then, Full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction. Finally, R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, Atailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Liver tissue

value: WT

value: refed DDC


title: Decidua, Control, rep2 [Th158_Decidua_S2_L001]


title: C3H,DDC_Withdrawn,week23

value: withdrawn from DDC


title: Salt stress in self rooted seedlings (6h) [ZS1]


title: Tag1F2_Tag01

value: CD11b+ cells


title: Self rooted seedling control (0h) [ZC3]

value: control


title: C3H,DDC_Fed,week19

value: fed the control diet with 0.1% DDC


title: inf_BMDMs 16 CEL-seq


title: C3H,Control,week19

value: fed the control diet


title: Tag1F12_Tag01


title: Self rooted seedling control (0h) [ZC2]


title: inf_BMDMs 15 CEL-seq


title: Tag1F10_Tag01


title: Self rooted seedling control (0h) [ZC1]


title: inf_BMDMs 14 CEL-seq


title: Salt stress treatment of grafted seedlings (96h) [PS15]

value: Grafted seedling


title: sifA_inf_3

data_processing:
The CEL-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10) and gene counting.
Each condition had 4 replicates; one replicate of naïve uninfected cells was excluded due to low coverage (~2M reads, uninfected_2.txt)
The package DESeq2 (Love et al., 2014) was used to normalized the data and identify differentially expressed genes between naïve, WT and ∆sifA infected cells.
Lowly expressed genes (mean expression across all conditions < 3 in log2 scale) were excluded from the analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample

extract_protocol:
Cells were harvested 20 hours post infection by a PBS wash followed by incubation of 10 min with ice-cold EDTA (5mM) and analyzed by flow cytometry (BD FACS Aria III) under continuous cooling at 4°C. Infected cells were sorted into 1.7ml low–bind tubes containing 25μl of lysis buffer (0.1% Triton in RNase-free water), placed immediately on dry ice and stored in minus 80.
Single cells were processed for libraries generation according to the Cel-seq protocol (Hashimshony et al., 2016)

treatment_protocol: SPI-2 media-grown S.T.m cultures of WT or ∆sifA strains were opsonized with 20% mouse serum for 30 min and washed with PBS. BMDMs were left uninfected or infected with WT or ∆sifA at MOIs of 2:1 and spun down for 5 min at 400g to synchronize internalization. After 30 min, cells were washed with media containing 50 μg/ml gentamicin to remove S.Tm that were not internalized. Fresh media containing 50 μg/ml gentamicin was then added back to the cells for the duration of infection

tag: infected with

value: ∆sifA


title: Tag1E9_Tag01

data_processing:
Fastq files were quality-controlled with FastQC and reads were then aligned using rnaSTAR to the GRCm38 (mm10) genome with addition of ERCC spike-in sequences. To obtain single cell gene expression matrices reads were counted with rnaSTAR using parameter “quantMode GeneCounts” and unstranded argument.
Assembly: mm10
Supplementary files format and content: Tab-separated counts per cell and cell metadata

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).

tag: tissue


title: Tag1F1_Tag01

tag: cell type


title: inf_BMDMs 13 CEL-seq


title: Salt stress treatment of grafted seedlings (96h) [PS14]


title: sifA_inf_4


title: sifA_inf_2


title: Salt stress treatment of grafted seedlings (96h) [PS13]


title: inf_BMDMs 17 CEL-seq


title: sifA_inf_1


title: Tag1E7_Tag01

tag: strain


title: inf_BMDMs 12 CEL-seq


title: inf_BMDMs 11 CEL-seq


title: WT_inf_4


title: Tag1E5_Tag01

tag: age


title: Salt stress treatment of grafted seedlings (48h) [PS12]


title: inf_BMDMs 10 CEL-seq


title: Tag1E4_Tag01


title: WT_inf_3


title: inf_BMDMs 9 CEL-seq


title: Salt stress treatment of grafted seedlings (48h) [PS11]


title: Tag1E3_Tag01


title: WT_inf_2


title: Salt stress treatment of grafted seedlings (48h) [PS10]


title: WT_inf_1


title: Salt stress treatment of grafted seedlings (24h) [PS9]


title: inf_BMDMs 7 CEL-seq


title: inf_BMDMs 6 CEL-seq


title: Salt stress treatment of grafted seedlings (24h) [PS8]


title: Tag1E12_Tag01


title: Salt stress treatment of grafted seedlings (24h) [PS7]


title: Tag1E11_Tag01


title: inf_BMDMs 4 CEL-seq


title: uninfected_1

value: uninfected


title: Tag1E10_Tag01


title: Salt stress treatment of grafted seedlings (12h) [PS6]


title: Tag1D9_Tag01


title: inf_BMDMs 5 CEL-seq

value: 20 hours post infection


title: uninfected_2


title: Salt stress treatment of grafted seedlings (12h) [PS5]

value: Salt stress


title: brain single cells, sham_ctrl_5

city: Beijing

first: Pan

last: Cui

address: No. 45 Changchun St, Xicheng District, Beijing, China 100053

department: Department of Neurology

institute: Xuanwu Hospital, Capital Medical University

data_processing:
Base-calling was performed using bcl2fastq software
Data were filtered using the fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it; if the reads contain a joint sequence, the joint sequence is cut off first; a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window; remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed; the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed; if the truncated read length is less than 50 bp, the entire read is removed; remove unmatched reads.
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
Reads were aligned to Mouse genome (GRCm38) using Hisat2/Tophat software with default parameters.
Using String Tie for readcount and FPKM calculation. Removed the genes or transcripts less than 100bp and genes with 0 expression in all samples.
The annotation of genes were perfomed based on the information obtained from the database of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Differential expression analyses were performed using the limma package.
Genome_build: GRCm38
Supplementary_files_format_and_content: genes.rawcount.anno.xlsx

source_name: sham Vdrf/f mice

extract_protocol:
Total RNA was extracted from microglia isolated from the ischemic brains of  Vdr-cKO and Vdrf/f mice using TRIzol reagent. Total RNA from each sample of sufficient quality, defined as RNA integrity number (RIN) > 7.0, was included for subsequent analysis.
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instruction

treatment_protocol: Three days after MCAO or sham procedure, primary microglia were isolated from Vdr-cKO mice and Vdrf/f littermate controls.

value: Brain

value: Microglia

value: 10-12 weeks

value: Vdrf/f

value: Sham


title: Tag1D8_Tag01


title: inf_BMDMs 3 CEL-seq


title: Salt stress treatment of grafted seedlings (12h) [PS4]


title: inf_BMDMs 8 CEL-seq


title: inf_BMDMs 2 CEL-seq


title: brain single cells, sham_ctrl_4


title: Tag1E2_Tag01


title: Tag1D7_Tag01


title: Salt stress treatment of grafted seedlings (6h) [PS3]


title: inf_BMDMs 1 CEL-seq


title: brain single cells, sham_ctrl_3


title: uninfected_3


title: uninfected_4


title: Salt stress treatment of grafted seedlings (6h) [PS2]


title: brain single cells, sham_ctrl_2


title: Salt stress treatment of grafted seedlings (6h) [PS1]


title: Tag1D6_Tag01


title: Tag1D5_Tag01


title: HT29

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Assembly: Cow genome assembly: ARS-UCD1.2
Supplementary files format and content: Tab-delimited text files including ensembl gene id and number of mapped reads.

organism: Bos taurus

source_name: adrenal gland

extract_protocol:
Total RNA was extracted from approximately 5 g of adrenal gland tissue using the TRIzol® (Invitrogen Corp, Carlsbad, CA.) following the manufacturer’s instructions.
Library preparation and subsequent RNA sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).

value: adrenal gland

value: in utero heat stressed

tag: time

value: weaning


title: DEN5d, replicate 1, scRNAseq

description: 10x Genomics

source_name: Tibialis anterior and gastrocnemius

value: Skeletal muscle-residents cells

value: Tibialis anterior and gastrocnemius

value: 12 weeks old


title: HT28


title: Grafted seedling control (0h) [PC3]

value: control


title: brain single cells, sham_ctrl_1


title: brain single cells, sham_cKO_3

source_name: sham Vdr-cKO mice

value: Vdr-cKO


title: Grafted seedling control (0h) [PC2]

value: Grafted seedling


title: HT31


title: HT25


title: brain single cells, sham_cKO_2


title: Tag1D12_Tag01

value: CD11b+ cells


title: Tag1D2_Tag01


title: Tag1D3_Tag01


title: Grafted seedling control (0h) [PC1]


title: brain single cells, postischemic_ctrl_4

source_name: postischemic Vdrf/f mice

value: MCAO


title: HT18


title: HT23


title: brain single cells, sham_cKO_1


title: brain single cells, postischemic_ctrl_3


title: HT8

value: birth


title: Tag1D11_Tag01


title: Tag1D10_Tag01


title: HT7


title: H1 CpGFI NeoR pool-TP53

type: genomic

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description:
tp53_pool
Processed data file: 205437180026_205437180004.igv
850 beadchip

hyb_protocol: The bisulfite converted DNAs were denatured by the 0.1N NaOH and amplified for 20 – 24 hours in the 37C hybridization chamber to produce a sufficient amount of  the DNA sample. The amplified DNAs were enzymatically fragmented on the 37C heat block for 1 hour and were precipitated for 30 min at 4C. For the hybridizing the DNAs onto Illumina beadchips, the precipitated DNAs were resuspended by RA1 solution according to the manufacturer protocol and the suspended DNAs with an appropriate volume were loaded onto the Inf Methyl EPIC 8 sample beadchip (San Diego, CA). The hybridication was performed for over the 16 hours within 24 hours.

scan_protocol: The image acquisition was carried out using the Illumina iScan System (San Diego, CA).

data_processing:
Raw data were processed and normalized by "SWAN" method using Bioconductor package "lumi".
The *igv processed data files represent SWAN-normalized Average Beta values.

label: Cy5 and Cy3

source_name: H1 hESCs with CpG free ssI at promoter CpG island of TP53, neoR pool

label_protocol: We followed the standard Infinium HD Methylation protocol guide and all reagents, which were required in the procedure, were purchased from the Illumina (San Diego, CA).

extract_protocol:
genomic DNA was extracted and purified from cells using Qiagen DNeasy Kit according to standard instructions
[bisulfite conversion protocol] The non-methylated cytosine residues of the purified genomic DNA sample were converted into uracil using EZ DNA Methylation Kit from Zymo Research (Irvine, CA).

value: pluripotent stem cell line

tag: integration of cpg free insert

value: Y

tag: dna methylation at target cgi


title: Tag1D4_Tag01

last: Androvic

institute: LMU Hospital, Institute for Stroke and Dementia Research


title: Tag1D1_Tag01


title: HT5


title: H1 CpGFITP53C2

description:
tp53_clone#9
Processed data file: 205437180026_205437180004.igv
850 beadchip

source_name: H1 hESCs with CpG free ssI at promoter CpG island of TP53, clone2

tag: cell line


title: Tag1C7_Tag01


title: BXSO115 CpGF-ssI-NeoR pool

description:
S15-MLH1-P4
Processed data file: 205437180001.igv
850 beadchip

source_name: iPSC neoR pool with CPG free insert at MLH1

value: iPSC

value: induced pluripotent stem cell


title: HT2


title: brain single cells, postischemic_ctrl_1

value: Brain

value: Microglia

value: 10-12 weeks

tag: genotype

value: Vdrf/f


title: HT4

value: adrenal gland

value: in utero heat stressed


title: brain single cells, postischemic_cKO_4

source_name: postischemic Vdr-cKO mice


title: brain single cells, postischemic_cKO_3


title: H1 CpGFITP53C1

description:
tp53_clone#4
Processed data file: 205437180026_205437180004.igv
850 beadchip

source_name: H1 hESCs with CpG free ssI at promoter CpG island of TP53, clone1


title: brain single cells, postischemic_cKO_2


title: HT1


title: CL22

value: in utero cooled

value: weaning


title: BXSO115 CpGF-ssI clone 2

description:
S15-MLH1-1-5
Processed data file: 205437180001.igv
850 beadchip

source_name: iPSC with CPG free insert at MLH1 clone 2


title: brain single cells, postischemic_cKO_1

value: Vdr-cKO


title: Tag1C4_Tag01


title: brain single cells, postischemic_ctrl_2


title: Tag1C5_Tag01


title: BXSO115 CpGF-ssI clone 1

description:
S15-MLH1-1-1
Processed data file: 205437180001.igv
850 beadchip

source_name: iPSC with CPG free insert at MLH1 clone 1


title: H1 CpGFINeoR pool-OCProCGI

description:
onecut1-CG3_pool
Processed data file: 205437180026_205437180004.igv
850 beadchip

source_name: H1 hESCs with CpG free ssI at intron CpG island of onecut1, neoR pool

value: N


title: BXSO115 control

description:
SXO115
Processed data file: 205437180001.igv
850 beadchip

source_name: iPSC control


title: CL20


title: Hap1-CpGF-ssI-NeoR pool

description:
HAP1-MLH1
Processed data file: 204365950122.igv
850 beadchip

source_name: Hap1 neoR pool with CpG free ssI at MLH1

value: chronic myelogenous leukemia cell line


title: H1 CpGFI NeoR pool OCintCGI

description:
onecut1-CG1_pool
Processed data file: 205437180026_205437180004.igv
850 beadchip

source_name: H1 hESCs with CpG free ssI at promoter CpG island of onecut1, neoR pool


title: Tag1C2_Tag01

value: CD11b+ cells


title: VarsSeqDNA

city: PALO ALTO

first: Rhiju

last: Das

address: 279 Campus Dr, B419 Beckman Center

institute: Stanford University

data_processing:
UMI-tools was used to extract randomized barcode sequences by identifying sequences directly downstream of primer binding sites, and paired-end reads were error-corrected using bbmerge.
Paired-end reads were aligned to intron reference sequences using bwa with default settings. Alignments were sorted using fgbio's SortBam and mate-pairs were annotated with fgbio's SetMateInformation.
Reads with the same barcode were grouped using fgbio's GroupReadsByUmi. Then, consensus reads were called using fgbio's CallMolecularConsensusReads with mostly default settings except for the flags -m 20 -M 5.
Consensus reads were quality filtered using fgbio's FilterConsensusReads with the flags -M 5 -q 20 -N 20 -E 0.01. With samtools, the resulting alignment file was sorted and paired-end consensus reads were retrieved. Paired-end reads were then merged with bbmerge using default settings. We kept only the consensus reads with highest coverage (primary consensus sequence) for each barcode, and we required that at most 5% of reads map to secondary consensus sequences. From the resulting consensus sequences, we obtained barcode mappings for designed variants for each of our 7 sub-libraries.
Assembly: S. cerevisiae intron reference sequences were obtained from Talkish, et al. 2019 (doi: 10.1371/journal.pgen.1008249).Coding ORF annotations were obtained from the Saccharomyces Genome Database for the S288C reference genome. Pre-mRNA reference sequences were obtained using the sacCer3 UCSC genome assembly.
Supplementary files format and content: For each sub-library, barcodes and corresponding variants are included along with coverage values. In files ending with conseus_coverage.fa, we provide pairs of barcodes and consensus sequences along with coverage values (number of sequencing reads supporting each consensus sequence). In files ending with complete.fa, we list all designed intron variant sequences for each sub-library, and in files ending with designed_var_barcodes.txt, we provide all barcodes and coverage values corresponding to each designed variant sequence. Samples are indexed as follows: S1 (QCR9), S2 (RPL28), S3 (RPS9B), S4 (RPL7A), S5 (RPS9A), S7 (RPS14B), and S8 (RPL36B).
Library strategy: Targeted gDNA sequencing

organism: Saccharomyces cerevisiae

source_name: Library integrated in PLH001

growth_protocol: Intron variant libraries were integrated into the genome of the S. cerevisiae strain PLH001 using homologous recombination and CRISPR/Cas9-induced double stranded breaks to increase efficiency. Our library included seven sub-libraries with variants of the introns in the following genes: QCR9, RPL28, RPS9B, RPL7A, RPS9A, RPS14B, and RPL36B. Integrated constructs included intron variants in their complete gene context with randomized 12N barcodes upstream of introns in 5' UTR regions. For both DNA and RNA sequencing, overnight cultures were grown from sub-library glycerol stocks at 30 oC in YPD liquid medium, diluted to OD600 0.1, and grown to OD600 0.5-0.6.

extract_protocol:
DNA was extracted using the YeaStar Genomic DNA Kit (Zymo Research).
We carried out a 7 cycle indexing PCR to amplify target intron library regions (complete variant sequences and barcode sequences) and add i5/i7 indices for demultiplexing sub-libraries in Illumina sequencing. We then amplified our samples for 11-14 PCR cycles with P5/P7 primers to obtain sufficient material for Illumina sequencing, and we size-selected the final library using RNACleanXP beads (Beckman Coulter).

value: Library integrated in PLH001


title: Tag1C6_Tag01

city: Munich

first: Peter

address: Feodor-Lynen-Strasse 17


title: Tag1C8_Tag01


title: Tag1C3_Tag01


title: CL19


title: Hela-CpGF-ssI-NeoR pool

description:
HeLa ctrl
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: Hela neoR pool with CpG free ssI at MLH1

value: Hela

value: cervical cancer line


title: Tag1C12_Tag01


title: Hap1

description:
HAP1-wild
Processed data file: 204365950122.igv
850 beadchip

source_name: Hap1 control


title: CL17

source_name: adrenal gland


title: Hela

description:
HeLa MLH1
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: Hela control


title: Tag1C11_Tag01


title: Jurkat

description:
Jurkat ctrl
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: Jurkat control

value: Jurkat

value: human T lymphocytes


title: CL13


title: Tag1C10_Tag01


title: CL7

value: birth


title: Tag1C1_Tag01


title: CL3


title: Tag1B9_Tag01


title: Tag1B7_Tag01


title: Jurkat-CpGF-ssI-NeoR pool

description:
Jurkat++
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: Jurkat neoR pool with CpG free ssI at MLH1

value: Y


title: CL5


title: Nt2D1-CpGF-ssI-NeoR pool

description:
Nt2D1-MLH1
Processed data file: 203299670104.igv
850 beadchip

source_name: Nt2D1 neoR pool with CpG free ssI at MLH1

value: embryonic carcinoma cell line (testes)


title: K562

description:
K562 control
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: K562 control


title: CL2


title: K562-CpGF-ssI-NeoR pool

description:
K562 CGI
Processed data file: 203299670008_203299670138.igv
850 beadchip

source_name: K562 neoR pool with CpG free ssI at MLH1


title: Nt2D1

description:
Nt2D1-WT
Processed data file: 203299670104.igv
850 beadchip

source_name: Nt2D1 control


title: Tag1B5_Tag01


title: CL1


title: Tag1B3_Tag01


title: Tag1B8_Tag01


title: ONT_FoB_BR4

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
Basecalling of reads was performed with guppy basecaller (4.0.11) in high accuracy mode. Reads with a mean sequence quality score higher than 7 were demultiplexed with the guppy_barcoder tool and processed with pychopper (2.5.0) in order to identify, orient and trim the full-length cDNA reads.
Pychopped reads were then aligned to mouse genome reference GRCm38 using minimap2 (2.17-r941) (Li et al, 2018, Bioinformatics, DOI: 10.1093/bioinformatics/bty191) with splice aware setting and analysed with FLAIR pipeline (Tang et al, 2020, Nat Commun, DOI: 10.1038/s41467-020-15171-6) for isoform identification.
Assembly: GRCm38
Supplementary files format and content: ONT_cDNAPCR_fullLength_counts.tsv: tab-delimited text file containing gene names and IDs together with the number of full length transcript isoforms detected for each gene in each sample, from FLAIR analysis.

source_name: spleen

growth_protocol: Single cell suspensions were prepared from spleen by passing the organ through a 70mm cell strainer. B cells were pre-enriched through negative selection (Miltenyi B cell isolation kit, cat # 130-090-862) and T1, T2, MZ and FoB cell subsets FACS-sorted using anti-CD19 (6D5), anti-CD93 (AA4.1), anti-CD23 (B3B4), anti-CD21 (7G6) and anti-IgM (II/41) antibodies.

extract_protocol:
Oxford Nanopore Technologies (ONT) sequencing libraries were prepared as described previously (Berrens et al, 2021, Nat. Biotech, DOI: 10.1038/s41587-021-01093-1; D'Angeli et al, 2022, Eur J Immunol, DOI: 10.1002/eji.202149781). Briefly, RNA was reverse transcribed using the Smart-seq2 protocol (Picelli et al, 2013, Nat Methods, DOI: 10.1038/nmeth.2639), cDNA was amplified using the KAPA HiFi Uracil+ hot start polymerase mix (Roche) and PCR products were purified using 0.6X AMPure XP beads (Beckman). Equal amount of cDNA libraries were pooled for a total of 200 fmol and sequenced with MinION R9.4.1 flow cell using the SQK-LSK109 kit on MinKNOW (21.02.1) according to manufacturers’ instructions.
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

treatment_protocol: B cell subsets were purified from 12-week old untreated mice

value: spleen

value: follicular B cells

value: male

tag: flow cytometry_markers


title: CL15

value: adrenal gland

value: in utero cooled


title: CL6


title: MCF7-CpGF-ssI-NeoR pool

description:
MCF7-MLH1
Processed data file: 203299670104.igv
850 beadchip

source_name: MCF7 neoR pool with CpG free ssI at MLH1

value: breast cancer cell line


title: MCF7

description:
MCF7-WT
Processed data file: 203299670104.igv
850 beadchip

source_name: MCF7 control

value: N


title: ONT_FoB_BR3

value: female


title: BT-6

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

hyb_protocol: DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research Corp), according to manufacturer recommendations, and hybridized in the Human Methylation 450 BeadChip microarrays (HM450K, Illumina), following the Illumina Infinium HD methylation protocol.

scan_protocol: Raw data was extracted using the iScan SQ scanner (Illumina) by GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 (Illumina), into IDAT files,

data_processing: The R package ChAMP was applied to the dataset. Signal intensities from probes type I and II were normalized using the updated version of BMIQ method.

source_name: bone

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the QIAsymphony equipment with the DSP DNA Mini Kit (Qiagen)

tag: subtypes

value: bone

tag: age (years)

tag: metastasis

tag: huvos grade

tag: tumor size (cm)


title: H1 control

description:
H1P31
Processed data file: 202835220094_202835220161.igv
850 beadchip

source_name: H1 hESC control

value: pluripotent stem cell line


title: Tag1B2_Tag01

value: CD11b+ cells


title: Tag1B11_Tag01


title: ONT_FoB_BR2

tag: Sex


title: ONT_FoB_BR1


title: BT-8


title: BT-9


title: H1 neomycin reistant pool with 30 bp HA CpG free insert

description:
MLH130-25
Processed data file: 202835220094_202835220161.igv
850 beadchip

source_name: H1 hESC neomycin resistant pool with ssI at MLH1 promoter CGI


title: BT-7


title: ONT_MZ_BR4

value: marginal zone B cells


title: H1-MLH1-PM-TECs-2

description:
24096_H1M6TEPD30_2
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 MLH1 promoter methylated derived thymic epithelial cells D21 of differentiation biological replicate

value: pluripotent derived thymic epithelial cell

tag: Stage

value: D30 of differentiation

value: N (was removed)


title: Tag1B1_Tag01

tag: tissue


title: ONT_MZ_BR3

tag: cell type


title: BT-3


title: Tag1B10_Tag01

tag: strain


title: H1-TEC-2

description:
24094_H1_TEPsD30_2
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 derived thymic epithelial cells at D21 of differentiation biological replicate 2


title: ONT_MZ_BR1


title: Tag1A6_Tag01

tag: age


title: Tag1B12_Tag01


title: Tag1A9_Tag01


title: ONT_MZ_BR2


title: Tag1A4_Tag01


title: H1-MLH1-PM-TECs-1

description:
24095_H1M6TEPD30_1
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 MLH1 promoter methylated derived thymic epithelial cells D21 of differentiation

value: Y


title: H1-MLH1-PM-CMs-2

description:
24092_H1M6CMD21_2
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 MLH1 promoter methylated derived cardiomyocytes D21 of differentiation biological replicate

value: pluripotent derived cardiomoycyte

value: D21 of differentiation


title: BT-4


title: ONT_T2_BR4

value: spleen

value: transitional 2 B cells


title: BT-5


title: BT-2


title: Tag1A3_Tag01


title: BT-1


title: OS-28

source_name: osteosarcoma

value: osteoblastic

value: male


title: ONT_T2_BR3


title: H1-MLH1-PM-CMs-1

description:
24091_H1M6CMD21_1
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 MLH1 promoter methylated derived cardiomyocytes D21 of differentiation


title: ONT_T2_BR2


title: H1 neomycin reistant pool with 20 bp HA CpG free insert

description:
MLH120
Processed data file: 202835220094_202835220161.igv
850 beadchip


title: OS-27


title: H1-CM1-2

description:
24090_H1CMD21_2
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 derived cardiomyocytes at D21 of differentiation biological replicate 2


title: OS-23


title: OS-26


title: H1-TEC-1

description:
24093_H1_TEPs_D30_1
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 derived thymic epithelial cells at D21 of differentiation


title: ONT_T2_BR1


title: H1-CM1-1

description:
24089_H1CMD21_1
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 derived cardiomyocytes at D21 of differentiation


title: H1-MLH1-PM-2

description:
24088_H1M6D0_2
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 hESC clone M6 post CIMR with CpG free insert removed by Cre biological replicate 2


title: ONT_T1_BR4

value: transitional 1 B cells


title: ONT_T1_BR3


title: Tag1A10_Tag01


title: OS-24


title: H1-MLH1-PM-1

description:
24087_H1M6D0_1
Processed data file: 201496710238_201496710121.igv
850 beadchip

source_name: H1 hESC clone M6 post CIMR with CpG free insert removed by Cre