title: DCC-2036_3

city: Hengyang

first: Xiguang

state: Hunan

address: #28 Changsheng Road

institute: University of South China

description: LoVo  (2×105/well) plated in 6-well plates were treated with 0 or 2.5 μM DCC-2036 for 48 h

data_processing:
PolyA-Seq is based on eukaryotic mrnas and partial long non-coding rnas (lncrnas) with a polyA-tailed structure at the 3' end, which is captured by polyA-tailed rnas for library-building sequencing. Subsequently, all genes and transcripts containing the polyA structure are detected for differential expression or structural variation, and molecular markers associated with diseases or traits are screened. PolyA-Seq can generate 6 g of Clean bases and accurately detect low abundance gene transcripts, which can reveal the complexity of the transcriptome, determine the structure of genes and transcripts, alternative splicing, RNA editing, non-coding rnas with polyA tails and new transcripts.
Total RNA→Oligo (dT enrichment）→PolyA RNA→RNA processing→Reverse transcription →synthetic cDNA library→DNA sequencing joint connection→PCR amplification library→The depth of the sequencing→Image recognition→RNA sequence information
After obtaining Raw Data, it is necessary to filter, de-linker and process low-quality reads first, and then evaluate the sequencing quality to obtain high-quality Data (Clean Data) . Clean Data was compared with the reference genome and the BAM file was obtained. For the detected mRNA, the Gene expression was further calculated and the differentially expressed genes between samples were analyzed, and the differentially expressed genes were analyzed by Gene Ontology (GO) and KEGG biopathway enrichment analysis. For the detected lncrnas, the lncRNA expression quantity and analysis were calculated accordingly, and the lncrnas were differentially expressed among the samples, and specific annotations were given.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Large intestine; Colon

growth_protocol: LoVo was cultured in Dulbecco's modified Eagle medium (DMEM, Gibco, Waltham, MA, USA) supplemented with 10% heat-activated fetal bovine serum (Biological Industries, Northern Kibbutz Beit Haemek, Israel) and 1% penicillin/streptomycin.

extract_protocol:
RNA was isolated using Trizol.
Illumina libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit as described previously using the protocol supplied by Fluidigm.

treatment_protocol: LoVo  (2×105/well) plated in 6-well plates were treated with/without 2.5 μM DCC-2036 for 48 h

value: Large intestine; Colon

value: LoVo

value: Adenocarcinoma

value: Dukes' type C


title: AL_46.2_LPS

status: Public on Jan 15 2025

type: RNA

city: Oullins-Pierre-Bénite

first: Marion

last: Debombourg

address: 165 chemindu grand revoyet

country: France

institute: biomerieux

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: Data were collected and analyzed using the nCounter Digital Analyze according to the manufacturer instructions (NanoStrings Technologies, Seattle, WA).

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, POLR2A)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Biotin & color-coded tag, 300 ng of total RNA from each sample was analyzed for the detection of a 144-gene panel according to the manufacturers instructions.

growth_protocol: Incubation inside a Truculture stimulation tube (from Myriad RBM), 37C, 22h.

extract_protocol: A modified protocol of the NucleoSpin 96 RNA tissue kit (Macherey-Nagel) was followed using a vaccum system

treatment_protocol: At the end of the incubation period, upon removal of the liquid supernatant cell pellets were resuspended in 2ml Trizol LS (Sigma) and vortexed for 2min, rested for 10 min at RT before storage at -80°C

tag: cohort

value: FIGHT

tag: status

value: Patient

tag: support

value: TruCulture

tag: stimulus

value: LPS


title: Sample_7_Tcell_Xenon

type: SRA

city: Boston

first: Wesley

last: Nogueira Brandao

state: Massachusetts

address: 60 Fenwood Rd

department: Neurology

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.

organism: Mus musculus

source_name: Tcells

growth_protocol: APP/PS1mice were kindly provided by Dr. Mathias Jucker (University of Tubingen). All animals received water and food ad libitum. Procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women's Hospital, Harvard Medical School, and Washington University School of Medicine

extract_protocol:
The microglia cells were isolated by cell sorter, and 1000 cells have their RNA extracted by Broad Institute using TCL buffer containing 1% Beta-Mercaptoethanol.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol65. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

treatment_protocol: We treated 3-month-old APP/PS1 mice with a single dose of 30% Xe for 40 minutes.

tag: genotype

tag: Sex

value: Female

tag: cell type

value: Tcells

tag: treatment

value: Xenon

tag: timepoint

tag: age

value: 3 months


title: DCC-2036_2

last: Chen

country: China

tag: tissue

tag: cell line


title: Sample_6_Tcell_Xenon


title: Sample_5_Tcell_Xenon


title: DCC-2036_1


title: AL_46.1_NUL

value: NUL


title: AL_44.2_LPS


title: Control_2

description: LoVo  (2×105/well) plated in 6-well plates were treated without  DCC-2036.


title: Control_3


title: AL_44.3_SEB

value: SEB


title: AL_44.1_NUL


title: AL_42.3_SEB


title: Sample_3_Tcell_AIR

value: AIR


title: Control_1


title: AL_42.2_LPS


title: 207030420010_R01C01

type: genomic

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

description: SAMPLE 22

hyb_protocol: Methylation EPICv2 beadarrays were performed according to the Infinium HD Methylation Assay Protocol, as previously described with minor changes. Eight µl of restored FFPE bs-DNA was used for each sample and 28 µl of hybridization volume was used when loading the microarray.

scan_protocol: Samples were scanned using Illumina's iScan according to manufacturer's recommendations for infinuim arrays

data_processing: Bioconductor (Version 3.17) package minifi (Version 1.43) using function 'preprocessIllumina'  Average beta

label: biotin/DNP

molecule: genomic DNA

source_name: Thyroid Tumor

label_protocol: Bisulfite conversion: Samples ranging from 50 ng to 500 ng of FFPE DNA was pipetted into strip tubes and processed using the EZ-96 DNA Methylation kit (Zymo Research Corp., CA, USA) following the manufacturer's recommendations for Infinium assays.

extract_protocol: Samples included in the study were all formalin-fixed for 8 hours followed by paraffin-embedding (FFPE) and stored at room temperature. All samples were extracted using either Covaris (FFPE DNA Kit, Covaris, Inc., MA, USA) or Purigen Biosystems (FFPE DNA Kit, Purigen Biosystems, CA, USA) following the manufacturer’s instructions.

tag: tissue preparation

value: FFPE

tag: tumor type

value: Medullary Thyroid


title: Sample_4_Tcell_Xenon


title: Sample_12_Microglia_Phagocytic_Xenon_IFNy blocker

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: plaint text  quantification file (quant.sf)

source_name: Phagocytic Microglia

growth_protocol: C57BL/6-J (Stock No. 000664, Jackson Laboratories) mice were purchased from the Jackson Laboratory. All animals received water and food ad libitum. Procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women's Hospital, Harvard Medical School, and Washington University School of Medicine

treatment_protocol: we injected fluorescently labeled apoptotic neurons into the cortex and hippocampus of C57BL/6 mice previously treated with an IFNg neutralizing antibody or an IgG isotype control followed by a Xe inhalation and microglia isolation

value: Phagocytic Microglia

value: IFNg Blocker-Xenon

value: 2 months


title: AL_42.1_NUL


title: Sample_11_Microglia_Phagocytic_Xenon_IFNy blocker


title: Sample_2_Tcell_AIR


title: R86_NA

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, TBP)

label_protocol: Biotin & color-coded tag, 300 ng of total RNA from each sample was analyzed for the detection of a 86-gene panel according to the manufacturers instructions.

growth_protocol: Patient's blood was directly collected in a PaxGene tube and then stabilized at room temperature for 2H

extract_protocol: Total RNA was extracted using the PaxGene Blood RNA kit (PreAnalytiX/QIAGEN) according to manufacturer instructions

treatment_protocol: After the 2h stabilization, the tube was stored at -80°C

value: REALISM

value: PaxGene


title: R83_NA

value: Healhty Volonteer


title: AL_41.2_LPS

value: FIGHT

value: Patient

value: TruCulture


title: AL_41.3_SEB


title: Sample_10_Microglia_Phagocytic_Xenon_IFNy blocker

value: Female


title: R81_NA


title: AL_41.1_NUL


title: R79_NA


title: 207030420010_R06C01

description: SAMPLE 18


title: Sample_1_Tcell_AIR

value: Tcells


title: R77_NA


title: Sample_9_Microglia_Phagocytic_Xenon_IFNy blocker


title: R75_NA


title: 207057130072_R05C01

description: SAMPLE 10


title: AL_40.3_SEB


title: iMEF, HP1B, rep2

city: Columbus

first: Mark

last: Parthun

state: Ohio

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

library_source: genomic

data_processing:
Samples were aligned using BWA with flag -M
Aligned data was filtered to remove reads mapping to mitochondrial DNA or unlocalized or unplaced contigs
Replicates were subsampled to the same library size.
Assembly: mm10
Supplementary files format and content: Bigwig files viewable in genome browser

source_name: iMEF

growth_protocol: Mouse embryonic fibroblasts were cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle’s High Glucose Medium supplemented with 10% FBS, 1% glutamine, and 1% Penn-Strep and passaged approximately every 2-3 days.

extract_protocol:
Cells were harvested using 2% trypsin and suspended in fresh media for counting
ChIP-seq was performed as previously described [Popova et al. (2021), Nuc. Ac. Res. https://doi.org/10.1093/nar/gkab1044]

value: iMEF

value: mouse embryonic fibroblast


title: iMEF, HP1B, rep1


title: Sample_7_Microglia_Phagocytic_Xenon_ISO

value: Iso-Xenon


title: Sample_8_Microglia_Phagocytic_Xenon_ISO


title: AL_40.2_LPS

value: LPS


title: AL_40.1_NUL

value: NUL


title: Sample_6_Microglia_Phagocytic_Xenon_ISO


title: R73_NA


title: iMEF, H3K27ac, rep2

data_processing:
Samples were aligned using bowtie2 with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Aligned data was filtered to remove reads mapping to mitochondrial DNA or unlocalized or unplaced contigs
Replicates were subsampled to the same library size.
Assembly: mm10
Supplementary files format and content: Bigwig file with genomic distribution of histone PTM viewable in genome browser
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested using 2% trypsin and suspended in fresh media for counting
CUT&Tag was performed according to Epicypher's CUTANA™ Direct-to-PCR CUT&Tag Protocol with a fixation step adapted from Kaya-Okur et al. (2020) (https://doi.org/10.1038/s41596-020-0373-x). 100,00 MEFs were harvested and rinsed with PBS, then incubated in Nuclear Extraction Buffer for 10 minutes on ice. For some samples, HEK293T cells were added to the MEFs at a 1:5 ratio before nuclei extraction, but this spike-in proved to be unreliable and was ignored for the data analysis. Nuclei were spun down and resuspended in PBS, then fixed by adding formaldehyde to a concentration of 0.1% and incubating 2 min at room temperature. Formaldehyde was quenched with two molar equivalents of glycine and cells were spun down, resuspended in Nuclear Extraction Buffer, and incubated for 10 minutes at room temperature with 10 uL activated Concavalin A beads to allow nuclei to bind to the beads. The nuclei/beads were separated with a magnet to allow removal of the supernatant, suspended in Antibody 150 Buffer with the appropriate dilution of primary antibody and incubated overnight at 4 °C. The next day, the primary antibody was replaced with secondary antibody and nuclei were incubated for 30 min at room temperature. Nuclei were rinsed twice with Digitonin 150 Buffer and incubated for 1 hour with pAG-Tn5 fusion transposase, followed by two rinses with Digitonin 300 Buffer. They were then incubated at 37 °C for 1 hour with 10 mM MgCl2 to activate the Tn5 Transposase. Tagmentation was stopped by rinsing with TAPS Buffer and samples were incubated in SDS Release Buffer at 58 °C for 1 hour to lyse nuclei and release the DNA. SDS was quenched in 0.5% TritonX-100. DNA libraries were amplified using CUTANA High-Fidelity 2X PCR Master Mix with Universal i5 primer and the appropriate barcoded i7 primer, and DNA was extracted using 1.3X AMPure beads.


title: Sample_5_Microglia_Phagocytic_Xenon_ISO


title: R71_NA


title: R69_NA


title: AL_34.2_LPS


title: iMEF, H3K27ac, rep1


title: AL_34.1_NUL


title: R67_NA


title: iMEF, H3K27ac, rep3


title: Sample_4_Microglia_Phagocytic_Air_ISO

value: Iso-Air


title: AL_34.3_SEB

value: SEB


title: 207030420010_R03C01

description: SAMPLE 15

value: FFPE

value: Medullary Thyroid


title: R65_NA

value: REALISM


title: 207057130180_R03C01

description: SAMPLE 21


title: iMEF, H3K9ac, rep3


title: AL_33.3_SEB


title: 207030420010_R04C01

description: SAMPLE 16


title: iMEF, H3K9ac, rep2


title: Sample_3_Microglia_Phagocytic_Air_ISO

value: Phagocytic Microglia

value: 2 months


title: Sample_2_Microglia_Phagocytic_Air_ISO


title: AL_33.2_LPS

value: FIGHT


title: Sample_1_Microglia_Phagocytic_Air_ISO


title: iMEF, H3K9ac, rep1


title: Sample_16_Microglia_Xenon 35%

treatment_protocol: C57BL/6 (WT) mice receive injection of apoptotic neurons in cortex and hippocampus. Two hours after the injection of apoptotic neurons, the mice were treated with Xe at four different concentrations, starting with 6%, 12%, 30%, and 35% for 40 minutes and euthanized 14 hours later. Microglia were isolated to RNAseq analysis.

value: WT

value: Xenon 35%


title: 207057130180_R02C01

description: SAMPLE 13


title: R62_NA

value: Patient

value: PaxGene


title: 207030420010_R02C01

description: SAMPLE 14


title: R64_NA


title: Sample_15_Microglia_Xenon 35%

value: Female


title: R58_NA


title: iMEF, H3K14ac, rep3

value: iMEF

value: mouse embryonic fibroblast


title: Sample_14_Microglia_Xenon 35%


title: iMEF, H3K14ac, rep2


title: R60_NA


title: AL_32.1_NUL

value: TruCulture


title: R52_NA


title: 207030420010_R05C01

description: SAMPLE 17


title: iMEF, H3K14ac, rep1


title: AL_33.1_NUL

value: NUL


title: AL_32.2_LPS

value: LPS


title: Sample_13_Microglia_Xenon 30%

value: Xenon 30%


title: iMEF, H3K27me3, rep3


title: 207057130072_R08C01

description: SAMPLE 11

value: FFPE


title: R50_NA


title: AL_30.3_SEB

value: SEB


title: AL_30.2_LPS


title: Sample_12_Microglia_Xenon 30%


title: iMEF, H3K27me3, rep2


title: R48_NA

value: REALISM


title: iMEF, H3K27me3, rep1


title: Sample_11_Microglia_Xenon 30%

value: Phagocytic Microglia


title: Sample_10_Microglia_Xenon 30%

value: 2 months


title: R44_NA


title: iMEF, H3K9me2, rep2


title: iMEF, H3K9me2, rep3


title: AL_28.2_LPS

value: FIGHT


title: R40_NA


title: iMEF, H3K9me2, rep1


title: AL_28.3_SEB


title: Sample_8_Microglia_Xenon 12%

value: WT

value: Xenon 12%


title: Sample_7_Microglia_Xenon 12%


title: iMEF, H3K9me3, rep3


title: iMEF, H3K9me3, rep2


title: AL_27.3_SEB

value: Patient


title: R36_NA

value: PaxGene


title: R38_NA


title: AL_27.2_LPS


title: Sample_6_Microglia_Xenon 6%

value: Female

value: Xenon 6%


title: R46_NA


title: AL_28.1_NUL


title: AL_27.1_NUL


title: Sample_5_Microglia_Xenon 6%


title: iMEF, H3K9me3, rep1

value: iMEF

value: mouse embryonic fibroblast


title: AL_30.1_NUL

value: TruCulture

value: NUL


title: R30_NA


title: Sample_9_Microglia_Xenon 12%


title: AL_21.3_SEB


title: iMEF, IgG, rep2

data_processing:
Samples were aligned using bowtie2 with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Aligned data was filtered to remove reads mapping to mitochondrial DNA or unlocalized or unplaced contigs
Replicates were subsampled to the same library size.
LADs were called on merged replicates using the HMMt package in R with a modified version of the HMMtBroadPeak function (see associated manuscript)
Assembly: mm10
Supplementary files format and content: Bigwig files viewable in genome browser
Supplementary files format and content: BED file of called LAD locations
Library strategy: CUT&RUN

extract_protocol:
Cells were harvested using 2% trypsin and suspended in fresh media for counting
CUT&RUN was performed with 500,000 MEFs according to EpiCypher's CUTANA™ CUT&RUN Protocol. For Lamin B1 CUT&RUN, cells were rinsed twice with wash buffer and bound to activated Concavalin A beads. For H3K9me2 and H3K14ac, nuclei were extracted before binding to Concavalin A beads. Samples were incubated overnight with primary antibody at the appropriate dilution in Antibody Buffer (1:50 for IgG, 1:100 for Lamin B1, H3K14ac, or H3K9me2). The next day, samples were rinsed twice with Digitonin Buffer and incubated for 10 minutes with pAG-MNase. After two more rinses with Digitonin Buffer, samples were then incubated in 2 mM CaCl2 for 2 hours at 4 °C. Samples were quenched with 33 uL STOP Buffer (containing E. coli spike-in DNA in the case of Lamin B1 and IgG samples) and incubated 10 min at 37 °C to release fragmented DNA, then beads were separated out of solution on a magnetic rack and the supernatant was transferred to new tubes. Libraries were prepared for next generation sequencing using the CUTANA CUT&RUN Library Prep Kit.


title: Sample_4_Microglia_Xenon 6%


title: iMEF, IgG, rep1


title: AL_21.2_LPS

value: LPS


title: iMEF, H3K14ac


title: Sample_2_Microglia_Non-Xenon

value: Non-Xenon


title: R34_NA


title: R26_NA


title: R28_NA


title: iMEF, H3K9me2, 39041


title: R32_NA


title: AL_21.1_NUL


title: R24_NA


title: iMEF, H3K9me2, ab1220


title: Sample_8_Microglia_IFNg-blocker

source_name: Microglia

treatment_protocol: We treated APP/PS1 mice at 6 months of age once a week for 2 weeks with the anti-IFNγ neutralizing antibody, administered 24 hours intraperitoneally before Xe exposure. After 14 days, we euthanized the animals and assessed microglial signatures

value: Microglia

value: IFNg-blocker

value: 6 months


title: Sample_1_Microglia_Non-Xenon

value: Phagocytic Microglia

value: 2 months


title: R22_NA

value: REALISM


title: AL_19.3_SEB

value: FIGHT

value: SEB


title: iMEF, LaminB1, rep2


title: AL_32.3_SEB

value: Patient


title: AL_19.2_LPS


title: R20_NA

value: PaxGene


title: iMEF, LaminB1, rep1


title: Sample_3_Microglia_Non-Xenon

value: WT

value: Female


title: R18_NA


title: Sample_6_Microglia_IFNg-blocker


title: e2_dmso_24hr_input_aH3K9me2_rep2

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

data_processing:
Technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Bigwigs normalized to sequencing depth were made from bed files using deeptools v3.5.1 using parameters: --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Bigwigs were normalized at 10kb resolution with 5kb sliding steps using a custom R (v4.1.2, "Bird Hippie") script.
Bigwigs normalized to input [log2(ChIP/Input)] were generated using custom R (v4.1.2, "Bird Hippie") script from 10kb normalized bigwigs.
Assembly: mm10
Supplementary files format and content: bigwigs normalized to sequencing depth
Supplementary files format and content: bigwigs normalized as log2(chip/input)
Supplementary files format and content: bed files of H3K9me2 domains.
Library strategy: ULI-NChIP

growth_protocol: ESCs were cultured  in KO-DMEM (Invitrogen) supplemented with L-Glutamine, penicillin-streptomycin, nonessential amino acids, β-mercaptoethanol, LIF and heat-inactivated fetal bovine serum (FBS).

extract_protocol:
Cells were collected in single cell suspension using trypsin and counted. The counted cells were then spun down and flash-frozen. ULI-NChIP was conducted according to the protocol published by Brind’Amour et al. (PMID 25607992). 1ug H3K9me2 antibody ab1220 was used.
ULI-NChIP libraries were prepared using the Thru-PLEX DNA-seq kit with adapters from Takara (cat. R400666). The quality of the libraries was checked using a DNA tape-station and sequencing conducted by the Weill Cornell Genomics core.
Ultra low input native ChIP (ULI-NChIP)

treatment_protocol: Cells were treated with DMSO for 24hr

value: ESC

tag: strain

value: BL6/129 hybrid

value: DMSO 24hr


title: AL_18.3_SEB

value: TruCulture


title: R14_NA


title: Sample_5_Microglia_IFNg-blocker


title: AL_18.2_LPS

value: LPS


title: e2_dmso_24hr_input_aH3K9me2_rep1


title: Sample_7_Microglia_IFNg-blocker

value: Microglia


title: 207057130180_R01C01

description: SAMPLE 12

value: FFPE

value: Medullary Thyroid


title: Sample_1_Microglia_IgG

value: IgG

value: 6 months


title: Sample_4_Microglia_IgG


title: AL_19.1_NUL

value: NUL


title: e2_dmso_24hr_chip_aH3K9me2_rep1


title: AL_17.3_SEB

value: FIGHT


title: e2_dmso_24hr_chip_aH3K9me2_rep2


title: AL_17.1_NUL


title: Sample_2_Microglia_IgG


title: R12_NA

value: REALISM


title: R10_NA

value: Patient


title: R08_NA

value: PaxGene


title: e2Merv_dtag_bulk_72hr_aIgG_cnr_rep4

data_processing:
Biological and technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Peaks were called on bed files using MACS2 v2.2.6 using parameters: -f BEDPE --nomodel --seed 123 --keep-dup all
Bigwigs were made from bed files using bedtools genomecov v2.30.0.
Bigwigs were z-normalized per chromsome arm using a custom R script.
Assembly: mm10
Supplementary files format and content: z-normalized bigwigs for merged replicates.
Supplementary files format and content: narrowpeak files of called peaks
Library strategy: CUT&RUN

growth_protocol: All cells cultured at 37C, 5% CO2.  ESC's were cultured in DMEM KO media containing FBS/LIF.

extract_protocol:
CUT&RUN on MERVL GFP- EHMT dTAG lines were treated with DMSO/dTAG for 72hrs , Sorted for gfp positive and negative population. Cut and Run performed using anti-DPPA4 antibody  was performed on 250k-450k cells per sample using BioMag Plus Concanavalin A beads (ConA beads, PolySciences NC1358578), 1:100 anti-DPPA4  ((AF3730)) or anti-IgG (EpiCypher 130042), and ProteinA/G MNase (EpiCypher). Fragmented DNA was isolated by phenolchloroform extraction and EtOH precipitation
CUT&RUN libraries were constructed using the Takara Thruplex Library Prep and Unique Dual Index kits. Cycles for PCR amplification were determined individually for each sample by qPCR. Libraries were size selected using SPRI beads (Beckman Coulter)

treatment_protocol: Live GFP+ and GFP- cells were sorted for CUT&RUN with DAPI on BD-Influx

value: dTAG 72HRS


title: AL_17.2_LPS


title: AL_18.1_NUL


title: R04_NA


title: e2Merv_dtag_gfpNeg_72hr_aIgG_cnr_rep1


title: AL_14.3_SEB

value: SEB


title: Sample_10_MG_XENON

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: salmon output including plain text quantification file (quant.sf)

growth_protocol: 5xFAD: MITRG mice were kindly provided by Dr. Mathew Blurton-Jones (UC Irvine). All animals received water and food ad libitum. Procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women's Hospital, Harvard Medical School, and Washington University School of Medicine

treatment_protocol: Xe treatment (Xe 30%, 40 minutes once a week) was initiated in 5xFAD-MITRG mice at 4 months of age and continued once a week until the animals reached 6 months of age.

value: Female

value: XENON

value: 6 Months


title: R86_SEB

value: TruCulture


title: Sample_3_Microglia_IgG


title: e2Merv_dtag_gfpPos_72hr_aDppa4_cnr_rep2

value: ESC

value: BL6/129 hybrid


title: AL_14.2_LPS

value: LPS


title: R06_NA


title: e2Merv_dtag_gfpPos_72hr_aDppa4_cnr_rep1


title: Sample_8_MG_XENON

value: Microglia


title: R86_NUL


title: AL_14.1_NUL


title: Sample_7_MG_XENON


title: Sample_6_MG_XENON


title: Sample_5_MG_AIR

value: AIR


title: AL_4.2_LPS


title: e2Merv_dtag_gfpNeg_72hr_aDppa4_cnr_rep1


title: R83_NUL

value: Healhty Volonteer


title: R83_SEB


title: R81_SEB


title: AL_3.3_SEB


title: Retina,2.5mo,donor 2,snATAC

city: La Jolla

first: Ying

last: Yuan

address: Palmilla Dr.

department: MATS

institute: UCSD

description: 2.5 mo old wild type mice retinal tissue_Left eye dissected

library_source: genomic single cell

data_processing:
CellRanger
Assembly: mm10
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: retina

extract_protocol:
The flash frozen retinal tissue along with RPE and choroid was harvested from 28days, 2.5month, 5month and 21month old mice. Each age point contained two biological replicates. Nuclei preparation was adapted from Lacar et al. 2016 (PMID: 27090946). Flash frozen mouse retina was resuspended in 1 mL of  douncing buffer consisting of 0.25M sucrose (S1888, Sigma), 25mM KCl (AM9610G, Invitrogen), 5mM MgCl2 (194698, Mp Biomedicals Inc.), 10 mM Tris-HCl pH 7.5 (15567027, Thermo Fisher Scientific), 1mM DTT (D9779, Sigma), 1X protease inhibitor (05056489001, Roche), 0.1% Triton X-100 (T8787-100ML, Sigma), and 0.5 U/ul RNasin RNase inhibitor (PAN21110, Promega) in molecular biology grade water (46000-CM, Corning). Frozen tissue was then transferred to a dounce homogenizer on ice and dounced 25 times with a loose plunger and 25 times with a tight plunger. Suspension was then passed through a Celltrix 30 μM filter (04-004-2326, Sysmex) and washed with 300 mL of douncing buffer before being centrifuged for 10 minutes at 1000 rcf in a swinging bucket centrifuge at 4°C with run setting 3/3. Pellet was then washed with an additional 1 mL of douncing buffer without Triton X-100, and split for single-nucleus ATAC-seq and single-nucleus RNA-seq in a ratio of 700 mL /300 mL.
Nuclei from dissociated tissue were permeabilized in 1 mL of  permeabilization buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT, 1x cOmplete EDTA-free protease inhibitor in PBS), pipette mixed, and incubated on ice for 10 minutes. Nuclei were then centrifuged at 500 rcf for 5 minutes and the supernatant was removed. Nuclei were resuspended in 500 µL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2000 nuclei/9 µL, and 2000 nuclei were dispensed into each well of one 96-well plate. For tagmentation, 1 µL barcoded Tn5 transposomes (58) was added using a BenchSmart 96 (Mettler Toledo), mixed five times and incubated for 60 min at 37°C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA were added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37°C for 15 min with shaking (500 rpm). Next, 10 µL 3x sort buffer (2% BSA, 2 mM EDTA in PBS) was added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 µM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 2n nuclei were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol) primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55°C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added and samples were PCR-amplified (72°C 5 min, 98°C 30 s, (98°C 10 s, 63°C 30 s, 72°C 60 s)×12 cycles, held at 12°C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x).

value: retina


title: R81_NUL

value: NUL


title: Sample_4_MG_AIR


title: Retina,5mo,donor 2,snATAC

description: 5mo old wild type mice  Right Eye


title: AL_4.3_SEB

value: FIGHT


title: AL_3.2_LPS

value: Patient


title: AL_4.1_NUL


title: Sample_9_MG_XENON


title: Sample_3_MG_AIR


title: Sample_2_MG_AIR


title: Retina,2.5mo,donor 1,snATAC


title: R79_NUL

value: REALISM


title: AL_3.1_NUL


title: e2Merv_dtag_gfpNeg_72hr_aDppa4_cnr_rep2

value: dTAG 72HRS


title: Retina,5 mo, donor 2,snRNA

description: A976 Left Eye

library_source: transcriptomic single cell

data_processing:
CellRanger
Assembly: mm10
Supplementary files format and content: CellRanger output files: RNA.barcodes.tsv.gz, RNA.features.tsv.gz, RNA.matrix.mtx.gz

molecule: nuclear RNA

extract_protocol: 10x snRNA-seq

value: Retina

value: 5 mo

tag: donor

value: donor 2


title: Retina,5mo,donor 1,snATAC

description: 5mo old wild type mice Left Eye


title: Sample_1_MG_AIR

value: Female

value: 6 Months


title: R77_SEB

value: TruCulture

value: SEB


title: Sample_16_Microglia_XENON, Cx3Cr1-CreERT2:Ifngr1Flox

growth_protocol: Cx3cr1CreERT2 (Stock No. 021160, Jackson Laboratories) and Ifngr1Flox (Stock No. 025394, Jackson Laboratories) mice were purchased from the Jackson Laboratory. All animals received water and food ad libitum. Procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women's Hospital, Harvard Medical School, and Washington University School of Medicine

treatment_protocol: The mice were treated with TAM to delete Ifngr1 one month before the injection of apoptotic neurons. Two hours after the injection of apoptotic neurons, the mice were treated with Xe (30%) for 40 minutes and euthanized 14 hours later.

value: Phagocytic Microglia

value: Male

value: XENON

value: 3 months


title: Retina,5 mo, donor 1, snRNA

description: A975 Left Eye

value: retina

value: donor 1


title: Sample_15_Microglia_XENON, Cx3Cr1-CreERT2:Ifngr1Flox


title: Retina,2.5mo,donor 2,snRNA


title: E233S-pSeSD-SisPerR, biol rep 2

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

description: The SisperR overexpression strain, biol rep 2

data_processing:
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the whole genome of S. islandicus REY15A (Guo, et al., 2011). Both building index of reference genome and aligning cleanreads to reference genome were used Bowtie2 (2.3.4.3).
HTSeq (v0.9.1) was used to count the reads numbers mapped to each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using theDESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on thenegative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<0.05and |log2(foldchange)| > 0 were set as the threshold for significantly differential expression.
Assembly: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Saccharolobus islandicus

source_name: microbial cells

growth_protocol: S. islandicus strains were grown in MTSUV medium (Basic mineral medium+Typtone+Sucrose+Uracil+Vatamin) for E233S and deletion mutant or MTSV medium for those carrying the pSeSD vector at 75 oC.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures were treated with 70 μM H2O2 when their OD(600nm) reached 0.2.

value: microbial cells

value: SisPerR overexpression

value: no treatment


title: R75_SEB

value: REALISM

value: Healhty Volonteer


title: Sample_13_Microglia_XENON, Cx3Cr1-CreERT2:Ifngr1Flox


title: Retina,2.5mo,donor 1,snRNA

value: Retina


title: R75_NUL

value: NUL


title: R79_SEB


title: Sample_14_Microglia_XENON, Cx3Cr1-CreERT2:Ifngr1Flox


title: R73_SEB


title: K20200116,Adelaide,Testis

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
We first removed all RNA-seq reads that mapped to ribosomal RNAs (rRNAs) in the reference koala genome. We annotated the rRNAs using RNAmmer54 (version 1.2) with default parameters and mapped RNA-seq reads to rRNAs using Bowtie2 (version 2.2.5) with default parameters. The remaining RNA-seq reads were mapped to the reference koala genome using STAR (version 020201). PCR duplicates were eliminated based on UMI tags and alignment information using Umitools (version 0.2.0). The resulting reads were then annotated to protein-coding genes, non-coding RNAs, and piRNA genes using HTSeq58 (version 0.9.1). Gene expression levels were quantified in reads per million unique mapped reads per kilobase (RPKM) using custom bash scripts.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the normalized expression levels of genes and piRNA clusters

organism: Phascolarctos cinereus

source_name: Testis

extract_protocol:
Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Strand-specific RNA sequencing libraries for were prepared as described in (Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012;3(1):9. Published 2012 Dec 28. doi:10.1186/1758-907X-3-90).  In brief, total RNA was isolated from frozen koala tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). RNAs greater than 200nt were selectively recovered using the RNA Clean & Concentrator-5 kit(Zymo Research).  RNA samples were fragmented and reverse transcribed. dUTP was incorportated during second strand synthesis for strand specificity. End repair and A-tailing was performed followed by adapter ligation and uracil-DNA glycosylase (UDG) treatment.  ERCC spike-ins and UMI tags are added to the libraries. Finally, the library was PCR amplified.

value: Testis

tag: Stage

value: adult

tag: location

value: Adelaide

tag: koala id


title: E233S-pSeSD-SisPerR, biol rep 3

description: The SisperR overexpression strain, biol rep 3


title: AL_2.1_NUL

tag: cohort

value: FIGHT

tag: status

value: Patient

tag: support

value: TruCulture


title: R73_NUL

tag: stimulus


title: K20200116,Adelaide,Liver

source_name: Liver

value: Liver


title: K20200104,Adelaide,Testis


title: E233S-pSeSD, biol rep 3

description: The wild type strain with empty vector, biol rep 3

tag: cell type

tag: genotype

value: WT with empty vector


title: R71_SEB

value: SEB


title: Sample_11_Microglia_AIR, Cx3Cr1-CreERT2:Ifngr1Flox

value: Phagocytic Microglia

tag: Sex

value: Male

tag: treatment

value: AIR

value: 3 months


title: E233S-pSeSD-SisPerR, biol rep 1

description: The SisperR overexpression strain, biol rep 1

value: microbial cells

value: SisPerR overexpression

value: no treatment


title: R77_NUL

value: REALISM

value: Healhty Volonteer

value: NUL


title: E233S-pSeSD, biol rep 2

description: The wild type strain with empty vector, biol rep 2


title: Sample_10_Microglia_AIR, Cx3Cr1-CreERT2:Ifngr1Flox

tag: age


title: R71_NUL


title: AL_2.2_LPS

value: LPS


title: K20200104,Adelaide,Liver

tag: tissue

value: adult

value: Adelaide


title: E233S-pSeSD, biol rep 1

description: The wild type strain with empty vector, biol rep 1


title: K20191231-2,Adelaide,Testis

value: Testis


title: Sample_9_Microglia_AIR, Cx3Cr1-CreERT2:Ifngr1Flox


title: AL_2.3_SEB

value: FIGHT

value: Patient

value: TruCulture


title: R69_SEB

value: SEB


title: ΔsisperR-H2O2, biol rep 3

description: The SisperR deletion strain treated with H2O2 for 6 h, biol rep 3

value: Sisfha knockout

value: H2O2 treatment


title: K20191231-2,Adelaide,Liver

value: Liver


title: Sample_8_Microglia_XENON, Ifngr1Flox

value: Phagocytic Microglia

value: Male

value: XENON

value: 3 months


title: K20191231-1,Adelaide,Testis


title: Sample_12_Microglia_AIR, Cx3Cr1-CreERT2:Ifngr1Flox

value: AIR


title: R69_NUL

value: REALISM

value: Healhty Volonteer

value: NUL


title: ΔsisperR-H2O2, biol rep 2

description: The SisperR deletion strain treated with H2O2 for 6 h, biol rep 2

value: microbial cells


title: ΔsisperR-H2O2, biol rep 1

description: The SisperR deletion strain treated with H2O2 for 6 h, biol rep 1


title: R67_SEB


title: Sample_7_Microglia_XENON, Ifngr1Flox


title: R67_NUL


title: ΔsisperR, biol rep 3

description: The SisperR deletion strain mock-treated for 6 h, biol rep 3

value: no treatment


title: K20190814,Adelaide,Testis

value: Testis

value: adult

value: Adelaide


title: Sample_5_Microglia_XENON, Ifngr1Flox


title: ΔsisperR, biol rep 2

description: The SisperR deletion strain mock-treated for 6 h, biol rep 2


title: K20191231-1,Adelaide,Liver


title: R65_SEB

value: TruCulture

value: SEB


title: Sample_4_Microglia_AIR, Ifngr1Flox


title: K20190814,Adelaide,Liver


title: R65_NUL


title: ΔsisperR, biol rep 1

description: The SisperR deletion strain mock-treated for 6 h, biol rep 1

value: Sisfha knockout


title: K20190727,Adelaide,Testis


title: R64_SEB

value: Patient


title: Sample_3_Microglia_AIR, Ifngr1Flox

value: Phagocytic Microglia


title: E233S-H2O2, biol rep 3

description: The wild type strain E233S treated with H2O2 for 6 h, biol rep 3

value: WT

value: H2O2 treatment


title: K20190727,Adelaide,Liver

value: Liver


title: R64_NUL


title: E233S-H2O2, biol rep 2

description: The wild type strain E233S treated with H2O2 for 6 h, biol rep 2


title: Poppy,Brisbane,Testis

data_processing:
We first removed all RNA-seq reads that mapped to ribosomal RNAs (rRNAs) in the reference koala genome. We annotated the rRNAs using RNAmmer54 (version 1.2) with default parameters and mapped RNA-seq reads to rRNAs using Bowtie255 (version 2.2.5) with default parameters. The remaining RNA-seq reads were mapped to the reference koala genome using STAR56 (version 020201). PCR duplicates were eliminated based on UMI tags and alignment information using Umitools57 (version 0.2.0). The resulting reads were then annotated to protein-coding genes, non-coding RNAs, and piRNA genes using HTSeq58 (version 0.9.1). Gene expression levels were quantified in reads per million unique mapped reads per kilobase (RPKM) using custom bash scripts.
Following rRNA removal, RNA-seq reads were aligned directly to transposon consensus sequences, as defined in our 2019 study, using Hisat2 (version 2.1.0) with parameters “-k 100 --no-mixed --no-discordant”. PCR duplicates were removed using Umitools, and reads mapping to multiple loci were counted as one divided by the number of times they map to the genome. Transposon expression levels were determined using Bedtools (version 2.27.1) and normalized to RPKM based on the total reads uniquely mapped to the koala genome. The final RPKM file contains expression in the sense strand and antisense strand respectively for each transposon."
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the normalized expression levels of genes and piRNA clusters
Supplementary files format and content: tab-delimited text files contain the normalized expression levels of transposons, separated in sense strand (2nd columns) and antisense strand (3rd column).

value: Brisbane

value: Poppy


title: Sample_1_Microglia_AIR, Ifngr1Flox

value: Male

value: AIR

value: 3 months


title: E233S-H2O2, biol rep 1

description: The wild type strain E233S treated with H2O2 for 6 h, biol rep 1

value: microbial cells


title: Mario,Brisbane,Testis

value: Testis

value: Mario


title: Sample_10_Astrocytes_XENON

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: salmon output including plain text  quantification file (quant.sf)

source_name: Astrocyte

value: Astrocyte

value: Female

value: XENON

value: 6 Months


title: E233S, biol repl 3

description: The wild type strain E233S mock-treated for 6 h, biol rep 3

value: no treatment


title: Sample_6_Microglia_XENON, Ifngr1Flox

value: Phagocytic Microglia


title: R62_NUL

value: REALISM

value: Patient

value: TruCulture

value: NUL


title: K98494,Brisbane,Testis

value: adult

value: Brisbane


title: E233S, biol repl 2

description: The wild type strain E233S mock-treated for 6 h, biol rep 2

value: WT


title: R60_NUL


title: E233S, biol repl 1

description: The wild type strain E233S mock-treated for 6 h, biol rep 1


title: R60_SEB

value: SEB


title: Sample_8_Astrocytes_XENON


title: Cove,Brisbane,Testis

value: Cove


title: Sample_7_Astrocytes_XENON


title: Burke,Brisbane,Testis

value: Testis

value: Burke


title: R58_SEB


title: ARS-5-2

city: Cerdanyola del Vallès

first: Andrés

last: Rico-Medina

state: Barcelona

address: C/ de la Vall Moronta SN

country: Spain

institute: CRAG

description: KO rep 3 technical 2

data_processing:
Raw reads were quality-checked using FastQC tool (v0.11.2), trimmed 13bp at the 3’ end quality-trimmed and filtered at a minimum quality score of 28 (Phred+33, minimum read length of 75bp) using trimmomatic software (v0.38).
Filtered reads were mapped to the Sorghum bicolor v3.0.1 genome (Phytozome) release using HISAT2 2.1.0 aligner and quantified at a gene level using FeatureCount software v1.6.2 on the Sorghum bicolor v3.1.1 annotation file (Phytozome).
For differential expression analysis, low-abundant raw counts were filtered out and remaining counts normalized by library size and TMM. Pairwise differentail expression analysis was performed using edgeR package (v3.34.1) in R (v4.1.1).
Assembly: Sorghum bicolor v3.0.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Sorghum bicolor

source_name: Root

growth_protocol: Freshly explanted sorghum embryos 13-17 days after anthesis were grown in vitro in MS0.5 media for 8 days at 28º in a growth chamber for 8 days

extract_protocol:
8 day old sorghum roots were cut in a laminar flow cabin, pooled and its RNA extracted using MAXWELL 16 LEV system by PROMEGA with the Plant RNA Kit. Total RNA was extracted, frozen, and sent to sequencing.
Stranded libraries were prepared using TrueSeq Stranded mRNA KIT (Ilumina). Paired-end sequencing (2x100bp) was performed using NovaSeq6000 (Ilumina) at minimum depth of 45M.

treatment_protocol: No treatment was applied

value: Root


title: Andy,Brisbane,Testis

value: Andy


title: Sample_6_Astrocytes_XENON

value: Astrocyte

value: Female

value: XENON


title: Sample_2_Microglia_AIR, Ifngr1Flox

value: Phagocytic Microglia

value: Male

value: AIR

value: 3 months


title: R58_NUL

value: REALISM

value: Patient

value: TruCulture

value: NUL


title: ARS-5-1

description: KO rep 3 technical 1


title: R52_SEB

value: SEB


title: K98314,Currumbin,Testis

value: adult

value: Currumbin


title: Sample_5_Astrocytes_AIR

value: 6 Months


title: R62_SEB


title: K98314,Currumbin,Liver

value: Liver


title: ARS-2-2

description: KO rep 2 technical 2

value: Root


title: Sample_4_Astrocytes_AIR

value: Astrocyte


title: Sample_9_Astrocytes_XENON

value: Female


title: ARS-2-1

description: KO rep 2 technical 1


title: R50_SEB


title: R52_NUL


title: ARS-1-2

description: KO rep 1 technical 2


title: R50_NUL


title: Sample_3_Astrocytes_AIR


title: K98224,Currumbin,Liver


title: Sample_1_Astrocytes_AIR


title: K98214,Currumbin,Ovary

source_name: Ovary

value: Ovary


title: Sample_2_Astrocytes_AIR


title: WT-5-2

description: WT rep 3 technical 2


title: K98214,Currumbin,Liver


title: R48_SEB


title: WT-5-1

description: WT rep 3 technical 1


title: Sample_9_Microglia_XENON

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.

growth_protocol: APP/PS1 mice were kindly provided by Dr. Mathias Jucker (University of Tubingen). All animal procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital, Harvard Medical School, and Washington University School of Medicine.

treatment_protocol: We utilized a newly designed inhalation chamber to house up to 12 mice with an airtight 8L volume and a gas recirculation system. Continuous monitoring of Xe, O2, and CO2 concentrations was conducted, with a CO2 absorbent used to maintain CO2 levels between 600-900 ppm. This new system maintained stable gas 30% Xenon concentrations throughout the 40-minute treatment period. The animals were treated once a week from 2-4 months of age.

value: XENON

value: 4 Months

value: Microglia


title: Sample_10_Microglia_XENON


title: K94283,SunshineCoast,Ovary

value: Sunshine Coast


title: K98224,Currumbin,Testis

value: Testis


title: R48_NUL

value: REALISM

value: Patient


title: K94283,SunshineCoast,Liver


title: Sample_8_Microglia_XENON


title: R46_SEB

value: TruCulture


title: WT-4-2

description: WT rep 2 technical 2


title: K94276,SunshineCoast,Testis


title: R46_NUL

value: NUL


title: WT-4-1

description: WT rep 2 technical 1


title: ARS-1-1

description: KO rep 1 technical 1


title: Sample_7_Microglia_XENON


title: WT-2-2

description: WT rep 1 technical 2


title: R44_SEB

value: SEB


title: Sample_6_Microglia_XENON


title: WT-2-1

description: WT rep 1 technical 1


title: K71362,SunshineCoast,Testis

value: adult


title: R40_SEB


title: Sample_5_Microglia_AIR

value: AIR


title: K71362,SunshineCoast,Liver

value: Liver


title: Sample_4_Microglia_AIR


title: R44_NUL


title: K98224,Currumbin,Testis,ONT

data_processing:
We used TEMP2-insertion (version 0.1.6) to identify new transposon insertions in Illumina and BGI DNA-seq data.
To leverage Nanopore long-read DNA-seq data for constructing transposon insertion sequences, we first employed Guppy-basecaller62 (version 5.0.16) with the high accuracy configuration to convert the Nanopore raw signals into raw reads. Subsequently, the raw reads were aligned to the koala genome using Minimap263 (version 2.17) with the parameters “-x map-ont”. Soft clipped reads (those with clipped 5´ or 3´ ends) and spanning reads (those containing internal deletions) were collected. A soft clipped read or spanning read was designated as supporting a transposon insertion if the soft clipped or deleted portion could be mapped back to transposon consensus sequences using Minimap2 with parameters “-x map-ont”. Adjacent reads supporting transposon insertions were clustered together and used for assembling the insertion sequence via wtdbg2 (version 2.5) with default parameters. An insertion with a sequence originating from both KoRV-A and PhER was classified as a recKoRV insertion, and the structure of recKoRV was defined accordingly for Currumbin and Sunshine Coast koalas. Hence, insertions with sequences solely from KoRV-A were deemed as full-length KoRV-A insertions.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the information of identified transposon insertions.
Library strategy: DNA-seq

extract_protocol:
Total DNA was isolated from koala tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen).
Short fragment PCR-free DNA-seq libraries was constructed and sequenced in BGI China or the Broad Institute. Long fragment DNA-seq libraries was constructed and sequenced in Cold Spring Harbor using the PromethION platform.

value: Currumbin


title: R40_NUL


title: Mtb sigH wk3 post-infection, rep4

city: Huntington

first: Sadia

last: Akter

state: WV

address: 1700 Third Ave.

department: Biomedical Sciences

institute: Marshall University

description:
Library name: sample23
10X genomics

data_processing:
demultiplexing, alignment, raw gene expression matrices were by the Cell Ranger software (10x Genomics, version 6.1.1) available on the 10x website
Assembly: Macaca fascicularis 5
Supplementary files format and content: tab seperated values files and matrix files

organism: Macaca fascicularis

source_name: BAL Cells

extract_protocol:
Single-cell suspensions from BAL obtained at different time points were collected and cryopreserved in Cryostor-CS10 (Biolife Solutions, USA) at -70ºC and then used for single cell RNAlibrary preparation as per manufacturer's instructions (10x genomics).
10x 3' GEX

value: BAL Cells

value: Airway cells, Leukocytes

value: Mtb infection after sigH vaccination

tag: time post_vaccination

value: 11 weeks

tag: time post_infection

value: 3 weeks


title: R38_SEB

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, TBP)


title: Mtb sigH wk3 post-infection, rep3

description:
Library name: sample22
10X genomics


title: Sample_3_Microglia_AIR

value: Female

value: 4 Months

value: Microglia


title: Mtb sigH wk3 post-infection, rep2

description:
Library name: sample21
10X genomics


title: R38_NUL

value: REALISM


title: K94276,SunshineCoast,Testis,ONT

value: Testis

value: SunshineCoast


title: Sample_2_Microglia_AIR


title: K20200116,Adelaide,Testis

data_processing:
We used TEMP2-insertion (version 0.1.6) to identify new transposon insertions in Illumina and BGI DNA-seq data.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the information of identified transposon insertions.
Library strategy: DNA-seq

extract_protocol:
Total DNA was isolated from koala tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen).
Short fragment PCR-free DNA-seq libraries was constructed and sequenced in BGI China or the Broad Institute.

value: Adelaide


title: Mtb sigH wk3 post-infection, rep1

description:
Library name: sample20
10X genomics


title: K94276,SunshineCoast,Liver

value: Sunshine Coast


title: BCG wk3 post-infection, rep4

description:
Library name: sample19
10X genomics

value: Mtb infection after BCG vaccination


title: R36_SEB

extract_protocol: A modified protocol of the NucleoSpin 96 RNA tissue kit (Macherey-Nagel) was followed using a vaccum system

value: Patient

value: TruCulture

value: SEB


title: R36_NUL

value: NUL


title: NC1-NC2-HC1-HC2

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: 10x Genomics

data_processing:
Data were analyzed using Seurat package (Version 5.0.1) in RStudio software (Version 4.3.3). We processed single-cell RNA-seq data using Seurat in RStudio, filtering out cells with unique molecular identifier counts below 200. We normalized gene expression data using LogNormalize in Seurat and identified the 2,000 most variable features using the vst method with FindVariableFeatures. The top 10 most variable genes were selected for labeling on a variable feature plot. All gene expressions were scaled to Z-scores with ScaleData. PCA was then conducted using the variable features, with visualization of the PCA results including cell and feature loadings, elbow plot, and dimension plots for the first 15 dimensions. We reduced dimensionality using UMAP on the top 9 principal components to create a UMAP plot for visualization. This data was visualized in two dimensions, clustered (FindClusters), and differentially expressed genes (DEGs) were pinpointed (FindMarkers). Cell types for the control samples were determined using DEGs and corresponding markers. Gene ontology of DEGs was analyzed with GSEA, setting thresholds at fold change over 0.5 and adjusted P-value below 0.05.
Assembly: mm10
Supplementary files format and content: tab separately values files and matrix files

source_name: skeletal muscle stem

extract_protocol:
Cells were immediately fixed and RNA was extracted commercially by GENEWIZ following 10X Genomics SOPs (PN-1000414).
Extracted RNA was prepared for sequencing commercially by GENEWIZ following 10X Genomics SOPs (PN-1000414).

value: skeletal muscle stem

tag: cell line

value: muscle stem

value: WT

value: multiplexed:High CO2, Normal CO2


title: K20191231-2,Adelaide,Testis

value: adult


title: BCG wk3 post-infection, rep3

description:
Library name: sample18
10X genomics

value: BAL Cells

value: Airway cells, Leukocytes

value: 11 weeks

value: 3 weeks


title: R34_SEB

value: REALISM


title: shoot; replicate 2; treated

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description: shoot; replicate 2; treated

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: TSV
Library strategy: BID-Seq

molecule: polyA RNA

organism: Zea mays

source_name: shoot

extract_protocol:
Total RNA isolation: total RNA was isolated according to TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation. PolyA+ RNA isolation: Dynabeads™ mRNA Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment, from the purified total RNA.
With 10 ng synthetic RNA oligos carrying 0%, 20%, 40%, 60%, 80%, or 100% pseudouridine, 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). To perform 3′-adapter ligation, 10 µl 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

value: shoot


title: BCG wk3 post-infection, rep2

description:
Library name: sample17
10X genomics


title: shoot; replicate 1; treated

description: shoot; replicate 1; treated


title: R34_NUL


title: BCG wk3 post-infection, rep1

description:
Library name: sample16
10X genomics


title: R32_SEB


title: shoot; replicate 2; input

description: shoot; replicate 2; input


title: K20190814,Adelaide,Testis

value: Testis

value: Adelaide


title: K20190727,Adelaide,Testis


title: shoot; replicate 1; input

description: shoot; replicate 1; input


title: Mtb-CDC1551 Wk3 post-infection, rep3

description:
Library name: sample15
10X genomics

value: Mtb infection


title: Mtb-CDC1551 Wk3 post-infection, rep2

description:
Library name: sample14
10X genomics


title: Sample_1_Microglia_AIR

extract_protocol:
The microglia cells were isolated by cell sorter, and 1000 cells have their RNA extracted by Broad Institute using TCL buffer containing 1% Beta-Mercaptoethanol.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol65. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

value: Female

value: AIR

value: 4 Months

value: Microglia


title: R30_SEB

value: Patient

value: TruCulture

value: SEB


title: K98214,Currumbin,Ovary,BGI-seq

value: Ovary

value: adult

value: Currumbin


title: stem; polysome; replicate 2

first: CHUAN

last: HE

address: 929 East 57th Street, GCIS E313

data_processing:
Sequencing data with read lengths between 29-35 bp were selected and mapped to the Arabidopsis reference genome (TAIR10) using the HISAT2 aligner. After mapping, coverage at each position along the ORFs was extracted using Ribotricer (https://github.com/smithlabcode/ribotricer), applying the recommended phase-score cutoff for Arabidopsis and default settings. Codon translation efficiency was defined as the reciprocal of the dwell time for each codon, calculated from the relative coverage of codons obtained from ribosome footprinting, and normalized by gene expression levels derived from RNA-seq.
Assembly: TAIR-10
Supplementary files format and content: xlsx
Library strategy: polysome-seq

organism: Arabidopsis

source_name: stem

growth_protocol: Col-0 accession of Arabidopsis were grown at 20 °C with 16 h of light per 24 h. Arabidopsis seedlings, and roots were harvested after growing on 1/2 Murashige and Skoog medium (MS) plates for 7 days. Arabidopsis shoots and roots were harvested after growing on 1/2 Murashige and Skoog medium (MS) plates for 14 days. Arabidopsis Rosetta leaves were harvested after growing in soil for 30 days. Arabidopsis cauline leaf, flower, stem and silique were harvested after flowering. Arabidopsis seeds were collected after the seeds are  totally dry

extract_protocol:
Total RNA isolation: three volume of LS trizol was added to the samples and mixed well for the RNA extract.
The RNA was run in 15% 10 Well TBU gel (EC6885BOX) to select RNA fragment on the size between 20 nt to 40 nt (Pre-stained ladder (DM253S) was used for size reference). Then, libraries were constructed following the procedures of NEB E7330S kit. The constructed libraries were sequenced on the Illumina HiSeq sequencing platform in single read mode with 100 bp per read.

treatment_protocol: The polysome profiling was conducted based on sucrose gradient method as previously published. Brifely, we first prepared the sucrose gradient buffer: Make 60 ml 5% (5 mL 60% sucrose + 49 mL H2O + 6 mL 10X buffer) and 50% (50 mL 60% sucrose + 4 mL H2O + 6 mL 10X buffer) sucrose each in 1X sucrose gradient buffer + 100 ug/ml CHX (Cycloheximide, C1988), 0.1% protease inhibitor and 0.1% SUPERaseIn. Then, place half 50% sucrose buffer at the bottom and half 5% sucrose buffer above to a high speed centeriguge tube (SETON 7042) and make the gradient sucrose buffer with Biocomp Gradient station. For sample preparation, we added the lysis buffer with 20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 100 µg/ml CHX, 1% Triton-X-100, freshly add 1:100 protease inhibitor (Roche), and 40 U/ml SUPERasin (Ambion) to 0.3g freshly grinded nine  Arabidopsis samples with two biological replicates. After 30min lysis, samples were centeriguged at 16,000 g for 15 min and the clear lysate was saved for further step. Then, 5µl Turbo DNase was added to the above 1ml lysate followed with room temperature incubation for 15 min. The lysate was then carefully placed on the top of gradient sucrose buffer and then centrifuged at 28,000 rpm for 3h at 4℃. After centrifuge, we collected the fraction by using Biocomp Gradient station and the 6th, 7th, 8th, 9~14th tubes were collected. At last, the collected tubes were mixed equally for further library preparation. Below is the procedures for the library preparison. We first measured the OD A260 of the mixed fraction of each sample described in the last step and then added RNase I (i.e., OD = 1, 300 ul add 9U RNase I), which followed with incubation at 37 oC for 30 min. After then, three volume of LS trizol was added to the samples and mixed well for the RNA extraction. Next, 300ul chloroform was added and mixed well for 5 min. The samples were then centrifuged for 15 min to collect the supernatant into a new 1.5 ml tube. Next, equal volume of 2-Propanol and 1uL GlycoBlue (AM9516) were added to the above supernatant. Then the above mixture was placed in -80 oC overnight for the RNA precipitation. After centrifuge for 15 min, the precipitation was washed by 70% EtOH and then 15 uL RNase-free H2O was added to resolve the RNA.

value: stem

tag: ecotype


title: K20200104,Adelaide,Testis

tag: Stage


title: K94283,SunshineCoast,Ovary

tag: location

value: SunshineCoast


title: Mtb-CDC1551 Wk3 post-infection, rep1

description:
Library name: sample13
10X genomics

value: BAL Cells

value: Airway cells, Leukocytes

value: 3 weeks


title: R30_NUL

source_name: whole blood

value: REALISM

value: NUL


title: stem; polysome; replicate 1


title: K20191231-1,Adelaide,Testis

value: Testis

value: Adelaide

tag: koala id


title: Mtb sigH wk3 post-vac, rep4

description:
Library name: sample12
10X genomics

value: sigH vaccination


title: K94276,SunshineCoast,Testis


title: K71362,SunshineCoast,Testis


title: R28_SEB

tag: cohort


title: silique; polysome; replicate 2

source_name: silique

value: silique


title: Mtb sigH wk3 post-vac, rep3

description:
Library name: sample11
10X genomics


title: R28_NUL

tag: status

value: Patient


title: silique; polysome; replicate 1


title: Mtb sigH wk3 post-vac, rep2

description:
Library name: sample10
10X genomics


title: R26_SEB

tag: support

value: TruCulture


title: shoot; polysome; replicate 2

value: shoot


title: RECQL5_IP exp2

city: Seville

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

description: anti-FLAG-immunoprecipitated DNA from W303-1AR5 + tetp::RECQL5 exp2

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction (IP) with the supernatant fraction (SUP) by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

organism: Saccharomyces cerevisiae

source_name: RECQL5, exp2, anti-FLAG

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in synthetic complete media plus glucose 2% and minus uracil to mid-log phase at 30°C

extract_protocol: ChIP was carried out as previously described (Katou et al., 2003, 2006): We disrupted 1.5 × 107 cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-FLAG monoclonal antibody M2 (Sigma-Aldrich) was used for ChIP.

tag: antibody

value: anti-FLAG

tag: cell cycle

value: asynchronous

tag: strain

value: W303-1AR5 + tetp::RECQL5


title: Mtb sigH wk3 post-vac, rep1

description:
Library name: sample9
10X genomics

tag: cell type


title: R32_NUL

tag: stimulus


title: R26_NUL


title: BCG wk3 post-vac, rep4

description:
Library name: sample8
10X genomics

tag: treatment

value: BCG vaccination


title: seedling; polysome; replicate 2

source_name: seedling

tag: tissue

value: seedling


title: RECQL5_SUP exp1

description: Input DNA from W303-1AR5 + tetp::RECQL5 exp1

source_name: RECQL5, exp1, none

tag: genotype


title: RECQL5_IP exp1

description: anti-FLAG-immunoprecipitated DNA from W303-1AR5 + tetp::RECQL5 exp1

source_name: RECQL5, exp1, anti-FLAG


title: R24_SEB

value: SEB


title: seedling; polysome; replicate 1


title: BCG wk3 post-vac, rep3

description:
Library name: sample7
10X genomics

value: BAL Cells

value: Airway cells, Leukocytes

tag: time post_vaccination

tag: time post_infection


title: R24_NUL

value: REALISM


title: seed; polysome; replicate 2

source_name: seed

value: seed

tag: ecotype


title: Atlantic salmon, pectoral fin, control

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

country: United Kingdom

institute: The University of Edinburgh

description: Library name: Sample 4

data_processing:
Genome indexing and library mapping was performed with STAR (version 2.7.10a).
Assembly: We appended the mitochondrial genome from the ENSEMBL V2 Atlantic salmon genome (Salmo_salar.ICSASG_v2.dna_rm.toplevel.fa.gz, v2, release 105, masked genome, assembly ID: GCA_000233375.4) to the ENSEMBL V3 Atlantic salmon genome (Salmo_salar.Ssal_v3.1.dna_rm.toplevel.fa.gz, v3.1, release 106, masked genome, assembly ID: GCA_905237065.2) for both the .gff and .fna files prior to indexing. For coho salmon, we appended this species’ mitochondrial genome (version NC_009263.1, NCBI) to the ENSEMBL V2 coho salmon genome (Oncorhynchus_kisutch.Okis_V2.dna_rm.toplevel.fa.gz, v2, release 106, masked genome, assembly ID: GCA_002021735.2) for both the .gff and .fna files prior to indexing.
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file

organism: Salmo salar

source_name: skin

extract_protocol:
Nuclei were extracted in accordance with Ruiz Daniels et al. (2023) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484441/). In brief, approximately 45 mg tissue samples were cut with scissors in 1 mL of TST buffer for 10 minutes on ice before being filtered through a 40 µm Falcon™ cell strainer (Thermo Fisher Scientific, catalog no. 08-771-2). A further 1 mL of TST and 3 mL of 1X PBS + BSA buffer were added to each sample before centrifuging at 4°C for 5 minutes at 500 g. Samples were resuspended in 1 mL 1X ST buffer filtered again through a 40 µm cell strainer, stained with Hoechst 33342 Solution (Thermo Fisher Scientific, catalog no. 62249) and then nuclei integrity was visually assessed using a fluorescent microscope. A disposable flow haemocytometer (C-Chip Neubauer Improved (100 µm depth), NanoEnTek, catalog no. DHC-N01) was then used to estimate nuclei counts.
Samples were processed with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10X Genomics) using the protocol outlined in the User Guide (CG000315 Rev C). Samples were diluted with nuclease-free water to a target concentration that would recover approximately 7000 nuclei in the final library. Samples were then loaded on the Chromium Controller for nuclei droplet formation. After subsequent nuclei and UMI barcoding and reverse transcription, resulting cDNA was then amplified, fragmented, and indexed with Truseq adapters and Illumina sample indexes.

value: skin

value: control


title: R22_SEB


title: RECQL5_SUP exp2

description: Input DNA from W303-1AR5 + tetp::RECQL5 exp2

source_name: RECQL5, exp2, none


title: BCG wk3 post-vac, rep2

description:
Library name: sample6
10X genomics

value: 3 weeks


title: seed; polysome; replicate 1


title: rosettaLeaf; polysome; replicate 2

source_name: rosetta

value: rosetta


title: R22_NUL

value: Patient

value: NUL


title: shoot; polysome; replicate 1

value: shoot


title: BCG wk3 post-vac, rep1

description:
Library name: sample5
10X genomics


title: naïve wk-1, rep4

description:
Library name: sample4
10X genomics


title: R20_SEB

value: TruCulture


title: rosettaLeaf; polysome; replicate 1


title: naïve wk-1, rep2

description:
Library name: sample2
10X genomics


title: R18_SEB


title: root; polysome; replicate 2

source_name: root

value: root


title: SSc3-2

city: Saga

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

country: Japan

institute: Saga Medical School

hyb_protocol: desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

label_protocol: Desalted Labeled RNA were prepared from 100ng total RNA Agilent’s miRNA Complete Labeling and Hyb Kit

extract_protocol: Total RNA from the fibroblasts was isolated with the NucleoSpin miRNA kit (Takara).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line


title: naïve wk-1, rep1

description:
Library name: sample1
10X genomics


title: SSc7-1


title: root; polysome; replicate 1


title: R18_NUL

last: Debombourg


title: SSc3-1


title: SSc7-2


title: R14_SEB


title: Cultured hypocotyl knat7 KNAT7-EYFP biol rep 3

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

institute: Graduate School of Science, The University of Tokyo

description: Library name: Sample 12

data_processing:
RNA-seq reads were mapped on the TAIR10 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- clip3pNbases, 50; -- quantMode GeneCounts parameters.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file for RNA-seq

organism: Arabidopsis thaliana

source_name: Hypocotyl

growth_protocol: Sample1~6: Seedlings were grown in MS liquid medium. Sample7~12: Seedlings were grown on MS agar plates in the dark.

extract_protocol:
RNA is harvested using FavorPrep Plant Total RNA Mini Kit. 0.5 µg of total RNA was used for the construction of sequence libraries.
RNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems).

treatment_protocol: Sample1~6: Seedling were cultured in MS liquid medium supplemented with 1.25 mg/L 2,4-D, 0.25 mg/L kinetin, and 10 µM bikinin for 3 days. Sample7~12: Hypocotyls of etiolated seedlings were excised and cultured in liquid MS medium supplemented with 1 mg/L kinetin, 0.1 mg/L 2,4-D, and 10 µM bikinin for 5 days.

value: Hypocotyl

value: knat7 KNAT7-EYFP

value: xylem differentiation


title: flower; polysome; replicate 2

source_name: flower

value: flower


title: Cultured hypocotyl knat7 KNAT7-EYFP biol rep 2

description: Library name: Sample 11


title: Atlantic salmon, dorsal fin,pectoral

description: Library name: Sample 3


title: R14_NUL


title: Cultured hypocotyl knat7 KNAT7-EYFP biol rep 1

description: Library name: Sample 10


title: flower; polysome; replicate 1


title: caulineLeaf; polysome; replicate 2

source_name: cauline

value: cauline


title: Cultured hypocotyl knat7 biol rep 3

description: Library name: Sample 9


title: M30-2


title: R12_SEB

value: SEB


title: R20_NUL

value: REALISM


title: R12_NUL


title: naïve wk-1, rep3

description:
Library name: sample3
10X genomics

source_name: BAL Cells

value: BAL Cells

value: Airway cells, Leukocytes


title: caulineLeaf; polysome; replicate 1


title: HC4

first: Ariel

last: Jaitovich

email: balnisj@amc.edu, jaitova@amc.edu

address: 47 New Scotland Ave.

department: MCP

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_116

data_processing:
Automated RPM normalization by S5 Torrent software produced RPM normalized CHP files and normalized counts.
CHP file analysis using ThermoFisher Transcriptome Analysis Console (TAC) Software.
Assembly: AmpliSeq_Mouse_Transcriptome_v1
Supplementary files format and content: RPM normalized .CHP files
Supplementary files format and content: Normalized absolute counts for all samples in one .xls file.

source_name: Skeletal muscle stem cells

growth_protocol: Pax7-GFP inducible reporter C57/B6 littermates were grown to 12 weeks of age then tamoxifen induced and treated for 4 weeks and collected at 16 weeks of age.

extract_protocol:
Mouse hind leg muscles from both legs were collected and enzymatically digested. Mononuclear cells were sorted with FACS and Pax7-GFP+ cells were collected. After sorting RNA was isolated with TriZol following standard techniques and DNA was digested.
Library construction was performed automatically by the Ion Chef robotic system following manufacturers protocols.

treatment_protocol: Mice at 12 weeks of age were all tamoxifen induced and placed in NC or HC conditions for 4 weeks.

value: Skeletal muscle stem cells

value: Primary stem cells

value: Pax7+ stem cells

value: Inducible Pax7-GFP C57BL/12

value: Hypercapnia


title: M30-1


title: Cultured hypocotyl knat7 biol rep 2

description: Library name: Sample 8


title: R10_SEB

first: Marion

value: Patient


title: Cultured hypocotyl knat7 biol rep 1

description: Library name: Sample 7


title: HC3

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_115

value: Inducible Pax7-GFP C57BL/11


title: R10_NUL

value: TruCulture

value: NUL


title: Cultured cotyledon knat7 KNAT7-EYFP biol rep 3

description: Library name: Sample 6

source_name: Cotyledon

value: Cotyledon

value: knat7 KNAT7-EYFP


title: HC2

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_114

value: Inducible Pax7-GFP C57BL/10


title: R08_SEB

source_name: whole blood


title: NDF5-2


title: Cultured cotyledon knat7 KNAT7-EYFP biol rep 2

description: Library name: Sample 5

value: xylem differentiation


title: R08_NUL


title: NC3

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_112

value: Inducible Pax7-GFP C57BL/8

value: Normocapnia


title: NDF5-1


title: Cultured cotyledon knat7 KNAT7-EYFP biol rep 1

description: Library name: Sample 4


title: Cultured cotyledon knat7 biol rep 3

description: Library name: Sample 3


title: R06_SEB

value: REALISM

value: SEB


title: R06_NUL


title: NC2

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_110

value: Skeletal muscle stem cells

value: Inducible Pax7-GFP C57BL/7


title: Cultured cotyledon knat7 biol rep 2

description: Library name: Sample 2


title: R04_SEB


title: Cultured cotyledon knat7 biol rep 1

description: Library name: Sample 1


title: ATACseq_T3M4_BI653048_Rep3

status: Public on Jan 14 2025

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample68

data_processing:
Paired end sequencing reads were filtered for adapter contamination with cutadapt/2.8 and mapped to the reference genome assembly hg38 using bowtie2 with --dovetail. BamTools Filter was used for removing low quality (mapQ >= 30) and mitochondrial reads. Resulting bam file was converted to a bed file with bedtools/2.30.0 bamtobed. Peak calling and bedgraph generation was performed using macs2 callpeak using shift and extend method to center peaks at 5’ cut site (shift -100 extension size 200). The data was visualized by using bedGraphToBigWig (ucscbigtools/11-Aug-2023).
Assembly: hg38
Supplementary files format and content: bigwigs for each condition, controls normalized to BI 653048 treatment
Supplementary files format and content: peakfile
Supplementary files format and content: Alternative control normalization against siGATA6

source_name: cell line

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol: For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.

value: cell line

value: PDAC


title: p146_2BC_backbone_S1

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description:
Library name: p146_2BC_backbone_S1
Mapping barcode pairs in parental plasmid backbone for dictionary generation.

library_source: other

data_processing:
Short-read data (p146 barcode pairs dictionary): Read counts corresponding to identical barcodes 1 and 2 were first piled up.  First, representation of barcodes (separately, summing reads from pairs with 3 or more counts) was inspected, revealing a trimodal distribution: low counts (<=5 reads) corresponding to likely sequencing or PCR errors (BC1: n=1010349, 2.5% of reads; BC2: n=1162035, 2.9% of reads), intermediate counts barcodes making up the bulk of the coverage (BC1=6345673 barcodes, 92.9% of reads; BC2: n=6596695 barcodes, 93.5% of reads), and high-count barcodes (BC1: n=827, 4.6% of reads; BC2: n=530 barcodes, 3.7% of reads), possibly emerging from low level of clonal expansion during cloning. In the case of BC2, a single sequence (ATAACGACTTGTGAGC) was drastically over-represented (2.5% of reads). This barcode and all other barcodes within a Levenshtein distance of 2 or less to it (n=402 barcode, 0.25% of reads) were not considered in downstream analysis to avoid spurious non-unique pairs. We note our barcode space was not saturated at that level of tolerance to mismatches (average of 3 BCs within our BC2 reads within Levenshtein distance of 2 to repeated 1-shufflings of the ATAACGACTTGTGAGC sequence). Further, barcodes with 10 or more consecutive Gs, or containing truncated BC (with the detected post-BC sequences: ATTAAAC for BC1, TAGCGCG for BC2) were removed, corresponding to a minute proportion of the library (BC1: n=9533, 1.1% of reads; BC2: n=3910 , 0.06% of reads). To avoid mismatches from high-representation barcodes being retained as spurious mid-counts barcodes, the list of mid-counts barcode was pruned by removing those within Levenshtein distance of 2 from the high-counts barcodes (number mid-counts barcodes removed in pruning process: BC1 n=16386; BC2 n=4747). All remaining pruned mid-counts barcodes were retained downstream (BC1: n=6321002; BC2: n=6588391). Finally, the high-counts barcodes were further error-corrected by generating an undirected graph connecting barcodes within Levenshtein distance of 2 or less. The most highly represented barcode from connected components were considered the valid barcode. Rare clusters composed of many well-represented barcodes (fold-change between max/min < 10 within cluster) were discarded as possibly ambiguous, leading respectively to n=609 and n=420 error-corrected high count BC1 and BC2 sets. All in all, these filtering steps generated a list of well-represented high quality barcodes (BC1: n=6321611, BC2: n=6588811). From these well-represented BC1 and BC2, we finally filtered on unique pairing between the two. Specifically, all paired barcodes with 2 or more reads were filtered for members present in both separately valid sets. Then, the proportion of reads to each barcode within a pair (e.g., number of reads to BC1 from a given pair over number of reads containing the same BC1 across all pairs in the library) was computed. Only pairs for which >99% of reads mapped to a unique pair were retained. This led to a final set of n=5586772 valid barcode pairs used for downstream assessment. Only exact matches to BC1 and BC2 constituents of these final pairs were used for filtering long-read data and setting the denominator in our barcode swap quantification.
ONT reads were processed by first searching for ‘signpost’ sequences, corresponding to constant regions flanking our barcodes, within the reads.
Signpost sequences:
Left BC1 upstream: CGCGTTTAAT
Left BC1 downstream: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
Right BC2 upstream: GATCCGTCGATCGACTGAGT
Right BC2 downstream: TAGCGCGCCATTAGGCATGA
To do so, we ran Smith-Waterman (ssw-align17, option -r) using the nanopore reads as target and signposts as query, and reformatted the output to collate alignment scores from all signposts for each target read. Reads for which all 4/4 signposts were detected (75% match or higher) in the concordant orientations and expected barcode order (BC1 position < BC2 for + strand, and vice versa). The sequences corresponding to barcodes, insert index (one for each library), and insert were obtained based on local position reference frames set by signpost positions and length and strand. All sequences were then converted for forward strand for downstream analysis (reverse complement for reads mapped to - orientation). Reads were demultiplexed based on the insert index by calculating the Levenshtein distance to the closest index from the expected list:
>>>>>>>>>>>>>>>
Insert class, Insert index, Primer used for insert amplification
p146 (parental), CTCTTCAGAT, NA
Short, homologous, AGACTCAAGT, o937
Short, non-homologous, GAGACGGTCA, o941
Mid-sized, homologous, AGACGATCTG, o938
Mid-sized, non-homologous, GAGACCCTAA, o942
Long, homologous, AGACATTGGC, o939
Long, non-homologous, GAGACCATCG, o943
>>>>>>>>>>>>>>>
The second best match was also retained. Any reads for which the best match was within a Levenshtein distance 1, and the difference to the second best match was at least 2 was deemed unambiguously demultiplexable. Finally, only reads with BC1 and BC2 (separately, i.e., irrespective of whether their pairing is correct) corresponding to exact match in our final set of barcodes in our dictionary of valid pairs were retained from quantification. Reads were deemed ‘full length’ with regards to BC-to-BC distance if they fell within the 1% to 99% size distribution from the size selected & digested reads. Only full BC-to-BC length reads were considered for quantification of main figure. Full ITR-to-ITR length boundaries for classification as full length read  were taken to be: plasmids parental p146: 800 to 1050 nt; plasmids all others: 2000 to 2500 nt, AAV all except p153×-mid and p153×-short: 2250 to 2750 nt, AAV p153×-mid: 1100 to 1400 nt, and AAV p153×-short: 500 to 750 nt.
To collate metadata on insert sequences, we aligned the inserts to both the E. coli genome (GCF000005845.2) and plasmid CN1839 (Addgene #163509) using minimap2 (version 2.28, option -x map-ont). Alignments with >0.65 fraction of matching bases (matching bases in alignment/alignment length including gaps) were retained. For a given read and start alignment position within the read, the best scoring (fraction of matching bases) alignment was retained. To further reduce redundant alignments to homologous sections, each read with multiple listed alignments was considered. Overlap (in the read reference frame) between alignments was computed, and alignments were considered redundant if they overlapped by >50% (in practice, the distribution of overlap was nearly perfectly bimodal between 0% and 100%), and the best alignment was retained. To properly categorize inserts overlapping with the end of the plasmid (minimap does not deal with circular chromosomes), reads with two disjoint alignments and one starting within position 5 or ending within 5 of the end of the plasmid were re-categorized as non-composite (unique overlapping the circular junction). Based on these, read inserts were then categorized based on whether they contained a non-mapped (based on our stringent procedure), a unique alignment (to either the E. coli genome or CN1839), or a composite alignment (two or more non-overlapping alignments to either the E. coli genome, CN1839, or both). Quantification  from the plasmid inserts aligned with expectations (homologous libraries entirely comprised of simple fragments mapping to the plasmid, non-homologous libraries coming from a mixture of both given the source material used for tagmentation).
Assembly: Custom constructs, N/A.
Library strategy: Custom amplicons

molecule: other

organism: synthetic construct

source_name: Escherichia coli (for plasmid amplification)

extract_protocol:
Plasmids were purified with Zymo MidiPrep kit. AAV samples were sequenced by Plasmidsaurus.
See manuscript for details on cloning of libraries p149-p154 (dually barcoded inserts flanked by AAV2 ITRs, with different insert lengths and class [homologous/non-homologous] between barcodes).  The library for barcode dictionary generation from parental backbone p146 was generated by amplifying by PCR (primers o945+o946v2 containing P5 and P7 Illumina adapters) the GFP stuffer insert flanked by the two barcodes using 5 ng starting template (50 uL reaction, Kapa Robust, standard conditions, 10 cycles) and followed by 1x ampure beads cleanup. The resulting library was sequenced using custom primers as a fraction of a NextSeq2000 P2 100 cycles run (read1: 42 cycles with o947, index1: 20 cycles with o761 Nextera_read1 [into SapI restriction site and GFP, not used], index2: 20 cycles with o948 [into GFP, not used], read2: 16 cycles with o762 Nextera_index2). Sequencing data was demultiplexed from other samples based on the first 10 indices of read1 (GATCCGTCGA) using bcl2fastq with base mask i10y*,y*,y*,y*, yielding 195.6M reads to associate barcodes from p146. BC1 (5’/left of insert) was on cycles 1 to 16 within read 2, BC2 (3’/right of insert) was on cycles 21 to 36 within read1.  For long read sequencing, inserts from the barcoded plasmids were released by MluI+NotI digestion and size selected on agarose (Zymoclean kit). Size selected inserts were pooled and submitted to Plasmidsaurus for a custom Oxford Nanopore sequencing project.  AAV preps were submitted to Plasmidsaurus for direct sequencing (which involves an annealing step, end-repair and adapter ligation) with Oxford Nanopore.


title: ATACseq_T3M4_BI653048_Rep2

description: Library name: Sample67


title: R04_NUL

city: Oullins-Pierre-Bénite

address: 165 chemindu grand revoyet

institute: biomerieux

growth_protocol: Incubation inside a Truculture stimulation tube (from Myriad RBM), 37C, 22h.


title: ATACseq_T3M4_DMSO_Rep3

description: Library name: Sample65


title: ATACseq_L36pl_BI653048_Rep3

description: Library name: Sample62


title: ATACseq_L36pl_BI653048_Rep1

description: Library name: Sample60


title: ATACseq_L36pl_BI653048_Rep2

description: Library name: Sample61


title: ATACseq_T3M4_DMSO_Rep2

description: Library name: Sample64


title: HC1

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_113

value: Primary stem cells

value: Pax7+ stem cells

value: Inducible Pax7-GFP C57BL/9

value: Hypercapnia


title: ATACseq_L36pl_DMSO_Rep2

description: Library name: Sample58


title: ATACseq_L36pl_DMSO_Rep1

description: Library name: Sample57


title: ATACseq_TCCPAN2_BI653048_Rep3

description: Library name: Sample56


title: ATACseq_TCCPAN2_BI653048_Rep2

description: Library name: Sample55


title: ATACseq_TCCPAN2_BI653048_Rep1

description: Library name: Sample54


title: ATACseq_TCCPAN2_siGATA6_Rep3

description: Library name: Sample53


title: ATACseq_TCCPAN2_siGATA6_Rep1

description: Library name: Sample51


title: ATACseq_TCCPAN2_siGATA6_Rep2

description: Library name: Sample52


title: ATACseq_TCCPAN2_Ctrl_Rep3

description: Library name: Sample50


title: ATACseq_TCCPAN2_Ctrl_Rep2

description: Library name: Sample49


title: ATACseq_TCCPAN2_Ctrl_Rep1

description: Library name: Sample48


title: NC1

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_109

value: Inducible Pax7-GFP C57BL/6


title: ATACseq_AsPC1_BI653048_Rep1

description: Library name: Sample45


title: ATACseq_AsPC1_BI653048_Rep3

description: Library name: Sample47


title: ATACseq_AsPC1_siGATA6_Rep3

description: Library name: Sample44


title: ATACseq_AsPC1_BI653048_Rep2

description: Library name: Sample46


title: ATACseq_AsPC1_siGATA6_Rep2

description: Library name: Sample43


title: ATACseq_AsPC1_siGATA6_Rep1

description: Library name: Sample42


title: ATACseq_T3M4_BI653048_Rep1

description: Library name: Sample66


title: ATACseq_AsPC1_Ctrl_Rep1

description: Library name: Sample39


title: ATACseq_T3M4_DMSO_Rep1

description: Library name: Sample63