title: pup-3(tm5089);pup-4(om141);pup-1/-2(om129)_mRNA-seq_rep3


title: pup-4(om141)_mRNA-seq_rep3

status: Public on Jul 17 2024

type: SRA

city: Bloomington

first: Leanne

last: Kelley

state: IN

address: 1001 E Third St

country: USA

institute: Indiana University

library_source: other

data_processing:
Basecalled with guppy_basecaller (v4.4.2), demultiplexed with guppy_barcoder (v4.4.2), FASTQ chunks within each genotype/replicate were combined into one FASTQ file using the cat command in Unix, reads were mapped to the transcriptome using minimap2 with the parameters '-ax map-ont --MD -k14' and using the RefSeq GCF 000002985.6 reference. In parallel, the non-basecalled FAST5 files were demultiplexed with the demux_fast5 (v4.1.1) command from the ont_fast5_api software and these were used as input for the find_tails command in the program tailfindr (polyu branch). The resulting tails count table and the SAM file from the mapping step were used as input for the annotate_tails function in tailfinder to produce the final counts table. This was loaded into R to convert to a matrix.
Assembly: RefSeq GCF 000002985.6
Supplementary files format and content: Total counts (not parsed by tail type) in a matrix

molecule: other

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: 1 day old adult hermaphrodites raised at 22°C

extract_protocol:
RNA was isolated from whole animals using the TRIzol (Invitrogen) method.
Ribosomal-depleted RNA was subjected to the Nano3P-seq protocol (modification of the ONT direct cDNA-seq kit, published by Begik et al. 2023).

tag: tissue

value: whole animal

tag: gender

value: hermaphrodite

tag: genotype

tag: developmental stage

value: 1-day adult


title: pup-3(tm5089);pup-4(om141);pup-1/-2(om129)_mRNA-seq_rep2


title: pup-1/-2(om129)_mRNA-seq_rep1


title: pup-1/-2(om129)_mRNA-seq_rep4


title: pup-2(tm4344)_mRNA-seq_rep4


title: pup-3(tm5089)_mRNA-seq_rep1


title: pup-2(tm4344)_mRNA-seq_rep3


title: pup-3(tm5089);pup-4(om141);pup-1/-2(om129)_mRNA-seq_rep1


title: pup-1(tm1021)_mRNA-seq_rep4


title: splenic monocytes, vanco gavaged + L654, rep3

status: Public on Jun 20 2024

city: Avon

first: Beiyan

last: Zhou

state: Connecticut

address: 263 Farmington Ave, Immunology

department: Immunology

institute: UCONN Health

description:
matrix column 11
VanLip3

library_source: transcriptomic

data_processing:
Reads in Fastq files were aligned using HISAT2 v2.2.1 on the GRCm38 index, with SAMtools v1.9 for BAM conversion.
A matrix of fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated using Stringtie v2.1.3 with Ballgown on the GRCm38 index.
FPKM data was converted to gene count data matrix using tximport v1.26.1 R package for differential gene expression analysis using DESeq2 v1.38.3 R package.
Assembly: GRCm38
Supplementary files format and content: comma separated file including unfiltered FPKM
Supplementary files format and content: comma separated file including unfiltered gene counts

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: in vivo

extract_protocol:
RNA was purified using miRNeasy Mini Kit (Qiagen, Cat 217084).
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA library prep kit following manufacter's protocols.

treatment_protocol: 2mg total/mouse/day of Vancomycin (Sigma-Aldrich, St. Louis, MO) (or water-control) was given as two oral gavage-administrations of 1mg via oral gavage for 6 days. Mice were then “rested” without antibiotics for 6 to 8 days and either received none or exogenous lipid L654 via retro-orbital administration on day 7, 9, and 11.

value: Spleen

tag: cell type

value: Monocyte

tag: strain

tag: treatment

value: Vancomycin gavage and L654

tag: Sex

value: Female


title: pup-4(om141)_mRNA-seq_rep2


title: pup-3(tm5089)_mRNA-seq_rep3


title: N2_mRNA-seq_rep2


title: pup-3(tm5089)_mRNA-seq_rep2


title: pup-2(tm4344)_mRNA-seq_rep2


title: pup-2(tm4344)_mRNA-seq_rep1


title: pup-1(tm1021)_mRNA-seq_rep2


title: Vanco gavaged, rep3 [RC6]

status: Public on Jun 12 2024

description: matrix column 8

treatment_protocol: 2mg total/mouse/day of Vancomycin (Sigma-Aldrich, St. Louis, MO) (or water-control) was given as two oral gavage-administrations of 1mg via oral gavage for 6 days. Mice were then “rested” without antibiotics for 6 to 8 days.

value: Vancomycin gavage


title: splenic monocytes, vanco gavaged + L654, rep2

description:
matrix column 10
VanLip2


title: splenic monocytes, vanco gavaged + L654, rep1

description:
matrix column 9
VanLip1


title: pup-1(tm1021)_mRNA-seq_rep1


title: pup-1(tm1021)_mRNA-seq_rep3


title: splenic monocytes, vanco gavaged, rep3

description:
matrix column 8
Van3


title: Normal Chow Diet 13

status: Public on May 15 2024

city: Dallas

first: Hao

last: Zhu

state: TX

address: 6000 Harry Hines Blvd.

department: Children’s Research Institute

institute: University of Texas Southwestern Medical Center

data_processing:
RNA-seq data was analyzed with nf-core/rnaseq (v3.14.0) pipeline. Default parameters were employed.
STAR was used to map the raw FastQ reads to the reference genome. Salmon was used to perform gene/transcript quantification.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

molecule: total RNA

source_name: liver

extract_protocol:
Trizol and the Qiagen RNeasy mini kit (#74104).
NuGen Ovation Mouse RNA-Seq Systems 1–16

treatment_protocol: Normal Chow Diet

value: liver

value: Littermate WT Cre BL6

value: Normal Chow Diet


title: splenic monocytes, vanco gavaged, rep2

description:
matrix column 7
Van2


title: Normal Chow Diet 10

value: Littermate WT Cre BL5


title: Normal Chow Diet 4

value: Littermate WT Cre BL2


title: C. senegalense total RNA-seq, native

status: Public on May 06 2024

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

data_processing:
RNA-seq data were processed using cutadapt v4.2 to remove adapter sequences, trim low-quality ends from reads, and exclude reads shorter than 18 bp.
Trimmed and filtered reads were mapped to a reference (ATCC25772 or concateinated BL21 genome (GenBank accession GCA_013166975.1) and plasmid) using bwa-mem2 v2.2.1 with default parameters. SAMtools v1.17 was used to filter uniquely mapped reads (MAPQ > 1), as well as used to sort and index the uniquely mapped reads.
Coverage tracks were generated using bamCoverage v3.5.1 with a bin size of 1, read extension to fragment size, and normalization by counts per million mapped reads (CPM) with exact scaling.
Assembly: For Cse native RNA-seq, the reference genome can be found at https://genomes.atcc.org/genomes/a91dae517b3c42e7. For all others, reference files can be found in Žedaveinytė et al. (2024) Supplementary table 3.
Supplementary files format and content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage v3.5.1.

organism: Clostridium senegalense

growth_protocol: E. coli str. BL21 (sSL0026) was transformed with plasmids encoding CboIStron with mutant tnpAS (pSL5878), CseIStron-1 (pSL6566) or CseIStron-2 with frameshifted tnpAS (pSL6630). Single colonies were inoculated in liquid LB with spectinomycin (100 µg mL−1) and grown overnight. The next day, the culture was used to inoculated 50 mL of liquid LB with spectinomycin (100 µg mL−1) and IPTG (0.1 mM) at 100× dilution and grown until OD600 reached 0.5. 1 ml of the culture was centrifuged at 6,000 rpm for 5 min and the resulting pellet was used for RNA extraction. A Clostridia strain encoding IStrons with ~80% similarity to the CboIStron experimentally characterized in this study was obtained from ATCC (strain 25772), where it was defined as belonging to an unknown species classification. Internal rRNA phylogenetic analysis led to the assignment of this strain as a member of species senegalense. C. senegalense was cultured from a lyophilized ATCC pellet in 5 mL of Gifu Anaerobic Medium Broth, Modified (mGAM; HyServe) in an anaerobic chamber (5% H2, 10% CO2 and 85% N2). All media was pre-reduced for ~24 hours before use in culturing. C. senegalense was then banked as a glycerol stock (final concentration 20%) and sub-cultured into 100 mL cultures of mGAM. The growth of these cultures was monitored with a spectrophotometer over ~6 h until a final OD600 of 0.4-0.6 was reached (exponential phase), at which point cultures were poured into two 50 mL conical tubes and cooled on ice for 10 min. The cultures were then centrifuged at 4,000 g for 10 min at 4 °C, the supernatant was decanted, and cell pellets were flash frozen in liquid nitrogen. Pellets were stored at -80 °C until RNA extraction and processing.

extract_protocol:
RNA from E. coli was extracted by resuspending cell pellet in 1 ml Trizol and incubating at room temperature for 10 min before adding 200 ul chloroform. The tubes were mixed and centrifuged at 12,000 g for 15 min at 4 °C. The aqueous phase was transferred to a new tube and purified using Monarch RNA Cleanup Kit (NEB). RNA was stored at -80 °C until library preparation. RNA from C. senegalense cell pellets were extracted in 96-well format using a silica bead beating-based protocol adapted from a prior study Ji et al., 2019, Nat Methods. Briefly, 200 µL of 0.1 mm zirconia silica beads (Biospec,) were added to each well of 96-well deep-well plates (Thermo Fisher Scientific). Next, cell pellets were resuspended in 500 µL DNA/RNA shield buffer (Zymo Research) and transferred to separate wells, and the plates were affixed with a sealing mat and centrifuged for 1 min at 4,500 g. To avoid overheating, the plates were vortexed for 5 s and incubated at −20 °C for 10 min before beating. Then, plates were fixed on a bead beater (Biospec) and subjected to bead beating for 5 min, followed by a 10 min cooling period. The bead beating cycle was repeated three times, and plates were then centrifuged at 4,500 g for 5 min to remove cell debris. Next, 60% of the bead beating volume was transferred to the Quick-RNA Miniprep Plus kit (Zymo Research), and RNA was purified using the manufacturer’s protocol for gram positive bacteria. RNA quality was assessed using the 260/280 nm ratio (~2.0) as measured by Nanodrop, and concentration was measured by the Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific) using the manufacturer’s protocol. RNA was stored at -80 °C until library preparation.
For total RNA-seq library preparation of samples from E. coli, 200 ng of purified total RNA was depleted for ribosomal RNA with Ribo-Zero Plus rRNA Depletion kit (illumina) following the manufacturers protocol and used for downstream library preparation. For samples from C. senegalense, 10 µg of purified RNA was treated with Turbo DNase I (Thermo Fisher Scientific) for 1 h at 37 °C using the manufacturer’s protocol. A 2× volume of Mag-Bind TotalPure NGS magnetic beads (Omega) was added to each sample, and the RNA was purified using the manufacturer's protocol. The RNA was then diluted in NEBuffer2 (NEB) and fragmented by incubating at 92 °C for 1.5 min. To generate RNA with 5′-monophosphate and 3′-hydroxyl ends, samples were treated with RppH (NEB) supplemented with SUPERase•In RNase Inhibitor (Thermo Fisher Scientific) for 30 min at 37 °C, followed by T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB) for 30 min at 37 °C. Samples were column-purified using RNA Clean & Concentrator-5 (Zymo Research), and the concentration was determined using the DeNovix RNA Assay (DeNovix). Illumina adapter ligation and cDNA synthesis were performed using the NEBNext Small RNA Library Prep kit. Dual index barcodes were added by PCR amplification (12 cycles), and the cDNA libraries were purified using the Monarch PCR & DNA Cleanup Kit (NEB). High-throughput sequencing was performed on an Illumina NextSeq 550 in paired-end mode with 75 cycles per end for E. coli samples and 150 cycles per end for C. senegalense samples.

tag: cell line


title: C. senegalense IStron-1 total RNA-seq, heterologous

organism: Escherichia coli


title: splenic monocytes, water gavaged, rep3

description:
matrix column 5
Con3

value: Water gavage


title: splenic monocytes, water gavaged, rep2

description:
matrix column 4
Con2


title: Vanco gavaged, rep2 [RC5]

description: matrix column 7


title: splenic monocytes, water gavaged, rep1

description:
matrix column 3
Con1


title: C. botulinum IStron total RNA-seq, heterologous


title: Normal Chow Diet 7

value: Littermate WT Cre BL3


title: C. botulinum dTnpB RIP

data_processing:
RNA-seq data were processed using cutadapt v4.2 to remove adapter sequences, trim low-quality ends from reads, and exclude reads shorter than 18 bp.
Trimmed and filtered reads were mapped to a reference (concatenated MG1655 genome (GenBank accession AKVX01000001.1) and plasmid) using bwa-mem2 v2.2.1 with default parameters. SAMtools v1.17 was used to filter uniquely mapped reads (MAPQ > 1), as well as used to sort and index the uniquely mapped reads.
Coverage tracks were generated using bamCoverage v3.5.1 with a bin size of 1, read extension to fragment size, and normalization by counts per million mapped reads (CPM) with exact scaling.
Assembly: Reference files can be found in Žedaveinytė et al. (2024) Supplementary table 3.
Supplementary files format and content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage v3.5.1.

growth_protocol: E. coli str. K-12 substr. MG1655 (sSL0810) was transformed with plasmids encoding ωRNA and 3×FLAG-CboTnpB (pSL5412) or 3×FLAG-CboTnpB(D189A) (pSL5413). Single colonies were inoculated in liquid LB with spectinomycin (100 µg mL−1) and grown overnight. The next day, the culture was used to inoculated 50 mL of liquid LB with spectinomycin (100 µg mL−1) at 100× dilution and grown until OD600 reached 0.5.

extract_protocol:
10 mL of culture was centrifuged at 4,000 g for 10 min at 4 °C, and the supernatant was removed. The pellet was washed once with 1 mL of cold TBS (20 mM Tris-HCl (pH 7.5 at 25 °C), 150 mM NaCl), centrifuged at 10,000 g for 5 min at 4 °C, the supernatant was removed, and the resulting pellet was flash-frozen in liquid nitrogen. Pellets were stored at -80 °C. Antibodies for immunoprecipitation were conjugated to magnetic beads as follows: for each sample, 30 μL Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 mL RIP lysis buffer (20 mM Tris-HCl (pH 7.5 at 25 °C), 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 mL RIP lysis buffer, combined with 10 μL anti-FLAG M2 antibody (Sigma-Aldrich, F3165), and rotated for >3 hours at 4 °C. Antibody-bead complexes were washed 3× to remove unconjugated antibodies, and resuspended in 30 μL RIP lysis buffer per sample. To generate cell lysates, flash-frozen pellets were first resuspended in 1.2 mL RIP lysis buffer supplemented with cOmplete Protease Inhibitor Cocktail (Roche) and SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). Cells were then sonicated for 1.5 min total (2 s ON, 5 s OFF) at 20% amplitude. To clear cell debris and insoluble material, lysates were centrifuged for 15 min at 4 °C at 21,000 g, and the supernatant was transferred to a new tube. At this point, a small volume of each sample (24 μL, or 2%) was set aside as the “input” starting material and stored at -80 °C.For immunoprecipitation, each sample was combined with 30 μL antibody-bead complex and rotated overnight at 4 °C. The next day, each sample was washed 3× with ice-cold RIP wash buffer (20 mM Tris-HCl (pH 7.5 at 25 °C), 150 mM KCl, 1 mM MgCl2). After the last wash, beads were resuspended in 1 mL TRIzol (Thermo Fisher Scientific) and incubated at RT for 5 min to allow separation of RNA from the beads. A magnetic rack was used to isolate the supernatant, which was transferred to a new tube and combined with 200 μL chloroform. Each sample was mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged for 15 min at 4 °C at 12,000 g. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research) and eluted in 15 μL RNase-free water. RNA from input samples was isolated in the same manner using TRIzol and column purification.
For RIP-seq library preparation (input and RIP eluates), 6 μL of RNA was diluted in FastAP Buffer (Thermo Fisher Scientific) supplemented with SUPERase•In RNase Inhibitor (Thermo Fisher Scientific) to a total volume of 18 μL, and fragmented by heating to 92 °C for 1.5 min. Each sample was treated with 2 μL TURBO DNase (Thermo Fisher Scientific) for 30 min at 37 °C and column-purified using the RNA Clean & Concentrator-5 kit (Zymo Research), eluting in 12.5 μL RNase-free water. RNA concentration was quantified using the DeNovix RNA Assay. Illumina sequencing libraries were prepared using the NEBNext Small RNA Library Prep kit, and libraries were sequenced on an Illumina NextSeq 500 in paired-end mode with 75 cycles per end.

tag: rip antibody

value: Monoclonal ANTI-FLAG M2 antibody (Sigma-Aldrich, cat. number:F1804)


title: C. senegalense IStron-2 total RNA-seq, heterologous


title: C. botulinum TnpB Input


title: Normal Chow Diet 1

value: Littermate WT Cre BL1


title: C. botulinum dTnpB Input


title: Water gavaged, rep2 [RC2]

description: matrix column 4


title: C. botulinum TnpB RIP


title: Water gavaged, rep1 [RC1]

description: matrix column 3


title: splenic monocytes, vanco gavaged, rep1

description:
matrix column 6
Van1


title: Vanco gavaged, rep1 [RC4]

description: matrix column 6


title: AR_136_rep2

status: Public on Apr 22 2024

data_processing:
RIP-seq: RIP-seq reads were processed using cutadapt (v4.2) to remove adapter sequences, trim low-quality ends from reads, and exclude reads shorter than 15 bp.
RIP-seq: Trimmed and filtered reads were mapped to a reference containing both the MG1655 genome (NC_000913.3) and plasmid sequences using bwa-mem2 v2.2.1, in paired-end mode with default parameters.
RIP-seq: SAMtools (v1.17) was used to filter for uniquely mapping reads using a MAPQ score threshold of 1, and to sort and index the unique reads.
RIP-seq: Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, read extension to fragment size, and normalization by counts per million mapped reads (CPM) with exact scaling. Coverage tracks were visualized using IGV.
Total RNA-seq: Data was processed as described for RIP-seq.
Total RNA-seq: For transcript-level quantification, the number of read pairs mapping to annotated transcripts was determined using featureCounts (v2.0.2). The resulting counts values were convert- ed to transcripts-per-million-mapped-reads (TPM) by normalizing for transcript length and sequencing depth. For differential expression analysis between genetically engineered Enterobacter strains, the counts matrix was first filtered to remove rows with fewer than 10 reads for at least 3 samples. The filtered matrix was then processed by DESeq2 (v1.40.2) in order to determine the log2(fold change) for each transcript between the experimental conditions, as well as the Wald test P value adjusted for multiple comparisons using the Benjamini-Hochberg approach. Significantly differentially expressed genes were determined by applying thresholds of |log2(fold change)| > 1 and adjusted P value < 0.05.
Assembly: NC_000913.3 (E. coli K-12 MG1655); CP021902.1 (Enterobacter cloacae AR_136); CP029716.1 (Enterobacter cloacae AR_154); CP021749.1 (Enterobacter cloacae AR_163); KQ089962.1 (Enterobacter sp. BIDMC93)
Supplementary files format and content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage
Supplementary files format and content: .xlsx file contains number of raw and uniquely mapped reads for obtained ChIP-seq

organism: Enterobacter cloacae

source_name: Liquid cell culture

growth_protocol: E. coli transformations were performed using a single plasmid encoding a TnpB protein and an ωRNA. TnpB and ωRNA were expressed using separate constitutive promoters. The E. coli growth protocol generally followed the ChIP-seq protocols that were previously described (Hoffmann, Kim, Beh et al. 2022; Meers et al. 2023). In brief, after 16 h incubation at 37 °C on LB-agar plates with antibiotics, colonies were scraped and resuspended in 1 ml of LB broth. The optical density at 600 nm was measured, and approximately 4.0 × 10^8 cells (equivalent to 1 ml of OD600 = 0.25) were spread onto two LB-agar plates containing antibiotics. We chose to culture cells on solid LB-agar to reduce any competition-induced effects of culturing in liquid LB media. Plates were incubated at 37°C for 24 h, after which compactly spaced colonies were present.

extract_protocol:
E. coli cells were scraped and spread onto the wall of a 50 ml conical tube in a thin layer, to allow for efficient resuspension and crosslinking in the next step.Crosslinking and immunoprecipitation generally followed our previous ChIP-seq protocols (Hoffmann, Kim, Beh et al., 2022; Meers et al., 2023), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to a separate tube containing 40 ml of LB medium (~1% final concentration), and the solution was mixed immediately by inverting. This solution was added to the conical tube containing the scraped cells, and the cells were fully resuspended in the LB-formaldehyde solution by vigorous vortexing at room temperature. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD at 600 nm was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
RIP-seq: Cells harvested for RIP-seq were cultured as described for ChIP-seq using an E. coli K12 MG1655 strain expressing sfGFP and mRFP (sSL3580). Colonies from a single plate were scraped and resuspended in 1 ml of TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl). Next, the OD600 was measured for a 1:20 mixture of the cell sus- pension and TBS buffer, and a standardized amount of cell material equivalent to 20 ml of OD600 = 0.5 was aliquoted. Cells were pelleted by centrifugation at 4,000 g and 4 °C for 5 min. The supernatant was discarded, and pellets were stored at -80 °C. Antibodies for immunoprecipitation were conjugated to magnetic beads as follows: for each sample, 60 μl Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 ml RIP lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 ml RIP lysis buffer, and combined with 20 μl anti-FLAG M2 antibody (Sigma-Aldrich), and rotated for >3 h at 4 °C. Antibody-bead complexes were washed 3× to remove unconjugated antibodies, and resuspended in 60 μl RIP lysis buffer per sample. Flash-frozen cell pellets were resuspended in 1.2 ml RIP lysis buffer supplemented with cOm- plete Protease Inhibitor Cocktail (Roche) and SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). Cells were then sonicated for 1.5 min total (2 sec ON, 5 sec OFF) at 20% amplitude. Lysates were cen- trifuged for 15 min at 4 °C at 21,000 g to pellet cell debris and insoluble material, and the supernatant was transferred to a new tube. At this point, a small volume of each sample (24 μl, or 2%) was set aside as the “input” starting material and stored at -80 °C. For immunoprecipitation, each sample was combined with 60 μl antibody-bead complex and rotated overnight at 4 °C. Next, each sample was washed 3× with ice-cold RIP wash buffer (20 mM Tris- HCl, 150 mM KCl, 1 mM MgCl2). After the last wash, beads were resuspended in 1 ml TRIzol (Thermo Fisher Scientific) and RNA was eluted from the beads by incubating at RT for 5 min. A magnetic rack was used to separate beads from the supernatant, which was transferred to a new tube and combined with 200 μl chloroform. Each sample was mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged for 15 min at 4 °C at 12,000 g. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research). RNA from input samples was isolated in the same manner using TRIzol and column purification. High-throughput sequencing library preparation was per- formed as described below for total RNA-seq of Enterobacter strains. Libraries were sequenced on an Illumina NextSeq 550 in paired-end mode with 75 cycles per end.
Total RNA-seq: Enterobacter cloacae strains (sSL3710, sSL3711, and sSL3712) were obtained from a CDC isolate panel (Enterobacterales Carbapenemase Diversity; CRE in ARIsolateBank), and an Enterobacter sp. BIDMC93 (sSL3690) was kindly provided by Ashlee M. Earl at the Broad Institute; strain information is listed in Supplementary Table 1. Biological replicates were obtained by isolating 3 individual clones of each Enterobacter strain on LB-agar plates and using these to inoculate overnight cultures in liquid LB media. All strains were grown at 37 °C without antibiotics and with agitation when in liquid medium (240 rpm), in a BSL-2 environment. For total RNA-seq library preparation, RNA was purified from 2 mL of exponentially growing cultures of sSL3690, sSL3710, sSL3711, and sSL3712, since RT-qPCR analyses of fliC expression showed that the TldR-mediated was more robust in exponential than in stationary phase. RNA was extracted using TRIzol and column purification (NEB Monarch RNA cleanup kit), and samples were then individually diluted in NEBuffer 2 (NEB) and fragmented by incubating at 92 °C for 1.5 min. The fragmented RNA was simultaneously treated with RppH (NEB) and TURBO DNase (Thermo Fisher Scientific) in the presence of SUPERase•In RNase Inhibitor (Thermo Fisher Scientific), in order to remove DNA and 5′ pyrophosphate. For further end repair to enable downstream adapter ligation, the RNA was treated with T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB). Samples were column-purified using RNA Clean & Concentrator-5 (Zymo Research), and the concentration was determined using the DeNovix RNA As- say (DeNovix). Illumina adapter ligation and cDNA synthesis were performed using the NEBNext Small RNA Library Prep kit, using 100 ng of RNA per sample. High-throughput sequencing was performed on an Illumina NextSeq 550 in paired-end mode with 75 cycles per end.

treatment_protocol: TnpB proteins were heterologously expressed in E. coli MG1655 using constitutive promoters.


title: AR_136_rep1


title: Normal Chow Diet 8

value: Littermate WT Cre BL4


title: AR_154_rep2


title: AR163_rep3


title: AR_154_rep1


title: Water gavaged, rep3 [RC3]

description: matrix column 5


title: AR_136_rep3


title: EsaTldR_RIP

source_name: Solid cell culture

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

tag: epitope tag_on_sample_protein

tag: induction parameters

value: constitutive expression, 24 h, 37°C

tag: flag-tagged protein


title: EceTldR_RIP


title: Efa2TldR_RIP


title: AR163_rep1


title: AR_154_rep3


title: EcaTldR_RIP


title: EmuTldR_RIP


title: Efa1TldR_rep2_RIP


title: EcaTldR_input

value: none (non-immunoprecipitated control sample)


title: EmuTldR_input


title: EhoTldR_RIP


title: EceTldR_input


title: Efa1TldR_rep2_input


title: BIDMC93_WT-guide_rep3

organism: Enterobacter sp. BIDMC93


title: BIDMC93_WT-guide_rep2


title: EsaTldR_input


title: BIDMC93_WT-guide_rep1


title: BIDMC93_NT-guide_rep3


title: BIDMC93_NT-guide_rep2


title: Tos_dTnpB_ChIP-seq_paired_raw

library_source: genomic

data_processing:
ChIP-seq paired-end reads were trimmed and mapped to a custom E. coli MG1655 reference genome (based on GenBank accession AKVX01000001.1) using fastp (Chen et al., 2018) and Bowtie2 (Langmead et al., 2012) with default parameters, respectively. The custom E. coli MG1655 strain has genomically encoded GFP and RFP genes, in between which custom TnpB target sites were inserted. A genomic lacZ/lacI region and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 366,386-367,588).
Mapped reads were sorted and indexed using the SAMtools software package (Li et al., 2009) (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option).
Alignments were normalised by CPM (counts per million) and RPKM (Reads Per Kilobase per Million mapped reads) and converted to 1 bp-bin bigwig files using the deepTools2 (Ramirez et al., 2016) command bamCoverage (--normalizeUsing CPM -bs 1 parameters; --normalizeUsing RPKM -bs 1 parameters, respectively).
After normalization, genome-mapping reads were visualised in IGV (Robinson et al., 2011). The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) (Quinlan et al., 2010) and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously (Cooper et al., 2018).
Peaks were called on pre-normalised alignments using MACS3 (Zhang et al., 2008), with the parameters -g 4500000 --nomodel --extsize 400 -q 0.05 -B, with respect to a non-immunoprecipitated control sample of Eco_dTnpB (-n option). The peak summit coordinates in the MACS3 output  summits.bed file were extended to encompass a 200-bp window using the following Bedtools command: bedtools slop -l 100 -r 99. Sequence motifs were identified using MEME ChIP (Bailey et al., 2009) with default parameters.
Assembly: AKVX01000001.1
Supplementary files format and content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage
Supplementary files format and content: .bed files were generated using MACS3 and represent peak calls and summit enrichment values
Supplementary files format and content: .xlsx file contains number of raw and uniquely mapped reads

molecule: genomic DNA

extract_protocol:
E. coli cells were scraped and spread onto the wall of a 50 ml conical tube in a thin layer, to allow for efficient resuspension and crosslinking in the next step.Crosslinking and immunoprecipitation generally followed our previous ChIP-seq protocols (Hoffmann, Kim, Beh et al., 2022; Meers et al., 2023), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to a separate tube containing 40 ml of LB medium (~1% final concentration), and the solution was mixed immediately by inverting. This solution was added to the conical tube containing the scraped cells, and the cells were fully resuspended in the LB-formaldehyde solution by vigorous vortexing at room temperature. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD at 600 nm was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in paired-end mode on the Illumina NextSeq platform. For each ChIP-seq sample, >2,000,000 raw reads (including genomic and plasmid-mapping reads) were obtained.

value: Solid cell culture

tag: chip antibody


title: AR163_rep2


title: Input_Eco_dTnpB_ChIP-seq_paired_raw


title: BIDMC93_rep2


title: BIDMC93_rep3


title: BIDMC93_rep1


title: Efa2TldR_input


title: Efa1TldR_rep1_RIP


title: Lec_dTnpB_ChIP-seq_paired_raw


title: BIDMC93_NT-guide_rep1


title: Kpi_dTnpB_ChIP-seq_paired_raw


title: Gst_TnpB2_ChIP-seq_paired_raw


title: EhoTldR_input


title: Emu_dTnpB_ChIP-seq_paired_raw


title: Ece_dTnpB_ChIP-seq_paired_raw


title: Eko2_dTnpB_ChIP-seq_paired_raw


title: Esa_dTnpB_ChIP-seq_paired_raw


title: Efa1TldR_rep1_input


title: Ero_dTnpB_ChIP-seq_paired_raw


title: Eho_dTnpB_ChIP-seq_paired_raw


title: Eko1_dTnpB_ChIP-seq_paired_raw


title: Ecl_dTnpB_ChIP-seq_paired_raw


title: Eca_dTnpB_ChIP-seq_paired_raw


title: AD4_AD5_CosMx

status: Public on Apr 19 2024

type: RNA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description: Contains information from coronal hemispheric sections of two 18M mice

hyb_protocol: NanoString ISH probes were prepared by incubation at 95°C for 2 min and immediately transferred to ice. The ISH probe mix (1 nM ISH probe, 40% formamide, 2.5% dextran sulfate, 0.2% BSA, 100 μg/mL salmon sperm DNA, 2X SSC, 0.1 U/μL SUPERase•In™ [Thermofisher] in DEPC H2O) was then pipetted into the chamber, and adhesives supplied with the chambers were applied to the ports of the chambers. Hybridization occurs at 37°C overnight after sealing the chamber to prevent evaporation. After ISH probe hybridization, the tissue sections were washed twice in a buffer composed of 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min each at room temperature, and then blocked with 100 mM NHS-acetate for 15 min. After blocking, the hydrophobic barrier was removed with a blade, and a custom-made flow cell was attached to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and between 20-23 fields of view (FoVs) were placed on each of the tissues to capture regions of interest (hippocampus and adjacent regions). RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. The tissue samples were incubated with antibodies  or Histone, glial fibrillary acidic protein (GFAP), 4′,6-diamidino-2-phenylindole (DAPI) and MOAB-2 for amyloid-β. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and Z-stack images for the  channels were captured.

data_processing:
Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. The expression matrices, metadata, and FOV files were read in using squidpy’s read_nanostring() function. Transcripts associated with negative probes were removed from the count matrices. Cells were manually assigned regional annotation based on visual alignment with the Allen Brain Mouse Atlas reference. Cells with a high or low number of genes or transcripts were removed. In order to identify likely mis-segmented doublets (i.e. two cells that were incorrectly identified as one cell during the segmentation process), scrublet was run on each of the hippocampal sections, separately. Cells that were assigned a high doublet probability were removed.
CosMx_mouse_combined.h5ad: cell-level normalized counts (.X field), cell-level raw counts (.layers['counts'] field), cell-level annotations (.obs field) (post-QC)

source_name: brain

label_protocol: The tissue was fixed with 10% neutral-buffered formalin (NBF) for 2 hours at 4°C and baked at 60°C for 30 minutes. Afterwards, the tissue was rehydrated with increasing ethanol concentrations. The tissue was digested with 1x Target Retrieval solution for 15min in a pressure cooker. The tissue sections were rinsed with DEPC H2O and with 100% ethanol. After the slides were dried at room temperature for 30 minutes. The tissue was digested with Protease A and Proteinase K for 30 minutes at room temperature. The sections were rinsed in PBS  and incubated in 1:400 diluted fiducials in 2X saline sodium citrate and Tween (SSCT; 0.001% Tween-20, Teknova) for 5 min at room temperature, and washed with 1X phosphate-buffered saline (PBS; ThermoFisher) for 5 min.     After digestion and fiducial placement, the tissue was fixed with 10% NBF for 1 min to maintain soft tissue morphology, then washed twice with Tris-glycine buffer (0.1M glycine [Sigma], 0.1M Tris-base [FisherScientific] in DEPC H2O) for 5 min, and washed with 1X PBS for 5 min. The fixed tissue was blocked using 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate; ThermoFisher) diluted in NHS-acetate buffer (0.1M NaP+0.1% Tween PH8 in DEPC H2O) for 15 min at room temperature and washed in 2X saline sodium citrate (SSC) for 5 min. Adhesive SecureSealTM Hybridization Chamber (Grace Bio-Labs) was placed to cover the tissue.

treatment_protocol: APP NL-G-F were sacrificed 18 months (18M) using a carbon dioxide overdose. Following cervical dislocation, brains were dissected. The left and right hemispheres were embedded in cold OCT and snap-frozen in isopentane chilled with liquid nitrogen and stored at -80°C. 10 µm thick tissue sections were cryosectioned and fixed.

tag: age

value: male

value: App NL-G-F

tag: disease

value: AD


title: Eco_dTnpB_ChIP-seq_paired_raw


title: Efa2_dTnpB_ChIP-seq_paired_raw


title: Efa1_dTnpB_ChIP-seq_paired_raw


title: AD2_AD3_CosMx


title: DMM00989

status: Public on Mar 01 2024

city: Manila

first: Jana Victoria

last: San Pedro

state: Manila

address: 623 Pedro Gil St.

department: Institute of Human Genetics

country: Philippines

institute: National Institutes of Health

hyb_protocol: The samples were processed according to the manufacturer's instructions/protocol using the Illumina DirectHyb HumanHT-12 v4.0 Expression Beadchip (Illumina, San Diego, CA, USA) comprising 47,231 oligonucleotide probes representing 34,602 genes and scanned on the Illumina HiScan System.

scan_protocol: The samples were processed according to the manufacturer's instructions/protocol. Acquisition of raw gene expression data and initial pre-processing was done via GenomeStudio Software version 2011.1 (Illumina).

data_processing:
All subsequent data processing and integration procedures were performed using R statistical programming language (version 3.5.1) and was done independently for each case-control study (i.e. T2DM, PAD, CAD, Ret, CVD, Neph). To ensure uniformity of raw data pre-processing procedures between the two different platforms for each analysis, raw gene expression values from the Illumina platform were forced to be positive through an offset via the lumi package, subjected to quantile normalization using the preprocessCore package and log-transformed via the Biobase package and R default functions. Collapsing of probes with multiple gene targets and inter-platform normalization (i.e. removal of batch effects and preservation of variance due to affliction through designated “Batch” and “Affliction” parameter values for each sample) were performed using WGCNA and the linear models for microarray data (limma) packages.
The sample data tables contain data that was normalized using cross-platform normalization and merging of the processed datasets. This method was done using the inSilicoMerging package in the R statistical programming language (version 3.5.1) following the empirical Bayes method (ComBat).

label: BIOTIN, CY3_HYB

organism: Homo sapiens

source_name: blood

label_protocol: Samples were labelled according to patient ID number and title of study (i.e., in this case, the study is about diabetes mellitus (DM) so for the first patient, the given label was DM00001, the second patient was DM00002, so on and so forth).

extract_protocol: Four (4) mL of whole blood were collected from participants upon recruitment and stored in ethylenediamine tetra acetic acid (EDTA) -containing blood tubes. The blood tubes were kept in ice-cold containers for transport. Within 2 hours of blood collection, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood through Ficoll density gradient centrifugation using Lymphoprep (Stemcell Technologies, Vancouver, Canada). Isolated PBMCs were temporarily stored at -80°C until RNA extraction. Total RNA was extracted from the PBMCs using QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. Quantification and OD260/280 determination of total RNA from PBMCs were performed using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Quality of the total RNA in terms of RNA Integrity Number (RIN) were analyzed on the 2200 TapeStation (Agilent Technologies, Santa Clara, CA) system using the TapeStation RNA analysis kits. RNA samples of good quantity (≥ 50ng/uL) and quality (RIN ≥ 3.5) were stored at -80°C until further use.

value: blood

value: Male

tag: sample group

value: Healthy

tag: comorbidity


title: DMM00953

tag: tissue

value: Female

value: DMCAD

value: with CAD


title: DMM00980


title: DMM00987


title: DMM01020


title: DMM00801


title: DMM01006


title: DMM01005


title: DMM00883


title: DMM00884


title: DMM00858


title: DMM00783


title: DMM00715


title: DMM00674


title: DMM00619


title: DMM00669


title: DMM00786

value: DMnoCAD

value: with no CAD


title: DMM00797


title: DMM00977


title: DMM00795


title: DMM00620


title: DMM00568


title: DMM00779


title: DMM00564


title: DMM00845


title: DMM00504


title: DMM00331


title: DMM00610


title: DMM00286


title: DMM00588


title: DMM00264


title: DMM00187


title: DMM00388


title: DMM00288


title: DMM00137


title: DMM00450


title: DMM00313


title: DMM00135


title: DMM00254


title: DMM00321


title: DMM00218


title: DMM00118


title: RS0041 (re-analysis)

status: Public on Feb 26 2024

city: Madrid

first: Luis

middle: Andrés

last: López Fernández

state: Madrid

address: Servicio Farmacia, Doctor Esquerdo 46

country: Spain

institute: Hospital General Universitario Gregorio Marañón

description:
re-analysis of GSM4818022
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx

data_processing:
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
Raw data per-gene counts were analyzed using the DESeq2 library combined with a non-parametrical procedure to identify differential gene-expression from RNA-seq data. After estimating size factors and gene dispersions by local fit type, a negative binomial generalize linear model (GLM, negative binomial Wald test was used to obtain the log2 fold changes (log2FC) for each gene by comparing 2 states between samples: responders and non-responders to anti-TNF drugs.
Assembly: Human sequenced genome GRCh38 v91
Supplementary files format and content: Tab-delimited text files include raw and normalized TPM values for each sample.

source_name: Blood

extract_protocol:
200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

treatment_protocol: A blood sample was collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) before the administration of the anti-TNF agent (week 0). Total whole blood RNA was extracted using PAXgene Blood RNA kits (PreAnalitiX) according to the manufacturer’s instructions. RNA concentrations were measured using the Quawell Q5000 Spectrophotometer (Quawell Technology Inc, San Jose, CA, USA). RNA integrity was verified using the Agilent RNA 6000 Nano Kit in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Extracted RNA was stored at −80 °C until further processing. All RNA samples fulfilled the following criteria: RNA integrity ˃7.

value: Blood

tag: disease state

value: pediatric inflammatory bowel disease

value: Anti-TNF

tag: response

value: Non-responder

tag: time

value: before initiation of treatment


title: DMM00134


title: DMM00156


title: DMM00059


title: DMM00081


title: DMM00145


title: PAZ0161 (re-analysis)

description:
re-analysis of GSM4818012
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: DMM00090


title: VR0161 (re-analysis)

description:
re-analysis of GSM4818010
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx

value: Responder


title: RM0161 (re-analysis)

description:
re-analysis of GSM4818018
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: DMM00002


title: RM0171 (re-analysis)

description:
re-analysis of GSM4818006
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: VV0011 (re-analysis)

description:
re-analysis of GSM4818000
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: VR0131 (re-analysis)

description:
re-analysis of GSM4818016
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: JC0121 (re-analysis)

description:
re-analysis of GSM4818004
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: GM0031 (re-analysis)

description:
re-analysis of GSM4818002
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: DMM00013


title: DMM00102


title: SJ039

description:
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx

data_processing:
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Sequencing reads were aligned to the human reference transcriptome (GRCh38, release v91) and quantified using RSem 1.3.1 (Li B et al. 2011).
Raw data per-gene counts were analyzed using the DESeq2 library combined with a non-parametrical procedure to identify differential gene-expression from RNA-seq data. After estimating size factors and gene dispersions by local fit type, a negative binomial generalize linear model (GLM, negative binomial Wald test was used to obtain the log2 fold changes (log2FC) for each gene by comparing 2 states between samples: responders and non-responders to anti-TNF drugs.
Assembly: Human sequenced genome GRCh38 v91
Supplementary files format and content: Tab-delimited text files include raw and normalized TPM values for each sample.

extract_protocol:
200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were sequenced at 650 pM on a P2 flow cell of the NextSeq 2000 (Illumina) to generate 60 bases single reads following the standard sequencing protocol. Reads were further processed using the bcl2fastq package v2.20 (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.


title: DMM00179


title: PAZ021


title: D0051 (re-analysis)

description:
re-analysis of GSM4818020
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: PM005_1 (re-analysis)

description:
re-analysis of GSM4818014
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: DMM00045


title: VR019


title: H12003


title: DMM00162


title: IL008


title: NJ037


title: DMM00076


title: RM0101 (re-analysis)

description:
re-analysis of GSM4818008
RawMatrix_T0_RvsNR.xlsx
NormalizationMatrix_T0_RvsNR_GS.xlsx


title: DMM00050


title: NJ035


title: PT015


title: SAL008


title: Lungs from Gprc5a-/- mouse 16 at end of exposure to saline [KOSB_8]

status: Public on Feb 16 2024

city: Houston

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite (version 3.0.1) provided by 10X Genomics. For read alignment of human and mouse scRNA-seq data, the human reference GRCh38 (hg38) and mouse reference GRCm38 (mm10) genomes were used, respectively. Detailed quality control (QC) metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, cells with low complexity libraries (in which detected transcripts are aligned to < 200 genes such as cell debris, empty drops, and low-quality cells) were filtered out and excluded from subsequent analyses. Likely dying or apoptotic cells where > 15% of transcripts derived from the mitochondrial genome were also excluded.  For scRNA-seq data of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice, we further removed potential droplets/dead cells with nFeature smaller than or equal to 500 and mitochondrial gene fraction larger than or equal to 15% using Seurat.
For scRNA-seq data, likely doublets or multiplets were identified and carefully removed through a multi-step approach. Briefly, doublets or multiplets were identified based on library complexity, whereby cells with high-complexity libraries in which detected transcripts are aligned to > 6,500 genes were removed, and also, based on cluster distribution and marker gene expression, whereby doublets or multiplets forming distinct clusters with hybrid expression features and/or exhibiting an aberrantly high gene count were also removed. Expression levels and proportions of canonical lineage-related marker genes in each identified cluster were carefully reviewed. Clusters co-expressing discrepant lineage markers were identified and removed. Doublets or multiplets were also identified using the doublet detection algorithm DoubletFinder. The proportion of expected doublets was estimated based on cell counts obtained prior to scRNA-seq library construction. Data normalization was then performed using Seurat on the filtered gene-cell matrix. Statistical assessment of possible batch effects was performed on non-malignant epithelial cells using the R package k-BET48 as described in our previous studies and Harmony was run with default parameters to remove batch effects present in the PCA space.  For ST profiling data, demultiplexed clean reads were aligned against the GRCm38 (mm10) mouse reference genomes by Spaceranger (version 2.0.0 for mouse ST data) with the Visium transcriptome probe set (mouse data probeset v1.0) and default parameter settings. Generated ST gene expression count matrices were then analyzed using Seurat v4.1.0 to perform unsupervised clustering analysis.
Assembly: mm10
Supplementary files format and content: Comma-separated values and matrix files

source_name: Lung

extract_protocol:
Murine lung single cells were  stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience). Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10XGenomics Chromium microfluidic chips. Spatial transcriptomic (ST) profiling of FFPE tissues of three Gprc5a-/- mouse samples was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations and as previously reported by our group.
Up to 10,000 cells per sample were partitioned into nanoliter-scale Gel beads-in-emulsion (GEMs) using Chromium Next GEM Single Cell 5' Gel Bead Kit v1.1 (1000169, 10XGenomics, ) and by loading onto Chromium Next GEM Chips G (1000127, 10XGenomics, Pleasanton, CA). GEMs were then recovered to construct single-cell gene expression libraries using the Chromium Next GEM Single Cell 5’ Library kit (1000166, 10XGenomics) according to the manufacturer’s protocol. Briefly, recovered barcoded GEMs were broken and pooled, followed by magnetic bead clean-up (Dynabeads MyOne Silane, 37002D, Thermo Fisher Scientific). 10X-barcoded full-length cDNA was then amplified by PCR and analyzed using Bioanalyzer High Sensitivity DNA kit (5067-4626, Agilent). Up to 50 ng of cDNA was carried over to construct gene expression libraries and was enzymatically fragmented and size-selected to optimize the cDNA amplicon size prior to 5’ gene expression library construction. Further, samples were subject to end-repair, A-tailing, adaptor ligation, and sample index PCR using Single Index Kit T Set A (2000240, 10XGenomics) to generate Illumina-ready barcoded gene expression libraries. Library quality and yield was measured using Bioanalyzer High Sensitivity DNA (5067-4626, Agilent) and Qubit dsDNA High Sensitivity Assay (Q32854, Thermo Fisher Scientific) kits. Indexed libraries were normalized by adjusting for the ratio of the targeted cells per library as well as individual library concentration and then pooled to a final concentration of 10 nM. Library pools were then denatured and diluted as recommended for sequencing on the Illumina NovaSeq 6000 platform. For ST profiling, regions of interest per tissue/sample, each comprising a 6.5 x 6.5 mm capture area, were selected based on careful annotation of Hematoxylin and Eosin (H&E)-stained slides that were digitally acquired using the Aperio ScanScope Turbo slide scanner (Leica Microsystems Inc., Buffalo Grove, IL). HALO software (Indica Labs, Albuquerque, NM) was used for pathological annotation (tumour areas, blood vessels, bronchioles, lymphoid cell aggregates, macrophages, muscle tissue, normal parenchyma, and reactive pneumocytes) of H&E histology images. Spot-level histopathological annotation visualization was generated using loupe browser (v6.3.0). Briefly, cloupe file generated from Spaceranger was loaded into loupe browser along with the annotation table file , the annotation visualization was then generated in svg format using the export plot tool. Spatial transcriptomic RNA-seq libraries were generated according to manufacturer’s instructions, each with up to ~3,600 uniquely barcoded spots. Libraries were sequenced on Illumina NovaSeq 6000 platform to achieve a depth of at least 50,000 mean read pairs/spot and at least 2,000 median genes/spot
For scRNA-seq analysis of lung tissues from Gprc5a-/- mice, lung single cells were stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience) to sort out epithelial and non-epithelial cells. Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10X Genomics Chromium microfluidic chips. Cells from Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice were processed similarly except for sorting by GFP. Spatial transcriptomic (ST) profiling of FFPE tissues was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations.

tag: cell type

value: Mouse lung cells

value: Lung

tag: genotype

value: 4 months


title: Lungs from Gprc5a-/- mouse 15 at end of exposure to saline [KOSB_7]


title: Lungs from Gprc5a-/- mouse 8 at end of exposure to NNK [KOKB_4]


title: Nematostella_vectensis_2

status: Public on Feb 05 2024

city: Freeville

first: Brent

last: Basso

state: NEW YORK

address: 1631 Dryden Rd.

department: Computational Biology

institute: Cornell University

data_processing:
FASTQ data was aligned and processed using the proseq2.0 pipeline developed by Danko lab (https://github.com/Danko-Lab/proseq2.0).
The mESC data was competitively aligned to a merged genome assembly of mm10 and dm3. Merging the two genome builds was performed using fastq merge.

organism: Nematostella vectensis

source_name: Nematostella vectensis

extract_protocol:
RNA extraction, run-on, and library preparation were executed according to “Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).” (PMID: 27442863).
Library prep was performed using Illumina custom adapters: Reverse 3' RNA adapter (/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT) and Reverse 5' RNA Adapter (5'-CCUUGGCACCCGAGAAUUCCA-3').

tag: assay

value: PRO-seq

tag: degron type

tag: dtag-13 treatment

value: untreated

tag: heat shock

value: no

tag: replicate


title: Lungs from Gprc5a-/- mouse 7 at end of exposure to NNK [KOKB_3]


title: H12004

tag: treatment


title: Perkinsus_marinus_1

organism: Perkinsus marinus

source_name: Perkinsus marinus


title: Sphaeroforma_arctica_2

organism: Sphaeroforma arctica

source_name: Sphaeroforma arctica


title: Perkinsus_marinus_2


title: Lungs from Gprc5a-/- mouse 6 at end of exposure to NNK [KOKB_2]


title: Lungs from Gprc5a-/- mouse 14 at end of exposure to saline [KOSB_6]


title: Lungs from Gprc5a-/- mouse 5 at end of exposure to NNK [KOKB_1]


title: Creolimax_fragrantissima_1

organism: Creolimax fragrantissima

source_name: Creolimax fragrantissima


title: Nematostella_vectensis_1


title: Sphaeroforma_arctica_1


title: Haloferax_mediterranei_3

organism: Haloferax mediterranei

source_name: Haloferax mediterranei


title: NJ029


title: Haloferax_mediterranei_2


title: Haloferax_mediterranei_1


title: Daphnia_pulex_2

organism: Daphnia pulex

source_name: Daphnia pulex


title: JC022


title: Daphnia_pulex_1


title: Strongylocentrotus_purpuratus

organism: Strongylocentrotus purpuratus

source_name: Strongylocentrotus purpuratus


title: Lungs from Gprc5a-/- mouse 13 at end of exposure to saline [KOSB_5]


title: mESCs NELFe, 15 -- S/L

source_name: Mouse mESCs

value: NELFe-dTAG

tag: media used to grow the cells

value: serum lift (S/L)


title: mESCs NELFe, 14 -- S/L


title: mESCs NELFe, 17 -- S/L + 30 mins dTAG

value: 60min dTAG


title: mESCs NELFe, 18 -- S/L + 30 mins dTAG


title: mESCs NELFe, 16 -- S/L + 30 mins dTAG


title: mESCs NELFe, 13 -- S/L


title: mESCs NELFe, 5 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG

value: yes


title: mESCs NELFe, 4 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG


title: mESCs NELFe, 2 -- 30 mins HS at 42


title: mESCs NELFe, 1 -- 30 mins HS at 42


title: mESCs NELFe, 3 -- 30 mins HS at 42


title: mESCs NELFb, 29 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG

value: NELFb-dTAG


title: mESCs NELFb, 28 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG


title: mESCs NELFb, 27 -- 30 mins HS at 42


title: mESCs NELFb, 25 -- 30 mins HS at 42


title: mESCs NELFb, 30 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG


title: mESCs NELFb, 26 -- 30 mins HS at 42


title: mESCs NELFb, 22 -- S/L + 1 hr dTAG


title: mESCs NELFb, 2 -- S/L


title: mESCs NELFb, 24 -- S/L + 1 hr dTAG


title: mESCs NELFb, 3 -- S/L


title: mESCs NELFb, 23 -- S/L + 1 hr dTAG


title: Dictyostelium_discoideum_2

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum


title: Capsaspora_owczarzaki_2

organism: Capsaspora owczarzaki

source_name: Capsaspora owczarzaki


title: Dictyostelium_discoideum_1


title: Capsaspora_owczarzaki_1


title: Escherichia_coli_c1

source_name: Escherichia coli


title: Dryas_iulia_H1

organism: Dryas iulia

source_name: Dryas iulia


title: Biperiden sample 18

status: Public on Dec 09 2023

city: Sao Paulo

first: Sintia

last: Belangero

address: Rua Botucatu

department: Morphology and Genetics

country: Brazil

institute: UNIFESP

data_processing:
miRge3.0 was used for adapter trimming, UMI deduplication and read alignment to reference hg38 genome using parameters specific to Qiagen miRNA Library Kit.
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

source_name: Blood serum extracellular vesicle

extract_protocol:
Approximately 10 hours after the last biperiden or placebo dose, blood samples were collected from each patient using BD Vacutainer Serum Separator Tubes. Serum was obtained after centrifugation, then frozen and maintained in -80C until processing. Extracellular vesicles (EVs) were isolated from each serum by sequential centrifugation, followed by use of miRCURY Exosome Isolation Kit Serum/Plasma (Qiagen). MicroRNAs from serum EVs were extracted using miRNeasy Serum/Plasma Advanced Kit (Qiagen).
miRNA libraries were prepared using Qiaseq miRNA Library Kit, then miRNA-seq was performed in a 1x75 format with NextSeq 500/550 High Output Kit v2.5 (75 cycles) (Illumina) using Illumina NextSeq 550.

treatment_protocol: Within approximately 12 hours following TBI, patients began receving, every 6 hours, either placebo or biperiden, intravenously. A total of 40 doses (5 mg of biperiden per dose) were administered per patient, as described in the clinical trial NCT01048138.

value: Blood serum extracellular vesicle

tag: sequencing batch

tag: biological sex

value: M

tag: tbi outcome

value: Alive

tag: pte development

value: No PTE development

value: Biperiden


title: Escherichia_coli_c2


title: Dryas_iulia_F1


title: Biperiden sample 17

tag: tissue


title: Biperiden sample 16


title: Biperiden sample 15


title: Escherichia_coli_c3


title: Biperiden sample 13

value: Deceased

value: Uncertain PTE development


title: Biperiden sample 14


title: mESCs NELFe, 6 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG


title: Biperiden sample 10

value: With PTE development


title: Biperiden sample 12


title: Biperiden sample 9


title: Biperiden sample 11

value: F


title: Biperiden sample 7


title: Biperiden sample 8


title: mESCs NELFb, 1 -- S/L

value: PRO-seq


title: Biperiden sample 3


title: Biperiden sample 5


title: Biperiden sample 4


title: Biperiden sample 6


title: Placebo sample 18

value: Placebo


title: Biperiden sample 2


title: Placebo sample 19


title: Biperiden sample 1


title: Placebo sample 17


title: Placebo sample 16


title: Placebo sample 12


title: Placebo sample 11


title: Placebo sample 15


title: Placebo sample 10


title: Placebo sample 14


title: Placebo sample 8


title: Placebo sample 5


title: Placebo sample 6


title: Placebo sample 3


title: Placebo sample 9


title: Placebo sample 2


title: Placebo sample 13


title: Placebo sample 7


title: Placebo sample 4


title: Placebo sample 1


title: 231-shGFP-N rep3

status: Public on Oct 18 2023

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description:
RNA-seq
231.xls
231-shGFP-H-3

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to hg38 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Assembly: hg38
Supplementary files format and content: excel files include counts of samples

growth_protocol: NCM460, RKO and MDA-MB-231 cells were purchased from American Type Culture Collection (ATCC). All these cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Hyclone). Human ESC H9 (also named WA09) were cultured on Matrigel (Corning)-coated plates in mTesR1 (STEMCELL Technologies) with 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara Bio) following the manufacturer’s instruction and subjected to quality control to inspect RNA integrity by Agilent Bioanalyzer 2100 (Agilent Technologies). RNAs were further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN).
RNA libraries were constructed using VAHTS Total RNA-Seq (H/M/R) Library PrepKit for Illumina (Vazyme) following manufacturer's protocol.

treatment_protocol: Cells under hypoxia culture were placed in the Hypoxia Incubated Workstation (Ruskinn) and flushed with a gas mixture of 1% O2, 5% CO2, and balanced N2.

tag: cell line

value: breast cancer cell

value: WT

value: 1percent O2 shGFP


title: 231-shGFP-H rep3

description:
RNA-seq
231.xls
231-shGFP-C-3

value: 21percent O2 shGFP


title: 231-shGFP-H rep2

description:
RNA-seq
231.xls
231-shGFP-C-2


title: 231-shGFP-H rep1

description:
RNA-seq
231.xls
231-shGFP-C-1


title: RKO-shGFP-N rep3

description:
RNA-seq
RKO.xls
RKO-shGFP-N-3

source_name: RKO

value: RKO

value: colorectal cancer cell


title: RKO-shGFP-N rep1

description:
RNA-seq
RKO.xls
RKO-shGFP-N-1


title: 231-shGFP-N rep2

description:
RNA-seq
231.xls
231-shGFP-H-2


title: RKO-shGFP-N rep2

description:
RNA-seq
RKO.xls
RKO-shGFP-N-2


title: RKO-shGFP-H rep3

description:
RNA-seq
RKO.xls
RKO-shGFP-H-3


title: NCM460-shGFP-N rep2

description:
RNA-seq
NCM460.xls
NCM460-shGFP-N-2

value: colon epithelial cell


title: NCM460-shGFP-N rep3

description:
RNA-seq
NCM460.xls
NCM460-shGFP-N-3


title: NCM460-shGFP-H rep3

description:
RNA-seq
NCM460.xls
NCM460-shGFP-H-3


title: RKO-shGFP-H rep1

description:
RNA-seq
RKO.xls
RKO-shGFP-H-1


title: NCM460-shGFP-N rep1

description:
RNA-seq
NCM460.xls
NCM460-shGFP-N-1


title: NCM460-shGFP-H rep2

description:
RNA-seq
NCM460.xls
NCM460-shGFP-H-2


title: H9-shGFP-H rep1

description:
RNA-seq
H9.xls
H9-shGFP-H-1

value: embryonic stem cell


title: H9-shGFP-N rep1

description:
RNA-seq
H9.xls
H9-shGFP-N-1


title: genomic DNA from venous blood 164

status: Public on Jun 26 2023

type: genomic

city: GAINESVILLE

first: Edward

last: Quinn

state: FL

address: 2033 Mowry Road

department: Anthropology

institute: University of Florida

description:
SV021b.2A.1.1
Normal venous blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended Illumina scanner settings

data_processing:
SeSame R package
matrix processed value definition: Average Beta after noob normalization
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: venous blood 164

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from venous blood using the QIAmp DNA Blood Mini Kit (Qiagen, Germantown, Maryland). The protocol was performed in two parts. Steps one through seven were performed at HEAL Africa Hospital to kill infectious agents and stabilize DNA prior to shipment to the University of Florida. Steps 8-11 were done at the University of Florida but modified them slightly - two AW1 washes and two AW2 washes were done instead of one wash each. We eluted three times in 45 ul TE buffer each time.

tag: gender

value: Female

tag: age

tag: birthweight

tag: dyad

tag: maternal age

tag: delivery mode

value: vaginal

tag: maternal alcohol

value: No

tag: parity

value: Primigravida

tag: gestational age

tag: war trauma

tag: chronic stress

tag: cohort

value: Sexual Violence Ward

value: FALSE

tag: replicate id

tag: dna methylation age

tag: age acceleration


title: genomic DNA from venous blood 163

description:
SV036bb.2.1a
Normal venous blood sample

source_name: venous blood 163

value: Male

tag: tissue

value: caesarean section

value: Yes

tag: replicate


title: genomic DNA from venous blood 162

description:
SV037b.1A.1.1
Normal venous blood sample

source_name: venous blood 162

tag: gender


title: genomic DNA from venous blood 160

description:
SV021bb.3A.2
Normal venous blood sample

source_name: venous blood 160

tag: age


title: H9-shGFP-H rep3

description:
RNA-seq
H9.xls
H9-shGFP-H-3

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: NCM460-shGFP-H rep1

description:
RNA-seq
NCM460.xls
NCM460-shGFP-H-1


title: H9-shGFP-N rep2

description:
RNA-seq
H9.xls
H9-shGFP-N-2


title: 10x scATACseq for Lin- cells from WT young mouse

status: Public on Aug 11 2023

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Chromium 10x v2 was processed using Cell Ranger (v6.0.0) with default parameters to generated single cell RNA sequencing data. Single cell RNAseq was sequenced on Novaseq S4 platform. Raw fastq files were demultiplexed using cellranger mkfastq from 10x Genomics. Then, the demultiplexed fastq files were aligned on mouse genome (refdata-gex-mm10-2020-A) provided by 10x Genomics. Scanpy (https://scanpy.readthedocs.io/en/stable/) was used to filter out cells with low UMI (<1,000) and cells with mitochondria reads percentage > 5%. Cells with less than 200 genes detected and genes expressed in less than 10 cells were also filtered out. Normalization and clustering analysis were using scanpy packages with default settings.
scATACseq data was prepared using Chromium 10x v2 kits and was demultiplexed using cellranger-atac mkfastq (cellranger-atac-1.2.0). The fastq files were aligned to mm10 (refdata-cellranger-atac-mm10-1.2.0) using Cellranger-atac count. ArchR (https://www.archrproject.com) was used to do quality control and data analysis. Specifically, the size of fragments and TSS enrichment were estimated, and doublet was removed. Clustering and gene scores calculation were performed based on the tutorial (https://www.archrproject.com/bookdown/index.html).
Bulk RNAseq data was mapped to mm10 using STAR (version=2.7.7a). Uniquely mapped reads was used to calculate raw counts for each gene and sample were inputted to DESeq2 R package to identify significantly differential expressed genes among groups.
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. Fastp was used to trim adaptor sequences from fastq data and remove 15 bp from the two ends of the reads based on Swift protocol. MCALL module in MOABS software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
For CMS-IP-seq analysis, raw FASTQ files were mapped to mm10 using BSMAP . Only uniquely mapped non duplicated reads were kept as input for MACS2  to call 5hmC enriched regions (peaks). Differential hydroxymethylation regions (DHMRs) were identified using DESeq2 with default parameters. Bam files were transformed to bigwig format, which can be used to visualize 5hmC signals in the UCSC genome browser.. H3K9me3 and H3K9me2 ChIPseq data was aligned on mm10 using bowtie2. The bam files were inputted to EDD (https://github.com/CollasLab/edd) to identify ChIPseq enriched regions.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; csv; txt

source_name: Lin- cells from bone marrow

growth_protocol: 6-8 weeks WT mice were used as WT-young; 12-24 months WT mice were used as WT-old;  6-8 weeks Tet2KO mice were used as Tet2KO-young; 12-24 months Tet2KO mice were used as Tet2KO-old;

extract_protocol:
RNA and DNA were purified using Qiagen AllPrep DNA/RNA micro kit.
1. Single-cell ATAC-seq libraries were generated by Chromium Single Cell ATAC Reagent Kits (10× Genomics); 2. Low amount RNA seq libraries were generated using Takara SMART-Seq Single Cell Kit; 3. CMSIP: 5hmC-containing genomic DNA were immunoprecipitated by CMS antibody after being bisulfite treated.  Immunoprecipitated DNA and input were proceed for Library generation by using zymo pico methyl kit. 4. CHIP seq: H3K9me2/3 binded chromatins were immunoprecipitated by H3K9me3 (ab8898) and H3K9me2 (ab1220). immunoprecipitated DNA and input were proceeded for library generation by using Takara ThruPLEX DNA library kit. 5. WGBS: Bisulfite conversions were performed by using Zymo lighting bisulfite kit and libraries were generated by using Swift Methyl kit for BS converted DNA.

treatment_protocol: mxCre_Dnmt3af/f mice were injected with 300 ul pIpC every other day for total 5 times

value: LSK

value: young


title: genomic DNA from venous blood 159

description:
SV063b.b.1.1
Normal venous blood sample

source_name: venous blood 159

tag: birthweight

tag: dyad

tag: maternal age

tag: delivery mode

tag: maternal alcohol


title: 231-shGFP-N rep1

description:
RNA-seq
231.xls
231-shGFP-H-1

value: breast cancer cell

value: WT

value: 1percent O2 shGFP


title: genomic DNA from venous blood 157

description:
SV008b.2A.1.1
Normal venous blood sample

source_name: venous blood 157

tag: parity

tag: gestational age

tag: war trauma

tag: chronic stress

tag: cohort


title: genomic DNA from venous blood 158

description:
SV048b.b.1.1 - eq100
Normal venous blood sample

source_name: venous blood 158

tag: tissue

tag: replicate

tag: replicate id

tag: dna methylation age

tag: age acceleration


title: H9-shGFP-N rep3

description:
RNA-seq
H9.xls
H9-shGFP-N-3

tag: cell line

tag: cell type

tag: genotype


title: genomic DNA from venous blood 154

description:
SV066bb.2.1
Normal venous blood sample

source_name: venous blood 154

tag: gender

tag: age

tag: birthweight

tag: dyad


title: genomic DNA from venous blood 156

description:
SV030b.b.1.1
Normal venous blood sample

source_name: venous blood 156

tag: maternal age

tag: delivery mode

tag: maternal alcohol

tag: parity


title: genomic DNA from venous blood 155

description:
SV003b.1A.1
Normal venous blood sample

source_name: venous blood 155

value: Multigravida

tag: gestational age

tag: war trauma

tag: chronic stress

tag: cohort


title: RKO-shGFP-H rep2

description:
RNA-seq
RKO.xls
RKO-shGFP-H-2

value: RKO

value: colorectal cancer cell

tag: treatment

value: 21percent O2 shGFP


title: genomic DNA from venous blood 153

description:
SV033bb.2A.1.1 (NOT 11/8/18)
Normal venous blood sample

source_name: venous blood 153

value: Female

tag: tissue

tag: replicate

tag: replicate id

tag: dna methylation age

tag: age acceleration


title: genomic DNA from venous blood 152

description:
SV016b.1A.1.1
Normal venous blood sample

source_name: venous blood 152

tag: gender

tag: age

value: vaginal

value: No


title: genomic DNA from venous blood 150

description:
SV039bb.2A.2
Normal venous blood sample

source_name: venous blood 150

tag: birthweight

tag: dyad

value: Sexual Violence Ward


title: genomic DNA from venous blood 148

description:
SV033bb.2
Normal venous blood sample

source_name: venous blood 148

tag: maternal age

tag: delivery mode

value: FALSE


title: genomic DNA from venous blood 146

description:
SV012bb.3a.1.1
Normal venous blood sample

source_name: venous blood 146

tag: maternal alcohol

tag: parity

value: Primigravida


title: H9-shGFP-H rep2

description:
RNA-seq
H9.xls
H9-shGFP-H-2

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype


title: genomic DNA from venous blood 161

description:
SV016bb.1
Normal venous blood sample

source_name: venous blood 161

tag: gestational age

tag: war trauma

tag: chronic stress

tag: cohort


title: genomic DNA from venous blood 145

description:
SV045bb.2a.1.1
Normal venous blood sample

source_name: venous blood 145

value: Male

tag: tissue

value: caesarean section

tag: replicate

tag: replicate id

tag: dna methylation age


title: genomic DNA from venous blood 147

description:
SV023b.b.1.1
Normal venous blood sample

source_name: venous blood 147

tag: gender

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 141

description:
SV029b.2A.1.1
Normal venous blood sample

source_name: venous blood 141

tag: dyad

tag: maternal age

tag: delivery mode

tag: maternal alcohol


title: genomic DNA from venous blood 149

description:
SV018bb.1A.2
Normal venous blood sample

source_name: venous blood 149

tag: parity


title: genomic DNA from venous blood 142

description:
SV037bb.2
Normal venous blood sample

source_name: venous blood 142

tag: gestational age


title: genomic DNA from venous blood 143

description:
SV068b.6m.1.1
Normal venous blood sample

source_name: venous blood 143

tag: war trauma


title: genomic DNA from venous blood 151

description:
SV067bb.1.1 -  quad3
Normal venous blood sample

source_name: venous blood 151

tag: chronic stress

value: TRUE


title: genomic DNA from venous blood 140

description:
SV019bb.2.1 - eq100
Normal venous blood sample

source_name: venous blood 140

tag: cohort


title: genomic DNA from venous blood 144

description:
SV003b.b.2.1
Normal venous blood sample

source_name: venous blood 144

tag: tissue


title: genomic DNA from venous blood 138

description:
SV040bb.2
Normal venous blood sample

source_name: venous blood 138

tag: replicate


title: genomic DNA from venous blood 137

description:
SV032b.1A.1.1
Normal venous blood sample

source_name: venous blood 137

tag: replicate id


title: genomic DNA from venous blood 136

description:
SV045bb.1a.1.1
Normal venous blood sample

source_name: venous blood 136

tag: dna methylation age


title: genomic DNA from venous blood 133

description:
SV041bb.2
Normal venous blood sample

source_name: venous blood 133

tag: gender


title: genomic DNA from venous blood 134

description:
SV050b.b.1.2
Normal venous blood sample

source_name: venous blood 134

tag: age


title: genomic DNA from venous blood 130

description:
SV071bb.1a.1.1
Normal venous blood sample

source_name: venous blood 130

tag: birthweight


title: genomic DNA from venous blood 127

description:
SV057b.b.1.1
Normal venous blood sample

source_name: venous blood 127

tag: age acceleration


title: genomic DNA from venous blood 139

description:
SV020bb.1a.2.1
Normal venous blood sample

source_name: venous blood 139

tag: dyad


title: genomic DNA from venous blood 123

description:
SV049bb.2a.1.1
Normal venous blood sample

source_name: venous blood 123

tag: maternal age


title: genomic DNA from venous blood 132

description:
SV017bb.2.1
Normal venous blood sample

source_name: venous blood 132

tag: delivery mode


title: genomic DNA from venous blood 131

description:
SV065bb.1.1 7/7/2018
Normal venous blood sample

source_name: venous blood 131

tag: maternal alcohol


title: genomic DNA from venous blood 135

description:
SV003b.2A.1.1
Normal venous blood sample

source_name: venous blood 135

tag: parity


title: genomic DNA from venous blood 129

description:
SV020b.2A.1.1
Normal venous blood sample

source_name: venous blood 129

tag: gestational age


title: genomic DNA from venous blood 126

description:
SV076bb.2a.2.1
Normal venous blood sample

source_name: venous blood 126

value: Yes

tag: war trauma


title: genomic DNA from venous blood 128

description:
SV011bb.3A.2
Normal venous blood sample

source_name: venous blood 128

tag: chronic stress


title: genomic DNA from venous blood 125

description:
SV008b.1A.1.1
Normal venous blood sample

source_name: venous blood 125

tag: cohort


title: genomic DNA from venous blood 121

description:
SV006bb.3a.1
Normal venous blood sample

source_name: venous blood 121

tag: tissue


title: genomic DNA from venous blood 120

description:
SV015bb.1
Normal venous blood sample

source_name: venous blood 120

tag: replicate


title: genomic DNA from venous blood 124

description:
SV011b.1A.1.1
Normal venous blood sample

source_name: venous blood 124

tag: replicate id


title: genomic DNA from venous blood 118

description:
SV035b.2A.1
Normal venous blood sample

source_name: venous blood 118

tag: dna methylation age


title: genomic DNA from venous blood 114

description:
SV064bb.1a.1.1
Normal venous blood sample

source_name: venous blood 114

tag: gender


title: genomic DNA from venous blood 122

description:
SV016bb.3a.1.1
Normal venous blood sample

source_name: venous blood 122

tag: age


title: genomic DNA from venous blood 119

description:
SV035b.b.1.1
Normal venous blood sample

source_name: venous blood 119

tag: birthweight


title: genomic DNA from venous blood 117

description:
SV008bb.1
Normal venous blood sample

source_name: venous blood 117

tag: age acceleration


title: genomic DNA from venous blood 116

description:
SV025b.b.1.1 - eq100
Normal venous blood sample

source_name: venous blood 116

tag: dyad


title: genomic DNA from venous blood 112

description:
C105bb.1.1
Normal venous blood sample

source_name: venous blood 112

tag: maternal age


title: genomic DNA from venous blood 111

description:
SV067b.b.1.1
Normal venous blood sample

source_name: venous blood 111

tag: delivery mode


title: genomic DNA from venous blood 110

description:
SV043bb.2A.2.1
Normal venous blood sample

source_name: venous blood 110

tag: maternal alcohol


title: genomic DNA from venous blood 113

description:
SV015b.2A.1.1
Normal venous blood sample

source_name: venous blood 113

tag: parity


title: genomic DNA from venous blood 106

description:
SV001b.2A.1.1
Normal venous blood sample

source_name: venous blood 106

tag: gestational age


title: genomic DNA from venous blood 104

description:
SV028b.b.1.1
Normal venous blood sample

source_name: venous blood 104

tag: war trauma


title: genomic DNA from venous blood 107

description:
SV061bb.2.1
Normal venous blood sample

source_name: venous blood 107

tag: chronic stress


title: genomic DNA from venous blood 103

description:
SV042bb.2.1
Normal venous blood sample

source_name: venous blood 103

tag: cohort


title: genomic DNA from venous blood 102

description:
SV029bb.3a.1.1
Normal venous blood sample

source_name: venous blood 102

tag: tissue


title: genomic DNA from venous blood 101

description:
SV001b.1A.1.1 - eq100
Normal venous blood sample

source_name: venous blood 101

tag: replicate


title: genomic DNA from venous blood 98

description:
SV006bb.1.1 6/2/2017
Normal venous blood sample

source_name: venous blood 98

tag: replicate id


title: genomic DNA from venous blood 92

description:
SV011b.6m.1.1
Normal venous blood sample

source_name: venous blood 92

tag: dna methylation age


title: genomic DNA from venous blood 99

description:
SV071bb.6m.1.1
Normal venous blood sample

source_name: venous blood 99

tag: gender


title: genomic DNA from venous blood 100

description:
SV018bb.2A.1.1 - dup3
Normal venous blood sample

source_name: venous blood 100

tag: age


title: genomic DNA from venous blood 96

description:
SV005b.2A.1.1
Normal venous blood sample

source_name: venous blood 96

tag: birthweight


title: genomic DNA from venous blood 115

description:
SV018bb.2.1
Normal venous blood sample

source_name: venous blood 115

tag: age acceleration


title: genomic DNA from venous blood 97

description:
SV067bb.1.1 - quad2 - eq100
Normal venous blood sample

source_name: venous blood 97

tag: dyad


title: genomic DNA from venous blood 95

description:
SV015bb.3A.2 - dup2a
Normal venous blood sample

source_name: venous blood 95

tag: maternal age


title: genomic DNA from venous blood 94

description:
SV008bb.3a.2.1
Normal venous blood sample

source_name: venous blood 94

tag: delivery mode


title: genomic DNA from venous blood 90

description:
SV009b.2A.1.1
Normal venous blood sample

source_name: venous blood 90

tag: maternal alcohol


title: genomic DNA from venous blood 91

description:
SV026b.1A.1.1
Normal venous blood sample

source_name: venous blood 91

tag: parity


title: genomic DNA from venous blood 89

description:
SV051b.b.1.1
Normal venous blood sample

source_name: venous blood 89

tag: gestational age


title: genomic DNA from venous blood 109

description:
SV073b.b.1.1
Normal venous blood sample

source_name: venous blood 109

tag: war trauma


title: genomic DNA from venous blood 108

description:
SV032bb.3a.1.1
Normal venous blood sample

source_name: venous blood 108

tag: chronic stress


title: genomic DNA from venous blood 85

description:
SV068bb.1a.2
Normal venous blood sample

source_name: venous blood 85

tag: cohort


title: genomic DNA from venous blood 105

description:
SV039b.1A.1.1
Normal venous blood sample

source_name: venous blood 105

tag: tissue


title: genomic DNA from venous blood 88

description:
SV065bb.2a.1.1
Normal venous blood sample

source_name: venous blood 88

tag: replicate


title: genomic DNA from venous blood 86

description:
SV021bb.1a.1.1
Normal venous blood sample

source_name: venous blood 86

tag: replicate id


title: genomic DNA from venous blood 87

description:
SV011bb.2
Normal venous blood sample

source_name: venous blood 87

tag: dna methylation age


title: genomic DNA from venous blood 83

description:
SV064b.b.1.1
Normal venous blood sample

source_name: venous blood 83

tag: gender


title: genomic DNA from venous blood 79

description:
SV046bb.2.1
Normal venous blood sample

source_name: venous blood 79

tag: age


title: genomic DNA from venous blood 82

description:
SV028b.2A.1.1 - eq101
Normal venous blood sample

source_name: venous blood 82

tag: birthweight


title: genomic DNA from venous blood 80

description:
SV052b.b.1.1
Normal venous blood sample

source_name: venous blood 80

tag: age acceleration


title: genomic DNA from venous blood 77

description:
SV043b.b.1.1
Normal venous blood sample

source_name: venous blood 77

tag: dyad