title: TnsC_deltaTniQ_crRNA-4_ChIP-seq_paired_raw

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

data_processing:
ChIP-seq single- and paired-end reads were trimmed and mapped to an E. coli BL21(DE3) reference genome (GenBank accession CP001509.3) using fastp [REF] and Bowtie2 [REF] with default parameters, respectively. Two genomic lacZ/lacI regions and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 335,600-337,101 and 748,601-750,390). Enrichment analysis on pDonor and pQCascade was performed by mapping reads (Bowtie2, default parameters) to the same E. coli BL21(DE3) reference genome concatenated to the respective pQCascade, pTnsABC and pDonor plasmid sequences used in each experiment. For those concatenated reference genome files, sequence elements were separated from one another by inserting 1,000 bp represented as Ns. Mapped reads were sorted and indexed using the SAMtools software package [REF] (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 RPKM (Reads Per Kilobase per Million mapped reads), as described previously [REF] and converted to 1 bp-bin bigwig files using the deepTools2 [REF] command bamCoverage (--normalizeUsing RPKM -bs 1 parameters). After normalization, genome- and plasmid-mapping reads were visualised in IGV [REF]. The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) [REF] 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 [REF]. Peaks were called on pre-normalised alignments using MACS3 [REF], with the following parameters: [-g 4500000 --nomodel --extsize 400 -q 0.05 -B]. A non-immunoprecipitated control library of Cas8 was used as an input for standardizing all library peak calls (-n option).  Heatmaps of peak calls were first generated by computing a heatmap matrix on the alignments using the deepTools function (computeMatrix reference-point) with default parameters. Subsequently, the deepTools function plotHeatmap was used on the heatmap matrices with the following parameters: [--whatToShow ‘heatmap and colorbar' --sortUsing max]. Venn diagrams were generated using custom R code on MACS3 peak output files. Sequence motifs were identified using MEME (version 4.12.0) with default parameters [REF]. Off-target mismatch analysis on peak calls was performed using a custom Python script. Briefly, a 200-bp sequence around each peak was examined, and the 10-bp sequence most closely matching a 5'-CN-3' PAM and the first 8-nt of the seed sequence, with the 6th bp set as N, was identified. The best-matching sequence was inferred to be the off-target binding site, and the full 34-bp PAM and target sequence was extracted for each peak.
Genome_build: CP001509.3
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

organism: Escherichia coli

source_name: Solid cell culture

growth_protocol: Transformations were performed using a three-plasmid system, according to the general transposition assay protocol that was previously described (Klompe et al. 2019). In brief, after 16 h incubation at 37 °C on LB-agar plates with antibiotics but no IPTG induction, colonies were scraped and resuspended in 1 ml of fresh LB. The optical density at 600 nm was measured, and approximately 4.0 × 108 cells (equivalent to 1 ml of OD600 = 0.25) were spread onto two LB-agar plates containing antibiotics and supplemented with 0.1 mM IPTG. 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 room temperature (~25 °C) for 44 h, during which time a bacterial lawn formed.

extract_protocol:
IPTG-induced 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 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 OD600 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 either single- or paired-end mode on the Illumina MiniSeq and NextSeq platform. For each ChIP-seq sample, >1,800,000 raw reads (including genomic and plasmid-mapping reads) were obtained.

treatment_protocol: Type I-F3 CRISPR-associated transposon proteins (Cas8/5, Cas7, Cas8, TniQ, TnsC, TnsB, TnsA) from Vibrio cholerase (as described in Klompe et al. 2019 and Vo et al. 2021) were heterologously expressed upon induction with 0.1 mM IPTG

tag: transposon protein

value: TnsC

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

tag: epitope-tag on sample protein


title: P. aeruginosa 5 h, replicate 3, run B

status: Public on Oct 31 2021

type: SRA

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

library_source: transcriptomic

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: NC_008463.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

molecule: polyA RNA

organism: Pseudomonas aeruginosa PA14

source_name: P. aeruginosa cultivated in LB medium

growth_protocol: 50 mL of LB medium was inoculated with an overnight culture to an OD600 of 0.05. The culture was grown for 10 h in a shaker at 37°C and 180 rpm. Two runs were performed on separate days.

extract_protocol:
For isolation and purification the RNeasy Plus kit (Qiagen) in combination with QIAshredder columns (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cell lysis was performed with 8 mg/mL lysozyme in Tris-EDTA-buffer (pH 8.0). RLT buffer with mecaptoethanol was added. Samples were frozen at -70°C for 60 min and then processed with QIAshredder columns. The remaining steps were performed according to the manufacturer's manual. After RNA elution, samples were treated with DNase (DNA-free Kit DNase Treatment & Removal, ambion).
RNA was fragmented (150–350 bp) by FastAP buffer (Thermo). End repair was performed with DNase (Thermo) and FastAP. Barcodes were ligated to each sample by T4 RNA ligase 1 (NEB). Samples were purified with the RNA Clean & Concentrator-25 Kit (Zymo). The RiboZero Bacteria Kit (Illumina) was used to remove ribosomal RNA. cDNA libraries were generated using SMARTscribe reverse transcriptase (Clonetech). Enrichment was done by AccuPrime HiFi Taq (Thermo) and all purification steps using RNAClean XP beads (Agencourt). Libraries were sequenced in paired-end mode on an Illumina Novaseq 6000 device (2 x 50 bp).

tag: strain

tag: time (h)

tag: replicate

tag: run

value: B


title: KO2_XRN607

city: Indianapolis

first: Travis

last: Johnson

state: IN

department: Biostatistics

country: USA

institute: Indiana University School of Medicine

data_processing:
alignmentSTAR 2.7.3a
quantificationRSEM 1.3.0 (gene level)
Genome_build: GRCm38
genome annotationgencode vM25

molecule: total RNA

organism: Mus musculus

source_name: Unstimulated

growth_protocol: For α-CD3-CD28 stimulation, sorted WT and Gpx4-deficient Treg cells were cultured in Click’s medium (plus β-mercaptoethanol) supplemented with 10% (vol/vol) FBS and 1% (vol/vol) penicillin–streptomycin.

extract_protocol:
RNA of WT and Gpx4-deficient Treg cells was extracted using the RNeasy Micro Kit (Qiagen)
RNA (600 ng/ sample) was used to prepare single indexed strand specific cDNA library using TruSeq stranded mRNA library prep kit (Illumina). The library prep was assessed for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer.

treatment_protocol: WT and Gpx4-deficient Treg cells were stimulated with plate-bound α-CD3-CD28 (5 μg/ml) for 4 h

tag: age

value: 11 weeks

tag: cell type

value: Treg


title: P. aeruginosa 5 h, replicate 2, run B


title: P. aeruginosa 6 h, replicate 1, run B


title: KO1_XRN606


title: Cobimetinib 24hr H3K27ac rep2

city: Boulder

first: Edward

middle: Boyi

last: Chuong

state: CO

address: JSC Biotech Building, 3415 Colorado Ave

department: BioFrontiers Institute and Molecular, Cellular & Developmental Biology Department

institute: University of Colorado Boulder

library_source: genomic

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=31 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the hg38 assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome were removed. For one sample (untreated H3K27ac rep2), the original and resequenced files were merged into one bam file. Peak calling was performed using complete and size subsetted alignment files with MACS2 v2.1.1 in a two-step process where separate sets of peaks were called with (1) single-end options ‘--format BAM --shift=-75 --extsize=150 --pvalue 0.01’ and (2) paired-end option ‘--format BAMPE --pvalue 0.01’, and then peaks were merged for each sample. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Genome_build: hg38
Supplementary_files_format_and_content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format
Supplementary_files_format_and_content: Tab-delimited text files including unfiltered narrowPeaks called by MACS2 in UCSC BED format

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal cancer cell line

growth_protocol: HCT116 cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in McCoy’s 5A (Gibco #16600082) supplemented 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
CUT&RUN pulldowns were generated using a protocol from Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). All buffers were prepared according to the “High Ca2+/Low Salt” section of the protocol using 0.05% digitonin. 500,000 viable cells were used for each pulldown. The following antibodies were used: rabbit anti-mouse IgG (1:100, Abcam #ab46540) and rabbit anti-H3K27ac (1:100, Abcam #ab4759). pA-MNase (gift from Steve Henikoff) was added to each sample following primary antibody incubation at a final concentration of 700 ng/mL. Chromatin digestion, release, and extraction was carried out according to Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). Pulldown success was determined by Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000 before proceeding with library preparation.
Libraries were generated using a modified protocol for use with the KAPA HyperPrep Kit. Briefly, the full volume of each pulldown (~30 uL) was diluted to 50 uL in nuclease-free water, and libraries were generated following the manufacturer’s protocol with the following modifications. Freshly diluted 0.200 uM single-index adapters were added to each library at a low concentration (9 nM) to minimize adapter dimer formation. Adapter-ligated libraries underwent a double-sided 0.8X/1.0X cleanup with KAPA Pure Beads. Purified, adapter-ligated libraries were amplified using the following PCR cycling conditions: 45 s at 98°C, 14x(15 s at 98°C, 10 s at 60°C), 60 s at 72°C. Amplified libraries underwent 2 double-sided 1.0X cleanups with KAPA Pure Beads. The final libraries were quantified using Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150bp paired-end reads.

treatment_protocol: Cells were either untreated or treated with 1 uM Cobimteinib or 100 ng/mL TNF-alpha for 24h.

tag: cell line

tag: antibody

value: Rabbit polyclonal H3K27ac (Abcam #ab4729)

tag: treatment

value: Cobimetinib

tag: timepoint


title: P. aeruginosa 5 h, replicate 1, run B


title: TnsC_crRNA-4_ChIP-seq_paired_raw_more-depth


title: TnsC_crRNA-NT_ChIP-seq_paired_raw


title: P. aeruginosa 5 h, replicate 3, run A

value: A


title: Cobimetinib 24hr IgG rep2

value: Rabbit anti-mouse IgG (Abcam #ab46540)


title: WT3_XRN588

value: WT


title: Cobimetinib 24hr H3K27ac rep1


title: WT2_XRN587


title: Cobimetinib 24hr IgG rep1


title: P. aeruginosa 6 h, replicate 2, run A


title: WT1_XRN586


title: P. aeruginosa 5 h, replicate 2, run A


title: Untreated H3K27ac rep1

value: untreated


title: P. aeruginosa 4 h, replicate 3, run B


title: Untreated H3K27ac rep2


title: Plate TM123 - Dclk1-tdTom+/CD49b+ cells

city: Munich

first: Moritz

last: Middelhoff

address: Ismaninger Str. 22

country: Germany

institute: TU München

description:
TM123_S4
K-2088
K-2089

data_processing:
Reads were aligned to genome (genome version GRCh38 human, GRCm38 mouse) using STAR v2.5.3a
BAM output was used as input into featureCounts v1.5.3 to assign alignments to genes
The UMI count matrix was used as filter for low quality cells by removing cells with a number of UMI counts less than 1000 and more than 100000
UMI counts were normalized to log2-CPM (count per million of reads) and used for differential expression analysis and for VIPER analysis
Differential expression analysis between injured and non-injured cell was computed by performing a bootstrap t-test with n=100 bootstraps
Supplementary_files_format_and_content: all_plates_umi_counts.csv

source_name: Plate TM123 - Dclk1-tdTom+/CD49b+ cells

extract_protocol:
Sorted cells were lysed and RT performed in-well on a 96-well plate
Sequencing libraries have been constructed using Nextera XT (Illumina) as previously described (Snyder et al., 2019)

value: Tam 3mg at 8wks, tissue collection 10d post Tam

tag: tissue

value: Intestinal adult LMMP tissue

value: CD49b+ glial cells


title: P. aeruginosa 4 h, replicate 2, run B


title: TnsB_deltaTnsC_crRNA-4_ChIP-seq_paired_raw

value: TnsB


title: TnsC_crRNA-287_ChIP-seq_paired_raw


title: P. aeruginosa 4 h, replicate 1, run B


title: Plate TM122 - Dclk1-tdTom+/CD49b- cells

description:
TM122_S3
K-2088
K-2089

source_name: Plate TM122 - Dclk1-tdTom+/CD49b- cells

value: CD49b- neuronal cells


title: TnsB_deltaTniQ_crRNA-4_ChIP-seq_paired_raw


title: Untreated IgG rep2


title: P. aeruginosa 4 h, replicate 2, run A


title: TnsB_deltapDonor_deltaTnsA_crRNA-4_ChIP-seq_single_raw


title: Plate TM119 - Dclk1-tdTom+/CD49b+ cells

description:
TM119_S4
K-1338
K-1339

source_name: Plate TM119 - Dclk1-tdTom+/CD49b+ cells

value: Tam 3mg at 9wks, IR 10.5Gy 7d post Tam, tissue collection 3d post IR (total trace 10d)


title: Plate TM121 - Dclk1-tdTom+/CD49b+ cells

description:
TM121_S2
K-1337
K-1302

source_name: Plate TM121 - Dclk1-tdTom+/CD49b+ cells

value: Tam 3mg at 9wks, tissue collection 10d post Tam


title: TnsC_crRNA-295_ChIP-seq_paired_raw

value: TnsC

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


title: P. aeruginosa 3 h, replicate 3, run B

value: B


title: Plate TM120 - Dclk1-tdTom+/CD49b- cells

description:
TM120_S1
K-1337
K-1302

source_name: Plate TM120 - Dclk1-tdTom+/CD49b- cells


title: TnsB_deltapDonor_crRNA-4_ChIP-seq_single_raw


title: Untreated IgG rep1


title: Human PBMCs IAV infected DI-treated

city: Hannover

first: Frank

last: Pessler

address: Feodor-Lynen-Str. 7-9

department: Experimental Infection Research

institute: Center for Experimental and Clinical Infection Research GmbH

description:
Single cell transcriptome from total 1411 human PBMCs untreated. Cell were IAV-infected and DI-treated.
PBMCs isolation: Primary human monocytes were isolated from buffy coat from a healthy blood donor by density gradient centrifugation (Histopaque™, Sigma-Aldrich)
Cell staining: Cells were stained with propidium iodide and dead cells and doublets were removed by FACS. Live cells (including those undergoing apoptosis) were used to make single cell suspensions using the 10x Genomics platform.
Barcoding and cDNA synthesis: The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer’s instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode.

data_processing:
Cell Ranger 1.3 (http://10xgenomics.com) was used to process Chromium  single  cell  3’  RNA-seq  output
cellranger count aligned to the pre-built human reference genome (hg19, GRCh38)
Raw counts were normalized by the global-scaling normalization method “LogNormalize”.
Principal component analysis score was used to determine the ‘dimensionality’ of all cells.
Scatter plots were obtained using the UMAP method. Cell clusters were identified as different cell populations based on the expression of recently published canonical markers
Genome_build: human reference genome (hg19, GRCh38)
Supplementary_files_format_and_content: filtered_feature_bc_matrix, tsv and mtx files
Supplementary_files_format_and_content: Seurat object

source_name: Human peripheral blood mononuclear cells

extract_protocol: The  cDNA  libraries  were  constructed  using  the  10x  ChromiumTM  Single  cell  3’  Library  Kit  according  to  the  manufacturer’s  original  protocol.   Libraries were sequenced on an Illumina NovaSeq 6000 2x50 paired-end kits using the following read length

treatment_protocol: cells were isolated from healthy donor and seeded as 4x106 cells/well in a 6 well plate and simultaneously infected for 12 h with strain PR8M (MOI=1) with or without IA (10 mM), DI (0.5 mM), or 4OI (25 µM). Thus, PBMC were not preincubated with the compounds before infection

value: Human primary cells


title: PBMCs uninfected DI treated

description:
Single cell transcriptome from total 1474 human PBMCs untreated. Cell were uninfected and treated with DI.
PBMCs isolation: Primary human monocytes were isolated from buffy coat from a healthy blood donor by density gradient centrifugation (Histopaque™, Sigma-Aldrich)
Cell staining: Cells were stained with propidium iodide and dead cells and doublets were removed by FACS. Live cells (including those undergoing apoptosis) were used to make single cell suspensions using the 10x Genomics platform.
Barcoding and cDNA synthesis: The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer’s instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode.


title: Sample 1

city: Shanghai

first: Deshui

last: Jia

address: 650 Xin Songjiang Road

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

description: The sample was collected from a  glioma patient who received surgery in Shanghai General Hospital. The patient did not receive any treatment before the surgery and was provided informed consent before the operation.

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.0). To remove low quality cells and likely multiplet captures,which is a major concern in microdroplet-based experiments, we apply a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where a certain percentage of counts belonged to mitochondrial genes. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count.Top variable genes across single cells were identified using the method described in Macosko et al[2]. Briefly, the average expression and dispersion were calculated for each gene, genes were subsequently placed into several bins based on expression.Principal component analysis (PCA) was performed to reduce the dimensionality on the log transformed gene-barcode matrices of top variable genes. Cells were clustered based on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in the percentage of expressed cells was used to identify significantly differentially expressed genes between clusters. Here, we use the R package SingleR[3], a novel computational method for unbiased cell type recognition of scRNA-seq to infer the cell of origin of each of the single cells independently and identify cell types.Differentially expressed genes(DEGs) were identified using the Seurat[1] package.P value < 0.05 and |log2foldchange| > 1 (or |log2foldchange| > 0.58) was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.2. [1] Butler A , Hoffman P , Smibert P , et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species[J]. Nature Biotechnology, 2018.[2] Macosko EZ, et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015;161:1202–1214.[3] Aran D , Looney A P , Liu L , et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibroticmacrophage[J]. Nature Immunology, 2019.
Genome_build: mm 10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Human glioma specimen

extract_protocol:
Fresh tissue was transported in cold PBS (Sigma-Aldrich) on ice. Tissue was washed three times with PBS to remove blood, then cut into tiny pieces (~1-2 mm3) and enzymatically dissociated in 1 mg/ml Type IV Collagenase in PBS for 45 min at 37 °C. The dissociation process was carried out in a shaking incubator with a speed of 50 r.p.m. Undigested masses were removed using 70-μm strainers (Corning), and red blood cells (RBC) were removed by RBC lysis buffer (Biolegend). The dissociated cells were washed twice with PBS containing 0.04% bovine serum albumin (BSA; Sigma-Aldrich). Finally, cell viability was examined by Trypan blue (Invitrogen) staining.
RNA libaries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacture's protocol.

value: 71  years old

tag: Sex

value: male


title: P. aeruginosa 3 h, replicate 2, run B


title: TnsB_crRNA-NT_ChIP-seq_paired_raw


title: TnsB_crRNA-4_ChIP-seq_paired_raw_more-depth


title: TnsC_crRNA-291_ChIP-seq_paired_raw


title: P. aeruginosa 4 h, replicate 3, run A

value: A


title: Plate TM118 - Dclk1-tdTom+/CD49b- cells

description:
TM118_S3
K-1338
K-1339

source_name: Plate TM118 - Dclk1-tdTom+/CD49b- cells


title: Human PBMCs IAV infected untreated

description:
Single cell transcriptome from total 1701 human PBMCs untreated. Cell were infected with IAV and untreated.
PBMCs isolation: Primary human monocytes were isolated from buffy coat from a healthy blood donor by density gradient centrifugation (Histopaque™, Sigma-Aldrich)
Cell staining: Cells were stained with propidium iodide and dead cells and doublets were removed by FACS. Live cells (including those undergoing apoptosis) were used to make single cell suspensions using the 10x Genomics platform.
Barcoding and cDNA synthesis: The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer’s instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode.


title: Plate TM116 - Dclk1-tdTom+/CD49b- cells

description:
TM116_S1
K-1335
K-1336

source_name: Plate TM116 - Dclk1-tdTom+/CD49b- cells


title: P. aeruginosa 3 h, replicate 1, run B


title: TnsB_crRNA-291_ChIP-seq_paired_raw


title: Human PBMCs uninfected control

description:
Single cell transcriptome from total 1870 human PBMCs untreated. Cell were uninfected and untreated.
PBMCs isolation: Primary human monocytes were isolated from buffy coat from a healthy blood donor by density gradient centrifugation (Histopaque™, Sigma-Aldrich)
Cell staining: Cells were stained with propidium iodide and dead cells and doublets were removed by FACS. Live cells (including those undergoing apoptosis) were used to make single cell suspensions using the 10x Genomics platform.
Barcoding and cDNA synthesis: The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer’s instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode.


title: TnsB_crRNA-295_ChIP-seq_paired_raw


title: Plate TM117 - Dclk1-tdTom+/CD49b+ cells

description:
TM117_S2
K-1335
K-1336

source_name: Plate TM117 - Dclk1-tdTom+/CD49b+ cells


title: P. aeruginosa 3 h, replicate 3, run A


title: P. aeruginosa 3 h, replicate 2, run A


title: Plate TM111 - Dclk1-tdTom+/CD49b+ cells

description:
TM111_S2
K-1296
K-1298

source_name: Plate TM111 - Dclk1-tdTom+/CD49b+ cells


title: P. aeruginosa 2 h, replicate 2, run B


title: Doxy/IKAROS RNP3

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
RNA-seq analysis was performed using the analysis pipeline developed by HCI Bioinformatic Core Facility (https://huntsmancancerinstitute.github.io/hciRscripts/hciR_scripts.html).
Briefly, the fastq files were firstly aligned using STAR aligned (v2.7.3a) using the following settings: --twopassMode Basic --outSAMtype BAM SortedByCoordinate  --limitBAMsortRAM 64000000000 --outBAMsortingBinsN 100  --quantMode TranscriptomeSAM --outWigType bedGraph --outWigStrand Unstranded
The count matrix was then calculated using the Subread FeatureCounts function (v1.6.3)
DESeq2 (v1.28.1) was used for differentially expressed genes analysis
Supplementary_files_format_and_content: gene expression matrix

source_name: Doxy/IKAROS RNP3

growth_protocol: CCRF-CEM cells were cultured in RPMI 1640 medium, 10% fetal bovine serum, 2 mM GlutaMAX-I, 100 U/mL penicillin and 100 μg/mL streptomycin

extract_protocol:
RNA was harvest with QIAGEN Rneasy Mini Kit and genomic DNA was remove with QIAGEN RNase-Free DNase Set
Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep kit and TruSeq RNA UD Indexes.

treatment_protocol: Cells were treated with vehicle (PBS) or doxycycline at 1uM for 24 hours

tag: cell lines

value: CCRF-CEM-GFI1-3XFLAG transfected with IKAROS CRISPR RNP

value: treated with Doxycycline for 24 hours


title: TnsB_crRNA-287_ChIP-seq_paired_raw


title: TniQ_crRNA-287_ChIP-seq_paired_raw

value: TniQ


title: Plate TM110 - Dclk1-tdTom+/CD49b- cells

description:
TM110_S1
K-1296
K-1298

source_name: Plate TM110 - Dclk1-tdTom+/CD49b- cells

value: Tam 3mg at 8wks, tissue collection 10d post Tam


title: Plate TM114 - Dclk1-tdTom+/CD49b- cells

description:
TM114_S3
K-1299
K-1301

source_name: Plate TM114 - Dclk1-tdTom+/CD49b- cells

value: Tam 3mg at 8wks, IR 10.5Gy 7d post Tam, tissue collection 3d post IR (total trace 10d)

value: Intestinal adult LMMP tissue


title: P. aeruginosa 2 h, replicate 1, run B

source_name: P. aeruginosa cultivated in LB medium


title: P. aeruginosa 2 h, replicate 3, run B


title: Doxy/IKAROS RNP2

source_name: Doxy/IKAROS RNP2


title: Doxy/IKAROS RNP1

source_name: Doxy/IKAROS RNP1


title: Input_Cas8_crRNA-4_ChIP-seq_paired_raw

source_name: Solid cell culture


title: HL60_BMI_KO_2

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequence reads were aligned to hg19 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Sambamba 0.5.5.
Deeptools was used to generate RPKM normalized bigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

tag: genotype

value: BMI1 knockout

tag: chip antibody


title: Plate TM115 - Dclk1-tdTom+/CD49b+ cells

description:
TM115_S4
K-1299
K-1301

source_name: Plate TM115 - Dclk1-tdTom+/CD49b+ cells

value: CD49b+ glial cells


title: Vehicle/IKAROS RNP2

source_name: Vehicle/IKAROS RNP2

value: Treated with PBS for 24 hours


title: Vehicle/IKAROS RNP1

source_name: Vehicle/IKAROS RNP1


title: P. aeruginosa 2 h, replicate 3, run A


title: Cas8_deltaTnsABC_crRNA-4_ChIP-seq_single_raw

tag: transposon protein


title: P. aeruginosa 1 h, replicate 3, run B


title: Cas8_deltaTniQ_crRNA-4_ChIP-seq_paired_raw

tag: epitope-tag on sample protein


title: TniQ_crRNA-4_ChIP-seq_single_raw

tag: strain


title: Cas8_crRNA-NT_ChIP-seq_paired_raw


title: HL60_WT

value: WT


title: si Opa1 3

city: Padova

first: Stephanie

last: Herkenne

state: Veneto

address: Via Ugo Bassi

department: Biology

country: Italy

institute: University of Padova

data_processing:
RNA Express Version 1.1.0 Illumina Base Space
RNA seq reads were aligned by using STAR ( reference genome HOMO SAPIENS UCSChg19)
Deseq2 version 1.6.3
Supplementary_files_format_and_content: csv files were generated by Deseq2 version 1.6.3

source_name: HUVECs

growth_protocol: HUVEC were grown on gelatin-coated plates with EGM-2 bullet kit medium (Lonza)

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen). Purity and quality of extracted RNA was evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories CA). High quality RNA with RNA Quality Indicator (RQI) score ≥ 9.5 was used for hybridization
RNA librairies were prepared by using TruSeq  stranded mRNA kit d'Illumina

treatment_protocol: HUVEC were transfected with 30 nM of siRNA using Dharmafect-4 reagent according to the manufacturer's instructions (Dharmacon, C0) for 24h

value: HUVECs pooled (Lonza)

tag: passage

value: passage p4


title: Cas8_crRNA-4_ChIP-seq_paired_raw_rep2

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


title: Vehicle/control RNP3

source_name: Vehicle/control RNP3

value: CCRF-CEM-GFI1-3XFLAG transfected with control CRISPR RNP


title: P. aeruginosa 1 h, replicate 1, run B

tag: time (h)

tag: replicate

value: B


title: si Opa1 1


title: sc3


title: Vehicle/control RNP2

source_name: Vehicle/control RNP2


title: Cas8_crRNA-295_ChIP-seq_paired_raw


title: Vehicle/control RNP1

source_name: Vehicle/control RNP1


title: P. aeruginosa 2 h, replicate 2, run A

tag: run


title: sc2

tag: cell type


title: Cas8_crRNA-287_ChIP-seq_paired_raw


title: Doxy/control RNP1

source_name: Doxy/control RNP1


title: P. aeruginosa 1 h, replicate 2, run A


title: Doxy/control RNP3

source_name: Doxy/control RNP3


title: P. aeruginosa 1 h, replicate 2, run B


title: sc1


title: Doxy/control RNP2

source_name: Doxy/control RNP2


title: si Opa1 2


title: 14D H3K4me2 rep1

status: Public on Oct 30 2021

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Burrows-Wheeler aligner with the minimum mapping quality filter of 20 was applied configurations…
ChIP-seq peak data targeting H3K4me1, H3K4me2, H3K4me3 and LSD1 (narrow peak data) had been generated using MACS2, the data consisting of observed peaks with a false discovery rate (FDR) cut off of 0.01. ChIP-seq peak data targeting H3K27me3 (broad peak data) had been generated using SICER peak caller, the data consisting of observed peaks with a FDR cut off of 0.01 as above. Peak data was read using custom R scripts, and exploratory analysis and peak annotation was done using R package ChIPseeker
Average profiles of ChIP-seq peaks binding to transcription start site (TSS) regions were inspected and visualized, using 3kb upstream and downstream TSS flanking sequences for the mapping. Peaks were annotated to the nearest TSS, with TSS region defined from -3kb to +3kb (default). R package DiffBind was used for generation of correlation heatmaps.
BEDtools multiIntersectBed and merge tools were used for detecting peak overlaps between the three time point samples, retaining the information on the peak existence in a sample. And for merging the overlapping peak intervals into continuous peak regions. TMM normalized read counts for the merged peaks were obtained using diffBind. Log2 fold change of normalized read counts between day 7 and day 0 samples, day 14 and day 0 samples as well as day 14 and day 7 samples were calculated
HOMER software was used for analyzing enrichment of known transcription factor (TF) motifs in ChIP-seq peaks and annotating the peaks with known motifs
Gene set enrichment of GOBP terms and KEGG pathway terms was performed using R package chipenrich with the genelocus definition set to 1 kb
Genome_build: mm10
Supplementary_files_format_and_content: Peak table

growth_protocol: αMEM+10% iFBS

extract_protocol:
Cross-link with 1% formaldehyde for 10 minutes RT. Incubate with 125 mM glycine 5 minutes RT. Collect cells to 50 ml falcon, centrifuge at 2500 RPM 5 min. Remove supernatant and replace with 3 ml of cold 1x TBS, don't resuspend. Centrifuge for 5 min 2500 rpm. Remove supernatant and store at -80C
Heating samples to 65 °C reversed cross-linking, and proteins were digested with proteinase K. Sequencing libraries were prepared, and massively parallel high-throughput sequencing was performed on an Illumina HiSeq 2000 system

treatment_protocol: Cells collected after 0d were treated with differentiation medium consisting of αMEM + 10% + 100 U/ml penicillin-streptomycin + iFBS + 50 µg/ml ascorbic acid + 10 mM β-glycerophosphate

tag: cell line

tag: time

value: 14 days of differentiation

value: Abcam ab7766

value: Differentiation treatment


title: 7d H3K4me2 rep1

value: 7 days of differentiation

tag: treatment


title: 14D H3K4me1 rep1

value: Cell Signaling Technology 5326 Lot1


title: 14D H3K4me3 rep1

value: Diagenode C15410003


title: 14D Input rep1

value: Sigma-Aldrich 12-370


title: 14D H3K27me3 rep1

value: Cell Signaling Technology 9733BC (C36B11)


title: 14D LSD1 rep1

value: Abcam ab17721


title: 7d H3K4me1 rep1


title: 7d H3K4me3 rep1


title: 7d LSD1 rep1


title: P. aeruginosa 1 h, replicate 3, run A

value: A


title: Cas8_crRNA-291_ChIP-seq_paired_raw

tag: antibody


title: 7d Input rep1


title: 0d H3K27me3 rep1

value: 0 days of differentiation

value: Growth medium


title: 0d LSD1 rep1


title: 0d Input rep1


title: 0d H3K4me1 rep1


title: 0d H3K4me3 rep1


title: 0d H3K4me2 rep1


title: 7d H3K27me3 rep1


title: KO_TAK2

city: L'Hospitalet de Llobregat

first: Antonio

last: Gentilella

state: Barcelona

address: granvia de l'Hospitalet, 199

department: ONCOBELL

country: Spain

institute: IDIBELL

data_processing:
Trimming of RNA-seq reads was performed with bbduk from BBTools suite to remove low quality bases, sequencing adapters and rDNA; Read alignment was performed with STAR version 2.6
Transcript and gene abundance quantification was performed with RSEM v(1.3.0) (58). GENCODE v29 was used for gene and transcript annotation. For differential expression analysis we used the statistical methods implemented in the DESeq2 R package. ERCC spike-ins were used to calculate normalization factors. Significance threshold was set at log2 fold change ≥1 and -log10 Q value ≥2
For the TSS analysis, we selected the sequencing reads that included part of the 3’ region of the RNA adapter oligo sequence ligated to the TAP-exposed 5’ termini (i.e. reads with at least the following 15 bp: 'CTGGCTTTGATGAAA') using GNU grep. We choose this specific oligo sequence to maximize both the oligo length and the number of reads with it. Next, we trimmed the oligo sequence with bbduk from BBTools suite (55) and aligned the sequencing reads to the human reference genome GRCh38 with STAR v(2.6) (57). We concatenated the two replicates with samtools cat (60) to increase the depth of coverage, obtaining a single alignment file with 282,495 mappable paired-end reads. We split the alignment file to obtain one per transcript, considering only protein coding, long noncoding and antisense transcripts based on GENCODE v19 annotation reference. We computed the coverage for the reference nucleotide systematically for all transcripts using samtools mpileup (60). TSS isoforms were determined at genome positions with an increase of coverage of more than 5 percent of the total coverage of a given transcript. We used GNU awk for performing calculations. We annotated as TOP isoforms those with the 5’ motif sequence “C[C/T][C/T]” and computed the percentage of TOP isoforms per gene using R. We made a bedgraph file with TSS coverage of all genes to visualize on IGV. In Figure 5e the corresponding circle-starting red lines display the 5’TOP-isoform transcripts
Genome_build: GENCODE v29

source_name: HCT116 LARP1 KO cells

growth_protocol: HCT116 cells Parental or LARP1 KO  were grown in DMEM 10% FBS.

extract_protocol:
1mg of polysomal lysates was resolved by ultracentrifugation on 10%-50% sucrose gradients. For each sample 20% volume of non-polysomal fractions from 40S to 80S peaks were pooled and spiked with a library of RNAs for normalization purposes across samples (ERCC spike-in mix, Thermo Fisher Scientific).
1μg of RNAs from two biological replicates from parental and LARP1 KO pools were depleted of rRNA with the Ribozero human, mouse, rat kit (Illumina) and  libraries for RNA-Seq were prepared. To identify the TSS of mRNAs protected by LARP1 with non-polysomes, 1 μg of the two parental RNA replicates was treated with alkalyne phosphates to blunt spourious 5’ termini, and CIP-treated RNAs were decapped with Tobacco Alkaline Phoshpatase (TAP, Epicentre). Exposed 5’ termini were ligated to an RNA oligo, then library were processed for RNA-Seq analysis.Differential analysis of non-polysomal transcripts upon TOR inhibition of parental / LARP1 KO cells. All libraries were sequenced on Illumina Novaseq 6000 platform in pair end mode resulting in 150 base length reads at Macrogen, Korea

treatment_protocol: Cells were treated for 48h with TAK228 at 250nM (drug was refreshed after 24h)

value: LARP1 KO

value: treatment with TAK228 at 250nM for 48h

tag: molecule subtype

value: Non-polysomal total RNA treated with Ribozero


title: KO_TAK1


title: ETC_T8_3

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

data_processing:
tophat2 --b2-very-sensitive
Conversion to bigWig R (3.5.1)
Genome_build: dm6
Supplementary_files_format_and_content: Genome coverage in bigWig format

organism: Drosophila melanogaster

source_name: Drosophila ph505 tumor cell line

growth_protocol: Drosophila ph505 cells were maintained at 25 °C in Shields and Sang M3 Insect medium (US Biological), supplemented with 2% Fetal Bovine Serum (FBS) (PAN Biotech), 2.5% fly extract, 5 µg/ml human insulin (Sigma), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Life Technologies) and subcultured every 3-7 days at a ratio of 1:(4-8).

extract_protocol:
RNA was extracted using an Arcturus PicoPure RNA Isolation kit (Applied Biosystems).
The library was prepared with SMARTSeq2 NexteraXT.

treatment_protocol: Drosophila ph505 cells a were treated with 5 μM 20-Hydroxyecdysone (Sigma) for 4, 8 or 16 hours.

value: Ecdysone 8 hours


title: PAR_TSS_2

description: same RNA sample as PAR_TAK_2 processed for TSS analysis

source_name: HCT116 parental cells

value: parental


title: PAR_TAK_2


title: PAR_TSS_1

description: same RNA sample as PAR_TAK_1 processed for TSS analysis


title: G_O_2

city: wuxi

first: Siyu

last: Liu

address: Street of River Deans, Binhu District, Wuxi City

institute: Jiangnan University Affiliated Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: Primary culture of skin fibroblasts

extract_protocol:
Primary culture of skin fibroblasts: Skin specimens were washed, cut into small pieces, and digested with 0.1% collagenases I for 4 h at 37 °C. Cells were then suspended in a culture medium (DMEM with 10% FBS, penicillin, and streptomycin) at 37 °C in 5% CO2. Set experiment grouping and collect fibroblasts, flash has frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin fibroblast


title: PAR_TAK_1


title: C1_1

value: Control


title: G1_2

value: GMQ


title: G1_1


title: C1_2


title: C1_3


title: Jejunum Patient_2 Monolayer-Matrigel

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids were grown and differentiated  as indicated in the manuscript

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated Controls

tag: tissue

value: Intestine

tag: segment

value: Jejunum

tag: format

value: Monolayer

tag: substrate

value: Matrigel

tag: sample type

value: Differentiated Jejunal Enteroids


title: Jejunum Patient_11 Monolayer-Collagen

value: Collagen


title: G1_3


title: Jejunum Patient_4 Monolayer-Matrigel


title: Jejunum Patient_11 Monolayer-Matrigel


title: G_O_3


title: Jejunum Patient_3 Monolayer-Matrigel


title: Jejunum Patient_2 Monolayer-Collagen


title: Jejunum Patient_4 Monolayer-Collagen


title: Jejunum Patient_6 3D-Matrigel


title: G_O_1


title: Jejunum Patient_11 Transwell-Matrigel

value: Transwell


title: Jejunum Patient_6 Monolayer-Collagen


title: Sachi

type: RNA

city: Nagakute

first: Sivasundaram

last: Karnan

address: 1-1 Yazako karimata, Buid:2,　Room:304

department: biochemistry

country: Japan

institute: aichi medical university

description: Gene expression in Sachi cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (G) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Sachi

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: KMS-11 and Sachi  cells were cultivated in RPMI1640   medium containing 10% FBS with penicillin-streptomycin. The cells were typically passaged at a split

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: KMS-11 and Sachi   cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Sachi

value: Human myeloma cell line

tag: gender

value: Female

tag: age

value: unknown

tag: genotype

value: wildtype


title: KMS-11-ARK5-KO#1

description: Gene expression in KMS-11-ARK5-KO#1 clone


title: Sachi-ARK5-KO#1

description: Gene expression in Sachi-ARK5-KO#1 clone


title: KMS-11-ARK5-KO#2

description: Gene expression in KMS-11-ARK5-KO#2 clone


title: Sachi-ARK5-KO#2

description: Gene expression in Sachi-ARK5-KO#2 clone


title: KMS-11

description: Gene expression in KMS-11 cells


title: Jejunum Patient_3 Monolayer-Collagen


title: Jejunum Patient_6 Transwell-Matrigel


title: Jejunum Patient_4 Transwell-Matrigel


title: Jejunum Patient_3 Transwell-Matrigel


title: Jejunum Patient_11 Transwell-Collagen


title: FNP-7 [Control]

city: NEW YORK

first: Philippe

last: Soriano

state: NY

address: 1468 Madison Avenue, Annenberg 25-70, Box 1020

department: Cell, Development, and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description: Control

data_processing:
Reads were pseudo-aligned to the mouse transcriptome (mm10 partial selective alignment method, downloaded from refgenie) using salmon 1.5.0 and the flags –validateMappings –gcBias –numBootstraps 30.
Pseudoalignments were processed with wasabi 1.0.1
Analysis with sleuth 0.30.0-4 with the flag gene_mode=true. Analysis was performed using a full model that accounted for genotype, litter/batch, and tissue-of-origin (for combined tissue analysis only) versus a reduced model consisting only of litter/batch (and tissue-of-origin). Fold-changes and q-values were computed using the Wald test.
Genome_build: mm10
Supplementary_files_format_and_content: An Excel file containing raw gene counts, tpm values, and differentially expressed genes for the mandible-only, FNP-only, and joint mandible+FNP datasets, as well as the variables used for each sample during sleuth analysis (litter, genotype, tissue).

source_name: nasal processes

extract_protocol:
Qiagen Rneasy Plus kit. Tissue was lysed by trituration in RLT buffer + BME
Library prep and sequencing was done by GeneWiz. It was for Illumina paired-end 150bp sequencing. mRNA was PolyA selected.

treatment_protocol: Embryos were dissected in ice-cold PBS and craniofacial prominences carefully removed and cleaned with fine forceps. They were immediately processed for RNA extraction.

value: FNP (LNP + MNP)

tag: developmental stage

value: Srf flox/+; Wnt1-Cre


title: Jejunum Patient_6 Monolayer-Matrigel


title: Jejunum Patient_2 Transwell-Matrigel


title: FNP-4 [Mutant]

description: Mutant

value: Srf flox/flox; Wnt1-Cre


title: FNP-8 [Control]

description: Control

value: Srf flox/+


title: Jejunum Patient_3 Transwell-Collagen


title: FNP-2 [Control]

description: Control

value: Srf flox/flox


title: FNP-5 [Mutant]

description: Mutant


title: Jejunum Patient_4 Transwell-Collagen

value: Intestine


title: FNP-6 [Mutant]

description: Mutant


title: Jejunum Patient_6 Transwell-Collagen

value: Jejunum


title: Jejunum Patient_2 Transwell-Collagen


title: FNP-3 [Mutant]

description: Mutant


title: Jejunum Patient_4 3D-Matrigel


title: Jejunum Patient_11 3D-Matrigel


title: Mand-8 [Control]

description: Control

source_name: mandible

value: mandible


title: FNP-1 [Control]

description: Control


title: Mand-7 [Control]

description: Control


title: Mand-6 [Mutant]

description: Mutant


title: Jejunum on Stiff Hydrogel (STJ3_2)

growth_protocol: 3D enteroids maintained in CMGF(+) were dissociated into single cells using trypsin, and seeded atop Matrigel-coated hydrogel surfaces at a density of 3x10^5 cells/cm2 for 1 day to form monolayers.

treatment_protocol: Simply grown on substrate

value: Monolayer

value: Hydrogel

tag: substrate stiffness

value: Stiff Hydrogel

tag: line

value: Jejunal Line - J3


title: Jejunum Patient_2 3D-Matrigel

value: Matrigel

value: Differentiated Jejunal Enteroids


title: Mand-3 [Mutant]

description: Mutant


title: Mand-5 [Mutant]

description: Mutant


title: Mand-2 [Control]

description: Control


title: Mand-4 [Mutant]

description: Mutant


title: Jejunum on Stiff Hydrogel (STJ11_1)

value: Jejunal Line - J11


title: Mand-1 [Control]

description: Control


title: Rh2-20 mg/kg + Doxorubicin 2mg/kg

city: Daejeon

first: Yee-Jin

last: Yun

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested. SureSelectXT RNA Direct Reagent kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were injected s.c. with 9×10^6 stable pool of MDA-MB-231 cells at day 0. Day 7, mice were randomly divided into six different groups: Control, Rh2 (20mg/kg), Rh2 (30mg/kg), Rh2 (20mg/kg) + Dox (2mg/kg), Rh2 (30mg/kg) + Dox (2mg/kg), and Dox (2mg/kg). then BALB/c nude mice were received injections of Dox dissolved in 0.9% saline every other day with cumulative dose of 22 mg/kg body weight. Rh2 dissolved in PBS + Tween 80 was injected every day during the treatment course (3 weeks).

value: heart

tag: strain

value: BALB/c nude (CAnN.Cg-Foxn1nu/Crl)

value: 6 weeks


title: Rh2-30 mg/kg + Doxorubicin 2mg/kg


title: Rh2-20 mg/kg


title: Jejunum on Soft Hydrogel (SOJ3_2)

value: Soft Hydrogel


title: Doxorubicin 2mg/kg

description: H-Dox


title: Jejunum on Stiff Hydrogel (STJ11_2)


title: Jejunum on Soft Hydrogel (SOJ3_1)


title: Jejunum on Soft Hydrogel (SOJ11_3)


title: Rh2-30 mg/kg


title: MEF LARP7 KO rep2

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using hisat2.
Count  per Million mapped reads (CPM) were calculated using HTseq
Genome_build: mm10

source_name: Mouse embryonic fibroblasts

growth_protocol: IMR90 human diploid fibroblast line was grown in MEM medium supplemented with 10% fetal bovine serum (FBS), L-glutamine, sodium pyruvate, nonessential amino and sodium bicarbonate. Mouse embryonic fibroblasts (MEFs) were isolated from E13.5 embryos of LARP7+/+ or LARP7-/- and grown in DMEM medium (Gibco) supplemented with 10% FBS.

extract_protocol:
Total RNA obtained from IMR90 cells and MEFs were extracted using a RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA and 1ug total RNA was used for sequencing library  construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IMR90 fibroblasts were infected with lentivirus expressing control shRNA or LARP7 shRNA, and then selected with puromycin (1μg/ml) for 7 days. The stable cell lines were maintained and passaged in the culture medium supplemented with 0.2 μg/ml puromycin.

tag: cell type

value: embryonic fibroblast


title: Jejunum on Stiff Hydrogel (STJ3_3)


title: Jejunum Patient_3 3D-Matrigel

tag: cell line


title: Jejunum on Medium Hydrogel (MJ3_3)

value: Medium Hydrogel


title: Jejunum on Medium Hydrogel (MJ3_2)


title: Jejunum on Soft Hydrogel (SOJ11_2)


title: Control

description: H-Control


title: Jejunum on Medium Hydrogel (MJ11_3)

description: Raw data: R2 available at SRA. R1 mate is not available.


title: Jejunum on Medium Hydrogel (MJ3_1)


title: MEF WT rep2


title: Jejunum on Medium Hydrogel (MJ11_2)


title: Jejunum on Medium Hydrogel (MJ11_1)


title: Jejunum on Stiff Hydrogel (STJ3_1)


title: MEF LARP7 KO rep1


title: MEF WT rep1


title: VU15_Mutant 28 day control

city: Nashville

first: Paul

middle: Brent

last: Ferrell

state: TN

address: 777 Preston Research Bldg., 2220 Pierce Ave.

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
Clean reads mapped to NCBI referene genome using STAR (v2.5) using Maximal Mapping Prefix
Expression quantified using HTSeq v0.6.1
DESeq2 R package (v2_1.6.3) used to evaluate for differential expression
Genome_build: NCBI
Supplementary_files_format_and_content: raw count and fpkm

source_name: Acute Myeloid Leukemia Cells

growth_protocol: Cells were grown per manufacturer's protocol and harvested at similar titers to ensure no additional variability.

extract_protocol:
RNeasy Mini Kit (Qiagen 74104)
Amplification and sequencing of RNA through Novogene

tag: mutation

tag: atcc cell line


title: Jejunum on Plastic (J3967)

value: Plastic


title: VU13_WT control

value: wtIDH


title: VU9_Mutant 28 day control


title: Jejunum on Soft Hydrogel (SOJ3_3)

value: Intestine

value: Jejunum


title: VU3_Mutant 28 day control


title: Jejunum on Stiff Hydrogel (J2st7)

value: Monolayer

value: Jejunal Line - J2


title: Jejunum on Stiff Hydrogel (J2st6)

value: Hydrogel

value: Stiff Hydrogel


title: VU7_WT control


title: Jejunum on Stiff Hydrogel (J2st5)


title: Jejunum on Soft Hydrogel (J2soft5)


title: VU1_WT control


title: h24_T85_Covid19_Remdesivir p20064_s070_EpiRNA_085_S170

city: Atlanta

first: Diego

last: Moncada

state: Georgia

address: 201 Dowman Dr

department: Pediatrics

institute: Emory University

description:
h24_T85_Covid19_Remdesivir
SARS-CoV-2_h24_Plus_Remdesivir

data_processing:
Hisat2 was used to align next-generation sequencing reads to the reference genome
SAMtools was used to sort BAM files.
FeatureCounts from the  Subread package was used to generate read counts expressed per gene
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: we used Alvetex (Reprocell) 200 μm-thick inert 3D scaffolds with >90% porosity (pore sizes of 36–40 μm, with interconnects of 12–14 μm). In brief, inserts were activated with 70% ethanol, coated overnight at 37ºC with rat-tail collagen I (3 mg/mL, Sigma) and seeded with NCI-H441 cells at 2.5×105 cells per 12-well insert. Cells were first grown in submerged cultures with DMEM/F12 supplemented with 10% heat-inactivated serum, penicillin, and streptomycin. After 2 days, cells were supplemented basally with serum-free DMEM/F12 with 10% Ultroser G (Pall Life Sciences) to establish ALI. Cultures were grown for 2 weeks at ALI and supplemented basally with fresh medium every 48 hours. At the end of two weeks, the filters were flipped and then infected with SARS-CoV-2 (or IAV or OC43) at an MOI of 0.1. For TM experiments, the ALI cultures were placed with the apical compartment exposed to RPMI, leukotriene B4 (LTB4, 100 nM) and CCL2 at 250 pg/mL. then. 1 ×106  blood monocytes were loaded onto the 200 μm-thick basal compartment of the Alvetex scaffold (situated upside), and allowed to migrate at 37°C at 5% CO2 through the collagen and epithelial layers into the apical compartment for 24 hours.

extract_protocol:
Filters containing epithelial cells were incubated with Trizol. RNA was extracted following standard chloroform extraction followed by a cleanup with sodium acetate precipitation. RNA quality and concentration were quantified using a Bioanalyzer (Agilent technologies, Inc.) and only samples with RIN>8.0 were used for sequencing.
Libraries were prepared using the TruSeq RNA Single Indexes Set B kit (Illumina) and AmPure beads (Beckman) and sequenced as paired end (100bp) by high seq rapid run (Illumina) with an aim of ~20 million reads per sample

treatment_protocol: In this model, small airway epithelium grown at air-liquid interface are infected with respiratory viruses (SARS-CoV-2, OC43, IAV) and in some instances blood monocytes were transmigrated across the air-liquid interface epithelium towards leukotriene B4 (LTB4) and CCL2 placed apically. Baricitnib and/or remdesivir were used where indicated to determine if these drugs had an effect on SARS-CoV-2 infection resolution.

value: Lung epithelial cells

tag: treatment

tag: condition

value: 24h Leucocytes transmigration


title: h24_T81_Covid19_Baricitinib p20064_s066_EpiRNA_081_S166

description:
h24_T81_Covid19_Baricitinib
SARS-CoV-2_h24_Plus_Baricitinib


title: Jejunum on Medium Hydrogel (J2med7)

tag: tissue

tag: segment


title: h24_T83_Covid19_Remdesivir p20064_s068_EpiRNA_083_S168

description:
h24_T83_Covid19_Remdesivir
SARS-CoV-2_h24_Plus_Remdesivir


title: Jejunum on Soft Hydrogel (J2sof6)

tag: format

tag: substrate


title: h24_T79_Covid19_Baricitinib p20064_s064_EpiRNA_079_S164

description:
h24_T79_Covid19_Baricitinib
SARS-CoV-2_h24_Plus_Baricitinib


title: Jejunum on Medium Hydrogel (J2md5)


title: h24_T75_Covid19_No_Drug p20064_s060_EpiRNA_075_S160

description:
h24_T75_Covid19_No_Drug
SARS-CoV-2_h24

value: 24 hours_post_SARS-CoV-2_Infection


title: Jejunum on Medium Hydrogel (J2med6)


title: Jejunum on Plastic (J2967)

value: Matrigel


title: h24_T77_Covid19_No_Drug p20064_s062_EpiRNA_077_S162

description:
h24_T77_Covid19_No_Drug
SARS-CoV-2_h24


title: Jejunum on Plastic (J2962)


title: h24_T84_NoInfection_Remdesivir p20064_s069_EpiRNA_084_S169

description:
h24_T84_NoInfection_Remdesivir
No_Infection_h24_Plus_Remdesivir

value: 24 hours_No_Infection_post_Remdesivir


title: h24_T80_NoInfection_Baricitinib p20064_s065_EpiRNA_080_S165

description:
h24_T80_NoInfection_Baricitinib
No_Infection_h24_Plus_Baricitinib

value: 24 hours_No_Infection_post_Baricitinib


title: Jejunum on Stiff Hydrogel (J11stiff5)

value: Jejunal Line - J11


title: Jejunum on Plastic (J2961)


title: h24_T82_NoInfection_Remdesivir p20064_s067_EpiRNA_082_S167

description:
h24_T82_NoInfection_Remdesivir
No_Infection_h24_Plus_Remdesivir


title: h24_T40_NoInfection_Baricitinib p20064_s053_EpiRNA_040_S153-2

description:
h24_T40_NoInfection_Baricitinib
No_Infection_h24_Plus_Baricitinib


title: Jejunum on Soft Hydrogel (J2sof7)

value: Soft Hydrogel


title: Jejunum on Plastic (A96WJ3_2)

value: Jejunal Line - J3


title: h24_T40_NoInfection_Baricitinib p20064_s053_EpiRNA_040_S153-1


title: Jejunum on Plastic (A96WJ11_2)

value: Plastic


title: h24_T38_NoInfection_Baricitinib p20064_s051_EpiRNA_038_S151-2

description:
h24_T38_NoInfection_Baricitinib
No_Infection_h24_Plus_Baricitinib


title: h24_T38_NoInfection_Baricitinib p20064_s051_EpiRNA_038_S151-1


title: Jejunum on Plastic (A96WJ11_3)


title: Jejunum on Plastic (A96WJ11_1)


title: Jejunum on Plastic (A96WJ3_1)


title: Jejunal Enteroid treated with non-pathogenic control E. Coli strain (J3_HS)

growth_protocol: The undifferentiated enteroids/colonoids monolayers were grown in CMGF(+) for 3 days and in differentiation media from days 3-5.

treatment_protocol: The differentiated monolayers were then infected with bacterial cultures at a multiplicity of infection of 10 for 3 hours

tag: sample type

value: Jejunal Enteroid

value: Collagen IV

value: non-pathogenic control E. Coli strain

tag: individual


title: h24_NT43R_Covid19 p20064_s015_EpiRNA_24_hours_minus_SARS_S115

description:
h24_NT43R_Covid19
SARS-CoV-2_h24

value: Baseline no transmigration


title: Jejunal Enteroid Mock treated (J3_Mock)

value: Intestine

value: Jejunum

value: Monolayer

value: Mock treated


title: h48_NT45_Covid19 p20064_s016_EpiRNA_48_hours_minus_SARS_S116

description:
h48_NT45_Covid19
SARS-CoV-2_h48

value: Lung epithelial cells

value: 48 hours_post_SARS-CoV-2_Infection


title: Jejunal Enteroid treated with enterohemorrhagic E. coli strain 8624 (J3_ehec)

value: enterohemorrhagic E. coli strain 8624


title: h48_NT45R_Covid19 p20064_s016_EpiRNA_48_hours_minus_SARS_S116

description:
h48_NT45R_Covid19
SARS-CoV-2_h48


title: h24_T78_NoInfection_Baricitinib p20064_s063_EpiRNA_078_S163

description:
h24_T78_NoInfection_Baricitinib
No_Infection_h24_Plus_Baricitinib

value: 24h Leucocytes transmigration


title: h24_NT41_OC43 Sample41_Epi24hour_DonorNA_OC43Infection_S37

description:
h24_NT41_OC43
OC43_h24

value: 24 hours_post_OC43_infection


title: h24_NT26_FLU Sample26_EpiTime_0_DonorNA_YesInfection_S18

description:
h24_NT26_FLU
PR8_Infection_48h

value: 48 hours_post_PR8_Infection


title: Jejunal Enteroid treated with extra-intestinal pathogenic E. coli (J3_expec)

value: extra-intestinal pathogenic E. coli


title: h24_NT25_FLU Sample25_EpiTime_0_DonorNA_YesInfection_S17

description:
h24_NT25_FLU
PR8_Infection_48h


title: Jejunal Enteroid treated with enteroaggregative E. coli strain 042 (J3_eaec)

value: enteroaggregative E. coli strain 042


title: h24_NT43_Covid19 p20064_s015_EpiRNA_24_hours_minus_SARS_S115

description:
h24_NT43_Covid19
SARS-CoV-2_h24

value: 24 hours_post_SARS-CoV-2_Infection


title: Jejunal Enteroid treated with aafA mutant (J3_aafA)

value: Jejunal Enteroid

value: aafA mutant


title: Jejunal Enteroid treated with non-pathogenic control E. Coli strain (J2_HS)

value: Collagen IV

value: non-pathogenic control E. Coli strain


title: h24_T76_NoInfection p20064_s061_EpiRNA_076_S161

description:
h24_T76_NoInfection
No_Infection

value: untreated


title: Jejunal Enteroid Mock treated (J2_Mock)

value: Intestine

value: Jejunum


title: h24_T74_NoInfection p20064_s059_EpiRNA_074_S159

description:
h24_T74_NoInfection
No_Infection


title: h24_T36_NoInfection p20064_s049_EpiRNA_036_S149-2

description:
h24_T36_NoInfection
No_Infection


title: Jejunal Enteroid treated with extra-intestinal pathogenic E. coli (J2_expec)

value: Monolayer


title: h24_T34_NoInfection p20064_s047_EpiRNA_034_S147-2

description:
h24_T34_NoInfection
No_Infection

value: Lung epithelial cells


title: h24_T36_NoInfection p20064_s049_EpiRNA_036_S149-1

description:
h24_T36_NoInfection
No_Infection


title: h24_T34_NoInfection p20064_s047_EpiRNA_034_S147-1

description:
h24_T34_NoInfection
No_Infection


title: Jejunal Enteroid treated with enterohemorrhagic E. coli strain 8624 (J2_ehec)


title: Jejunal Enteroid treated with aafA mutant (J2_aafA)


title: iPS, 120 h, untransfected, replicate 2

city: Kyoto

first: Hirohide

last: Saito

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Life Science Frontiers

institute: Kyoto University

data_processing:
Sequenced reads were filtered by fastp 0.12.4 with parameters -i $rawpath -h $html -j $json -o $outpath -q 15 -n 5 -l 15 -w $core --adapter_sequence=GATCGGAAGAGCACACGTCTGAACTCCAGTCA.
The reads were mapped to custom human genome including EGFP and Bsd gene by STAR 2.7.9a with parameters --runThreadN $core --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --genomeDir $star_index --readFilesCommand zcat --readFilesIn $fastq_path
The uniquely mapped reads were counted using htseq-count 0.13.5 with parameters --format bam --stranded reverse --idattr gene_name $star_path $GTF
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include read counts.

source_name: iPS

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina) with IDT for Illumina TruSeq RNA UD Indexes (Illumina), quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

value: iPS

tag: replicate

value: untransfected

tag: time point


title: iPS, 120 h, selected, replicate 2

value: selected


title: h0_NT30_NoInfection Sample30_EpiTime_0_DonorNA_NoInfection_S34

description:
h0_NT30_NoInfection
No_Infection

value: Baseline no transmigration


title: iPS, 96 h, untransfected, replicate 2

value: 96 hr


title: Jejunal Enteroid Mock treated (J11_Mock)

value: Mock treated


title: bcg5 - BCG|No BBN

city: Baltimore

first: Kara

last: Lombardo

state: Maryland

address: 600 N Wolfe St

department: Urology

institute: Johns Hopkins Medical Institutions

description: Twenty-six transcripts are reserved by the system for positive, negative, binding and purification controls.

hyb_protocol: Hybridization was carried out for 16 hours at 65degrees celsius in a thermal cycler

scan_protocol: Nanostring Mus musculus Myeloid Innate Immunity panel was run

data_processing: Raw data counts  were normalized by first thresholding to exceed mean +1 standard deviation of negative controls, then scaled by a positive control normalization factor to correct for total counts and additionally scaling with a set of predefined housekeeping genes, as described in the NanoString user documentation.

label: biotin

source_name: BBN bladder tumor

label_protocol: 100ug of RNA was labeled with Reporter Codeset and Capture Probset

growth_protocol: BBN was admistered in drinking water of mice ad libitum for 12 weeks resulting in the development of bladder cancer

extract_protocol: RNA was isolated from fresh bladder tissue following sacrifice and total RNA was extracted using Qiagen RNeasy Kit

treatment_protocol: Treatment with 100ul of TICE strain BCG (1x10^8 CFU) was initiated at week 12 and instilled into the bladder for 1 hour weekly for 3 weeks; Radiotherapy was administered as a single beam of external radiation at 15Gy at week 12.

tag: bbn

value: No

value: BCG

tag: tumor stage

value: Benign


title: bcg8 - BCG|Yes BBN

value: Yes

value: Benign, acute+chronic inflammation


title: iPS, 72 h, untransfected, replicate 2

value: 72 hr


title: Jejunal Enteroid treated with extra-intestinal pathogenic E. coli (J11_expec)

value: Jejunal Enteroid

value: Collagen IV

value: extra-intestinal pathogenic E. coli


title: bcg4 - BCG|No BBN


title: h0_NT30_NoInfection Sample30_EpiTime_0_DonorNA_NoInfection_S20

description:
h0_NT30_NoInfection
No_Infection

value: untreated


title: Jejunal Enteroid treated with enterohemorrhagic E. coli strain 8624 (J11_ehec)

value: Intestine

value: Jejunum

value: Monolayer

value: enterohemorrhagic E. coli strain 8624


title: h0_NT28_NoInfection Sample28_EpiTime_0_DonorNA_NoInfection_S32

description:
h0_NT28_NoInfection
No_Infection

value: Lung epithelial cells

value: Baseline no transmigration


title: h0_NT27_NoInfection Sample27_EpiTime_0_DonorNA_NoInfection_S31

description:
h0_NT27_NoInfection
No_Infection


title: iPS, 72 h, selected, replicate 2

value: iPS

value: selected


title: rad9 - Radiation|Yes BBN

value: Radiation

value: CIS


title: rad8 - Radiation|Yes BBN

value: Yes


title: Jejunal Enteroid treated with enteroaggregative E. coli strain 042 (J11_eaec)

value: enteroaggregative E. coli strain 042


title: rad3 - Radiation|No BBN

value: No

value: Benign


title: Jejunal Enteroid treated with enteroaggregative E. coli strain 042 (J2_eaec)

value: Jejunal Enteroid

value: Collagen IV


title: iPS, 120 h, untransfected, replicate 1

value: untransfected


title: H7_hESCs_DLG2_KO2_60d_3 [s_36]

city: Cardiff

first: Eunju

last: Shin

state: Wales

address: Hadyn Ellis Building,Maindy Road.

department: Neuroscience & Mental Health Research Institute, School of Medicine.

country: United Kingdom

institute: Cardiff University

data_processing:
All samples were modelled after the long-rna-seq-pipeline used by the PsychENCODE Consortium and available at https://www.synapse.org/#!Synapse:syn12026837. Briefly, the fastq files from Illumina HiSeq4000 were assessed for quality by using FastQC tool (v0.11.8) and trimmed for adapter sequence and low base call quality (Phred score < 30 at ends) with cutadapt (v2.3).
The mapping of the trimmed reads was done using STAR (v2.7.0e) and the BAM files were produced in both genomic and transcriptomic coordinates and sorted using samtools (v1.9). The aligned and sorted BAM files were further assessed for quality using Picard tools (v2.20.2). GRCh38.p13 was used as the reference genome and the comprehensive gene annotations on the primary assembly from Gencode (release 32) used as gene annotation. Gene and transcript-level quantifications were calculated using RSEM (v1.3.1). Both STAR and RSEM executions were performed using the psychENCODE parameters.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: All hESC lines were maintained at 37°C and 5% CO2 in 6 well cell culture plates (Greiner) coated with 1% Matrigel hESC-Qualified Matrix (Corning) prepared in Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12, Thermo Fisher Scientific). Cells were fed daily with Essential 8 medium (E8, Thermo Fisher Scientific) and passaged at 80% confluency using Versene solution (Thermo Fisher Scientific) for 1.5 minutes at 37°C followed by manual dissociation with a serological pipette. All cells were kept below passage 25 and confirmed as negative for mycoplasma infection.

extract_protocol:
Total transcriptome RNA was isolated from triplicate wells for all cell lines at each time point (days 15, 20, 30 and 60) by lysing cells in TRIzol Reagent (Thermo Fisher Scientific) followed by purification with the PureLink RNA Mini Kit (Thermo Fisher Scientific). RNA quality control (QC) was performed with the RNA 6000 Nano kit analysed using the 2100 Bioanalyzer Eukaryote Total RNA Nano assay (Agilent).
cDNA libraries for sequencing were produced using the KAPA mRNA HyperPrep Kit for Illumina Platforms (Kapa Biosystems) and indexed with KAPA Single-Indexed Adapter Set A + B (Kapa Biosystems). Library quantification was by Qubit 1x dsDNA HS Assay kit (Thermo Fisher Scientific) and QC by High Sensitivity DNA kit analysed using the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent).

treatment_protocol: Two guide RNAs targeting exon 22 of the human DLG2 gene, covering the first PDZ domain, were designed using a web-based tool (crispr.mit.edu) and cloned into two plasmids containing D10A nickase mutant Cas9 with GFP (PX461) or Puromycin resistant gene (PX462). H7 hESCs (WiCell) were nucleofected using P4 solution and CB150 programme (Lonza) with 5µg of plasmids, FACS sorted on the following day and plated at a low density (~70 cells/cm2) for clonal isolation. 19 clonal populations were established with 6 WT and 13 mutant lines after targeted sequencing of the exon 22. One WT and two homozygous knockout lines were chosen for study. Differentiation to cortical projection neurons was achieved using the dual SMAD inhibition protocol (Chambers et al., 2009) with modifications (embryoid body to monolayer and replacement of KSR medium with N2B27 medium) suggested by Cambray et al., 2012.

tag: cell line/type

value: H7 hESCs

tag: genotype

tag: age


title: iPS, 96 h, selected, replicate 2

tag: cell line

value: 96 hr


title: Jejunal Enteroid treated with non-pathogenic control E. Coli strain (J11_HS)

value: Intestine

value: Jejunum

value: Monolayer

value: non-pathogenic control E. Coli strain


title: iPS, 120 h, selected, replicate 1

value: iPS


title: ctrl9 - No treatment|Yes BBN


title: ctrl8 - No treatment|Yes BBN


title: h0_NT29_NoInfection Sample29_EpiTime_0_DonorNA_NoInfection_S19

description:
h0_NT29_NoInfection
No_Infection

tag: cell type

value: Lung epithelial cells

value: untreated

value: Baseline no transmigration


title: iPS, 96 h, untransfected, replicate 1

tag: treatment


title: bcg3 - BCG|No BBN

value: BCG


title: H7_hESCs_DLG2_KO2_60d_2 [s_35]


title: Ileal Enteroid treated with non-pathogenic control E. Coli strain (I9_HS)

value: Ileum

value: Ileal Enteroid


title: Ileal Enteroid treated with extra-intestinal pathogenic E. coli (I9_expec)

value: extra-intestinal pathogenic E. coli


title: H7_hESCs_DLG2_KO2_60d_1 [s_34]


title: Ileal Enteroid treated with enterohemorrhagic E. coli strain 8624 (I9_ehec)

value: enterohemorrhagic E. coli strain 8624


title: ctrl4 - No treatment|No BBN

value: No

value: Benign


title: Ileal Enteroid treated with enteroaggregative E. coli strain 042 (I9_eaec)

value: Collagen IV

value: enteroaggregative E. coli strain 042


title: iPS, 72 h, untransfected, replicate 1

value: untransfected

value: 72 hr


title: ctrl3 - No treatment|No BBN


title: Ileal Enteroid treated with aafA mutant (I9_aafA)

value: Intestine

value: Monolayer

value: aafA mutant


title: H7_hESCs_DLG2_KO1_60d_1 [s_31]

value: H7 hESCs


title: Jejunal Enteroid treated with aafA mutant (J11_aafA)

value: Jejunum

value: Jejunal Enteroid


title: H7_hESCs_DLG2_KO1_60d_2 [s_32]


title: iPS, 72 h, selected, replicate 1

value: iPS

value: selected


title: H7_hESCs_DLG2_WT_60d_3 [s_30]

value: wild type


title: 293FT, 72 h, untransfected, replicate 2


title: ctrl2 - No treatment|No BBN


title: Ileal Enteroid Mock treated (I4_Mock)

value: Ileum

value: Ileal Enteroid

value: Mock treated


title: bcg7 - BCG|Yes BBN

value: Yes

value: BCG

value: Benign, acute+chronic inflammation


title: bcg6 - BCG|Yes BBN


title: 293FT, 48 h, untransfected, replicate 2

value: untransfected

value: 48 hr


title: 293FT, 24 h, untransfected, replicate 2

value: 24 hr


title: Ileal Enteroid treated with non-pathogenic control E. Coli strain (I4_HS)

value: Intestine

value: Monolayer

value: Collagen IV

value: non-pathogenic control E. Coli strain


title: iPS, 96 h, selected, replicate 1

value: 96 hr


title: Ileal Enteroid treated with extra-intestinal pathogenic E. coli (I4_expec)

value: extra-intestinal pathogenic E. coli


title: H7_hESCs_DLG2_KO1_60d_3 [s_33]

value: H7 hESCs


title: H7_hESCs_DLG2_WT_60d_2 [s_29]

value: wild type


title: H7_hESCs_DLG2_WT_60d_1 [s_28]


title: 293FT, 48 h, untransfected, replicate 1


title: 293FT, 72 h, untransfected, replicate 1

value: 72 hr


title: Ileal Enteroid treated with enterohemorrhagic E. coli strain 8624 (I4_ehec)

value: Ileum

value: Ileal Enteroid

value: enterohemorrhagic E. coli strain 8624


title: bcg2 - BCG|No BBN

value: No

value: BCG

value: Benign


title: H7_hESCs_DLG2_KO2_30d_3 [s_27]


title: bcg1 - BCG|No BBN


title: 293FT, 24 h, untransfected, replicate 1

value: untransfected


title: H7_hESCs_DLG2_KO2_30d_2 [s_26]


title: Ileal Enteroid treated with enteroaggregative E. coli strain 042 (I4_eaec)

value: enteroaggregative E. coli strain 042


title: Ileal Enteroid treated with extra-intestinal pathogenic E. coli (I3_expec)

value: Intestine


title: rad7 - Radiation|Yes BBN

value: Yes

value: Radiation

value: CIS


title: Ileal Enteroid treated with aafA mutant (I4_aafA)

value: Monolayer

value: Collagen IV

value: aafA mutant


title: rad6 - Radiation|Yes BBN


title: H7_hESCs_DLG2_KO2_30d_1 [s_25]

value: H7 hESCs


title: Ileal Enteroid treated with enteroaggregative E. coli strain 042 (I3_eaec)


title: rad1 - Radiation|No BBN


title: 293FT, 48 h, GFP, replicate 2

value: GFP

value: 48 hr


title: rad2 - Radiation|No BBN


title: 293FT, 72 h, GFP, replicate 2

value: 72 hr


title: Ileal Enteroid treated with non-pathogenic control E. Coli strain (I103_HS)

value: Ileum

value: Ileal Enteroid

value: non-pathogenic control E. Coli strain


title: 293FT, 72 h, GFP, replicate 1


title: ctrl7 - No treatment|Yes BBN


title: 293FT, 24 h, GFP, replicate 2

value: 24 hr


title: H7_hESCs_DLG2_KO1_30d_1 [s_22]


title: 46C_GO_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from GENERGY BIO company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of GENERGY BIO.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: 46C mouse embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina X ten was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

value: 5uM GO


title: Ileal Enteroid Mock treated (I103_Mock)

value: Intestine

value: Mock treated


title: H7_hESCs_DLG2_KO1_30d_2 [s_23]


title: H7_hESCs_DLG2_KO1_30d_3 [s_24]


title: 46C_GO_1


title: 293FT, 24 h, GFP, replicate 1


title: ctrl6 - No treatment|Yes BBN

value: Yes


title: 46C_NT_1

value: Control medium


title: 293FT, 48 h, GFP, replicate 1


title: Ileal Enteroid treated with enterohemorrhagic E. coli strain 8624 (I103_ehec)

value: Monolayer

value: enterohemorrhagic E. coli strain 8624


title: ctrl1 - No treatment|No BBN

value: No

value: Benign


title: 293FT, 24 h, selected, replicate 2

value: selected


title: Ileal Enteroid treated with aafA mutant (I103_aafA)

value: Collagen IV

value: aafA mutant


title: H7_hESCs_DLG2_WT_30d_1 [s_19]

value: H7 hESCs

value: wild type


title: H7_hESCs_DLG2_WT_30d_2 [s_20]


title: 46C_NT_2


title: Duodenal Enteroid Mock treated (D9_Mock)

value: Duodenum

value: Duodenal Enteroid


title: H7_hESCs_DLG2_KO2_20d_3 [s_18]


title: Duodenal Enteroid treated with non-pathogenic control E. Coli strain (D9_HS)

value: non-pathogenic control E. Coli strain


title: 293FT, 48 h, selected, replicate 2

value: 48 hr


title: H7_hESCs_DLG2_WT_30d_3 [s_21]


title: H7_hESCs_DLG2_KO2_20d_2 [s_17]


title: F22O4, liver, RNA-Seq

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
Reads were filtered based on their length, pairing, and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the Xenopus genome (10.0 assembly) using HISAT2.
The Cufflinks (v0.0.7) tool was applied to HISAT2 alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
The Cuffmerge (v0.0.6) toll was used to merge transcriptome
Cuffdiff (v0.0.7) toll was used for differential  gene expression  analysis. Control mRNAseq data have been have been deposited on NCBI Gene Expression Omnibus (GEO) (accession no GSE150911).
Supplementary_files_format_and_content: Cuffdiff file.txt

organism: Xenopus tropicalis

source_name: Liver

extract_protocol:
For each biological replicate, the RNAqueous®-4PCR Kit (Ambion, Austin USA) was used to extract the total RNA from 15 mg of liver according to manufacturer instructions
RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina, San Diego, USA) and sequenced on an Illumina GAIIx sequencer as 75 bp reads

treatment_protocol: F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). Females from F1 and F2 generation were not exposed.

tag: common name

value: tropical clawed frog

tag: generation and f0-treatment

value: F2 generation control

tag: Sex

value: female


title: H7_hESCs_DLG2_KO2_20d_1 [s_16]


title: F22O5, liver, RNA-Seq


title: H7_hESCs_DLG2_KO1_20d_3 [s_15]


title: 293FT, 72 h, selected, replicate 1

value: 72 hr


title: 293FT, 72 h, selected, replicate 2


title: Duodenal Enteroid treated with extra-intestinal pathogenic E. coli (D9_expec)

tag: tissue

value: Intestine

tag: segment

tag: format

value: Monolayer

value: extra-intestinal pathogenic E. coli


title: F22O3, liver, RNA-Seq


title: 293FT, 48 h, selected, replicate 1


title: Duodenal Enteroid treated with enterohemorrhagic E. coli strain 8624 (D9_ehec)

tag: sample type

tag: substrate

value: enterohemorrhagic E. coli strain 8624

tag: individual


title: F22O2, liver, RNA-Seq


title: H7_hESCs_DLG2_KO1_20d_2 [s_14]


title: Duodenal Enteroid treated with enteroaggregative E. coli strain 042 (D9_eaec)

value: enteroaggregative E. coli strain 042


title: F22O1, liver, RNA-Seq


title: 293FT, 24 h, selected, replicate 1

tag: replicate

value: selected

tag: time point

value: 24 hr


title: HeLa, 72 h, untransfected, replicate 2

source_name: HeLa

value: HeLa

value: untransfected


title: Duodenal Enteroid treated with non-pathogenic control E. Coli strain (D4_HS)

value: Duodenum

value: Collagen IV


title: H7_hESCs_DLG2_WT_20d_3 [s_12]

tag: cell line/type

value: H7 hESCs

value: wild type


title: Duodenal Enteroid Mock treated (D4_Mock)

value: Duodenal Enteroid

value: Mock treated


title: HeLa, 72 h, untransfected, replicate 1


title: HeLa, 48 h, untransfected, replicate 2

value: 48 hr


title: H7_hESCs_DLG2_KO2_15d_3 [s_9]

tag: genotype


title: F12O4, liver, RNA-Seq

value: tropical clawed frog

value: F1 generation control

value: female


title: HeLa, 24 h, untransfected, replicate 2


title: Duodenal Enteroid treated with extra-intestinal pathogenic E. coli (D4_expec)

value: Intestine

value: Monolayer

value: extra-intestinal pathogenic E. coli


title: F12O2, liver, RNA-Seq


title: H7_hESCs_DLG2_WT_20d_2 [s_11]

tag: age


title: F12O3, liver, RNA-Seq


title: F12O6, liver, RNA-Seq


title: Duodenal Enteroid treated with enteroaggregative E. coli strain 042 (D4_eaec)

value: enteroaggregative E. coli strain 042


title: F12O1, liver, RNA-Seq


title: H7_hESCs_DLG2_KO2_15d_2 [s_8]


title: HeLa, 24 h, untransfected, replicate 1

tag: cell line

value: 24 hr


title: Duodenal Enteroid treated with aafA mutant (D4_aafA)

value: aafA mutant


title: H7_hESCs_DLG2_KO1_20d_1 [s_13]


title: F22M4, liver, RNA-Seq

value: F2 generation (From F0 Mixture exposed)

value: Liver


title: Duodenal Enteroid treated with aafA mutant (D9_aafA)

value: Duodenum

value: Collagen IV


title: Duodenal Enteroid treated with extra-intestinal pathogenic E. coli (D3_expec)


title: H7_hESCs_DLG2_WT_20d_1 [s_10]

value: H7 hESCs

value: wild type


title: HeLa, 72 h, GFP, replicate 2

value: HeLa

value: GFP

value: 72 hr


title: F22M5, liver, RNA-Seq

value: tropical clawed frog


title: H7_hESCs_DLG2_KO1_15d_3 [s_6]


title: Duodenal Enteroid treated with enterohemorrhagic E. coli strain 8624 (D4_ehec)

value: Duodenal Enteroid

value: enterohemorrhagic E. coli strain 8624


title: HeLa, 48 h, GFP, replicate 2

value: 48 hr


title: HeLa, 48 h, untransfected, replicate 1

value: untransfected


title: Duodenal Enteroid treated with enterohemorrhagic E. coli strain 8624 (D3_ehec)

value: Intestine

value: Monolayer


title: F22M3, liver, RNA-Seq

value: female


title: Duodenal Enteroid treated with enteroaggregative E. coli strain 042 (D3_eaec)

value: enteroaggregative E. coli strain 042


title: F22M2, liver, RNA-Seq

value: F2 generation (From F0 Mixture exposed)

value: Liver


title: H7_hESCs_DLG2_KO2_15d_1 [s_7]


title: H7_hESCs_DLG2_WT_15d_3 [s_3]


title: F22M1, liver, RNA-Seq


title: Duodenal Enteroid Mock treated (D103_Mock)

value: Duodenum

value: Collagen IV

value: Mock treated


title: HeLa, 48 h, GFP, replicate 1

value: HeLa


title: HeLa, 24 h, GFP, replicate 1

value: GFP

value: 24 hr


title: Duodenal Enteroid treated with non-pathogenic control E. Coli strain (D103_HS)

value: non-pathogenic control E. Coli strain


title: Duodenal Enteroid treated with aafA mutant (D103_aafA)

value: Duodenal Enteroid

value: aafA mutant


title: F12M13, liver, RNA-Seq

value: tropical clawed frog

value: F1 generation (From F0 Mixture exposed)


title: F12M9, liver, RNA-Seq


title: HeLa, 72 h, selected, replicate 2

value: selected

value: 72 hr


title: HeLa, 48 h, selected, replicate 2

value: 48 hr


title: F12M8, liver, RNA-Seq

value: female


title: HeLa, 72 h, GFP, replicate 1


title: IMR90 shLARP7 rep2

source_name: IMR90 human fibroblasts

tag: cell type

value: fibroblasts


title: IMR90 WT rep2

value: WT


title: HeLa, 24 h, selected, replicate 2

tag: treatment


title: F12M4, liver, RNA-Seq

tag: common name

value: Liver


title: Colonoid Mock treated (C9_Mock)

value: Intestine

value: Colon

value: Colonoid

value: Monolayer

value: Collagen IV


title: HeLa, 24 h, GFP, replicate 2

value: HeLa

value: GFP

value: 24 hr


title: Colonoid treated with enterohemorrhagic E. coli strain 8624 (C9_ehec)

value: enterohemorrhagic E. coli strain 8624


title: H7_hESCs_DLG2_KO1_15d_1 [s_4]

value: H7 hESCs


title: H7_hESCs_DLG2_KO1_15d_2 [s_5]


title: F12M1, liver, RNA-Seq

value: tropical clawed frog

tag: generation and f0-treatment

value: F1 generation (From F0 Mixture exposed)


title: H7_hESCs_DLG2_WT_15d_2 [s_2]

value: wild type


title: Colonoid treated with non-pathogenic control E. Coli strain (C9_HS)

value: non-pathogenic control E. Coli strain


title: IMR90 WT rep1

value: fibroblasts


title: HeLa, 48 h, selected, replicate 1

value: selected

value: 48 hr


title: Colonoid treated with enteroaggregative E. coli strain 042 (C9_eaec)

value: Intestine

value: enteroaggregative E. coli strain 042


title: H7_hESCs_DLG2_WT_15d_1 [s_1]


title: Colonoid treated with extra-intestinal pathogenic E. coli (C9_expec)

value: Colon

value: Colonoid

value: extra-intestinal pathogenic E. coli


title: HeLa, 72 h, selected, replicate 1

value: HeLa

value: 72 hr