title: Infection2_D11p_SEQ2

data_processing:
For each sample, fastq files originating from multiple sequencing runs were concatenated and processed using an analytical pipeline derived from the DropSeq pipeline v. 1.12, as described in (Gierahn et al., 2017) (https://github.com/broadinstitute/Drop-seq).
Briefly, reads were converted to a bam file using picard v. 2.9.0-1-gf5b9f50-SNAPSHOT, tagged with cell and transcript barcodes, and subsequently sequencing adapters and polyadenosine tracts were trimmed. Upon regenerating fastq files, reads were aligned with STAR v. 2.5.3a (Dobin et al., 2013) against the aforementioned tri-genome reference. Genomic features of the aligned reads were annotated using the combined species-gene symbol nomenclature including gene and exon of origin when relevant. Bead synthesis errors were assessed and when possible, altered unique molecular identifiers (UMIs) were repaired. Cell barcode abundance was tallied, and gene expression was called for the top 10,000 cell barcodes.
Count matrices of genes x cells were imported in the R v. 3.6 statistical environment and Seurat v.3 was used as the primary analytical package (Satija et al., 2015). Count matrices were merged into a single Seurat object, which was split by the sample of origin. Human, murine and P. vivax genes and transcripts counts were tallied for each cell barcode.
Genome_build: Tri-genome hg19, mm10 (ENSEMBL release as used in Macosko et al. Cell 2015) and PvP01 v1.
Supplementary_files_format_and_content: Tab-delimited text files containing unfiltered genes x cell-barcode matrices in MatrixMarket format (10K cells called for each sample). Three files are reported: for "Experiment 2", a pre-parasite capture count matrix is provided (containing host and parasite data for 10K cells per sample), as well as a post-capture file, which contains data for 10K cells called upon sequencing the captured libraries, added to the corresponding reads tallied pre-capture for each matching cell barcode. For "Experiment 1" the post-capture data only (10K cells/sample).

organism:
Plasmodium vivax
Homo sapiens
Mus musculus

source_name: day 11

extract_protocol:
Briefly, MPCCs were first treated with AP20187 (0.5 mM) for 30 minutes at 37°C to partially deplete the fibroblast cells via apoptosis. After washing, the cultures were dissociated by Trypsin (0.25%) 5-minute treatment at 37°C.
For the scRNA-seq analysis, an updated Seq-Well protocol including a second-strand synthesis step was employed (Hughes et al., 2020). A suspension with 10-15,000 cells (pooled from duplicate MPCC wells) was then loaded onto a functionalized-polydimethylsiloxane array preloaded with uniquely barcoded mRNA capture beads. For each time-point in the two independent infections, two separate arrays were loaded with P. vivax-infected samples, and single arrays for mock and naïve samples. After cells had settled into wells, the array was sealed with a hydroxylated polycarbonate membrane with a pore size of 10 nm, facilitating buffer exchange while permitting cell lysis, mRNA transcript hybridization to beads, and bead removal before proceeding with reverse transcription. The obtained bead-bound cDNA product then underwent Exonuclease I treatment to remove excess primer before proceeding with second-strand synthesis and PCR amplification. To capture parasite reads from Seq-Well, full length cDNAs were amplified an additional 5 cycles using Kapa HiFi polymerase including a 3-minute extension time to increase concentration for capture. 200-300 ng of cDNA was concentrated using a speedvac, reconstituted in 3.4 L water and hybridized for 32 hours as previously described (Gural et al., 2018). 10 L of capture material was amplified for 15 cycles following the standard protocol. Captured cDNA was then prepared into Illumina libraries using NexteraXT (Illumina). Final libraries were quality controlled using Fragment Analyzer (Agilent) and qPCR prior to Illumina sequencing (NextSeq500). Sequencing of captured parasite transcripts was performed for the two infection batches.

treatment_protocol: MPCCs were infected with fresh sporozoites obtained through hand dissection of P. vivax-infected mosquitoes. For mock samples, MPCCs were exposed to material from non-infected mosquito salivary glands (matched number of dissected mosquitoes and processed similarly as the infected counterparts). Naïve samples received the culture media used for the infections. Pi4K treatments were conducted from days 5 to 8 after infection.

value: P. vivax in primary human hepatocytes, with 3T3-J2s

value: infection with 100K P. vivax sporozoites


title: Infection2_D11p_SEQ1

status: Public on Feb 25 2022

type: SRA

city: Paris

first: Liliana

last: Mancio-Silva

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description:
Two processed data files represent the sequencing of the library upon its construction (pre-capture), as well as a re-sequencing post-enrichment for parasite-derived transcript (post-capture data).
Precapture_Infection2.tar
Postcapture_merged_Infection2.tar

library_source: transcriptomic

molecule: polyA RNA

growth_protocol: Primary human hepatocytes were seeded on collagen-micropatterned 96-well plates and surrounded with murine embryonic fibroblasts 3T3-J2s as detailed previously (March et al., 2015). For the scRNA-seq analysis, MPCCs were established using 3T3-J2s expressing an inducible apoptosis switch (Chen et al., 2020).

tag: cell type

tag: infection

tag: treatment


title: E11.5_SP-4

city: Edinburgh

first: Mona

last: Elhendawi

state: Midlothian

address: 7 George Square

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt
were aligned to the Mus musculus reference genome (GRCh38; from Ensembl) using STAR
The raw count data were filtered to remove very low-expressed genes (genes consisting predominantly of near-zero counts)
Reads were normalised using the weighted trimmed mean of M-values method.
Differential analysis (comparing each ES-derived progenitor group to the E11.5 embryonic counterpart group or the E12.5 counterpart group) was carried out using edgeR4.
Genome_build: GRCh38; from Ensembl
Supplementary_files_format_and_content: Microsoft Excel Comma Separated Values file

molecule: total RNA

organism: Mus musculus

source_name: Stromal progenitor cells

extract_protocol:
Total RNA was isolated from sorted cells (35,000 – 100,000 cells) using RNeasy Plus micro kit. Organoids were dissociated and processed as per the kit protocol
100 ng of total RNA/sample was used for sequencing library preparation using an Illumina TruSeq stranded mRNA kit. Sequencing was performed using a Novaseq S1 50 Paired-end run to produce 50-64-million read-pairs per sample.

value: E 11.5 stromal progenitor cells

tag: cell source

tag: strain/cell line

value: CD1 mice


title: Drosophila Adult-1hr-6-4_rep2

city: Chapel Hill

first: Aziz

last: Sancar

state: NC

address: 120 Mason Farm Rd. CB#7260

country: USA

institute: University of North Carolina at Chapel Hill

description:
Drosophila Adult-6-4_rep2
Low molecular DNA

library_source: genomic

data_processing:
Base calling was performed with Illumina’s bcl2fastq pipeline v.2.20.0.
Quality control was done using fastqc v0.11.8.
Adapter sequences were removed with Cutadapt v2.9 using sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG.
Identical reads were removed using fastx_toolkit v0.0.14 to avoid PCR duplicates.
Reads were aligned to dm6 genome assembly of Drosophila melanogaster using Bowtie2 v2.4.1 with the option --very-sensitive.
Abundance of dimers sensitive to damage (TT for CPD; TC, CC, CT or TT for 6-4; GG for cisplatin) for each position on oligomers of the same length were calculated.
For CPD and 6-4 photoproducts, reads shorter than 26 nt an longer than 28 nt were filtered out. For cisplatin reads shorter than 27 nt an longer than 29 nt were filtered out.
Damage pinpointing was done by searcing for sensitive dimers 6 - 9 nt upstream of the 3' end of the reads for CPD and 6-4, and 7 - 9 nt for cisplatin.
Read counts on transcribed and non-transcribed strands were obatained using bedtools v2.29 with parameters -c -wa -S -F 0.5 and -c -wa -s -F 0.5 respectively.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files were created using bedtools genomecov from bedtools v2.29 and bedGraphToBigWig from UCSCtools v320.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila Adults

growth_protocol: Drosophila were kept at 25°C, light-dark:12hr-12hr and fed with standard cornmeal medium. S2 Cells were cultured at 27°C in Schneider’s medium with heat-inactivated fetal bovine serum at 10% and with 200 µg/ml hygromycin antibiotic. Cells were passaged when they reached 80-90% confluence.

extract_protocol:
After repair, samples (embryo, larvae, pupae ,adults or s2 cells) were collected with ice-cold PBS and washed several times. 320 µl TE pH 8.0 was added to each sample and samples were ground. After grinding, 40 µl 10% SDS was added to each sample and samples were incubated at 70°C for 30 minutes. After incubation, 100 µl 5 M NaCl was added to each sample and they were incubated at 4°C overnight.
After overnight incubation, samples from each developmental phase were centrifuged at high speed at 4 degress for one hour.  Supernatants were processed for excision or XR-Seq assay. Briefly, supernatants were incubated with 5 µL Rnase A and then 5 µL Proteinase K, purified, and then immunoprecipitated with anti-CPD, anti-6-4 (P-P) or anti-cisplatin antibodies.  Immunoprecipitates were then either radiolabeled and excision products were separated on 10-11% sequencing gels, or, for  XR-seq assay, immunoprecipitates were ligated to the adaptors, purified by a second immunoprecipitation, and DNA damages were reversed (using photoreactivation for photoproducts, and cyanide treatment for cisplatin damage). Libraries were generated by PCR and then sequenced.
OTHER: XR-Seq

treatment_protocol: For these experiments, Drosophila adults were isolated with fly food containing 5% sucrose and 6% agar for two hours during which time they laid eggs. After the adults were removed, embryos were collected and irradiated with predetermined doses of UV-B, and then were allowed to repair in the dark for predetermined times. Larvae and pupae were transferred to 100 mm plates and irradiated with UV-B and allowed to repair in the dark. After repair, samples (embryo, larvae, pupae and adults) were collected with ice-cold PBS and washed several times. 320 µl TE pH 8.0 was added to each sample and samples were ground. After grinding, 40 µl 10% SDS was added to each sample and samples were incubated at 70°C for 30 minutes. After incubation, 100 µl 5 M NaCl was added to each sample and they were incubated at 4°C overnight.S2 Cells were irradiated with 20 J/m2 UV-C or indicated concentrations of Cisplatin (150uM or 200uM). Following predetermined repair times, plates were placed on ice and cells were harvested by scraping, washed with ice-cold PBS, pelleted, and transferred to Eppendorf tubes. osophila adults were collected on a CO2 panel for UVB irradiation.  Flies were then returned to their vials and allowed to repair in the dark for predetermined times. Cells were irradiated with 20 J/m2 UV-C or indicated concentrations of Cisplatin (150uM or 200uM) and then fresh medium was added. Following predetermined repair times, plates were placed on ice and cells were harvested by scraping, washed with ice-cold PBS, pelleted, and transferred to Eppendorf tubes.

tag: repair time

tag: strain

tag: damage ip antibody

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: IP_ChIP-seq_RNMT_1

city: Glasgow

first: Shang

last: Liang

address: Garscube Estate

institute: CRUK Scotland Institute

data_processing:
Sequencing was performed with a read length of 2×75 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
The bigWig files were generated by deepTools (Ramírez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showed the reads per kilobase per million (RPKM) of ChIP read densities within the 10bp windows of genomic region for each sample.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were were grown in Glasgow's Minimum Essential Medium with 10% Knockout Serum Replacement, 1% Non-Essential Amino Acids , 2 mM L-Glutamine, 1 mM sodium pyruvate, 0.35 μM β-mercaptoethanol and 100 U/ml recombinant LIF. mESCs were cultured in 0.1% gelatin-coated flasks or dishes at 37 °C with 5 % CO2.

extract_protocol:
Cells were cross-linked by 1% formaldehyde for 10 min. Then the glycine was added to quench the reaction. The cell lysates were prepared as described (Varshney et al., 2018).The chromatin was sonicated in Bioruptor (Diagenode) at high power for 20 min (30 s on/off, 20 cycles). 25-50 micrograms of the sonicated chromatin were used for each IP. 50μl (10%) from each diluted extract for IP were taken as the inputs. For ChIP using anti-HA beads, 20μL of anti-HA magnetic beads (Pierce) were added to lysates from CMTR1/RNMT KI cells (as IPs) and E14 cells (as control) for 4°C overnight incubation. For RNAP II ChIP, 2μg of anti-Rpb1 (CST 14958) were added to lysates from E14 cells for 4 °C overnight reaction before the incubation with protein G Dynabeads (Life Technologies) for additional 2 hours. The beads were washed and eluted as described (Varshney et al., 2018) before the proteinase K treatment and reverse crosslinking at 42 °C overnight. The eluted DNA was purified by the QIAquick PCR purification kit (QIAGEN).
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos (Index Primers Set 1) for Illumina.

treatment_protocol: For RNAP II ChIP, cells were treated with the control scramble siRNA or CMTR1 specific siRNAs for 36 hours.

value: Embryonic stem cells

tag: cell line

value: HA-GFP-Rnmt KI E14

value: untreated

tag: antibody

value: anti-HA magnetic beads (Pierce 88836)


title: Drosophila Adult-16hr-CPD_rep1

description:
Drosophila Adult-CPD_rep1
Low molecular DNA

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: E11.5_SP-3


title: E12.5_NP-1

source_name: Nephron progenitor cells

value: E 12.5 nephron progenitor cells


title: Input_ChIP-seq_CMTR1

value: HA-GFP-Cmtr1 KI E14


title: Infection2_D8p_SEQ1

source_name: day 8


title: Infection2_D8p_SEQ2


title: Drosophila Adult-30min-6-4_rep2


title: E11.5_SP-2


title: Infection2_D11_SEQ2

value: non-treated


title: IP_ChIP-seq_CMTR1_3


title: Drosophila Adult-30min-CPD_rep2

description:
Drosophila Adult-CPD_rep2
Low molecular DNA


title: Infection2_D11_SEQ1


title: Drosophila Adult-15min-6-4_rep2


title: E11.5_NP-4

value: E 11.5 nephron progenitor cells


title: E11.5_SP-1


title: Infection2_D8_SEQ2


title: IP_ChIP-seq_CMTR1_1


title: IP_ChIP-seq_CMTR1_2


title: Drosophila Adult-15min-CPD_rep2


title: E11.5_NP-3


title: Drosophila Pupa-2hr-6-4_rep1

description:
Drosophila Pupa-6-4_rep1
Low molecular DNA

source_name: Drosophila Pupa

value: yw


title: Infection2_D5_SEQ2

source_name: day 5


title: E11.5_NP-2


title: X3xTG_SCD1i_IVO398_HPP

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

institute: Gustave Roussy

description: These samples were compared to 10 month samples only

data_processing:
Samples were sequenced on Nextseq 500 High Output Flowcell single-end 75nt reads
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M23, based on Ensembl 98) using STAR version 2.5.1b
Raw readcounts were obtained directly from STAR, concatenated and annotated
Genome_build: GRCm38
Supplementary_files_format_and_content: combined tab-delimited raw count matrix

source_name: Hippocampus

extract_protocol:
Hippocampi from unoperated or pump-implanted mice were dissected and immediately flash frozen on dry ice. Total RNA was extracted with TRIzol (Invitrogen) and chloroform (Invitrogen). RNA was then purified with the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. 400 ng of total RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For ICV infusions of SCDi or vehicle, mice were locally injected with buprivacaine (Hospira) and operated under isoflurane anesthesia (Baxter). Brain cannulae attached to Alzet osmotic pumps were stereotaxically implanted at 0.0mm antero-posterior and 0.9mm lateral to Bregma  and the pumps placed under the back skin according to manufacturer`s instructions. 28-day Alzet osmotic pumps were used in these experiments (0.11 μl/h infusion rate, model 1004; Durect). The SCD inhibitor (SCDi, ab142089, abcam) was dissolved in DMSO and infused at a final concentration of 80 µM in sterile aCSF. Vehicle pumps contained equal volumes as the SCDi pumps (0.8% DMSO/aCSF).

tag: age

value: 10 months

value: 28 day ICV SCDi


title: X3xTG_SCD1i_IVO394_HPP


title: Drosophila Pupa-2hr-CPD_rep1

description:
Drosophila Pupa-CPD_rep1
Low molecular DNA


title: Drosophila Adult-1hr-CPD_rep1


title: Infection2_D8_SEQ1

value: P. vivax in primary human hepatocytes, with 3T3-J2s


title: E11.5_NP-1

value: Embryonic day (E) 11.5


title: Infection2_D5_SEQ1

value: infection with 100K P. vivax sporozoites


title: X3xTG_SCD1i_IVO386_HPP


title: X3xTG_SCD1i_IVO390_HPP


title: Drosophila Larva-2hr-6-4_rep1

description:
Drosophila Larva-6-4_rep1
Low molecular DNA

source_name: Drosophila Larva


title: Drosophila Larva-2hr-CPD_rep1

description:
Drosophila Larva-CPD_rep1
Low molecular DNA


title: K4

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

country: China

institute: shenzhen people's hospital

description: primary hepatocytes were isolated from C57BL/6 mice

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: primary hepatocyte

extract_protocol:
RNA was harvested from lysates using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: primary hepatocyte

value: transfected with lentivirus expressing KLF10

value: 8 week-old


title: WT_SCD1i_IVO396_HPP


title: Infection2_D4_SEQ1

source_name: day 4


title: K3


title: K5


title: Infection2_D1_SEQ2

source_name: day 1


title: Drosophila Embryo-2hr-CPD_rep1

description:
Drosophila Embryo-CPD_rep1
Low molecular DNA

source_name: Drosophila Embryo


title: WT_SCD1i_IVO392_HPP


title: Drosophila Adult-female-2hr-6-4_rep1

description:
Drosophila Adult-6-4_rep1
Low molecular DNA

source_name: Drosophila Adults-female

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: Infection2_D1_SEQ1


title: K2


title: Drosophila Embryo-2hr-6-4_rep1

description:
Drosophila Embryo-6-4_rep1
Low molecular DNA


title: X3xTG_DMSO_IVO397_HPP

value: 28 day ICV DMSO


title: WT_SCD1i_IVO388_HPP


title: NC5

value: transfected with lentivirus expressing negative control


title: K1


title: Drosophila Adult-male-2hr-6-4_rep1

source_name: Drosophila Adults-male


title: Drosophila Adult-female-2hr-CPD_rep1

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: X3xTG_DMSO_IVO389_HPP


title: NC4


title: SH-SY5Y TRPM2 KO28 - Doxo 24h - replicate 2

city: Hershey

first: Fernanda

last: Festa

state: PA

address: 500 University Dr BMR C7846

department: Pediatrics

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78). EdgeR was used to fit the read counts to the negative binomial model along with generalized linear model (GLM) and differentially expressed genes were determined by the likelihood ratio test method implemented in the edgeR package. Significance was defined to be those with q-value < 0.05 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR). The list of differentially expressed genes was analyzed with Ingenuity Pathway Analysis (Qiagen).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing the result of edgeR differential expression analysis and CPM (copy per million) values for each sample

organism: Homo sapiens

source_name: SH-SY5Y TRPM2 KO28 - Doxo 24h

growth_protocol: Endogenous TRPM2 was depleted with CRISPR technology, using pCas9-guide TRPM2 gRNA vector  (target sequence GAGGAAAGCTGGCTCGGAGC) and donor vector containing 600-bp left and right homologous arms to the TRPM2 gene with GFP and puromycin markers (OriGene Technologies Inc.; Rockville, MD). As a negative control, pCas9-guide scrambled gRNA vector was used. Either TRPM2 gRNA vector or scrambled vector was co-transfected with donor vector into SH-SY5Y (wildtype) neuroblastoma cells using the Neon Transfection System(Invitrogen), following the manufacturer’s instructions. Cells were passed up to 8 passages with 0.5ug/ml of puromycin selection. Single-cell clones were generated and the TRPM2 genomic DNA was verified by RT-PCR, sequencing and Western blot analysis.

extract_protocol:
Two control clones (Scr13 and Scr16) and two TRPM2 knockout clones (TRPM2 KO11 and TRPM2 KO28) were incubated with or without Doxorubicin (0.3 uM) for 24 h. Each condition was performed in duplicate, cells were collected and RNA was isolated using RNeasy Mini Kit (Qiagen) before being subjected to total RNA sequencing (RNAseq)
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing.

treatment_protocol: SH-SY5Y TRPM2 KO and SH-SY5Y Scr cells were cultured in 50% DMEM and 50% Ham’s F-12 (DMEM/F-12 50/50) media supplemented with 10% heat-inactivated FBS. Cells were plated at 70-80% confluence and incubated for 24 hours with regular media (untreated cells) or regular media supplemented with 0.3 uM Doxorubicin (Doxo treated).

value: neuroblastoma

tag: vector

value: pCas9-guide vector with TRPM2 gRNA

tag: genotype

value: TRPM2 KO

tag: markers

value: GFP + puromycin

value: Doxorubicin


title: X3xTG_DMSO_IVO393_HPP

value: 10 months


title: Drosophila Adult-male-2hr-CPD_rep1


title: X3xTG_DMSO_IVO385_HPP


title: SH-SY5Y TRPM2 KO28 - untreated - replicate 2

source_name: SH-SY5Y TRPM2 KO28 - untreated

value: untreated


title: SH-SY5Y TRPM2 KO28 - untreated - replicate 1


title: Infection2_D4_SEQ2

value: P. vivax in primary human hepatocytes, with 3T3-J2s

value: non-treated


title: NC3


title: SH-SY5Y TRPM2 KO28 - Doxo 24h - replicate 1


title: Drosophila Adult-yw-2hr-CPD_rep1

value: yw


title: WT_DMSO_IVO395_HPP


title: SH-SY5Y Scr16 - Doxo 24h - replicate 2

source_name: SH-SY5Y Scr16 - Doxo 24h

value: pCas9-guide vector with Scramble gRNA

value: control


title: Drosophila Adult-2hr-6-4_rep1

source_name: Drosophila Adults


title: NC2

value: primary hepatocyte

value: 8 week-old


title: NC1


title: WT_DMSO_IVO391_HPP

value: 28 day ICV DMSO


title: NASH5

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample.

source_name: liver

extract_protocol:
liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

value: WD+CCl4 treated

value: 20 week-old


title: WT_DMSO_IVO387_HPP


title: SH-SY5Y Scr16 - Doxo 24h - replicate 1

value: neuroblastoma


title: WT_DMSO_IVO383_HPP


title: SH-SY5Y Scr16 - untreated - replicate 2

source_name: SH-SY5Y Scr16 - untreated


title: SH-SY5Y Scr16 - untreated - replicate 1


title: Input_rep1

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

data_processing:
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage.
Genome_build: dm3
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: Drosophila S2 cells were maintained in Schneider’s medium (Gibco) supplemented with 10% FBS (Sigma) and 1% penicillin–streptomycin (Sigma).

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Drosophila S2 cells


title: X3xTG_8M_197079_L.HPP

description: These samples were compared to 8M samples only

value: 8 months


title: NASH3


title: METTL3_ChIP_rep2

value: METTL3 (Bethyl, #A301-567A)


title: X3xTG_8M_197078_L.HPP


title: NASH2


title: Drosophila Adult-2hr-CPD_rep1

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: SH-SY5Y Scr13 - Doxo 24h - replicate 1

source_name: SH-SY5Y Scr13 - Doxo 24h

value: GFP + puromycin

value: Doxorubicin


title: SH-SY5Y Scr13 - Doxo 24h - replicate 2


title: METTL3_ChIP_rep1


title: SH-SY5Y Scr13 - untreated - replicate 2

source_name: SH-SY5Y Scr13 - untreated

value: untreated


title: NAFL5

value: 12 weeks high fat diet fed


title: X3xTG_8M_195825_L.HPP


title: WT_8M_197232_L.HPP


title: Input_rep2


title: NASH4


title: SH-SY5Y TRPM2 KO11 - Doxo 24h - replicate 2

source_name: SH-SY5Y TRPM2 KO11 - Doxo 24h

value: pCas9-guide vector with TRPM2 gRNA

value: TRPM2 KO


title: WT_8M_197231_L.HPP

source_name: Hippocampus


title: SH-SY5Y TRPM2 KO11 - Doxo 24h - replicate 1


title: 12_VBTM3_Day8PCas

data_processing:
Reads were aligned against Plasmodium vivax PvP01 from PlasmoDB v. 34 (Sept 2017) using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction PvivaxP01 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries(Li and Dewey, 2011): rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference.
Posterior mean estimates (pme) of counts and estimated TPMs were retrieved.
Genome_build: PvP01 (PlasmoDB v. 34)
Supplementary_files_format_and_content: Tab-delimited text files with RSEM  pme counts andlog2-transformed pme RPKM outputs

organism: Plasmodium vivax

source_name: day 8

growth_protocol: Primary human hepatocytes were seeded on collagen-micropatterned 96-well plates and surrounded with murine embryonic fibroblasts 3T3-J2s as detailed previously (March et al., 2015). For the scRNA-seq analysis, MPCCs were established using 3T3-J2s expressing an inducible apoptosis switch (Chen et al., 2020). MPCCs were infected with fresh sporozoites obtained through hand dissection of P. vivax-infected mosquitoes. Naïve samples received the culture media used for the infections.

extract_protocol:
Total RNA was extracted with TRIzol® (Invitrogen), DNAse treated and purified using the RNeasy MinElute Cleanup Kit (Qiagen). Prior Trizol, samples with iCas9-GFP 3T3-J2 cells were treated with a chemical inducer of dimerization (B/B Homodimerizer) to partially deplete the fibroblast cells via apoptosis.
RNA was quality controlled using an AATI Fragment Analyzer and 100ng was prepared following the SureSelectXT RNA Direct protocol version A0. Illumina libraries were quantitated using the Fragment Analyzer and by qPCR and sequenced as a single end 40nt read using a HiSeq2000.

treatment_protocol: To obtain hypnozoite-enriched samples, P. vivax-infected MPCCs were dosed with a schizont-specific drug Pi4K inhibitor (MMV390048, 1 µM) for 3 days starting on day 5 after infection.

value: P. vivax in primary human hepatocytes, with iCasp9-GFP 3T3-J2s

tag: collection

value: B/B Homodimerizer-treated

tag: parasite isolate


title: 11_VBTM3_Day8Cas

tag: cell type

value: non-treated


title: WT_8M_196849_l.HPP


title: WT_8M_196848_L.HPP


title: NAFL2

value: liver


title: 9_VBTM3_Day3Cas

source_name: day 3


title: NASH1

value: WD+CCl4 treated


title: SH-SY5Y TRPM2 KO11 - untreated - replicate 1

source_name: SH-SY5Y TRPM2 KO11 - untreated


title: TGFb1_M_3

first: Yin Celeste

last: Cheuk

address: 180 Fenglin Road, Shanghai,China

institute: Department of Urology, Zhongshan Hospital, Fudan University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100)
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome(Mus musculus),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam)
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam)
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64)
StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs
Genome_build: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus_c57bl6nj/
Supplementary_files_format_and_content: FPKM and count

source_name: bone marrow MSCs

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp

value: treated with TGF-Beta1 and M-MDSC sup


title: 14_VBTM3_Day11PCas

source_name: day 11


title: Lactating-3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Paired-end 75bp sequencing was undertaken on an Illumina NextSeq 500 and FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.30.1
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Mammary gland

extract_protocol:
RNA was isolated from freshly sorted cells with the RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription cDNA libraries were prepared from 2000 cells following the SMART-Seq v4 Ultra Low Input RNA Kit protocol.
All libraries were barcoded and multiplexed onto one run of an Illumina NextSeq 500 sequencer.

tag: background strain

value: Ductal macrophages

tag: Stage

value: Lactating


title: X3xTG_8M_195824_L.HPP

value: 8 months

tag: treatment


title: Lactating-2


title: TGFb1_M_2


title: NAFL4

value: 20 week-old


title: in vitro control and cytokine-induced memory-like NK cells (adt_gex)

city: St Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 S Euclid Ave, Campus Box 8007

department: Department of Medicine

institute: Washington University

description: 451 cNK-ctrl-ML

data_processing:
Library strategy: 5'v1 10x Genomics CITE-seq with hashtagging
Fastq files were aligned to combined human and mouse genome (GRCh38 & mm10) using 10x Genomics CellRanger 3.0.1 with default settings and feature barcoding reference file for cite-seq antibodies and hashtagging alignment and counts.
The filtered_feature_bc_matrix was used as input into Seurat for processing.  Since cellranger 3.0 is limited to two data modalities, the hashtag and GEX matrix was used for hashtag and GEX measurements, and the adt and GEX matrix was used for measurements of the other oligonucleotide tagged antibodies.
Genome_build: GRCh38 & mm10
Supplementary_files_format_and_content: matrix, features, and barcodes files consist of the 3 file types as output into the filtered_feature_bc_matrix from CellRanger and used as input into Seurat.

source_name: peripheral blood mononuclear cells

extract_protocol:
Donor peripheral blood NK cells were isolated from a LRS chamber, and cultured into control and memory-like NK cells according to PMID: 32614951.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-18 cycles before being cleaned up using SPRIselect beads. The supernatant was then collected for the Cell Surface Protein Library.  Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation.  GEX (Gene Expression) and TotalSeq C Feature libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits with Feature Barcode technology for Cell Surface Protein(v1 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Single Cell 5’ Library and Gel Bead Kit (PN-1000006), Chromium Single Cell A Chip Kit (PN-1000152), Chromium Single Cell 5' Feature Barcode Library Kit, 16 rxns (PN-1000080), Chromium Single Index Kit T for GEX (PN-1000213, Chromium Single Cell Single Index Kit N Set A for Feature (PN – 1000212) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x8x151 sequencing recipe according to manufacturer protocol.

value: natural killer cells


title: SH-SY5Y Scr13 - untreated - replicate 1

value: neuroblastoma

value: pCas9-guide vector with Scramble gRNA

value: control

value: GFP + puromycin


title: in vitro control and cytokine-induced memory-like NK cells (hastag_gex)

description: 451 cNK-ctrl-ML


title: 13_VBTM3_Day11Cas


title: NAFL3

value: 12 weeks high fat diet fed


title: Lactating-1


title: TGFb1_M_1


title: Si_METTL3_INTS11_PRO_Seq_for METTL3_INTS11_KD_Rep2

data_processing:
Paired-end reads were trimmed to remove adaptors and low-quality reads using fastp (0.21.0). Trimmed reads mapping to rRNAs were excluded using bowtie2. The remaining reads were then aligned to dm6 (Drosophila) and hg19 (Homo Sapiens) genome assembly using bowtie2.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: MCF-7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco), 50 units/mL penicillin and 50 μg/mL streptomycin (Hyclone SV30010).

extract_protocol:
Nascent biotin-labeled RNA was isolated from permeabilized cells.
Strand specific RNA library preparation  was carried as methods described (PMID: 31809743)

treatment_protocol: For knockdown, MCF-7 cells were seeded in a 6-well plate, and transfected with RNAiMAX (Invitrogen, 13778-150) according to the manual. Cells were harvested after three days.


title: 7_VBTM3_Day11P

value: P. vivax in primary human hepatocytes, with 3T3-J2s


title: Si_METTL3_INTS11_PRO_Seq_for METTL3_INTS11_KD_Rep1


title: Pregnant-3

value: Pregnant


title: 10_VBTM3_Day5Cas

source_name: day 5

value: P. vivax in primary human hepatocytes, with iCasp9-GFP 3T3-J2s

value: B/B Homodimerizer-treated


title: SH-SY5Y TRPM2 KO11 - untreated - replicate 2

value: pCas9-guide vector with TRPM2 gRNA

value: TRPM2 KO

value: untreated


title: NAFL1

value: liver


title: 5_VBTM3_Day8P

value: non-treated


title: TGFb1_G_3

value: treated with TGF-Beta1 and G-MDSC sup


title: TGFb1_G_2


title: Pregnant-2

value: Ductal macrophages


title: 8_VBTM3_Day1cas

source_name: day 1


title: Si_INTS11_PRO_Seq_for METTL3_INTS11_KD_Rep2


title: Pregnant-1


title: 4_VBTM3_Day8


title: 3_VBTM3_Day5


title: Si_INTS11_PRO_Seq_for METTL3_INTS11_KD_Rep1


title: TGFb1_G_1


title: Post-weaning-3

value: Post weaning


title: Si_METTL3_PRO_Seq_for METTL3_INTS11_KD_Rep2


title: 6_VBTM3_Day11


title: TGFb1_3

value: treated with TGF-Beta1


title: Post-weaning-2


title: 1_VBTM3_Day1


title: TGFb1_2


title: Si_METTL3_PRO_Seq_for METTL3_INTS11_KD_Rep1


title: 2_VBTM3_Day3


title: TGFb1_1


title: Post-weaning-1


title: Si_Ctrl_PRO_Seq_for METTL3_INTS11_KD_Rep2


title: Infection1_D14p_Inf_100

description:
Processed data file contains the post-parasite capture data.
Postcapture_Infection1.tar

source_name: day 14

tag: infection

value: infection with 100K P. vivax sporozoites


title: Virgin-3

value: Virgin


title: Control_3


title: Infection1_D14p_Inf_50

value: infection with 50K P. vivax sporozoites


title: Control_2


title: Virgin-2


title: Si_METTL3_PRO_Seq_for METTL3_KD_Rep2


title: Virgin-1


title: OGT Control 28days after PHX

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
Illumina software used for basecalling
Raw fastq file were read and aligned using STAR
subread feature count was used to perform strand-specific read counting.
edgeR was utlize to normalized the data
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: OGT-Control Whole Liver

extract_protocol:
Total RNA was extracted using TRIZOL methods from ~50mg of liver.
RNA libraries were prepared for sequencing using standard Illumina protocols Tecan universal plus mRNA-seq.

value: Liver

value: OGTfl/y

tag: procedure

value: PHX

tag: timepoint

value: 28 Day


title: Control_1

tag: strain


title: Si_METTL3_PRO_Seq_for METTL3_KD_Rep1


title: OGT-KO 28days after PHX

source_name: OGT-KO Whole Liver

value: OGT-/y


title: Si_Ctrl_PRO_Seq_for METTL3_KD_Rep2


title: OGA Control 28days after PHX

source_name: OGA-Control Whole Liver

value: OGAfl/fl


title: Infection1_D8p_Inf_50

value: P. vivax in primary human hepatocytes, with 3T3-J2s


title: Infection1_D8p_Inf_100


title: 4-4-A

city: Chengdu

first: litao

last: liu

address: Shuxi Road  36

institute: Chengdu Kanghong Pharmaceutical Co., Ltd.

description: Keluoxin-treatment

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 22
Supplementary_files_format_and_content: Mus_musculus_mmu_novoalign_premiRNA

source_name: Retinal

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135-155 bp PCR amplified fragments (corresponding to 15-35 nt small RNAs).

value: retinal

tag: agent

value: Keluoxin-treatment


title: 4-6-A

description: Keluoxin-treatment


title: 4-3-A

description: Keluoxin-treatment


title: DCIS2_scRNA

city: Houston

first: Anil

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description: scRNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Genome_build: hg19

growth_protocol: Single cell suspensions are made from fresh tumors

extract_protocol:
RNAs afe extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

treatment_protocol: samples are collected before treatment

value: fresh tumor

tag: sample type

value: surgical sample


title: DCIS2_ST

description: spatial capture technology


title: Si_Ctrl_PRO_Seq_for METTL3_KD_Rep1


title: OGA-KO 28days after PHX

source_name: OGA-KO Whole Liver

value: OGA-/-


title: Infection1_D11_Inf_100

data_processing:
For each sample, fastq files originating from multiple sequencing runs were concatenated and processed using an analytical pipeline derived from the DropSeq pipeline v. 1.12, as described in (Gierahn et al., 2017) (https://github.com/broadinstitute/Drop-seq).
Briefly, reads were converted to a bam file using picard v. 2.9.0-1-gf5b9f50-SNAPSHOT, tagged with cell and transcript barcodes, and subsequently sequencing adapters and polyadenosine tracts were trimmed. Upon regenerating fastq files, reads were aligned with STAR v. 2.5.3a (Dobin et al., 2013) against the aforementioned tri-genome reference. Genomic features of the aligned reads were annotated using the combined species-gene symbol nomenclature including gene and exon of origin when relevant. Bead synthesis errors were assessed and when possible, altered unique molecular identifiers (UMIs) were repaired. Cell barcode abundance was tallied, and gene expression was called for the top 10,000 cell barcodes.
Count matrices of genes x cells were imported in the R v. 3.6 statistical environment and Seurat v.3 was used as the primary analytical package (Satija et al., 2015). Count matrices were merged into a single Seurat object, which was split by the sample of origin. Human, murine and P. vivax genes and transcripts counts were tallied for each cell barcode.
Genome_build: Tri-genome hg19, mm10 (ENSEMBL release as used in Macosko et al. Cell 2015) and PvP01 v1.
Supplementary_files_format_and_content: Tab-delimited text files containing unfiltered genes x cell-barcode matrices in MatrixMarket format (10K cells called for each sample). Three files are reported: for "Experiment 2", a pre-parasite capture count matrix is provided (containing host and parasite data for 10K cells per sample), as well as a post-capture file, which contains data for 10K cells called upon sequencing the captured libraries, added to the corresponding reads tallied pre-capture for each matching cell barcode. For "Experiment 1" the post-capture data only (10K cells/sample).

extract_protocol:
Briefly, MPCCs were first treated with AP20187 (0.5 mM) for 30 minutes at 37°C to partially deplete the fibroblast cells via apoptosis. After washing, the cultures were dissociated by Trypsin (0.25%) 5-minute treatment at 37°C.
For the scRNA-seq analysis, an updated Seq-Well protocol including a second-strand synthesis step was employed (Hughes et al., 2020). A suspension with 10-15,000 cells (pooled from duplicate MPCC wells) was then loaded onto a functionalized-polydimethylsiloxane array preloaded with uniquely barcoded mRNA capture beads. For each time-point in the two independent infections, two separate arrays were loaded with P. vivax-infected samples, and single arrays for mock and naïve samples. After cells had settled into wells, the array was sealed with a hydroxylated polycarbonate membrane with a pore size of 10 nm, facilitating buffer exchange while permitting cell lysis, mRNA transcript hybridization to beads, and bead removal before proceeding with reverse transcription. The obtained bead-bound cDNA product then underwent Exonuclease I treatment to remove excess primer before proceeding with second-strand synthesis and PCR amplification. To capture parasite reads from Seq-Well, full length cDNAs were amplified an additional 5 cycles using Kapa HiFi polymerase including a 3-minute extension time to increase concentration for capture. 200-300 ng of cDNA was concentrated using a speedvac, reconstituted in 3.4 L water and hybridized for 32 hours as previously described (Gural et al., 2018). 10 L of capture material was amplified for 15 cycles following the standard protocol. Captured cDNA was then prepared into Illumina libraries using NexteraXT (Illumina). Final libraries were quality controlled using Fragment Analyzer (Agilent) and qPCR prior to Illumina sequencing (NextSeq500). Sequencing of captured parasite transcripts was performed for the two infection batches.

value: non-treated


title: Infection1_D14_Inf_100


title: OGA Control 14days after PHX

value: 14 Day


title: OGA-KO 14days after PHX


title: DCIS1_scRNA

description: scRNAseq


title: DCIS1_ST

description: spatial capture technology


title: Si_Ctrl_PRO_Seq_for METTL3_INTS11_KD_Rep1


title: Infection1_D14_Inf_50


title: Infection1_D11p_Inf_50


title: Infection1_D11p_Inf_100

value: infection with 100K P. vivax sporozoites


title: 4-1-A

description: Keluoxin-treatment


title: 4-2-A

description: Keluoxin-treatment


title: 4-5-A

description: Keluoxin-treatment


title: Infection1_D8_Inf_100


title: Infection1_D11_Inf_50


title: 118.H.2

city: Madison

first: Daniel

middle: M

last: Tremmel

state: WI

address: 1111 Highland Ave, WIMR 5168

institute: University of Wisconsin

data_processing:
Illumina bcl2fastq v2.20
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: edgeR_blocked-design_S2-H2.xlsx (MS Excel)

source_name: Isolated human islets_hydrogel culture

growth_protocol: Upon receival, islets were embedded in hP-HG, or cultured in suspension. PIM(R) medium was used, all samples were cultured in ultra-low attachments plates.

extract_protocol:
All samples were pelleted and lysed with TRIzol. RNA was extracted from the TRIzol with the addition of chloroform and the upper phase was combined with an equal volume of 100% ethanol and trasferred to a QIAGEN Rneasy Mini Kit column, the kit protocol was followed.
Takara SMARTer Total RNA Seq Kit v2 Pico Input kit and purified with AMPure XP Beads

treatment_protocol: Islets in the H group were embedded into hP-HG at a concentration of 8 mg/mL and a density of 100 IEQ/10 uL of gel. Gels were pipetted into 5 uL constructs.

value: Isolated human islets

value: Hydrogel culture


title: 118 S.2

source_name: Isolated human islets_suspension culture

value: Suspension culture


title: Infection1_D8_Inf_50

source_name: day 8

value: infection with 50K P. vivax sporozoites


title: 2-5-A

description: model

value: model


title: 2-4-A

description: model


title: 115 H.2


title: Infection1_D5_Inf_100


title: Myl1-Cre; Sirt6 flox/flox, rep 2

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Genome_build: mm10
Supplementary_files_format_and_content: Expression_Profile.mm10.gene.txt: tab-delimited text files include FPKM values for each Sample

source_name: Muscle

extract_protocol:
Gastrocnemius muscles tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

value: Gastrocnemius muscle

tag: age

value: 20 weeks

value: Muscle-specific Sirt6 KO


title: Sirt6 flox/flox, rep 3

value: WT


title: Myl1-Cre; Sirt6 flox/flox, rep 1


title: 2-3-A

description: model

value: retinal


title: 115.S.2


title: 109 H.2


title: Infection1_D1_Inf_100

value: P. vivax in primary human hepatocytes, with 3T3-J2s


title: Myl1-Cre; Sirt6 flox/flox, rep 3


title: Infection1_D5_Inf_50


title: 2-2-A

description: model


title: Sirt6 flox/flox, rep 1


title: 2-6-A

description: model


title: Infection1_D1_Inf_50


title: 109 S.2


title: WT DMSO, 3xTg DMSO, WT SCDi, 3xTg SCDi

description: Pooled multiplexed samples containing cells from WT DMSO, 3xTg DMSO, WT SCDi and 3xTg SCDi animals

data_processing:
Pooled mutliplexed library was sequenced on the NovaSeq 6000 platform
Resulting fastq files were processed using BD's Rhapsody WTA analysis pipeline on the Seven Bridges Platform using default parameters and the GRCm38 reference genome with gencodevM19-20181206 transcriptome annotation
Output Unfiltered MOI count matrices were processed on a Galaxy implementation of standard scanpy 1.4.3 processing pipeline.
Resulting .h5Anndata object was imported into R's Seurat package for further analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited Unfiltered single cell MOI matrix
Supplementary_files_format_and_content: tab-delimited metadata table for all cells
Supplementary_files_format_and_content: processed .rds object with metadata
Supplementary_files_format_and_content: tab-delimited metadata table for microglial cells after reanalysis

source_name: Hippocampus

extract_protocol:
Mice received a lethal dose of ketamine (Bimeda-MTC)/xylazine (Bayer Healthcare) and were then perfused transcardially with phosphate-buffered saline (PBS) followed by rapid dissected of the ipsilateral hippocampi from each mouse into ice cold HBSS. Hippocampi were dissociated into single cells and each sample was pooled to obtain 4 mice per group, then the cells were labeled with CD45 mouse immune multiplexing kit (BD Biosciences, USA), counted and 10 000 cells per sample were multiplexed, ready for single-cell capture. The viability of cells in all samples was 80-95%. Single-cell capture was performed on the BD Rhapsody Single-Cell Analysis System (BD, USA), the DNA from each cell attached to a barcoded bead was subsequently retrieved and libraries were prepared using the whole transcriptome analysis (WTA) amplification kit (BD Biosciences) according to the manufacturer’s recommendations.
Single cell RNA libraries were generated using the BD Rhapsody 3' WTA kit with sample multiplexing using the BD Mouse Immune Single-Cell Multiplexing Kit
Single cell RNAseq

value: C57BL/6J x 129S1 and B6;129-Psen1tm1MpmTg(APPSwe,tauP301L)1Lfa/Mmjax

value: 10 months

value: 28 day ICV DMSO or SCDi


title: Kidney Rep13 Pre

status: Public on Feb 24 2022

type: RNA

city: Cambridge

first: Sarah

last: Hosgood

address: Addenbrooke's hospital, Hills road

department: Department of Surgery

institute: University of Cambridge

hyb_protocol: Hybridisation was performed according to the manufacturer's protocol (Nanostring)

scan_protocol: After hybridisation, samples were loaded on The Prep station where the targets RNA were purified and immobilized onto the cartridge. The cartridge was then transferred to the Digital Analyser for imaging and analysis

data_processing: Data were processed and normalised on the advanced Nsolver software

label: molecular barcode

source_name: renal cortex

extract_protocol: Total RNA including small RNAs was extracted

treatment_protocol: Kidney biopsies taken before and after 1h of normothermic perfusion were stored in RNA later

tag: donor age

tag: donation type

value: DBD

tag: left/ right kidney

value: Right


title: Kidney Rep11 Pre


title: Kidney Rep16 Pre

value: Left


title: Kidney Rep16 1h NMP


title: Kidney Rep06 1h NMP


title: Kidney Rep13 1h NMP


title: Kidney Rep 11 1h NMP


title: Sirt6 flox/flox, rep 2

tag: tissue

tag: genotype


title: genomic DNA_FK1679

type: genomic

city: Guangzhou

first: Liang

last: Li

state: Guangdong

address: Shatai Road 1023

department: Department of Medical Genetics

institute: Southern Medical University

description: kidney transplantation

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the Axiom Human Whole Genome Microplate Array according to the Affymetrix's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneTitan MC.

data_processing:
Raw data CEL files were typed using Axiom Analysis Suite 3.1.51, with each locus assigned to a specified type based on a series of metrics.
Each row is a case, and each column is a SNP, and the SNP genotype form a matrix table.

label: Biotin

source_name: genomic DNA

label_protocol: As per manufacturer

extract_protocol: Genomic DNA was obtained from the peripheral blood of patients and extracted using the TIANamp Blood DNA Kit. DNA quality and quantity was assessed using a Micro UV Spectrophotometer and agarose gel electrophoresis.

tag: gender

value: male


title: genomic DNA_FK1714

description: kidney transplantation


title: genomic DNA_FK1681

description: kidney transplantation


title: genomic DNA_FK1690

description: kidney transplantation


title: genomic DNA_FK1704

description: kidney transplantation

value: female


title: genomic DNA_FK1708

description: kidney transplantation


title: genomic DNA_FK1682

description: kidney transplantation


title: genomic DNA_FK1685

description: kidney transplantation


title: genomic DNA_FK1676

description: kidney transplantation


title: genomic DNA_FK1692

description: kidney transplantation


title: genomic DNA_FK1680

description: kidney transplantation


title: Kidney Rep06 Pre


title: genomic DNA_FK1674

description: kidney transplantation


title: genomic DNA_FK1630

description: kidney transplantation


title: 2-1-A

description: model


title: genomic DNA_FK1625

description: kidney transplantation


title: genomic DNA_FK1671

description: kidney transplantation


title: genomic DNA_FK1689

description: kidney transplantation


title: genomic DNA_FK1639

description: kidney transplantation


title: genomic DNA_FK1613

description: kidney transplantation


title: genomic DNA_FK1616

description: kidney transplantation


title: genomic DNA_FK1569

description: kidney transplantation


title: genomic DNA_FK1607

description: kidney transplantation


title: genomic DNA_FK1612

description: kidney transplantation


title: genomic DNA_FK1610

description: kidney transplantation


title: genomic DNA_FK1557

description: kidney transplantation


title: genomic DNA_FK1554

description: kidney transplantation


title: genomic DNA_FK1586

description: kidney transplantation


title: genomic DNA_FK1538

description: kidney transplantation


title: genomic DNA_FK1652

description: kidney transplantation


title: genomic DNA_FK1431

description: kidney transplantation


title: genomic DNA_FK1319

description: kidney transplantation


title: genomic DNA_FK1452

description: kidney transplantation


title: genomic DNA_FK1314

description: kidney transplantation


title: genomic DNA_FK1391

description: kidney transplantation


title: genomic DNA_FK1385

description: kidney transplantation


title: genomic DNA_FK1490

description: kidney transplantation


title: genomic DNA_FK1455

description: kidney transplantation


title: genomic DNA_FK1527

description: kidney transplantation


title: genomic DNA_FK1405

description: kidney transplantation


title: genomic DNA_FK1423

description: kidney transplantation


title: genomic DNA_FK1304

description: kidney transplantation


title: genomic DNA_FK1390

description: kidney transplantation


title: genomic DNA_FK1519

description: kidney transplantation


title: genomic DNA_FK1439

description: kidney transplantation


title: genomic DNA_FK1342

description: kidney transplantation


title: genomic DNA_FK1301

description: kidney transplantation


title: genomic DNA_FK1285

description: kidney transplantation


title: genomic DNA_FK1163

description: kidney transplantation


title: genomic DNA_FK1195

description: kidney transplantation


title: genomic DNA_FK1149

description: kidney transplantation


title: genomic DNA_FK1146

description: kidney transplantation


title: genomic DNA_FK1131

description: kidney transplantation


title: genomic DNA_FK1140

description: kidney transplantation


title: genomic DNA_FK1102

description: kidney transplantation


title: genomic DNA_FK1106

description: kidney transplantation


title: genomic DNA_FK1068

description: kidney transplantation


title: genomic DNA_FK1119

description: kidney transplantation


title: genomic DNA_FK1029

description: kidney transplantation


title: genomic DNA_FK1048

description: kidney transplantation


title: genomic DNA_FK1026

description: kidney transplantation


title: genomic DNA_FK1012

description: kidney transplantation


title: genomic DNA_FK1006

description: kidney transplantation


title: genomic DNA_FK997

description: kidney transplantation


title: genomic DNA_FK1008

description: kidney transplantation


title: genomic DNA_FK975

description: kidney transplantation


title: genomic DNA_FK995

description: kidney transplantation


title: genomic DNA_FK967

description: kidney transplantation


title: genomic DNA_FK964

description: kidney transplantation


title: genomic DNA_FK958

description: kidney transplantation


title: genomic DNA_FK931

description: kidney transplantation


title: genomic DNA_FK987

description: kidney transplantation


title: genomic DNA_FK955

description: kidney transplantation


title: genomic DNA_FK896

description: kidney transplantation


title: genomic DNA_FK907

description: kidney transplantation


title: genomic DNA_FK891

description: kidney transplantation


title: genomic DNA_FK861

description: kidney transplantation


title: genomic DNA_FK856

description: kidney transplantation


title: genomic DNA_FK872

description: kidney transplantation


title: genomic DNA_FK851

description: kidney transplantation


title: genomic DNA_FK901

description: kidney transplantation


title: genomic DNA_FK855

description: kidney transplantation


title: genomic DNA_FK817

description: kidney transplantation


title: genomic DNA_FK850

description: kidney transplantation


title: genomic DNA_FK807

description: kidney transplantation


title: genomic DNA_FK1127

description: kidney transplantation


title: genomic DNA_FK782

description: kidney transplantation


title: genomic DNA_FK716

description: kidney transplantation


title: genomic DNA_FK843

description: kidney transplantation


title: genomic DNA_FK776

description: kidney transplantation


title: genomic DNA_FK755

description: kidney transplantation


title: genomic DNA_FK713

description: kidney transplantation


title: genomic DNA_FK717

description: kidney transplantation


title: genomic DNA_FK706

description: kidney transplantation


title: genomic DNA_FK938

description: kidney transplantation


title: genomic DNA_FK699

description: kidney transplantation


title: genomic DNA_FK669

description: kidney transplantation


title: genomic DNA_FK697

description: kidney transplantation


title: genomic DNA_FK668

description: kidney transplantation


title: genomic DNA_FK653

description: kidney transplantation


title: genomic DNA_FK660

description: kidney transplantation


title: genomic DNA_FK652

description: kidney transplantation


title: genomic DNA_FK641

description: kidney transplantation


title: genomic DNA_FK648

description: kidney transplantation


title: genomic DNA_FK610

description: kidney transplantation


title: genomic DNA_FK628

description: kidney transplantation


title: genomic DNA_FK564

description: kidney transplantation


title: genomic DNA_FK559

description: kidney transplantation


title: genomic DNA_FK549

description: kidney transplantation


title: genomic DNA_FK543

description: kidney transplantation


title: genomic DNA_FK540

description: kidney transplantation


title: genomic DNA_FK531

description: kidney transplantation


title: genomic DNA_FK528

description: kidney transplantation


title: genomic DNA_FK467

description: kidney transplantation


title: genomic DNA_FK473

description: kidney transplantation


title: genomic DNA_FK506

description: kidney transplantation


title: genomic DNA_FK461

description: kidney transplantation


title: genomic DNA_FK655

description: kidney transplantation


title: genomic DNA_FK464

description: kidney transplantation


title: genomic DNA_FK457

description: kidney transplantation


title: genomic DNA_FK451

description: kidney transplantation


title: genomic DNA_FK454

description: kidney transplantation


title: genomic DNA_FK443

description: kidney transplantation


title: genomic DNA_FK419

description: kidney transplantation


title: genomic DNA_FK439

description: kidney transplantation


title: genomic DNA_FK438

description: kidney transplantation


title: genomic DNA_FK437

description: kidney transplantation


title: genomic DNA_FK423

description: kidney transplantation


title: genomic DNA_FK415

description: kidney transplantation


title: genomic DNA_FK416

description: kidney transplantation


title: genomic DNA_FK586

description: kidney transplantation


title: genomic DNA_FK389

description: kidney transplantation


title: genomic DNA_FK374

description: kidney transplantation


title: genomic DNA_FK555

description: kidney transplantation


title: genomic DNA_FK363

description: kidney transplantation


title: genomic DNA_FK362

description: kidney transplantation


title: genomic DNA_FK532

description: kidney transplantation


title: genomic DNA_FK406

description: kidney transplantation


title: genomic DNA_FK378

description: kidney transplantation


title: genomic DNA_FK413

description: kidney transplantation


title: genomic DNA_FK351

description: kidney transplantation


title: genomic DNA_FK356

description: kidney transplantation


title: genomic DNA_FK338

description: kidney transplantation


title: genomic DNA_FK341

description: kidney transplantation


title: genomic DNA_FK345

description: kidney transplantation


title: genomic DNA_FK344

description: kidney transplantation


title: genomic DNA_FK337

description: kidney transplantation


title: genomic DNA_FK333

description: kidney transplantation


title: genomic DNA_FK334

description: kidney transplantation


title: genomic DNA_FK332

description: kidney transplantation


title: genomic DNA_FK327

description: kidney transplantation


title: genomic DNA_FK329

description: kidney transplantation


title: genomic DNA_FK317

description: kidney transplantation


title: genomic DNA_FK310

description: kidney transplantation


title: genomic DNA_FK302

description: kidney transplantation


title: genomic DNA_FK300

description: kidney transplantation


title: genomic DNA_FK303

description: kidney transplantation


title: genomic DNA_FK309

description: kidney transplantation


title: genomic DNA_FK298

description: kidney transplantation


title: genomic DNA_FK296

description: kidney transplantation


title: genomic DNA_FK295

description: kidney transplantation


title: genomic DNA_FK290

description: kidney transplantation


title: genomic DNA_FK288

description: kidney transplantation


title: genomic DNA_FK283

description: kidney transplantation


title: genomic DNA_FK284

description: kidney transplantation


title: genomic DNA_FK264

description: kidney transplantation


title: genomic DNA_FK272

description: kidney transplantation


title: genomic DNA_FK263

description: kidney transplantation


title: genomic DNA_FK265

description: kidney transplantation


title: genomic DNA_FK262

description: kidney transplantation


title: genomic DNA_FK261

description: kidney transplantation


title: genomic DNA_FK250

description: kidney transplantation


title: genomic DNA_FK255

description: kidney transplantation


title: genomic DNA_FK246

description: kidney transplantation


title: genomic DNA_FK249

description: kidney transplantation


title: genomic DNA_FK243

description: kidney transplantation


title: genomic DNA_FK245

description: kidney transplantation


title: genomic DNA_FK239

description: kidney transplantation


title: genomic DNA_FK258

description: kidney transplantation


title: genomic DNA_FK234

description: kidney transplantation


title: genomic DNA_FK236

description: kidney transplantation


title: genomic DNA_FK297

description: kidney transplantation


title: genomic DNA_FK227

description: kidney transplantation


title: genomic DNA_FK224

description: kidney transplantation


title: genomic DNA_FK218

description: kidney transplantation


title: genomic DNA_FK216

description: kidney transplantation


title: genomic DNA_FK209

description: kidney transplantation


title: genomic DNA_FK225

description: kidney transplantation


title: genomic DNA_FK207

description: kidney transplantation


title: genomic DNA_FK204

description: kidney transplantation


title: genomic DNA_FK202

description: kidney transplantation


title: genomic DNA_FK200

description: kidney transplantation


title: genomic DNA_FK197

description: kidney transplantation


title: genomic DNA_FK196

description: kidney transplantation


title: genomic DNA_FK193

description: kidney transplantation


title: genomic DNA_FK185

description: kidney transplantation


title: genomic DNA_FK186

description: kidney transplantation


title: genomic DNA_FK184

description: kidney transplantation


title: genomic DNA_FK178

description: kidney transplantation


title: genomic DNA_FK165

description: kidney transplantation


title: genomic DNA_FK173

description: kidney transplantation


title: genomic DNA_FK162

description: kidney transplantation


title: genomic DNA_FK231

description: kidney transplantation


title: genomic DNA_FK144

description: kidney transplantation


title: genomic DNA_FK229

description: kidney transplantation


title: genomic DNA_FK156

description: kidney transplantation


title: genomic DNA_FK142

description: kidney transplantation


title: genomic DNA_FK135

description: kidney transplantation


title: genomic DNA_FK124

description: kidney transplantation


title: genomic DNA_FK119

description: kidney transplantation


title: genomic DNA_FK114

description: kidney transplantation


title: genomic DNA_FK109

description: kidney transplantation


title: genomic DNA_FK107

description: kidney transplantation


title: genomic DNA_FK106

description: kidney transplantation


title: genomic DNA_FK092

description: kidney transplantation


title: genomic DNA_FK103

description: kidney transplantation


title: genomic DNA_FK177

description: kidney transplantation


title: genomic DNA_FK098

description: kidney transplantation


title: genomic DNA_FK091

description: kidney transplantation


title: genomic DNA_FK084

description: kidney transplantation


title: genomic DNA_FK151

description: kidney transplantation


title: genomic DNA_FK169

description: kidney transplantation


title: genomic DNA_FK155

description: kidney transplantation


title: genomic DNA_FK081

description: kidney transplantation


title: genomic DNA_FK128

description: kidney transplantation


title: genomic DNA_FK125

description: kidney transplantation


title: genomic DNA_FK118

description: kidney transplantation


title: genomic DNA_FK129

description: kidney transplantation


title: genomic DNA_FK074

description: kidney transplantation


title: genomic DNA_FK057

description: kidney transplantation


title: genomic DNA_FK066

description: kidney transplantation


title: genomic DNA_FK059

description: kidney transplantation


title: genomic DNA_FK076

description: kidney transplantation


title: genomic DNA_FK054

description: kidney transplantation


title: genomic DNA_FK072

description: kidney transplantation


title: genomic DNA_FK063

description: kidney transplantation


title: genomic DNA_FK078

description: kidney transplantation


title: genomic DNA_FK112

description: kidney transplantation


title: genomic DNA_FK104

description: kidney transplantation


title: genomic DNA_FK053

description: kidney transplantation


title: genomic DNA_FK046

description: kidney transplantation


title: genomic DNA_FK041

description: kidney transplantation


title: genomic DNA_FK038

description: kidney transplantation


title: genomic DNA_FK035

description: kidney transplantation


title: genomic DNA_FK023

description: kidney transplantation


title: genomic DNA_FK034

description: kidney transplantation


title: genomic DNA_FK010

description: kidney transplantation


title: genomic DNA_FK033

description: kidney transplantation


title: genomic DNA_FK011

description: kidney transplantation


title: genomic DNA_FK007

description: kidney transplantation


title: genomic DNA_FK004

description: kidney transplantation


title: genomic DNA_FK080

description: kidney transplantation


title: genomic DNA_FK002

description: kidney transplantation


title: 48_208-12R-pEM

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: CD4+ Tcells

extract_protocol:
After isolation, cells were resuspended in PBS containing 2 mM EDTA and spun for the removal of contaminating platelets. Prior to sorting, peripheral CD4+ T-cells were enriched with the use of magnetic beads and column purification (Miltenyi Biotec). Enriched peripheral CD4+ T-cells were then stained with previously determined volumes of the following fluorescently conjugated mAbs: CD3-APC-Cy7 or -AF700 (clone SP34-2), CCR7-PE-Cy7 (clone 3D12), CD8-APC-Cy7 (clone SK1), CD45RA-APC (clone 5H9), CD95-PE-Cy5 (clone DX2), (CD62L-PE (clone SK11) from BD Bioscience; CD28-ECD (clone CD28.2) from Beckman Coulter, CD4-BrilliantViolet650 (clone OKT4), CD8-BV421 (clone RPA-T8) from Biolegend. Circulating populations for sorting were defined as follows: naive, CD45RA+CCR7+CD95-CD62L+; TSCM, CD45RA+CCR7+CD95+CD28+CD62L+; TCM, CD45RA-CD95+CCR7+CD62L+; and TEM, CD95+CCR7−. RNA was purified using QIAGEN Micro RNEasy columns, and RNA quality assessed using Agilent Bioanalyzer.
10 ng of total RNA was used as input for mRNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified mRNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq 3000 using (151 bp SR) at an average read depth of 23 M.

treatment_protocol: Twelve Indian rhesus macaques (RMs), including 5 males and 7 females, were infected i.v. with 103 TCID50 of SIVmac251. Starting at day 11 post-infection, all 12 animals were initiated on triple ART consisting of two reverse transcriptase inhibitors (PMPA/tenofovir and FTC/emtricitabine) and one integrase inhibitor (dolutegravir). After 14-15 weeks on ART and plasma viral load suppression <80 copies/ml for at least 4 weeks, 8 RMs additionally received the CBP/β-catenin inhibitor PRI-724 while the 4 remaining RMs were maintained on ART only and served as controls (Figure 1). Among the PRI-724-treated group, 5 RMs received 6 cycles (one week on/one week off) of PRI-724 at 10mg/kg/day administered subcutaneously (s.c.). Based on results from a concurrent dose ranging study (Fig. S1), an additional 3 RMs received 12 weeks of uninterrupted PRI-724 at 20mg/kg/day s.c., a dose that was found to be safe in healthy RMs.

tag: subject id

tag: Sex

value: Male

tag: cell type

value: effector memory T-cells (EM)

value: Control

tag: dose


title: 45_208-12R-pNAIVE

value: naive CD4+ T-cells (NAIVE)

tag: treatment


title: 47_208-12R-pCM

value: central memory T-cells (CM)


title: 44_192-12R-pEM

value: Female


title: 46_208-12R-pSCM

value: stem cell memory CD4+ T-cells (SCM)


title: 43_192-12R-pCM


title: 41_192-12R-pNAIVE


title: 40_182-12R-pEM


title: 39_182-12R-pCM


title: 38_182-12R-pSCM


title: 37_182-12R-pNAIVE


title: 36_150-12R-pEM


title: 42_192-12R-pSCM


title: 33_150-12R-pNAIVE


title: 35_150-12R-pCM


title: 31_183-12R-pCM

value: Treated


title: 34_150-12R-pSCM


title: 30_183-12R-pSCM


title: 28_RZf15-pEM


title: 26_RZf15-pSCM


title: 24_RAe15-pEM


title: 22_RAe15-pSCM


title: 23_RAe15-pCM


title: 21_RAe15-pNAIVE


title: 20_180-12R-pEM


title: 19_180-12R-pCM


title: 18_180-12R-pSCM


title: 17_180-12R-pNAIVE


title: 16_155-12R-pEM


title: 15_155-12R-pCM


title: 32_183-12R-pEM


title: 13_155-12R-pNAIVE


title: S2_dev_STARRseq_input

city: Wien

first: Bernardo

middle: P

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
Library strategy: STARR-seq
Paired-end genome-wide UMI-STARR-seq RNA and DNA input reads (36 bp) were mapped to the Drosophila genome (dm3), excluding chromosomes U, Uextra, and the mitochondrial genome, using Bowtie v.1.2.2. Mapping reads with up to three mismatches and a maximal insert size of 2kb were kept. For paired-end RNA reads that mapped to the same positions, we collapsed those that have identical UMIs (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts. We further computationally selected both RNA and input fragments of length 150-250 bp to only capture active sequences derived from short fragments.
After processing the two biological replicates separately, we pooled both replicates for developmental and housekeeping screens for further analyses.
Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of STARR-seq and input. We performed hypergeometric tests to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Peaks that had a hypergeometric p-value <= 0.001 and a corrected enrichment over input greater than 3 were defined as enhancers.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files contain normalized genome-wide coverage. Plain text files contain enhancer peaks, including the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

organism: synthetic construct

source_name: whole genome library (in STARR-seq vector)

growth_protocol: Schneider 2 cells were grown in Schneider’s Medium supplemented with 10% heat inactivated FBS (Sigma; F7524) at 27ºC. Cells were passaged every 2-3 days.

extract_protocol: 24h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer   s protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/  l for 45 minutes (min) at 37C. The reactions were then subjected to cleanup with Beckman-Coulter AMPure XP beads (Product No: A63881), at a ratio of 1:1.8. STARR-seq transcripts were specifically reverse transcribed using a gene specific primer (CTCATCAATGTATCTTATCATGTCTG), followed by RNaseA digest. After second strand synthesis (primer: TTGGTAAAGCCACCATGGAAAAG*G) we introduced a 10 bp unique molecular identifier (UMI) at the 3' end of the STARR-seq transcript (primer:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G), followed by a PCR step across the spliced intron junction of the mature STARR-seq transcript (primers: AAGCCACCATGGAAAAG*G*C*C*A*T and CAAGCAGAAGACGGCATACG*A). Samples were amplified for Illumina sequencing with an Illumina i5 adapter and a custom i7 index primer (CAAGCAGAAGACGGCATACGAGA*T). All PCR steps were performed using the KAPA HiFi HotStart ReadyMix (Roche; Material Number 7958927001), and cleaned up with Beckman-Coulter AMPure XP beads (Product No: A63881) at an appropriate ratio. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019 for more details.

tag: cell line

value: y; cn bw sp - sequenced strain (Adams et al. 2000)

value: PCR amplified Plasmid library

tag: promoter

value: developmental (DSCP)


title: 25_RZf15-pNAIVE


title: 12_204-12R-pEM


title: PRRX1 low Day 4 cells, rep1

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: processed data.xlsx: Excel file includes counts for each sample.

source_name: PRRX1 low Day 4 cells

growth_protocol: Differentiation protocol: hPSCs (3 × 10^4) were suspended in 1 ml of StemFit (Ajinomoto) containing 10 µM Y27632 (Wako), and 4 µl of iMatrix511 was added to a 3.5-cm culture dish. The culture medium was replaced the next day with fresh StemFit without Y27632. After culturing for 2 or 6 days, the cells were washed with PBS, and differentiation was induced by changing the culture medium at each time point. Chemically defined CDM2 medium was used as basal culture medium, and cytokines or other chemicals were added to prepare each differentiation medium. The composition of CDM2 basal medium was as follows: 50% IMDM (+ GlutaMAX, + HEPES, + sodium bicarbonate; Gibco) + 50% F12 (+ GlutaMAX; Gibco) + 1 mg/ml polyvinyl alcohol (Sigma-Aldrich) + 1% v/v concentrated lipids (Gibco) + 450 μM monothioglycerol (Sigma-Aldrich) + 7 μg/ml insulin (Sigma-Aldrich) + 15 μg/ml transferrin (Sigma-Aldrich) + 1% v/v penicillin/streptomycin (Gibco). The composition of cytokines or other chemicals in the media was as follows: mid-primitive streak (CDM2 basal medium + 30 ng/ml ACTIVIN A + 40 ng/ml BMP4 + 6 µM CHIR99021 + 100 nM PIK90 + 10 µM Y27632), LPM (CDM2 medium + 1 µM A-83-01 + 30 ng/ml BMP4 + 1 µM C59 + 10 µM Y27632), LBM-like (CDM2 basal medium +1 µM A-83-01 + 0.5 µM LDN-193189 + 3 µM CHIR99021 + 150 nM vismodegib + 10 µM Y27632).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacturer`s instruction. The initial amount of total RNA was 1000 ng.

value: limb bud mesenchymal cells

tag: origin

value: human iPSC


title: PRRX1 positive LBM-like cells, rep2

source_name: PRRX1 positive LBM-like cells


title: 27_RZf15-pCM


title: SK-MEL-147_8_IFNgamma_sgSTUB1_Rep2

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Fastq files were mapped to the human reference genome (Homo.sapiens.GRCh38.v77) using Tophat v2.1 with default settings for single-end data. The samples were used to generate read count data using HTSeq-count (V0.10.0).
Genome_build: hg38
Supplementary_files_format_and_content: Text fie with read count data

source_name: Melanoma cell line

growth_protocol: Cells were cultured with DMEM supplemented with 9% FBS and pen/strep in 5% CO2 incubator at 37 degree

extract_protocol:
RNA was extracted using RLT buffer (Qiagen, 79216)
Librararies were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2*106 D10 and SK-MEL-147 melanoma cells expressing either sgCtrl or sgSTUB1 were plated per dish in 10 cm cell culture dishes 48 hours prior to IFNγ treatment. Melanoma cells were subsequently treated with 25 ng/ml IFNγ or vehicle for 8 hours.

tag: time (hours)

value: IFNgamma

tag: guide

tag: replicate


title: 29_183-12R-pNAIVE


title: 10_204-12R-pSCM


title: 11_204-12R-pCM


title: SK-MEL-147_8_IFNgamma_sgSTUB1_Rep1


title: 9_204-12R-pNAIVE


title: SK-MEL-147_8_IFNgamma_sgCTR_Rep2

value: sgCTR


title: 8_91-12R-pEM


title: SK-MEL-147_8_IFNgamma_sgCTR_Rep1


title: 6_91-12R-pSCM


title: 5_91-12R-pNAIVE


title: SK-MEL-147_8_Tcells_sgSTUB1_Rep2

value: Tcells


title: 4_89-12R-pEM


title: SK-MEL-147_8_Tcells_sgSTUB1_Rep1


title: 3_89-12R-pCM


title: PRRX1 low Day 4 cells, rep2


title: 1_89-12R-pNAIVE


title: SK-MEL-147_8_Tcells_sgCTR_Rep2


title: 2_89-12R-pSCM


title: PRRX1 positive LBM-like cells, rep1


title: SK-MEL-147_8_Tcells_sgCTR_Rep1


title: D10_8_IFNgamma_sgSTUB1_Rep2


title: HCT116_oligo_library_STARRseq_rep2

data_processing:
Library strategy: STARR-seq
Oligo library UMI-STARR-seq RNA and DNA input reads (150 bp) were mapped to a reference containing 249 bp long sequences containing both wildtype and mutated fragments from the Drosophila library using Bowtie v.1.2.2. We demultiplexed reads by the i5 and i7 indexes and subsequently by the oligo identity, since this library contained oligos from other experiments. Mapping reads with the correct length, strand and with no mismatches (to identify all sequence variants) were kept. Both DNA and RNA reads were collapsed by UMI (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts.
We excluded oligos with less than 10 reads in any of the input replicates and added one read pseudocount to oligos with zero RNA counts. The enhancer activity of each oligo in each screen was calculated as the log2 fold-change over input, using both replicates, using DESeq2. We used the counts of wildtype negative regions in each library as scaling factors between samples. This normalization only changes the position of the zero and consequently does not affect the calculation of log2 fold-changes or the p-values for the statistical tests used.
Genome_build: hg19 (custom oligo library)
Supplementary_files_format_and_content: Table of all 22,900 human enhancer sequences and their motif-mutant sequences included in the oligo library, with genomic coordinates, oligo sequence, experiment, mutated motif, read counts for each screen and final enhancer activity (log2).

source_name: HCT-116 cells

growth_protocol: Human colon cancer cell line HCT116 was grown in DMEM (Gibco; 52100-047) supplemented with 10% heat inactivated FBS (Sigma; F7524) and 1% L-Glutamine (Sigma; G7513) at 37ºC. Cells were passaged every 2-3 days.

extract_protocol: 6h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer's protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/ul for 45 minutes (min) at 37C. The reactions were then subjected to cleanup with Beckman-Coulter AMPure XP beads (Product No: A63881), at a ratio of 1:1.8. STARR-seq transcripts were specifically reverse transcribed using a gene specific primer (CTCATCAATGTATCTTATCATGTCT), followed by RNaseA digest. After second strand synthesis (primer: GTCGTGAGGCACTGGGCA*G) we introduced a 10 bp unique molecular identifier (UMI) at the 3'end of the STARR-seq transcript (primer: CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G), followed by a PCR step across the spliced intron junction of the mature STARR-seq transcript (primers: TCGTGAGGCACTGGGCAG*G*T*G*T*C and CAAGCAGAAGACGGCATACG*A). Samples were amplified for Illumina sequencing with an Illumina i5 adapter and a custom i7 index primer (CAAGCAGAAGACGGCATACGAGA*T). All PCR steps were performed using the KAPA HiFi HotStart ReadyMix (Roche; Material Number 7958927001) and cleaned up with Beckman-Coulter AMPure XP beads (Product No: A63881) at an appropriate ratio. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019 for more details.

tag: sample type

value: PCR amplified cDNA (STARR-seq transcript)


title: 7_91-12R-pCM

value: Male


title: D10_8_IFNgamma_sgCTR_Rep1


title: D10_8_Tcells_sgSTUB1_Rep2


title: HCT116_oligo_library_STARRseq_rep1


title: D10_8_IFNgamma_sgCTR_Rep2


title: D10_8_Tcells_sgCTR_Rep2


title: D10_8_IFNgamma_sgSTUB1_Rep1


title: SK-MEL-147_4_IFNgamma_sgSTUB1_Rep2


title: SK-MEL-147_4_Tcells_sgSTUB1_Rep2


title: Hyper3

city: Vienna

first: Dominika

last: Lukovic

address: Waehringer Guertel 18-20

department: Internal Medicine II

institute: Medical University of Vienna

data_processing:
Alignment [code: STAR    --runThreadN 32    --outSAMattributes All    --outSAMtype BAM SortedByCoordinate    --quantMode GeneCounts    --genomeDir Sscrofa11.1_index    --readFilesIn rawReads    --outFileNamePrefix 15619    --readFilesCommand gunzip -c    --outReadsUnmapped Fastx    --outWigType wiggle ]
Counting reads into genes [EnsemblIDs](code: python3 -m HTSeq.scripts.count -f bam -r pos -t exon --additional-attr=gene_name stranded=reverse  15618Aligned.sortedByCoord.out.bam genes.gtf > 15618.counts). Mapped reads were counted into the Ensembl  Sscrofa 11.1 gene model using HTSeq Python package (Python3 Version 3.9, HTSeq-Count Version 0.11.1)9 applying parameters:  -m union stranded=revers.
Differential expression analysis[comparison between experimental group and control group]; (code: deseq2Data <- DESeqDataSetFromMatrix(countData=rawCounts, colData=sampleData, design= ~ treatment). Raw reads were transformed based on library size using DESeq2 package with subsequent rlog transformation. Statistically significantly deregulated genes were determined by generalized linear models fitted to the corresponding contrast (each treatment versus control group). The estimated coefficients and standard errors for all contrasts were used for calculation of moderated t-statistics, moderated F-statistics, and the log-odds of differential expression by empirical Bayes shrinkage of the standard errors towards a common value.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: counted reads in .txt files

organism: Sus scrofa

source_name: anterior wall

extract_protocol:
The specimens were homogenized using Precellys lysing kit CK28 beads (VWR, Vienna, Austria) in Qiazol lysis buffer (Qiagen, Hilden, Germany) and total RNA was isolated using the RNeasy® Tissue kit (Qiagen, Hilden, Germany).
The total RNA fractions of the myocardial samples were subjected to mRNA deep sequencing using the Illumina (San Diego, CA, USA) platform. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) was utilized for mRNA fragmentation and enrichment. Fragmented and primed mRNA was reverse transcribed to cDNA. The cDNA library was synthesized and enriched using the NEBNext Ultra Directional RNA Library Kit (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on the HiSeq 2500 platform to a mean depth of 15–20 million paired-end reads per sample at the Core Facility of the Medical University of Vienna.

treatment_protocol:
Nineteen pigs (Sus scrofa, female large whites) were included into five groups receiving either Doxorubicin (DOX, n=5) or liposomal encapsulated Doxorubicin, Myocet (MYO, n=5), undergoing reperfused myocardial infarction (RemoLV, n=3) or induced artificial aortic isthmus stenosis (Hyper, n=3). The fifth group served as sham-operated control group (Control, n=3). Animals in groups DOX and MYO received either Doxorubicin (DOX) or liposomal doxorubicin-citrate complex (Myocet®, MYO) in 3 cycles (Day 1, 22, 43) of cytostatic treatment in doses equivalent to human treatment regimens (60 mg/m2 body surface area). The DOX and MYO experiments had to be prematurely terminated after 3 months (FUP) due to bad health conditions of the animals.  Domestic pigs in the group RemoLV were sedated by subcutaneous administration of 12mg/kg ketamine hydrochloride, 1mg/ kg xylazine, and 0.04 mg/kg atropine after overnight fasting. After endotracheal intubation, the anesthesia was deepened with 1.5-2.5 vol % isoflurane, 1.6- 1.8 vol % O2, and 0.5 vol % N2O. A 6F introduction sheath (Terumo Medical Corporation, Somerset, NJ, USA) was inserted into the right femoral artery. Following administration of 200 IU/kg of heparin, 6F right coronary guiding catheters were introduced into the left and right coronary ostium to perform selective angiography of the left and right coronary arteries.  Catheter-based reperfused anterior wall myocardial infarction was induced by the inflation of a coronary-angioplasty balloon (2.75 mm diameter, 15 mm length; Maverick, Boston Natick, MA, USA) at 5 atm for 90 min in the mid part of the left anterior descending coronary artery. Reperfusion was initiated via balloon deflation. The animals were allowed to recover from the anesthesia. FUP investigations and myocardial tissue sampling was performed at 6-month.  For pressure overload-induced myocardial fibrosis (Hyper), a bare metal stent (9 mm of diameter, 20 mm of length, Cordis S.M.A.R.T. CONTROL, Cordis, Fremont, California) was implanted in the descending thoracic aorta of the juvenile pigs. Natural enlargement of thoracic aorta by growing animals reaching the diameter of 1.8 cm resulted in induced artificial aortic thoracic stenosis by constant 9 mm stent. The developing artificial aortic isthmus stenosis resulted in a slowly developing severe myocardial hypertrophy and diffuse myocardial fibrosis during the 6 Mo FUP.  After the predefined FUP, the animals were euthanized, and the hearts were explanted. Myocardial samples from the anterior wall in groups DOX, MYO and Hyper were collected, while remote posterior wall myocardial area from the remodeled LV was excised in group RemoLV.  Sham operated animals in the same age of the animals of other groups served as Controls (n=3).
Myocardial tissue samples (~30mg) of the left ventricle (for RemoLV, non-ischemic myocardium) were washed with PBS, minced into small pieces and transferred into cryotubes containing 1.2 ml RNAlater®(Ambion, Austin, TX, USA). The samples were firstly incubated overnight at 4°C, then transferred to -80 °C.

value: Myocardium

tag: follow-up (fup)

value: 6 months after implantation of coronary stent

value: Artificial isthmus stenosis


title: Hyper2


title: Control1

value: 6 months

value: Control


title: SK-MEL-147_4_IFNgamma_sgSTUB1_Rep1


title: Control2


title: RemoLV2

source_name: posterior wall

value: 6 months after percutaneous coronary occlusion

value: Percutaneous coronary occlusion 90 min.


title: RemoLV1


title: Control3


title: Hyper1


title: SK-MEL-147_4_Tcells_sgSTUB1_Rep1


title: SK-MEL-147_0_CTR_sgSTUB1_Rep2

value: CTR


title: MYO5

value: 3 months after 1st injection

value: Myocet treated


title: RemoLV3


title: D10_8_Tcells_sgSTUB1_Rep1


title: SK-MEL-147_4_IFNgamma_sgCTR_Rep2


title: SK-MEL-147_0_CTR_sgSTUB1_Rep1


title: MYO3


title: D10_8_Tcells_sgCTR_Rep1


title: MYO2