title: MEFs-SAG-bio-rep-3

first: Douglas

last: Menke

state: Georgia

address: 500 DW Brooks drive

department: Genetics

institute: University of Georgia

description: Cells were collected from M. musculus stage E11.5 embryo and were grown until passage 3. After passage 3, the cells were split and seeded with equal density into two wells of a 24-well plate (passage 4).  24 hours after the SAG exposure, total RNA was collected.

data_processing:
Read quality  was checked with FastQC v0.11.8.
AS-LEF  and ASEC-1  reads were aligned to the Asag2.1 genome (Geneva et al,2022);  MEF  reads were aligned to mm10; read alignments were performed using HISAT2 v2.1.0
Sample similarity and batch effects were examined by principal component analysis (PCA)
Differentially expressed genes between SAG treated and untreated samples  were identified by DEseq2 v1.36.0
For primary embryonic fibroblasts in both species batch effects were corrected by using biological replicates as the batch variable in during DEG analysis.
WGS reads were aligned to Asag2.1 genome and genome coverage per scaffold was calculated using pileup.sh from BBMap
For SNP calling - Picard toolkit was used to remove duplicate reads and then BCFtools was used to identify SNPs
Assembly: Anolis sagrei samples: Asag2.1 (Geneva et al,2022) and for Mus musculus samples: mm10
Supplementary files format and content: Excel and csv files containing normalized read count,differentially expressed genes between SAG treated and untreated samples with base mean and log2fold change values , A variant call format file for ASEC-1 SNP data

source_name: embryonic limb buds

growth_protocol: Cells were grown at 29°C at 5% CO2  in the growth medium (1X DMEM with 4.5 g/L glucose,  10% heat-inactivated fetal bovine serum (FBS), 1X glutamine, 1X Pen/Strep/amphoterin).

extract_protocol:
Adherent cells were collected in lysis buffer and total RNA was isolated using the mirVana RNA Isolation Kit (ThermoFisher Scientific)
For WGS- A cell pellete collected from a confluent 10cm tissue culture plate was processed
Libraries were constructed with TruSeq Stranded mRNA Sample Prep Kit for Illumina and sequenced on the Illumina NextSeq platform
For WGS- Libraries were constructed from NEBNext Ultra II FS DNA library prep kit for Illumina

treatment_protocol: Equal-density cells were seeded into two wells. After the cells reached confluency, the growth medium was replaced by the DMEM medium containing 1% FBS. After 48 hr of serum starvation, SAG solution prepared in DMEM medium with 1% FBS was added into one well, and volume equivalent DMSO solution prepared in  DMEM medium with 1% FBS was added into the other well.

value: ICR

tag: developmental stage

value: primary embryonic fibroblasts

tag: growth temperature


title: MEFs-SAG-bio-rep-4

status: Public on Dec 15 2023

type: SRA

city: Athens

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

tag: passages

tag: treatment


title: MEFs-SAG-bio-rep-5


title: HctYH_OF3A_1-1-I3-G14

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF3A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-1-I3-H13


title: SW480trps1_1,biol rep 1

city: beijing

first: wenjie

last: liu

address: No. 17 Nanli, Panjiayuan, Chaoyang District

country: China

institute: National Cancer Center/National Clinical  Research Center for Cancer/Cancer  Hospital

data_processing:
Illumina NovaSeq platform
RNA-seq raw reads were trimmed by Skewer (v0.2.2) to remove adapter sequences
then aligned to the human hg19 reference genome by STAR (v2.4.2a)
RSEM (1.2.29) were used to determine expression abundance quantification.
Differentially expressed genes (DEGs) were selected based on |fold change| >=2 and adjusted P-value < 0.05 thresholds by edge R.
Assembly: GENCODE(v19)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HCT116 and SW480 were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA from HCT116 and SW480 cells was extracted by Trizol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared by TruSeq Ribozero kit following manufacturer's protocols.

treatment_protocol: TRPS1 overexpressed stable cells (empty vector, Con; wild type, WT; and R544Q mutant, MT) using these two cell lines were constructed and confirmed by Western blot

tag: cell line

value: epithelial

tag: genotype

value: TRPS1-WT overexpression


title: SW480Control3,biol rep 3

value: WT


title: HCT116R544QL3,biol rep 3

value: TRPS1-MT overexpression


title: HctYH_OF3A_1-1-I3-G1


title: HctYH_OF3A_1-1-I3-F2


title: serum_mESC_500cells_SOX2_CR

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data

source_name: serum mESC

growth_protocol: serum mES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: wild type

tag: chip-antibody

value: Sox2 (Abclonal, A11936)


title: serum_mESC_5000cells_SOX2_CR


title: MEFs-SAG-bio-rep-1


title: MEFs-SAG-bio-rep-2


title: HctYH_OF3A_1-1-I3-F14


title: MEFs-DMSO-bio-rep-5

value: DMSO


title: HctYH_OF3A_1-1-I3-E2


title: ICM_SOX2_CR_rep1

source_name: E3.5 ICM

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.

value: C57BL/6J x  PWK/PhJ


title: serum_mESC_200cells_SOX2_CR


title: HCT116R544QL1,biol rep 1


title: ASEC-1-WGS

description: Genomic DNA was colected from ASEC-1 cells

organism: Anolis sagrei

source_name: immortalized cell line, torso region

value: wild caught

value: derived from stage 6 embryo

value: embryonic fibroblast cell line


title: HctYH_OF3A_1-1-I3-F13


title: HCT116R544QL2,biol rep 2


title: ASEC-1-SAG-rep-4

description: Total RNA was collected 48 hours after the SAG exposure


title: MEFs-DMSO-bio-rep-4


title: HctYH_OF3A_1-1-I3-E1


title: HctYH_OF3A_1-1-I3-F1


title: SW480Control1,biol rep 1


title: HctYH_OF3A_1-1-I3-E14


title: HCT116trps1L3,biol rep 3


title: MEFs-DMSO-bio-rep-2


title: ASEC-1-SAG-rep-2


title: HCT116trps1L2,biol rep 2


title: ASEC-1-SAG-rep-3


title: ASEC-1-SAG-rep-1


title: HctYH_OF3A_1-1-I3-E13


title: MEFs-DMSO-bio-rep-1

description: Cells were collected from M. musculus stage E11.5 embryo and were grown until passage 3 . After passage 3, the cells were split and seeded with equal density into two wells of a 24-well plate (passage 4).  24 hours after the SAG exposure, total RNA was collected.


title: HctYH_OF3A_1-1-I3-D2


title: HCT116ControlL3,biol rep 3


title: ASEC-1-DMSO-rep-4


title: HctYH_OF3A_1-1-I3-D1


title: ASEC-1-DMSO-rep-3


title: HCT116ControlL2,biol rep 2


title: 25_Postnatal day 15 Pde1c-Cre+/- Noninjected biological replicate 2

city: Trondheim

first: Giulia

last: Quattrocolo

address: Olav Kyrres gate 9

department: Kavli Institute for Systems Neuroscience

country: Norway

institute: NTNU

data_processing:
MultiQC v1.9.dev0  pipeline -> b'github.com/gcfntnu/gcf-workflows/tree/main commit 37aea83293e215ab97ec49c6967a1987d2eccf4f'
Sequence reads were trimmed for adaptor sequence, quality controled, and categorized by RNA subtype using fastp (report: multiqc_GCF-2021-808.html)
Pseudoalignment by Kallisto
Trimmed sequence reads were mapped to GrCM39/mm11 using R software and ENSDb
Read count extraction and normalization were performed using R software and TMM
Assembly: GrCM39 mus musculus
Supplementary files format and content: tab-delimited text files include total reads for each Sample, dataframe includes TMM for all nonzero genes

source_name: Hippocampus

extract_protocol:
Tissue was homogenized and processed using Nucleospin RNA extraction kit from Machery Nagel.
RNA libraries for RNA-seq were prepared using Lexogen Corall mRNA kit following manufacturer's protocols.

tag: tissue

value: Brain

value: Hippocampus

value: Control (No injection)

tag: age (postnatal_day)


title: HCT116ControlL1,biol rep 1


title: ASEC-1-DMSO-rep-2


title: HctYH_OF3A_1-1-I3-D14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 23_Postnatal day 15 Pde1c-Cre-/- Noninjected biological replicate 2


title: HctYH_OF3A_1-1-I3-D13

value: Female


title: MEFs-DMSO-bio-rep-3

value: ICR

value: primary embryonic fibroblasts


title: GSDMD KO lung rep3

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Assembly: GRCm38
Supplementary files format and content: txt file with  normalized counts for each sample and each gene, includes gene annotations
Supplementary files format and content: txt file with raw counts for each sample and each gene

molecule: polyA RNA

source_name: lung

extract_protocol:
TRIzol RNA extraction from lung tissue.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

value: GSDMD KO

value: lung

tag: day post sars-cov-2


title: GSDMD KO lung rep2


title: AS-LEFs-SAG-bio-rep-5

description: Cells were collected from A. sagrei embryos and were grown until passage 3. After passage 3, the cells were split and seeded with equal density into two wells of a 24-well plate (passage 4). 24 hours after the SAG exposure, total RNA was collected.

value: stage 5-6


title: ASEC-1-DMSO-rep-1


title: HctYH_OF3A_1-1-I3-C2

value: nuclear RNA + genomic DNA


title: HCT116trps1L1,biol rep 1

value: epithelial

value: TRPS1-WT overexpression


title: 21_Postnatal day 30 Pde1c-Cre+/- Noninjected biological replicate 2


title: GSDMD KO lung rep1


title: HctYH_OF3A_1-1-I3-C14


title: AS-LEFs-SAG-bio-rep-4


title: HctYH_OF3A_1-1-I3-C1


title: HctYH_OF3A_1-1-I3-C13


title: 20_Postnatal day 30 Pde1c-Cre+/- Noninjected biological replicate 1


title: 22_Postnatal day 15 Pde1c-Cre-/- Noninjected biological replicate 1


title: WT lung rep3

value: WT


title: 19_Postnatal day 30 Pde1c-Cre-/- Noninjected biological replicate 2


title: AS-LEFs-SAG-bio-rep-3

value: wild caught


title: AS-LEFs-SAG-bio-rep-2

value: 200nM SAG


title: 18_Postnatal day 30 Pde1c-Cre-/- Noninjected biological replicate 1


title: 24_Postnatal day 15 Pde1c-Cre+/- Noninjected biological replicate 1


title: WT lung rep1


title: HctYH_OF3A_1-1-I3-B2


title: AS-LEFs-SAG-bio-rep-1


title: AS-LEFs-DMSO-bio-rep-5

value: DMSO


title: 16_Postnatal day 15 Pde1c-Cre+/- Injected biological replicate 3

value: Brain

value: Cre-DTA AAV injection


title: 17_Postnatal day 15 Pde1c-Cre+/- Injected biological replicate 4

value: Hippocampus


title: 15_Postnatal day 15 Pde1c-Cre+/- Injected biological replicate 2


title: AS-LEFs-DMSO-bio-rep-3


title: JCP_1260, rfx1 deletion, YP maltose plate, biological replicate 3

city: Houston

first: Jose

middle: Christian

last: Perez

state: TX

address: 6431 Fannin

institute: UTHealth Houston

data_processing:
Sequenced reads were trimmed for adaptor sequence and Quality cutoff 20 using Galaxy Cutadapt (Galaxy Version 3.7+galaxy0).
The reads were mapped to C. albicans Build 21 genome using RNA STAR (Galaxy Version v2.7.8a+galaxy0) with modification of these selected paramaters: with-gtf, --twopassMode, GeneCounts, --outSAMmapqUnique, --outSAMstrandField intronMotif, --alignIntronMin 9.
Counting of aligned reads in the BAM file that overlap features in a GFF file was executed with htseq-count (Galaxy version 0.9.1) with reverse stranded mode.
Differentially expressed genes from count files were determined using DESeq2(Galaxy Version 2.11.40.7+galaxy1).
Assembly: Candida albicans Build 21
Supplementary files format and content: TABULAR text file includes counts (after htseq-count) for each sample
Supplementary files format and content: Tab-delimited text file with all genes from DESeq2

organism: Candida albicans

source_name: colonies grown on agar

growth_protocol: Yeast extract peptone (YP) containing maltose (2%) agar incubated at 30°C for 48 hours

extract_protocol:
RiboPure™ RNA purification kit for yeast (Ambion, Life Technologies)
Directional mRNA library preparation (with poly A enrichment) according to standard operating procedures of Novogene Corporation Inc.

treatment_protocol: Colonies scraped off the plates using RNAlater (Invitrogen)

value: colonies grown on agar

value: a/alpha leu2-delta/LEU2 rfx1-delta/ rfx1-delta

value: YP maltose agar at 30°C for 48h


title: WT lung rep2


title: AS-LEFs-DMSO-bio-rep-4

value: primary embryonic fibroblasts


title: HctYH_OF3A_1-1-I3-B14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: JCP_1260, rfx1 deletion, YP maltose plate, biological replicate 1


title: AS-LEFs-DMSO-bio-rep-2

value: stage 5-6


title: 13_Postnatal day 15 Pde1c-Cre-/- Injected biological replicate 4


title: JCP_978, WT, YP maltose plate, biological replicate 3

value: a/alpha leu2-delta/LEU2


title: HctYH_OF3A_1-1-I3-B13

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-1-I3-A1


title: HctYH_OF3A_1-1-I3-A2


title: 11_Postnatal day 15 Pde1c-Cre-/- Injected biological replicate 2


title: JCP_978, WT, YP maltose plate, biological replicate 1


title: AS-LEFs-DMSO-bio-rep-1


title: JCP_978, WT, YP maltose plate, biological replicate 2


title: HctYH_OF3A_1-1-I3-B1


title: HctYH_OF3A_1-1-I3-A14


title: 14_Postnatal day 15 Pde1c-Cre+/- Injected biological replicate 1


title: HctYH_OF3A_1-1-I3-A13


title: 9_Postnatal day 15 Pde1c-Cre-/- Injected biological replicate 1


title: K_H (∆Ms_4236 hypoxia)

city: Chongqing

first: Hongxiang

last: Xu

address: Tiansheng Road

institute: Southwest University

data_processing:
Base Calling:CASAVA
Data filtering: Cutadapt
Read alignment:Hisat2
Abundance measurement:Subread
DEG analysis: DESeq2
Assembly: Mycolicibacterium smegmatis MC2155(ASM1500v1)
Supplementary files format and content: counts file

organism: Mycolicibacterium smegmatis MC2 155

source_name: bacterial cell

extract_protocol:
The M. smegmatis strains grew in 7H9 media under normoxia and hypoxia for three days. Then, the bacteria were harvested and washed with 1x PBS, and pellets were preserved through liquid nitrogen and kept at -80°C. Then, the samples were quality-checked, and sequence alignment analysis was performed to evaluate the ribosomal RNA contamination rate and to confirm transcriptome quality through sequence saturation and gene coverage. Then, after the quality check, differential expression analysis was performed. Qualitatively, transcriptome sequencing was performed using an Illumina HiSeq X platform. NR, Swiss-Prot, KEGG, Pfam, COG, and GO software performed the differential expression analysis on the RNA sequencing reads. Genes were significantly differentially regulated with log2 (fold change) | > 1 and P< 0.005.
After the samples pass the test, use magnetic beads with Oligo (dT) to enrich Eukaryote mRNA. Subsequently, a fragmentation buffer was added to randomly interrupt the mRNA. Using mRNA as a template, the first strand of cDNA was synthesized using six base random primers. Then, buffer, dNTPs, and DNA polymerase I were added to synthesize the second strand of cDNA. The double stranded cDNA was purified using AMPure XP beads. The purified double stranded cDNA was subjected to end repair, A-tail addition, and sequencing connections. Then, AMPure XP beads were used for fragment size selection, and PCR enrichment was performed to obtain the final cDNA library.

value: bacterial cell

value: hypoxia


title: K (∆Ms_4236 normoxia)

value: normoxia


title: 12_Postnatal day 15 Pde1c-Cre-/- Injected biological replicate 3


title: JCP_1260, rfx1 deletion, YP maltose plate, biological replicate 2


title: mouse reared in enriched environment D73

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCm38.p6
Supplementary files format and content: xls file include read count values for each Sample

source_name: brain

extract_protocol:
RNA was harvested by using Rneasy miniplus kit. Total 1.6μg of RNA  was used for the construction of sequencing libraries
total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular.

value: brain

tag: group

value: enriched environment

value: Standard rearing


title: mouse reared in enriched environment D77


title: 8_Postnatal day 30 Pde1c-Cre+/- Injected biological replicate 4

value: Brain

value: Cre-DTA AAV injection


title: H (WT hypoxia)

value: WT


title: HK2 cells-M-KD2, Input

city: Hefei

first: Xiao ming

last: Ment

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

description:
M1_Input,M3_Input--M-KD1_Input,M-KD2_Input.different.transcript.txt
M1_Input,M3_Input--M-KD1_Input,M-KD2_Input.all.transcript.txt

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222)/exomePeak was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by  CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)/MetDiff/exomePeak.
Assembly: hg19
Supplementary files format and content: peak text files
Supplementary files format and content: tab-delimited text files include different transcript for each group, bigwig files

source_name: TNF-α-stimulated HK2 cells with silencing of METTL3

growth_protocol: HK2 were cultured in 5% FBS-containing HyClone™DMEM/F12 medium in 95% air and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol. The quantity and integrity of RNA yield was assessed by using the K5500(Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. m6A antibody immunoprecipitation RNA was quality control with Qubit(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA).
RNA were fragmented to approximately 200bp. Then, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®(Life Technologies, USA) and then sequenced on Illumina （Illumina,USA）platformat with pair-end 150bp at Ribobio Co. Ltd (Ribobio, China).

treatment_protocol: HK2 cells were treated with TNF-α (10 ng/ml) for 24 h after knockdown of METTL3 by siRNA.

value: Human kidney tubular epithelial cell line

value: METTL3 knockdown

value: TNF-α

tag: rip antibody


title: mouse reared in enriched environment D68


title: WT (normoxia )


title: 7_Postnatal day 30 Pde1c-Cre+/- Injected biological replicate 3

value: Hippocampus


title: HK2 cells-M-KD1, MeRIP


title: mouse reared in standard environment control D53

value: standard environment control


title: 6_Postnatal day 30 Pde1c-Cre+/- Injected biological replicate 2


title: HK2 cells-M-KD1, Input


title: 5_Postnatal day 30 Pde1c-Cre+/- Injected biological replicate 1


title: mouse reared in standard environment control C78


title: mouse reared in standard environment control D47


title: HK2 cells-M3, MeRIP

source_name: TNF-α-stimulated HK2 cells

value: control


title: tsrRNAi_2

city: New York

first: Mary

last: Baylies

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: PE50 run

data_processing:
FASTQ files were mapped to Drosophila genome using STAR aligner (STAR-STAR_2.5.0a)
PICARD tools was used for post processing and conversion to BAM format.
Count matrix was generated using HTSeq (HTSeq-0.5.3)
Assembly: dm6
Supplementary files format and content: comma-separated .csv table including normalized counts for each sample

organism: Drosophila melanogaster

source_name: Adult body wall musculature

growth_protocol: Larvae grown to late third instar stage

extract_protocol:
Trizol extraction
RNA libraries were prepared using SMARTerAmpSeq

treatment_protocol: Tissue-specific knockdown under Mhc promotor

value: Adult body wall musculature

value: Muscle enriched

value: Mhc-Gal4>UAS-twinstarRNAi (biol rep2)

value: tsr knockdown


title: HK2 cells-M-KD2, MeRIP


title: 4_Postnatal day 30 Pde1c-Cre-/- Injected biological replicate 4


title: tsrRNAi_1

description: PE50 run

value: Mhc-Gal4>UAS-twinstarRNAi (biol rep1)


title: 3_Postnatal day 30 Pde1c-Cre-/- Injected biological replicate 3


title: mouse exposed to stress C76

value: brain

value: stress


title: HK2 cells-M1, MeRIP


title: mCherryRNAi_2

description: PE50 run

value: Mhc-Gal4>UAS-mCherryRNAi (biol rep2)

value: control knockdown


title: 2_Postnatal day 30 Pde1c-Cre-/- Injected biological replicate 2

value: Brain

value: Cre-DTA AAV injection


title: HK2 cells-M3, Input

value: Human kidney tubular epithelial cell line


title: mouse exposed to stress C77

value: Standard rearing


title: HK2 cells-M1, Input

value: TNF-α


title: mouse exposed to stress C52


title: mCherryRNAi_1

description: PE50 run

value: Mhc-Gal4>UAS-mCherryRNAi (biol rep1)


title: 1_Postnatal day 30 Pde1c-Cre-/- Injected biological replicate 1

value: Hippocampus


title: tsrRNAi_3

description: PE50 run

value: Mhc-Gal4>UAS-twinstarRNAi (biol rep3)


title: mCherryRNAi_3

description: PE50 run

value: Adult body wall musculature

value: Mhc-Gal4>UAS-mCherryRNAi (biol rep3)


title: genomic DNA from Whole Blood for 206644410118_R08C01 sample

status: Public on Dec 14 2023

type: genomic

city: Nizhny Novgorod

first: Alena

last: Kalyakulina

address: Gagarin avenue, 23

country: Russia

institute: Lobachevsky State University

description: 206644410118_R08C01 is sample from Central

hyb_protocol: DNA was quantified using the DNA Quantitation Kit Qubit dsDNA BR Assay (Thermo Fisher Scientific) and 250 ng was bisulfite-treated using the EpiMark Bisulfite Conversion Kit (NEB) with case and control samples randomly distributed across arrays.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Minfi R package standard protocol. Average beta values were obtained using preprocessRaw and getBeta functions.
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: sample type

value: genomic

value: F

tag: region

value: Central


title: genomic DNA from Whole Blood for 206644410075_R05C01 sample

description: 206644410075_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 206644410179_R03C01 sample

description: 206644410179_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240111_R08C01 sample

description: 206103240111_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240165_R04C01 sample

description: 206103240165_R04C01 is sample from Central

value: M


title: genomic DNA from Whole Blood for 206103240111_R01C01 sample

description: 206103240111_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240107_R08C01 sample

description: 206103240107_R08C01 is sample from Yakutia

value: Yakutia


title: genomic DNA from Whole Blood for 206103240107_R03C01 sample

description: 206103240107_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240107_R04C01 sample

description: 206103240107_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240107_R07C01 sample

description: 206103240107_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280135_R02C01 sample

description: 206112280135_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240107_R06C01 sample

description: 206103240107_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240107_R05C01 sample

description: 206103240107_R05C01 is sample from Yakutia


title: adult population at day 6 of adulthood, biological rep2

type: RNA

first: Niki

last: Chondrogianni

state: Attiki

address: Leof. Vasileos Konstantinou 48

department: ICB - Institute of Chemical Biology

country: Greece

institute: National Hellenic Research Foundation

description: Gene expression data from population of C. elegans at day 6 of adulthood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  C. elegans GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were backgroung corrected, quantile-normalized, log2 transfrormed with oligo::rma() function using R in R-studio environment.

label: biotin

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans Day 6 wt adults

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Standard procedures for strain maintenance and culture. C. elegans strain N2 provided by the CGC. Cultures were maintained at 20⁰C in fresh nematode growth medium (NGM) plates seeded with the OP50 strain of Escherichia coli.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: M9 buffer was applied, the nematodes were all grown following the standard procedure for wt strain and aged without any further interventions.

value: synchronized population

value: wild type, N2 Bristol

value: Day 6 of adulthood


title: genomic DNA from Whole Blood for 205809370103_R06C01 sample

description: 205809370103_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240107_R02C01 sample

description: 206103240107_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370103_R07C01 sample

description: 205809370103_R07C01 is sample from Yakutia


title: adult population at day 1 of adulthood, biological rep2

description: Gene expression data from population of C. elegans at day 1 of adulthood

source_name: Caenorhabditis elegans Day 1 wt adults

value: Day 1 of adulthood


title: adult population at day 12 of adulthood, biological rep1

description: Gene expression data from population of C. elegans at day 12 of adulthood

source_name: Caenorhabditis elegans Day 12 wt adults

value: Day 12 of adulthood


title: adult population at day 1 of adulthood, biological rep3


title: adult population at day 6 of adulthood, biological rep1


title: adult population at day 1 of adulthood, biological rep1


title: adult population at day 6 of adulthood, biological rep3


title: genomic DNA from Whole Blood for 205809370103_R08C01 sample

description: 205809370103_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240107_R01C01 sample

description: 206103240107_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370103_R05C01 sample

description: 205809370103_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240102_R08C01 sample

description: 206103240102_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206103240102_R05C01 sample

description: 206103240102_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240102_R03C01 sample

description: 206103240102_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240102_R01C01 sample

description: 206103240102_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370103_R04C01 sample

description: 205809370103_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370094_R07C01 sample

description: 205809370094_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240102_R07C01 sample

description: 206103240102_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370103_R03C01 sample

description: 205809370103_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370103_R02C01 sample

description: 205809370103_R02C01 is sample from Yakutia


title: adult population at day 12 of adulthood, biological rep2


title: genomic DNA from Whole Blood for 206103240102_R06C01 sample

description: 206103240102_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240102_R02C01 sample

description: 206103240102_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 206103240102_R04C01 sample

description: 206103240102_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R06C01 sample

description: 205809370094_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370103_R01C01 sample

description: 205809370103_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370094_R08C01 sample

description: 205809370094_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R04C01 sample

description: 205809370094_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370088_R07C01 sample

description: 205809370088_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R03C01 sample

description: 205809370094_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370088_R05C01 sample

description: 205809370088_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R05C01 sample

description: 205809370094_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R01C01 sample

description: 205809370094_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370094_R02C01 sample

description: 205809370094_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370088_R06C01 sample

description: 205809370088_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370088_R02C01 sample

description: 205809370088_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370088_R01C01 sample

description: 205809370088_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370088_R08C01 sample

description: 205809370088_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370081_R08C01 sample

description: 205809370081_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370088_R04C01 sample

description: 205809370088_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370088_R03C01 sample

description: 205809370088_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R06C01 sample

description: 205809370081_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R07C01 sample

description: 205809370081_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R07C01 sample

description: 205809370080_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R03C01 sample

description: 205809370081_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R01C01 sample

description: 205809370081_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R02C01 sample

description: 205809370081_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R08C01 sample

description: 205809370080_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R03C01 sample

description: 205809370080_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R04C01 sample

description: 205809370080_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R06C01 sample

description: 205809370080_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R05C01 sample

description: 205809370080_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R02C01 sample

description: 205809370080_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370080_R01C01 sample

description: 205809370080_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R07C01 sample

description: 205809370073_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R06C01 sample

description: 205809370073_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R04C01 sample

description: 205809370073_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R01C01 sample

description: 205809370073_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R07C01 sample

description: 205809370064_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R08C01 sample

description: 205809370064_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R02C01 sample

description: 205809370064_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370073_R02C01 sample

description: 205809370073_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R05C01 sample

description: 205809370073_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R05C01 sample

description: 205809370081_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R06C01 sample

description: 205809370064_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370081_R04C01 sample

description: 205809370081_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370026_R06C01 sample

description: 205809370026_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370064_R05C01 sample

description: 205809370064_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R04C01 sample

description: 205809370064_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370064_R03C01 sample

description: 205809370064_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370026_R08C01 sample

description: 205809370026_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370026_R07C01 sample

description: 205809370026_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370073_R08C01 sample

description: 205809370073_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370026_R03C01 sample

description: 205809370026_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 205809370026_R02C01 sample

description: 205809370026_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370026_R01C01 sample

description: 205809370026_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R08C01 sample

description: 206112280009_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370073_R03C01 sample

description: 205809370073_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R06C01 sample

description: 206112280009_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R05C01 sample

description: 206112280009_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R03C01 sample

description: 206112280009_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R04C01 sample

description: 206112280009_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370064_R01C01 sample

description: 205809370064_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 206112280009_R01C01 sample

description: 206112280009_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280005_R08C01 sample

description: 206112280005_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370026_R05C01 sample

description: 205809370026_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 206112280005_R07C01 sample

description: 206112280005_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280005_R02C01 sample

description: 206112280005_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205809370026_R04C01 sample

description: 205809370026_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R07C01 sample

description: 205724780168_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 206112280005_R06C01 sample

description: 206112280005_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780168_R04C01 sample

description: 205724780168_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 206112280005_R03C01 sample

description: 206112280005_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280009_R02C01 sample

description: 206112280009_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780168_R08C01 sample

description: 205724780168_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R03C01 sample

description: 205724780168_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R01C01 sample

description: 205724780168_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R05C01 sample

description: 205724780168_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R02C01 sample

description: 205724780168_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780167_R07C01 sample

description: 205724780167_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780167_R06C01 sample

description: 205724780167_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 206112280009_R07C01 sample

description: 206112280009_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280005_R01C01 sample

description: 206112280005_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780167_R05C01 sample

description: 205724780167_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780167_R08C01 sample

description: 205724780167_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780168_R06C01 sample

description: 205724780168_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 205724780161_R08C01 sample

description: 205724780161_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R07C01 sample

description: 205724780161_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R06C01 sample

description: 205724780161_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R04C01 sample

description: 205724780161_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R05C01 sample

description: 205724780161_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280005_R04C01 sample

description: 206112280005_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R03C01 sample

description: 205724780161_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R02C01 sample

description: 205724780161_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 206112280005_R05C01 sample

description: 206112280005_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780161_R01C01 sample

description: 205724780161_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R07C01 sample

description: 205724780160_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R08C01 sample

description: 205724780160_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R05C01 sample

description: 205724780160_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R04C01 sample

description: 205724780160_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R06C01 sample

description: 205724780160_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R02C01 sample

description: 205724780160_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R08C01 sample

description: 205724780068_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R01C01 sample

description: 205724780160_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R03C01 sample

description: 205724780068_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R07C01 sample

description: 205724780068_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R01C01 sample

description: 205724780068_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R05C01 sample

description: 205724780068_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R06C01 sample

description: 205724780068_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R07C01 sample

description: 205724790046_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R06C01 sample

description: 205724790046_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R08C01 sample

description: 205724790046_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R04C01 sample

description: 205724790046_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R05C01 sample

description: 205724790046_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R02C01 sample

description: 205724790046_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R01C01 sample

description: 205724790046_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790046_R03C01 sample

description: 205724790046_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R07C01 sample

description: 205724790027_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R08C01 sample

description: 205724790027_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R03C01 sample

description: 205724790027_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R06C01 sample

description: 205724790027_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R07C01 sample

description: 205724790012_R07C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R08C01 sample

description: 205724790012_R08C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R04C01 sample

description: 205724790027_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R01C01 sample

description: 205724790027_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R03C01 sample

description: 205724790012_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780068_R02C01 sample

description: 205724780068_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R02C01 sample

description: 205724790012_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R04C01 sample

description: 205724790012_R04C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790027_R02C01 sample

description: 205724790027_R02C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R06C01 sample

description: 205724790012_R06C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724780160_R03C01 sample

description: 205724780160_R03C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 205724790012_R05C01 sample

description: 205724790012_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 204373100096_R06C01 sample

description: 204373100096_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 205724790012_R01C01 sample

description: 205724790012_R01C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 204367460065_R08C01 sample

description: 204367460065_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490072_R08C01 sample

description: 204367490072_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100096_R08C01 sample

description: 204373100096_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100094_R06C01 sample

description: 204373100094_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460065_R06C01 sample

description: 204367460065_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490072_R06C01 sample

description: 204367490072_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490072_R04C01 sample

description: 204367490072_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 205724790027_R05C01 sample

description: 205724790027_R05C01 is sample from Yakutia


title: genomic DNA from Whole Blood for 204373100094_R02C01 sample

description: 204373100094_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490010_R04C01 sample

description: 204367490010_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460032_R02C01 sample

description: 204367460032_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100099_R07C01 sample

description: 204373100099_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490010_R08C01 sample

description: 204367490010_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490018_R06C01 sample

description: 204367490018_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490058_R06C01 sample

description: 204367490058_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460024_R03C01 sample

description: 204367460024_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460050_R06C01 sample

description: 204367460050_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460050_R04C01 sample

description: 204367460050_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460056_R06C01 sample

description: 204367460056_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460096_R08C01 sample

description: 204367460096_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460056_R04C01 sample

description: 204367460056_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460050_R08C01 sample

description: 204367460050_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460056_R02C01 sample

description: 204367460056_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204365940156_R03C01 sample

description: 204365940156_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490058_R02C01 sample

description: 204367490058_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460096_R06C01 sample

description: 204367460096_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490072_R02C01 sample

description: 204367490072_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204365940156_R02C01 sample

description: 204365940156_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460096_R03C01 sample

description: 204367460096_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460050_R02C01 sample

description: 204367460050_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100094_R04C01 sample

description: 204373100094_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460024_R01C01 sample

description: 204367460024_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204365940156_R01C01 sample

description: 204365940156_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490058_R07C01 sample

description: 204367490058_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490058_R04C01 sample

description: 204367490058_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590123_R07C01 sample

description: 204390590123_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950080_R08C01 sample

description: 204365950080_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590123_R05C01 sample

description: 204390590123_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590123_R03C01 sample

description: 204390590123_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950080_R06C01 sample

description: 204365950080_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950080_R04C01 sample

description: 204365950080_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204365940156_R04C01 sample

description: 204365940156_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460056_R08C01 sample

description: 204367460056_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590107_R03C01 sample

description: 204390590107_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950013_R07C01 sample

description: 204365950013_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950013_R05C01 sample

description: 204365950013_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590108_R07C01 sample

description: 204390590108_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590123_R01C01 sample

description: 204390590123_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950080_R01C01 sample

description: 204365950080_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590086_R06C01 sample

description: 204390590086_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590108_R01C01 sample

description: 204390590108_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590108_R03C01 sample

description: 204390590108_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590107_R05C01 sample

description: 204390590107_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460032_R08C01 sample

description: 204367460032_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590086_R07C01 sample

description: 204390590086_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590086_R02C01 sample

description: 204390590086_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460032_R06C01 sample

description: 204367460032_R06C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590086_R04C01 sample

description: 204390590086_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590107_R01C01 sample

description: 204390590107_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460044_R05C01 sample

description: 204367460044_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950045_R03C01 sample

description: 204365950045_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590108_R05C01 sample

description: 204390590108_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460057_R07C01 sample

description: 204367460057_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460057_R04C01 sample

description: 204367460057_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460057_R02C01 sample

description: 204367460057_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950045_R05C01 sample

description: 204365950045_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950045_R01C01 sample

description: 204365950045_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460044_R01C01 sample

description: 204367460044_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100099_R05C01 sample

description: 204373100099_R05C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460032_R03C01 sample

description: 204367460032_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204390590107_R07C01 sample

description: 204390590107_R07C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490010_R02C01 sample

description: 204367490010_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490018_R02C01 sample

description: 204367490018_R02C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460032_R04C01 sample

description: 204367460032_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204365950013_R01C01 sample

description: 204365950013_R01C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490058_R08C01 sample

description: 204367490058_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367460044_R03C01 sample

description: 204367460044_R03C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490018_R04C01 sample

description: 204367490018_R04C01 is sample from Central


title: genomic DNA from Whole Blood for 204373100094_R08C01 sample

description: 204373100094_R08C01 is sample from Central


title: genomic DNA from Whole Blood for 204367490018_R08C01 sample

description: 204367490018_R08C01 is sample from Central


title: Pt#15_LDC_end_stimulation_alpha

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Joining R1 and R2 reads from the paired end sequencing
Demultiplexing of the sequencing results according to the barcodes used for samples multiplexing
Analysis of the TCR clonotypes was carried out using the MiXCR software (version 3.0.5)
Library strategy: TCR-seq

source_name: Bone Marrow Patient:Pt15

extract_protocol:
Complementarity determining region (CDR) 3 sequences of TCR alpha and beta chains were amplified by using a modified RACE approach
Total RNA extracted from dextramer-sorted T cell cultures and from T lymphocytess serially stimulated with Leukemic Dendritic cells was reverse transcribed and amplified using primers specific for α/β chain constant regions and for the template switching sequence added during cDNA synthesis. A double barcoded strategy was used: each individual sample was unequivocally tagged with a barcoded fusion primer specific for the constant TCR genes in addition to the barcoded template switching primer used during cDNA synthesis. PCR amplicons were purified using the AmPure beads (Beckman Coulter) and sequenced with the Illumina MiSeq_600v3.

tag: time point

value: LDC serial stimulation


title: Pt#12_MAGE-A2#1_and_2_betas

source_name: Patient PBMCs:Pt12

value: Dextramer plus aCD3/aCD28 stimulation


title: Pt#15_LDC_end_stimulation_beta


title: Pt#10_hTERT#3_and_4_alphas

source_name: Patient PBMCs:Pt10


title: Pt#12_MAGE-A2#1_and_2_alphas


title: Pt#10_hTERT#2_beta


title: Pt#10_hTERT#2_alpha


title: Pt#12_Surv_beta


title: Pt#10_hTERT#1_beta


title: genomic DNA from Whole Blood for 204365950013_R03C01 sample

description: 204365950013_R03C01 is sample from Central


title: PT#3_WT1#1_and_2_and_3_betas

source_name: Patient PBMCs:Pt3


title: genomic DNA from Whole Blood for 204367490010_R06C01 sample

description: 204367490010_R06C01 is sample from Central


title: PT#3_WT1#1_and_2_and_3_alphas


title: PT#11_WT1#1_and_2_betas

source_name: Patient PBMCs:Pt11


title: Pt#10_hTERT#3_and_4_betas


title: Pt#10_hTERT#1_alpha


title: Pt#13_LDC_end_stimulation_beta

source_name: Bone marrow Patient PBMCs:Pt13


title: Pt#2_WT1#2_and_3_alphas

source_name: Patient PBMCs:Pt2


title: Pt#12_Surv_alpha


title: Pt#2_WT1#1_alpha


title: Pt#2_WT1#2_and_3_betas


title: Pt#13_LDC_end_stimulation_alpha


title: Pt#2_WT1#1_beta


title: Pt#5_WT1#1_and2_betas

source_name: Patient PBMCs:Pt5


title: Pt#5_WT1#1_and2_alphas


title: PT#11_WT1#1_and_2_alphas


title: Pt#3_WT1#4_beta


title: Pt#14_LDC_end_stimulation_alpha

source_name: Bone Marrow Patient:Pt14


title: Pt#3_WT1#4_alpha


title: Pt#14_LDC_end_stimulation_beta


title: mc2_MLLEx9

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description:
SAGCFN_23_00895
i5 (ACGGAACA) i7 (ATCACACG)

data_processing:
*library strategy: amplicon-seq
High-throughput sequencing was performed using Illumina MiSeq
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorith (versions 2.7.0)
Aligned with default parameters
Using featureCounts (v.1.6.4), reads were assigned to each exonic region and derived the raw counts.
Assembly: hg38

growth_protocol: Human HEK293 cells were grown in 10% FBS containuing DMEM in 12-well trays. All human cell lines in this study were incubated at 37 oC with 5% CO2.

extract_protocol:
RNA was extracted 24hrs post-transfection using TriZOL and Direct-zol RNA extration columns (Zymo Research). Two micrograms of total RNA was digested with 5 units of RNase R (Biosearch Technologies, RNR07250) for one hour at 37℃ to remove linear RNA. CircRNA was purified using RNeasy MinElute columns (Qiagen) as recommended by the manufacturer, and eluted in 14 µL of water. Reverse transcription was performed with 12 µL of circRNA as described above, using circRNA-specific primers appended with 12-nucleotide unique molecular identifier (UMI) and Illumina reverse adapter sequences. A single round of PCR was then performed using Q5 high fidelity DNA polymerase (NEB) with exon-specific primers appended with Illumina forward adapter sequence. Exonuclease digestion was then performed with thermolabile exonuclease I (NEB, M05685) to remove excess primers (37℃ for 4 minutes then 80℃ for 1 minute). Twenty-five cycles of PCR were then performed using Q5 high fidelity DNA polymerase (NEB) and Illumina forward and reverse adapter primers (98℃ 10 s, 60℃ 20 s, 72℃ 10 s). The reactions were then subjected to agarose gel electrophoresis (1% agarose, 1⨉ TAE, 20 V/cm, 30 mins). Amplicons (~250 bp) were excised from the gel, recovered using Qiaquick (Qiagen), and eluted in 30 µL of water (7-14 ng/µL final concentration).
Libraries and sequencing were prepared by the South Australian Genomics Centre (SAGC) using the illumina "16S Metagenomic Sequencing Library Preparation Protocol" with the following changes; 10 µl of Amplicon product was purified using a 1:0.8 ratio of XP beads (Beckman Coulter), with beads resuspended in a final volume of 10 µl of nuclease-free water. For indexing, 10 µl of cleaned amplicon product was used with 5 µl of  IDT UDI indexes (Integrated DNA Technologies) per sample. Final products were quantified by Nanodrop nanospectrophometer (ThermoFisher Scientific) and separated by LabChip (Perkin Elmer) using the HT DNA NGS 3K Reagent Kit (Revvity) to confirm library size and quantities. Libraries were pooled at equimolar concentrations and run on the MiSeq (illumina) Paired-end 150 using 5 pM with 20% PhiX.

treatment_protocol: HEK293 cells in 12-well plates were transfected with 1.6 µg of CircRNA Mini (mc) or mc2 plasmid.


title: mc2_EGFREx19_20

description:
SAGCFN_23_00894
i5 (CGCATGAT) i7 (CACCTGTT)


title: mc_BCREx9_14

description:
SAGCFN_23_00891
i5 (GAGACGAT) i7 (AGAACGAG)


title: mc2_BCREx9_14

description:
SAGCFN_23_00892
i5 (CTTGTCGA) i7 (TGCTTCCA)


title: somatotrope cell line GH3, input, rep1

city: Carbondale

first: Buffy

middle: Sue

last: Ellsworth

state: IL

address: 1135 Lincoln Dr

department: Department of Physiology

institute: Southern Illinois University

description: input for GH3 cells

data_processing:
ChIPseq reads were aligned to the rn6 genome using the BWA algorithm with default settings. Only reads that pass Illumina's purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the analysis. Duplicate reads were removed.
peak calling was performed using MACS 2.1.0

organism: Rattus norvegicus

source_name: somatotrope cell line

growth_protocol: GH3 cells were maintained in DMEM:F12 media supplemented with 10% donor equine serum and 2.5% fetal bovine serum. The media was changed every 48 hours and cells were passaged every fourth day at approximately 80% confluency.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes, quenched with glycine, and e pellet was then washed twice in 1X PBS and 0.5% Igepal, then once more but with added protease inhibitors. The cells were pelleted one final time, supernatant removed, and pellet flash frozen and sent to Active Motif.
50 micrograms of chromatin was prepared using the ChIP-IT High Sensitivity kit

value: somatotrope cell line

tag: chip antibody


title: mc2_MLLT2Ex3_4

description:
SAGCFN_23_00896
i5 (CGGCTAAT) i7 (CCGTAAGA)


title: somatotrope cell line GH3, FOXO1 Ab, rep1

description: ChIPseq for FOXO1 in GH3 cells


title: Standard Treatment (Control)

city: Brisbane

first: Onkar

middle: Rajesh

last: Mulay

state: QLD

address: Carmody Road

institute: University of Queensland

description: PSC-CM

data_processing:
The sequencing data were further processed to generate FASTQ files and the raw count matrix using the SpaceRanger pipeline. Raw NovaSeq BCL output file was converted to fastq file using SpaceRanger mkfastq V1.3.0 and bcl2fastq2-V2.17.1.
A hybrid reference genome was made from combining Sscrofa11.1 (reference annotation Sscrofa11.1.105.gtf) with GRCh38-3.0.0 (genome build GRCh38.p12) using SpaceRanger mkref.
The trimmed fastq reads were mapped to the hybrid genome using SpaceRanger count, which is based on STAR splicing-aware alignment.
Assembly: hg38 and Sscrofa11.1
Supplementary files format and content: .h5 file, .csv file, .jpg file and .png file
Library strategy: Spatial Transcriptomics (10X Visium)

organism:
Homo sapiens
Sus scrofa

source_name: heart

extract_protocol:
Formalin-fixed paraffin-embedded tissue from Level 1 blocks was used for spatial transcriptomics analysis of engrafted PSC-CMs. Using a tissue microarray punch, we collected 3mm diameter samples of tissue from regions confirmed to contain PSC-CM grafts. The samples were melted down and re-embedded into four 6mm x 6mm paraffin blocks, each containing 3 samples.
FFPE blocks were sectioned and placed onto a Visium slide then dried, dewaxed, deparaffinized, and stained as in the tissue optimisation procedure. After permeabilization, cDNA was synthesised using standard unlabelled nucleotides, followed by second strand synthesis. The libraries were sequenced in a NovaSeq SP100 V1.5 kit.

value: heart

tag: cell type

value: hESCs derived day 15 cardiomyocytes

value: contains gCaMP6f fluorescent calcium reporter, female landrace swine

tag: treatment

value: standard treatment


title: RA Treatment

description: RA-PSC-CM

value: retinoic acid treatment


title: SW480 cells, siKRAS, 72h

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

data_processing:
The quality of reads was evaluated using FASTQC
Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered using Trimmomatic
he cleaned reads were aligned to the human genome (hg38) using STAR
Counts and transcripts per million (TPM) for each condition were estimated from mapped reads using RSEM
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM for each sample

source_name: cell line

growth_protocol: SW480 cells were maintained in RPMI supplmeneted with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using mirVana miRNA isolation kit (Thermo Fisher Scientific)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads in Illumina platform

treatment_protocol: Prior to 3D cultures, CRC cell lines were seeded in 2D conditions in six-well plates, cultured for approximately 16 hours and then transfected using Lipofectamine RNAiMAX (Invitrogen, Thermo Fisher Scientific, USA) in reduced-serum Opti-MEM medium (Gibco, Thermo Fisher Scientific, USA) according to the manufacturer’s guidelines. Gene silencing was performed using ON-TARGETplus SMARTpool small interfering RNA specific for KRAS (siKRAS; L-005069-00-0010) from Dharmacon (USA) at a final concentration of 10 nM. A non-targeting (siControl) siRNA (D-001810-01-50; ON-TARGETplus Non-targeting siRNA #1) was used as negative control at the same concentration as the siRNA targeting KRAS. Twenty-four hours post-transfection, cells were harvested with 0.05% Trypsin-EDTA (Gibco, Thermo Fisher Scientific, USA) for 5 min at 37ºC, resuspended in completed medium, and seeded in 3D CoSeedis

value: cell line

value: colorectal cancer

value: siKRAS


title: SW480 cells, siKRAS, 48h


title: SW480 cells, siControl, 48h

value: siControl


title: SW480 cells, siKRAS, 24h


title: SW480 cells, siKRAS, 12h


title: SW480 cells, siControl, 24h


title: LS174T cells, siKRAS, 72h

growth_protocol: LS174T cells were maintained in DMEM supplmeneted with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) in humidified atmosphere with 5% CO2 at 37ºC


title: LS174T cells, siKRAS, 24h


title: LS174T cells, siControl, 72h


title: LS174T cells, siControl, 48h


title: mc2_EGFREx2_20

description:
SAGCFN_23_00893
i5 (TTCCAAGG) i7 (CTTCGACT)


title: LS174T cells, siControl, 12h


title: LS174T cells, siControl, 24h


title: LS174T cells, siKRAS, 12h


title: SW480 cells, siControl, 72h


title: HCT116 cells, siKRAS, 12h

data_processing:
The quality of reads was evaluated using FASTQC
Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered using Trimmomatic
he cleaned reads were aligned to the human genome (hg38) using STAR
Counts and transcripts per million (TPM) for each condition were estimated from mapped reads using RSEM
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: Excel file includes TPM for each sample

growth_protocol: HCT116 cells were maintained in RPMI supplmeneted with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) in humidified atmosphere with 5% CO2 at 37ºC

tag: time


title: HCT116 cells, siControl, 48h


title: HCT116 cells, siControl, 12h


title: HCT116 cells, siKRAS, 48h


title: SW480 cells, siControl, 12h


title: HCT116 cells, siControl, 72h


title: hBMSC_siControl_day7_3

city: Guangzhou

first: Zheting

last: Liao

address: 1838 North Guangzhou Avenue

institute: Sourthern Medical University

data_processing:
The raw image data files obtained from high-throughput sequencing (Illumina HiSeq) are transformed into sequencing sequence raw data through CASAVA1.4 base calling analysis. the results are stored in FASTQ file format.
Raw reads were then cleaned using trim_galore v0.6.0, mapped to hg38.
Assembly: hg38
Supplementary files format and content: text file includes raw counts for each sample

source_name: bone marrow derived mesenchymal stem cells

extract_protocol:
RNA extraction utilized column purification kits (Absin, abs60026), with purity assessed by Nanodrop spectrophotometry (Thermo Scientific)
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Preparation Kit following manufacturer's protocols.

value: WT

value: osteogenic differentiation


title: HCT116 cells, siKRAS, 24h


title: hBMSC_siCPM_day7_3

value: bone marrow derived mesenchymal stem cells

value: CPM knockdown


title: hBMSC_siCPM_day7_2


title: hBMSC_siControl_day7_2


title: HCT116 cells, siControl, 24h


title: hBMSC_siCPM_day7_1


title: HCT116 cells, siKRAS, 72h


title: CT29 EVT Mock A 72 HPI

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

description:
21_29_EVT_72_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

data_processing:
Sequencing reads were trimmed to remove adapter sequences with Trimmomatic using default parameters.
Trimmed reads were aligned to a concatenated reference file that contained the human (hg38) and TB40e-BAC4 (NCBI EF999921.1) genomes with STAR version 2.7.2a using the default parameters.
Gene count tables were prepared with featureCounts.
Assembly: hg38 + TB40e-Bac4 [NCBI EF999921.1]
Supplementary files format and content: text file includes raw counts for each sample mapped to hg38
Supplementary files format and content: text file includes raw counts for each sample mapped to HCMV TB40e-Bac4 (NCBI EF999921.1)

growth_protocol: CT27 (RCB4936) and CT29 (RCB4937) cells were  maintained using "TS culture protocol_V2" (doi: 10.1073/pnas.1916019116)  and differentiated as previously described (doi: 10.1016/j.stem.2017.11.004).

extract_protocol:
Total RNA was extracted using a RNeasy Mini kit (Qiagen).
SMARTer Pico Mammalian V2 kit (Takara)
TruSeq Stranded mRNA (Illumina)

treatment_protocol: Cells were either mock or HCMV (TB40/Ewt-mCherry) infected at a MOI of 1.

value: Extravillous trophoblasts

value: Mock 72 HPI


title: CT27 EVT CMV A 72 HPI

description:
19_27_EVT_72_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Infected 72 HPI


title: CT27 EVT Mock A 72 HPI

description:
17_27_EVT_72_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: LS174T cells, siKRAS, 48h


title: CT29 EVT CMV A 48 HPI

description:
15_29_EVT_48_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Infected 48 HPI


title: CT29 EVT Mock B 48 HPI

description:
14_29_EVT_48_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Mock 48 HPI


title: CT29 EVT Mock A 48 HPI

description:
13_29_EVT_48_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT CMV A 72 HPI

description:
23_29_EVT_72_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: hBMSC_siControl_day7_1


title: CT29 EVT CMV B 48 HPI

description:
16_29_EVT_48_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT Mock B 72 HPI

description:
18_27_EVT_72_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT CMV B 72 HPI

description:
24_29_EVT_72_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT Mock B 72 HPI

description:
22_29_EVT_72_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT CMV B 72 HPI

description:
20_27_EVT_72_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT CMV B 48 HPI

description:
12_27_EVT_48_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT CMV A 48 HPI

description:
11_27_EVT_48_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT Mock B 48 HPI

description:
10_27_EVT_48_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT CMV A 24 HPI

description:
7_29_EVT_24_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Infected 24 HPI


title: CT27 EVT Mock B 24 HPI

description:
2_27_EVT_24_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Mock 24 HPI


title: CT27 EVT Mock A 48 HPI

description:
9_27_EVT_48_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT CMV B 24 HPI

description:
8_29_EVT_24_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT Mock B 24 HPI

description:
6_29_EVT_24_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 EVT Mock A 24 HPI

description:
5_29_EVT_24_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT Mock A 24 HPI

description:
1_27_EVT_24_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB CMV B 72 HPI

description:
24_29_STB_72_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: Syncytiotrophoblast


title: CT29 STB CMV A 72 HPI

description:
23_29_STB_72_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: genomic DNA from Whole Blood for 204367460044_R07C01 sample

description: 204367460044_R07C01 is sample from Central

source_name: Whole Blood

value: genomic

tag: age

tag: Sex

value: M

value: Central


title: CT29 STB Mock B 72 HPI

description:
22_29_STB_72_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

tag: cell line


title: CT27 EVT CMV A 24 HPI

description:
3_27_EVT_24_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

tag: genotype


title: CT29 STB Mock A 72 HPI

description:
21_29_STB_72_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB CMV B 72 HPI

description:
20_27_STB_72_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB CMV A 72 HPI

description:
19_27_STB_72_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB Mock B 72 HPI

description:
18_27_STB_72_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB Mock A 72 HPI

description:
17_27_STB_72_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB CMV B 48 HPI

description:
16_29_STB_48_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB CMV B 48 HPI

description:
12_27_STB_48_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB Mock B 48 HPI

description:
14_29_STB_48_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB Mock A 48 HPI

description:
9_27_STB_48_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB CMV A 48 HPI

description:
11_27_STB_48_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB CMV A 48 HPI

description:
15_29_STB_48_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB Mock A 48 HPI

description:
13_29_STB_48_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB Mock B 48 HPI

description:
10_27_STB_48_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB CMV B 24 HPI

description:
8_29_STB_24_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB CMV A 24 HPI

description:
7_29_STB_24_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB Mock A 24 HPI

description:
5_29_STB_24_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 EVT CMV B 24 HPI

description:
4_27_EVT_24_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB CMV A 24 HPI

description:
3_27_STB_24_C_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 STB Mock B 24 HPI

description:
6_29_STB_24_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 mCherry high B 72 HPI

description:
29_HBH_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Trophoblast Stem Cells

value: Infected 72 HPI mCherry high


title: CT27 STB CMV B 24 HPI

description:
4_27_STB_24_C_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv

value: WT


title: CT29 mCherry low B 72 HPI

description:
29_HBL_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Infected 72 HPI mCherry low


title: CT29 mCherry high A 72 HPI

description:
29_HAH_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 STB Mock B 24 HPI

description:
2_27_STB_24_M_B
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT27 STB Mock A 24 HPI

description:
1_27_STB_24_M_A
Bierle_Project_014_raw_Gencode_v38_counts.csv
Bierle_Project_014_raw_EF999921.1_counts.csv


title: CT29 mCherry low A 72 HPI

description:
29_HAL_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 Mock A 72 HPI

description:
27_MA_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry high B 72 HPI

description:
27_HBH_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry low A 72 HPI

description:
27_HAL_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry high A 72 HPI

description:
27_HAH_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry low A 48 HPI

description:
27_HAL_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Infected 48 HPI mCherry low


title: CT27 mCherry high B 48 HPI

description:
27_HBH_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Infected 48 HPI mCherry high


title: CT29 Mock A 72 HPI

description:
29_MA_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry low B 48 HPI

description:
29_HBL_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry high B 48 HPI

description:
29_HBH_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry low B 48 HPI

description:
27_HBL_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry high A 48 HPI

description:
27_HAH_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry low B 72 HPI

description:
27_HBL_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry low A 24 HPI

description:
29_HAL_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Infected 24 HPI mCherry low


title: CT29 mCherry high A 48 HPI

description:
29_HAH_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry high A 24 HPI

description:
29_HAH_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Infected 24 HPI mCherry high


title: CT29 Mock B 48 HPI

description:
29_MB_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 Mock A 48 HPI

description:
29_MA_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry high B 24 HPI

description:
27_HBH_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry high B 24 HPI

description:
29_HBH_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 mCherry low A 48 HPI

description:
29_HAL_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 Mock B 48 HPI

description:
27_MB_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 Mock B 72 HPI

description:
27_MB_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Mock 72 HPI


title: CT29 mCherry low B 24 HPI

description:
29_HBL_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 Mock B 24 HPI

description:
29_MB_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 Mock B 72 HPI

description:
29_MB_72
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 Mock A 24 HPI

description:
27_MA_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 Mock B 24 HPI

description:
27_MB_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT27 mCherry low A 24 HPI

description:
27_HAL_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: D3 mock

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
alignment with Rsubread
counting with featureCounts
Assembly: GRCh38.103
Supplementary files format and content: csv file containing raw read counts

source_name: Human monocyte-derived Macrophages

growth_protocol: Human monocyte-derived Mφ were differentiated from peripheral blood mononuclear cells (PBMCs) isolated from Leucocyte Reduction System Chambers (LRSCs) from healthy blood donors via density gradient centrifugation using Lymphopreb (Nycomed Pharma). After isolation of PBMCs, 80 x 106 PBMCs were seeded in 10 cm² dishes (Cat. No. 664-160, Greiner Bio-one) to allow monocyte adherence in adherence medium [RPMI1640 (Lonza), 1% human AB serum (Sigma Aldrich), Penicillin-Streptomycin-Glutamine solution (Sigma Aldrich) and 10 mM HEPES (Lonza)], for 75 minutes. After adherence of monocytes, the non-adherent fraction (NAF) was collected and frozen for mixed lymphocyte reaction (MLR) assays (described below). To discard all non-adherent cells, dishes were washed three times with 10 ml of pre-warmed RPMI1640 without supplements. Subsequently, monocytes were differentiated into human Mφ in differentiation medium [RPMI1640 (Lonza), 10% human AB serum (Sigma Aldrich), Penicillin-Streptomycin-Glutamine solution (Sigma Aldrich), 10 mM HEPES (Lonza)] and recombinant M-CSF (20 ng/ml, PeproTech). Fresh medium and recombinant M-CSF (20 ng/ml, PeproTech) was added on day 3. To analyze the effect of sCD83 on human monocyte derived differentiation, sCD83 (25 µg/ml) or the corresponding amount of PBS was added as a control on day 0 as well as on day 3. On day 6, human monocyte-derived Mφ were harvested by using a cell scraper (Sarstedt, Cat. No.: 83.1830) and used for subsequent phenotypical and functional analyses.

extract_protocol:
Total RNA was isolated using the RNAeasy Mini Kit. 1 µg of RNA was sent for RNA sequencing (Novogene)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Monocytes were differentiated into human Mφ in differentiation medium [RPMI1640 (Lonza), 10% human AB serum (Sigma Aldrich), Penicillin-Streptomycin-Glutamine solution (Sigma Aldrich), 10 mM HEPES (Lonza)] and recombinant M-CSF (20 ng/ml, PeproTech). Fresh medium and recombinant M-CSF (20 ng/ml, PeproTech) was added on day 3. To analyze the effect of sCD83 on human monocyte derived differentiation, sCD83 (25 µg/ml) or the corresponding amount of PBS was added as a control on day 0 as well as on day 3. On day 6, human monocyte-derived Mφ were harvested by using a cell scraper (Sarstedt, Cat. No.: 83.1830) and RNA was extracted.

value: Human monocyte-derived Macrophages

value: PBS


title: D2 sCD83


title: CT27 mCherry low B 24 HPI

description:
27_HBL_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: CT29 Mock A 24 HPI

description:
29_MA_24
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv


title: D3 sCD83


title: D2 mock


title: TIGITnegative replicate3

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

data_processing:
Data quality control (adapter trimming, minimum Phred score 30, minimum read length 50 bp) was performed using fastp 27 (version 0.19.5).
Quality trimmed reads were mapped to human reference genome (GRCh38) using the STAR aligner 28 (version 2.7.9a).
Reads aligned to each gene feature were counted using the featureCounts 29 program from Subread package (version 1.6.1).
Differential expression (DE) analysis was performed using the edgeR method 30 (version 3.32.1).
Assembly: GRCh38
Supplementary files format and content: Excel file containing raw counts for each sample

source_name: human NK cells from peripheral blood

extract_protocol:
mirVana miRNA Isolation Kit
Samples were analyzed by Agilent Bioanalyzer, with DV200 > 80 and RIN > 8.4 for all samples. Libraries were prepared by GeneWiz. Sample libraries contained at least 30 million paired-end reads with length of 250 bp.

value: human NK cells from peripheral blood


title: CT27 Mock A 48 HPI

description:
27_MA_48
Bierle_Project_013_raw_Gencode_v38_counts.csv
Bierle_Project_013_raw_EF999921.1_counts.csv

value: Mock 48 HPI


title: TIGITnegative replicate1


title: TIGITlow replicate3


title: TIGITnegatve replicate2


title: D1 sCD83


title: D1 mock