title: TgN3840_vector

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: TLA material

data_processing:
All scripts are available at https://github.com/lldelisle/scriptsForWilleminEtAl2021. Adapter and low quality bases were removed with cutadapt v1.16.
Reads were mapped on mm10 or 4 copies of the fosmid with the following orientation (->-><-->) called fosmid_TH_TT_HH with bowtie2 version 3.2.5 in end-to-end very sensitive mode. For mm10, only reads with mapping quality above 30 were kept (samtools version 1.9).
Coverage was performed with bedtools (2.27.1).
Unaligned reads were split at the CATG sequence and only reads over 25bp were kept. These reads were mapped in end-to-end very sensitive mode on mm10 and the fosmid sequence and only reads mapping to none of them were kept.
Finally these reads are mapped on mm10 in very-sensitive local mode and coverage is computed with bedtools.
Genome_build: mm10 or fosmid_TH_TT_HH (https://github.com/lldelisle/scriptsForWilleminEtAl2021/blob/master/TLA/fasta/TgN3840_fosmid_TH_TT_HH.fa)
Supplementary_files_format_and_content: *_q30_cov.bw: bigwig of coverage of end-to-end mapping on mm10
Supplementary_files_format_and_content: *_unaligned_CATG_split_nomm10noTgN3840_fosmid_localMapped_onmm10.bw: bigwig of coverage of local mapping on mm10 of reads that did not mapped full length on mm10, split at CATG, still not mapping on mm10 or fosmid in end-to-end mode
Supplementary_files_format_and_content: *_onTgN3840_fosmid_TH_TT_HH.bw: coverage end-to-end on 4 copies of fosmid tail-to-head, tail-to-tail, head-to-head

source_name: Brains

extract_protocol:
Cells were dissociated with collagenase type XI (Sigma-Aldrich, C7657). The cell suspension was strained, and chromatin was crosslinked for 10 minutes at room temperature in 1X PBS/10% FCS containing 2% formaldehyde. Crosslinking was blocked by ice-cooling and ice-cold glycine addition. Following cell lysis, nuclei pellets were resuspended in 1X Cutsmart Buffer (NEB), followed by SDS addition to a final concentration of 0.28%. Samples were incubated at 37°C while shaking for 30 minutes, after which TritonX-100 was added to quench SDS. Crosslinked chromatin was primarily digested using NlaIII (4-cutter; NEB). Ligation was carried out with T4 DNA Ligase, after which reverse crosslinking was performed using proteinase K at 65°C. Proteinase K removal was achieved using phenol-chlorofphorm DNA purification with ethanol precipitation. Secondary restriction was performed using NspI (5-cutter recognizing a subset of NlaIII sites; NEB). Secondary ligation was carried out with T4 DNA Ligase in diluted conditions. After ethanol precipitation, DNA was purified using the QIAquick PCR Purification Kit.
TLA inverse PCR was performed using 800 ng template DNA (for 8 reactions in total), viewpoint-directed inverse PCR primers (listed in S2 Table, Willemin et al 2021) and the Phire Hot Start II DNA Polymerase (Thermo Fisher Scientific) following the manufacturer’s program with 2 minutes extension time and annealing at 55°C. After purification of the PCR products, TLA library preparation was achieved by Tn5 tagmentation using the Nextera DNA Flex Library Prep (Illumina) protocol, independently for each viewpoint.

tag: embryonic day


title: 78831 [minus_young_H3K4me3]

status: Public on Jul 05 2021

type: SRA

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

country: Germany

institute: Leipzig University

library_source: genomic

data_processing:
The sequenced reads underwent a quality trimming using cutadapt to ensure a minimum read length of 40 bases and a Phred quality score above 20.
The high-quality reads were mapped to the mouse reference genome NCBI37/mm9 (GRCh37/hg19) using the software tool segemehl 0.2.0 with parameter settings “-s -t 8”.
Histone modification peaks were identified by applying MACS 1.4.2 with the H3pan data as control and the following parameter settings: “--nomodel -w --space = 30 --bw 300 --pvalue 1e-5 --shiftsize 200".
The histone modification peak lists were summarized for each genotype and treatment. A peak is accepted, if it is detected in both replicates or in one replicate with a high reliability (MACS fold enrichment > 5.0). Finally, a peak is assigned to be within the promoter region of genes ((TSS) ± 1000 bases) and the gene bodies. If the overlap with a promoter or body region is at least 5%, the respective gene-associated histone is considered as modified.
X- and Y-chromosome is excluded from the analysis.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Processed data is stored in comma separated value format and provides modification profiles of mouse genes. The list includes those genes that show a modification in at least one of the lysines K4 or K27 of histone 3 only. If the lysine is modified, the respective value is '1', otherwise '0' (unmodified). In the respective columns (Plus_Young_H3K4me3, Plus_Young_H3K27me3, Plus_Old_H3K4me3, Plus_Old_H3K27me3, Minus_Young_H3K4me3, Minus_Young_H3K27me3, Minus_Old_H3K4me3, Minus_Old_H3K27me3), Plus/Minus identifies the genotype, though Plus is associated with Msh2+/+ and Minus is associated with Msh2-/-. Young/Old refers to short/long term organoid culture of 4 and 20 weeks aged organoids. In addition, beside the gene's name, the following data is provided: ensID: Ensembl transcription ID, chr: chromosome, strand, txStart, txEnd: start and end position.

molecule: genomic DNA

organism: Mus musculus

source_name: Intestinal organoid (jejunum)

growth_protocol: 6 cm of the jejunum was used to generate intestinal organoids of 8 month old Msh2-/- and Msh2+/+ mice

extract_protocol:
Chromatin was prepared from up to 50 mg jejunum using SDS Shearing Buffer and the truChlP Tissue Chromatin Shearing Kit (Covaris, Brighton, UK) according to the manufacturer´s instructions. ChIPs were run on the IP-Star compact system using the Auto iDeal ChIP-seq kit for histones (Diagenode, Seraing, Belgium) according to the manufacturer’s direct method for ChIP preparation. For ChIP-seq validation shredded intestinal tissue was cross-linked in 1% formaldehyde for 8 min at room temperature and homogenized in ZR 2.0 mm BashingBead™ Lysis Tubes (Zymo Research Corp., Tustin, US) with a Precellys24 homogenization device (VWR International GmbH, Darmstadt, Germany). ChIP assays were performed with minor modifications as described [Mannefeld et al. 2009]. DNA from 15 mg tissue was used in each IP with H3K4me3, H3K27me3, and H3pan premium rabbit polyclonal antibodies (Diagenode). A non-targeting IgG rabbit antibody (Cell Signaling, Leiden, Netherlands) was used as a control for non-specific signals. 1 µl of purified chromatin was applied for semi-quantitative real-time PCR using the absolute qPCR SYBR Green Mix (Thermo) performed with the ABI 7500 RealTime PCR System (Applied Biosystems, Forster City, US).
Library preparations were performed according to the TrueSeq LT PCR free or TruSeq Nano DNA Kit instructions (Illumina, San Diego, USA). Sequencing was performed on the Illumina HiSeq 4000 with 76 bp paired-end sequencings.

treatment_protocol: Organoids were split once/week and cultured with or without 1 mM aspirin (Sigma) for a further 18 weeks. After the first and 18th week organoids were stored into liquid nitrogen. These frozen organoids were recultured simultaneously in IntestiCult™ mouse organoid growth medium (Stemcell Technologies GmbH, Cologne, Germany) with or without 1 mM aspirin for further two weeks and analyzed afterwards.

tag: strain

tag: genotype

tag: animal id

tag: treatment

tag: tissue

value: jejunum

tag: age

value: 1 week

tag: chip antibody


title: TgN3840_CS38

description: TLA material


title: E12_Limbs_Wt

description: Hi-C material

data_processing:
All scripts are available at https://github.com/lldelisle/scriptsForWilleminEtAl2021. Fastq from NextSeq and HiSeq were concatenated then processed with HiCUP version 0.7.3 (or a modified version of it).
Then pairs were exported in the juicebox format with custom script.
40kb bin matrices were built and balanced with cooler version 0.8.10
TADs were called with hicFindTADs version 3.6 with window size of 240kb or 480kb
Genome_build: mm10 or TgN3840 (custom genome based on mm10)
Supplementary_files_format_and_content: validPairs: sorted pairs in juicebox format: (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse) pos = middle of the fragment
Supplementary_files_format_and_content: cool: balanced matrix in cool format at 40kb bins
Supplementary_files_format_and_content: bed: TADs with 240kb or 480kb window size
Supplementary_files_format_and_content: _mm10 indicates it is mapped on mm10
Supplementary_files_format_and_content: _TgN3840 indicates it is mapped on TgN3840

source_name: Whole limbs

extract_protocol:
Cells were dissociated with collagenase type XI. The cell suspension was strained, and chromatin was crosslinked for 10 minutes at room temperature in 1X PBS/10% FCS containing 2% formaldehyde. Crosslinking was blocked by ice-cooling and ice-cold glycine addition. Following cell lysis, nuclei were resuspended in 1X NEBuffer 3.1 (NEB) containing SDS to a final concentration of 0.11%. The samples were incubated at 65° for 10 minutes, followed by ice-cooling and TritonX-100 addition for SDS quenching. Crosslinked chromatin was digested using DpnII (NEB). Biotin fill-in was performed using biotin-14-dATP, non-biotinylated dCTP/dGTP/dTTP and DNA Polymerase I, Large (Klenow) Fragment with 3’->5’ exonuclease activity (NEB, M0210). Blunt-end ligation was achieved with T4 DNA Ligase. NaCl and SDS were added to the samples to a final concentration of 260 mM and 0.86%, respectively, followed by incubation overnight at 68°C with agitation. Chromatin reverse crosslinking was performed using proteinase K at 56°C. Proteinase K removal was achieved through two rounds of phenol-chloroform DNA extraction with a final ethanol precipitation. Sonication was carried out using a Covaris E220 sonication device with 175 W peak incident power, 200 cycles per burst and for a treatment time of 90 seconds. A 1:8:1 size selection was performed using SPRI beads with magnetic separation. Biotin pull-down was achieved using Dynabeads MyOne Streptavidin C1 with magnetic separation. Repair of DNA fragment ends was carried out using T4 Polynucleotide Kinase, T4 DNA Polymerase and DNA Polymerase I, Large (Klenow) Fragment with 3’->5’ exonuclease activity. A-tailing was performed with a DNA Polymerase I, Large (Klenow) Fragment lacking both 5’->3’ and 3’->5’ exonuclease activities in 1X NEBuffer 2 containing dATP.
Hi-C library preparation was achieved by ligation of TruSeq (Illumina) paired-end Y adapters following the manufacturer’s instructions using T4 DNA Ligase. Library amplification was carried out using the Herculase II Fusion DNA Polymerase following the manufacturer’s instructions (with an extension time of 15 seconds and annealing at 65°C).

value: Wild-type


title: 84577 [plus_young_H3K4me3]


title: E12_Limbs_TgN3840

description: Hi-C material


title: E12_Limbs_control_input

description: Input material

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForWilleminEtAl2021.
Nextera adapter and low quality bases were removed with cutadapt v1.16. Reads were mapped with default parameters with bowtie2 2.3.4.1 on mm10 or TgN3840.
When mapped on mm10, reads with mapping quality below 30 were discarded.
Peaks were called with macs2 version 2.1.1.20160309 (without specifying the input).
The bedgraph from macs2 was normalized to the million tags used in macs2. Then average of both replicates was computed.
For the copy number analysis: ChIPmentation input of mutant and control animals were processed as follow: adapter and low quality bases were removed with cutadapt version 1.16, mapping was done with bowtie2 2.3.5 on mm10. Alignments with mapping quality below 30 were discarded with samtools version 1.9 and PCR duplicates were removed with picard version 2.19.
The 8 bam files of the controls were merged. For the mutant bam and the sample bam, the region chr2:71M-78M was extracted and shifted. FREEC version 11.5 was used.
Genome_build: mm10 or TgN3840 (custom genome based on mm10)
Supplementary_files_format_and_content: *rep1*bedgraph or *rep2*bedgraph: coverage from macs2 on the specified genome (not normalized)
Supplementary_files_format_and_content: *neq2*bedgraph: average of normalized coverage for both replicates on the specified genome
Supplementary_files_format_and_content: *Wt*bedgraph: normalized coverage from reanalysis of published ChIP from our lab.
Supplementary_files_format_and_content: *bed: narrowPeak from macs2
Supplementary_files_format_and_content: *ratio.bedgraph = output of FREEC the ratio of the normalized coverage in each 1kb or 2kb bin between the sample and the control times 2.
Supplementary_files_format_and_content: *meanRatio.bedgraph = output of FREEC the estimated copy number (using maximum likelihood) from the ratio.
Supplementary_files_format_and_content: _mm10 indicates it is mapped on mm10
Supplementary_files_format_and_content: _TgN3840 indicates it is mapped on TgN3840

extract_protocol:
Tissues were dissected in ice-cold cold 1X PBS and crosslinking was performed for 15 minutes at room temperature in 1X PBS containing 1% formaldehyde (Thermo Fisher Scientific, 28906). Crosslinking was stopped using Stop Solution (Active Motif, ChIP-IT HS Kit) and tissues were washed three times in ice-cold 1X PBS containing Detergent (Active Motif, 1:20). Tissues were resuspended in Chromatin Prep Buffer (Active Motif, ChIP-IT HS Kit) containing cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail (Sigma-Aldrich, 1 tablet in 10 mL), homogenized using a Polytron and nuclei were released using a Dounce homogenizer with type B (tight) pestle (Active Motif). Released nuclei were resuspended in sonication buffer (50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 0.25% SDS) containing protease inhibitors. Chromatin was fragmented using a Bioruptor Pico sonication device (Diagenode), with the following settings: 4-7 times (20-30 seconds ON, 30 seconds OFF). A fraction of the samples (see total input DNA) was preserved. Anti-CTCF (Active Motif, 61311) or Anti-RAD21 (Abcam, ab992) antibodies were then incubated with Dynabeads Protein A (Thermo Fisher Scientific, 10001D) for 3 hours on a rotating wheel at 4°C, followed by two washes in RIPA with low salt concentration (LS, 140 mM NaCl) containing BSA (1 mg/mL). Samples were incubated with the antibody-coupled beads on a rotating wheel at 4°C overnight for chromatin immunoprecipitation, after which the following washes were performed in the presence of protease inhibitors: 2 washes in RIPA-LS, 2 washes in RIPA with high salt concentration (HS, 500 mM NaCl), 2 washes in RIPA containing LiCl and 1 wash in 10 mM Tris-HCl pH 8. Tagmentation was performed using the Tagment Enzyme 1 (Tn5, Illumina) for 2 minutes at 37°C, followed by washes with RIPA-LS and TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8); once each. ChIPed DNA was eluted using ChIP elution buffer (10 mM Tris-HCl pH 8, 5 mM EDTA pH 8, 300 mM NaCl, 0.4% SDS) containing proteinase K for 1 hour at 55°C and 6 hours at 65°C. The same previous step as well as all the following were also carried out on the total input DNA. DNA was purified using the MinElute PCR Purification Kit (Qiagen).
ChIP library preparation was performed as in (Schmidl et al., 2015), using indexed Nextera custom primers (Buenrostro et al., 2013) and pre-heated KAPA HiFi HotStart ReadyMix (Roche) following the manufacturer’s instruction (with an extension time of 30 seconds and annealing at 63°C). The resulting libraries were purified and size-selected using SPRI beads with magnetic separation.
ChIPmentation

value: Wild-type on CS38-40 region


title: E12_Limbs_TgN3840_input

description: Input material


title: D2-1

city: Beijing

first: Jinbo

last: Cheng

state: Beijing

address: No. 27 Taiping Road, Haidian District Beijing

country: China

institute: Beijing Institute of Basic Medical Science

library_source: transcriptomic

data_processing:
Aliquots of mRNA were extracted and purified by NucleoSpin RNA Plus XS kit.
Libraries were constructed using the Smart-Seq2 method.
Sequenced with 10G depth and paired-end reads on an Illumina Hiseq platform for PE150.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Read_count.xlsx: Matrix table with raw gene counts for every gene and every sample.

molecule: total RNA

source_name: Microglia cells 2 for Calhm2 cKO/AD

extract_protocol:
Microglia was isolated from mice brain, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Calhm2 cKO

tag: diagnosis

value: Alzheimer's disease

value: 6 months

value: Brain

tag: cell type

value: Isolated microglia


title: E12_Limbs_TgN3840_CTCF

description: ChIP material

value: Anti-CTCF (Active Motif, 61311)


title: D1

source_name: Microglia cells 1 for Calhm2 cKO/AD


title: C1

source_name: Microglia cells 1 for WT/AD

value: WT


title: C2

source_name: Microglia cells 2 for WT/AD


title: A1

source_name: Microglia cells 1 for WT

value: No Alzheimer's disease


title: A2

source_name: Microglia cells 2 for WT


title: B2

source_name: Microglia cells 2 for Calhm2 cKO


title: 78833 [minus_young_H3K27me3]


title: Exp3_SKF_JQ1_24h_N6

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description: rRNA depleted library

data_processing:
Fastq files were trimmed with TrimGalore.
Quality control was performed with FastQC.
Reads were aligned to Ensembl rat genome Rnor_6.0.94 using STAR.
Transcripts were assembled using StringTie.
Differential expression analysis was performed using DEseq2.
Genome_build: Rnor_6.0.94
Supplementary_files_format_and_content: *ctab.txt: Tab-delimited text files include FPKM values.

organism: Rattus norvegicus

source_name: primary striatal neuron

extract_protocol:
Qiagen RNeasy Mini Kit.
NEBNext rRNA-depleted stranded (HMR).

value: primary striatal neuron

value: Neonatal, DIV 7

value: SKF/JQ1 24h


title: Exp3_SKF_24h_N6

description: rRNA depleted library

value: SKF/DMSO 24h


title: Exp3_DMSO_24h_N6

description: rRNA depleted library

value: DMSO/DMSO 24h


title: Exp3_JQ1_24h_N5

description: rRNA depleted library

value: DMSO/JQ1 24h


title: Exp3_DMSO_24h_N5

description: rRNA depleted library


title: Exp3_JQ1_24h_N6

description: rRNA depleted library


title: B1

source_name: Microglia cells 1 for Calhm2 cKO


title: Exp2_SKF_iBD2_60m_N1

description: rRNA depleted library

value: SKF/iBD2 60min


title: CaPPZ1+BM+MSB_3

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome.
Tophat (version 2.1.1) and Bowtie (version 2.3.4.1) bioinformatics tools were used for the mapping and generating bam files, and htseq-count (from “HTSeq” framework, version 0.6.1p1) to generate read counts of A and B alleles.
The read counts of the corresponding A and B alleles were merged and these merged values were used for differential expression analysis using DESeq2 (version 1.24.0)
Genome_build: C. albicans SC5314 (candida genome database; Genome: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/archive/C_albicans_SC5314_version_A22-s07-m01-r85_chromosomes.fasta.gz, features: http://www.candidagenome.org/download/gff/C_albicans_SC5314/archive/C_albicans_SC5314_version_A22-s07-m01-r85_features_with_chromosome_sequences.gff.gz)
Supplementary_files_format_and_content: RNAseq.xlsx (Excel file includes row counts data for A and B alleles)

organism: Candida albicans

source_name: ΔCaPPZ1 fungal cells

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The yeast pre-cultures were grown in 5 ml YPD medium at 37 ºC for 18 h.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. The single read 75 bp long sequencing reads were generated on Illumina NextSeq500 instrument. Approximately 16–36 million reads per samples were generated.

treatment_protocol: The pre-cultures were diluted to 0.1 OD640 in YPD ± 2 mM BM then were grown at 37 ºC. MSB was added in the final concentration of 1.5 mM at 4 h incubation time. Fungal cells were collected after 5 h inoculation (at 1 h following MSB stress treatment) by centrifugation (5 min of 4000 × g at 4°C).The cells were washed three times with phosphate-buffered saline (PBS) and stored at -70°C until use.

value: deletion mutant type

value: BM+MSB


title: Exp2_SKF_60m_N2

description: rRNA depleted library

value: SKF/DMSO 60min


title: CaPPZ1+BM+MSB_2


title: Ssbp1_TruSeq_KO_brep3_trep2 [586H_2]

status: Public on Jul 06 2021

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Where applicable, technical replicates were pooled.
Sequenced reads were aligned to the mouse genome (GRCm38.p6 primary assembly, masked for nuclear mitochondrial sequences) using STAR v2.7.3a and the GENCODE vM24 gene annotation with a customised mitochondrial annotation.
Gene expression quantification was performed with Salmon v1.1.0 (-l ISR --seqBias) in alignment-based mode on the transcriptome alignment produced by STAR using a transcriptome sequence file generated with gffread v0.11.7.
Differential expression analysis was performed with DESeq2 1.26.0 using counts summarised by tximport 1.14.0 and effect size estimation performed using apeglm v1.8.1.
Full fragment length mitochondrial coverage profiles were generated with samtools v1.10 and bedtools v2.26.0, and normalised to total reads mapped to mitochondria.
Genome_build: GRCm38.p6

growth_protocol: SSBP1+/loxp were mated with mice expressing cre-recombinase under ckmm (the muscle creatinine kinase) promoter. All mice maintaining an inbred C57BL/6N nuclear background were housed in a 12-hour light/dark cycle at 21°C and fed ad libitum on a standard mouse food (ssniff RM-H Low-Phytoestrogen).

extract_protocol:
RNA was isolated from total hearts from three Ssbp1+/+ and Ssbp1-/- mice, using a bead-beating RNA extraction strategy based on the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing libraries were prepared according to the Illumina Tru-Seq protocol.

tag: strain background

value: inbred C57BL/6N nuclear background

value: Heart


title: Exp2_SKF_60m_N1

description: rRNA depleted library


title: CaPPZ1+BM+MSB_1


title: E12_Limbs_TgN3840_RAD21

description: ChIP material

value: Anti-RAD21 (Abcam, ab992)


title: Exp2_iBD2_60m_N2

description: rRNA depleted library

value: DMSO/iBD2 60min


title: CaPPZ1+MSB_3

value: MSB


title: 78835 [minus_young_H3pan]

value: jejunum

value: 1 week


title: Exp2_iBD2_60m_N1

description: rRNA depleted library

value: primary striatal neuron


title: CaPPZ1+MSB_2


title: Exp2_DMSO_60m_N2

description: rRNA depleted library

value: Neonatal, DIV 7

value: DMSO/DMSO 60min


title: Exp3_SKF_24h_N5

description: rRNA depleted library

value: SKF/DMSO 24h


title: CaPPZ1+MSB_1


title: Exp2_DMSO_60m_N1

description: rRNA depleted library


title: Exp3_SKF_JQ1_24h_N5

description: rRNA depleted library

value: SKF/JQ1 24h


title: Exp2_SKF_iBD2_60m_N2

description: rRNA depleted library


title: Exp1_SKF_JQ1_60m_N6

description: rRNA depleted library

value: SKF/JQ1 60min


title: Exp1_SKF_JQ1_60m_N5

description: rRNA depleted library


title: CaPPZ1+BM_1

value: BM


title: Exp1_SKF_60m_N6

description: rRNA depleted library


title: CaPPZ1_3

value: deletion mutant type

value: untreated


title: QMY23+BM+MSB_3

source_name: QMY23 fungal cells

value: wild type

value: BM+MSB


title: QMY23+BM+MSB_2


title: Exp1_SKF_60m_N5

description: rRNA depleted library

value: SKF/DMSO 60min


title: Exp1_JQ1_60m_N6

description: rRNA depleted library

value: DMSO/JQ1 60min


title: Exp1_DMSO_60m_N6

description: rRNA depleted library


title: Exp1_JQ1_60m_N5

description: rRNA depleted library


title: Exp1_DMSO_60m_N5

description: rRNA depleted library


title: QMY23+MSB_3


title: QMY23+MSB_2


title: CaPPZ1+BM_2


title: cisplatin-treated group tumor2

city: GAINESVILLE

first: Lingtao

last: Jin

state: FL

address: 2033 Mowry Rd, UF CGRC 356

country: USA

institute: University of Florida

data_processing:
CleanData (fastq format): Remove low quality readsthat contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). [Software: perl scripts in house, cutadapt]
Mapping to genomethe genome of ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/: Map the reads of each sample to the reference genome, [Software: HISAT2]
Transcripts assembly (gtf format): Assemble transcripts of each sample independently, [Software: StringTie]
Merged all assemblies to create a StringTie merged gtf, [Software: StringTie, gffcompare]
mRNAs expression profiling: StringTie was used to perform expression level for mRNAs by calculating FPKM [Software: StringTie]
Differentially expressed mRNAs: The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [Software: Rpackage - edgeR]
Genome_build: Homo sapiens GRCh38 DNA, release 96
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample and each gene

molecule: polyA RNA

organism: Homo sapiens

source_name: cell line xenograft tumor

growth_protocol: The KB-3-1 tumors were grown in 6-week old female athymic nude mice after subcutaneous injection into the right frank.

extract_protocol:
High quality total RNA was extracted using RNeasy Plus micro kit  with  gDNA removed  (Cat: #74034, Qiagen, Hilden, Germany). The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.  Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: The tumor bearing mice were treated with 0.5 mg/kg and 5 mg/kg at 5 and 10 days, respectively after xenograft.

tag: cell line

value: Cisplatin


title: CaPPZ1+BM_3


title: QMY23+BM_2


title: cisplatin-treated group tumor3


title: QMY23+MSB_1

value: MSB


title: PBS-treated group tumor3

value: PBS


title: QMY23+BM_3


title: cisplatin-treated group tumor1


title: PBS-treated group tumor2


title: QMY23_3


title: QMY23+BM_1


title: PBS-treated group tumor1


title: CaPPZ1_1


title: CaPPZ1_2


title: QMY23_2


title: QMY23_1


title: QMY23+BM+MSB_1


title: RAF_DRNM_4 [H01824]

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

description:
H01824
mRNA

data_processing:
16S rRNA: After assembling the reads using SeqPrep, subsequent identification of chimera with ChimeraSlayer and manual verification, chimera were removed from the data set. The sequences were further analyzes using QIIME 1.9.0.
RNA-Seq: After quality filtering (fastq_illumina_filter, prinseq-lite, cutadapt), sequencing reads were mapped against the Drosophila melanogaster reference BDGP6 using TopHat v2.1.0 with sensitive option. The read counts per transcript were calculated with the Python script HTSeq v0.6.1p1 using the mode ‘intersection-strict’.
Genome_build: Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files include read counts per gene for each sample.
Supplementary_files_format_and_content: otu_table_mc50_w_tax_wochimera_ctrl_50filtered.txt: Tab-delimited text file includes read counts per OTU for each sample.

organism: Drosophila melanogaster

source_name: midguts of 15 Drosophila melanogaster individuals

growth_protocol: We used homozygous flies containing esg-Gal4, UAS-GFP, tubulin-Gal80ts on the 2nd chromosome, and UAS-Luciferase on the 3rd chromosome and crossed them to homozygous UAS-RAFgof flies to obtain the F1 generation with a temperature inducible tumor phenotype. As a control we crossed EGT;Luc2 to w1118 wildtype flies. All fly lines were raised on a cornmeal based standard medium at 20 °C. The F1 generation was shifted to 29 °C 5-7 days post eclosion to induce the expression of UAS-dependent genes.

extract_protocol:
DNA for 16S rRNA sequencing was extracted with the DNeasy Blood & Tissue Kit (Qiagen, #69504) following the manufacturer´s protocol for Pretreatment for Gram-Positive Bacteria, followed by the protocol for Purification of Total DNA from Animal Tissues. For RNA isolation 15 midguts per treatment were dissected in S2 medium, immediately transferred to a 2 ml screw cap tube containing 1 ml RNA Magic (Bio-Budget, #56-1000-100) and homogenized for 2 min at 3.25 m/sec using a bead mill homogenizer with 3 zirconium beads per tube. The homogenate was incubated for 5 min at RT and stored at -20 °C until further processing. Samples were thawed on ice for subsequent RNA isolation. 200 μl chloroform were added into each tube. Tubes were inverted (not vortexed) several times to provide homogenous mixing and incubated for 5 min at RT prior to 15 min centrifugation at 12.000 xg and 4 °C. The upper aqueous phase was transferred into a new tube (about 500 μl) and 500 μl 99% EtOH were added. The samples were centrifuged for 45 min at 17.000 xg and 4 °C after vigorously inverting the tubes for 30 sec. The supernatant was carefully removed and the RNA containing pellet was washed by adding 200 μl 99% EtOH and centrifuging for 5 min at 12.000 xg and 4 °C. The supernatant was completely removed and the pellet was air-dried for 3 min. The pellet was subsequently resuspended in 13 ml RNase-free ddH2O.
The bacterial variable regions 1 and 2 of 16S rRNA genes were amplified as described by Rausch et al. (2016). RNA-Seq libraries were created with the TruSeq Stranded mRNA Library Kit (Illumina, San Diego, USA).

treatment_protocol: We used a standard corn meal based medium for all stock flies and crossings. All assays were conducted on low-melt fly food containing 1.5% agar, 2% bacto yeast extract and 7% corn syrup (NM). The medium was boiled and supplemented with 0.1% propionic acid and 0.3% nipagin to prevent microbial growth. For dietary restriction (DR) the amount of bacto yeast was reduced to 0.1%. The recurrent diet consisted of an alternating regimen of four days DR followed by feeding on NM for three days.

value: Midguts

tag: disease state

value: Cancer

tag: diet

value: DRNM

tag: feeding time

value: 13 days


title: RAF_DRNM_1 [H01821]

description:
H01821
mRNA

value: DR


title: RAF_DRNM_3 [H01823]

description:
H01823
mRNA


title: RAF_DRNM_2 [H01822]

description:
H01822
mRNA


title: Ranger20Post_Stress

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

description:
Ranger20Post_Stress_GTAGAG_L006_R1_001
post-stress

data_processing:
Sequence reads were quality trimmed for adaptor sequences with 5 bases minimum overlap and 0.1 error rate and quality filtered with threshold of Phred quality score 20 using cutadapt
Quality filtered reads were further mapped to genome assembly for Homo sapiens (hg19) using bowtie mapper and mirdeep2 tool
miRNA quantification was performed using mirbase and hairpin fasta files from mirbase for mature and precursor miRNAs identification.
miRNA counts were further normalized by library size using TMM (Trippled mean median) normalization
Genewise negative binomial generalized linear model was used to fit the counts and using contrast function differentially expression miRNA has been identified.
Genome_build: hg19
Supplementary_files_format_and_content: processed files format is tab delimited matrix for all QC passed and normalized samples

source_name: plasma

growth_protocol: Plasm was isolated from whole blood samples drawn from RASP cadets before and immediately after the RASP training

extract_protocol:
Micro RNAs were extracted from 200 ul of plasma samples using miRCURY RNA isolation kit, Biofluids (Exiqon) using manufacturer's guidelines.  Small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.  A fraction of ﬁve microliter of total RNA was used for library preparation as quantiﬁcation is below the detection limit.
Five microliters of total RNA was ligated with 30 and 50 adaptors followed by reverse transcription with SuperScript II Reverse Transcriptase (Invitrogen) and unique indexes were introduced during PCR ampliﬁcation for 15 cycles.
A multiplexed pool consisting of equimolar amounts of small RNA-derived libraries was prepared. The 140–150 nt region containing the microRNA fraction of the library was excised from a 6 % polyacrylamide gel after electrophoresis, ethanol-precipitated and quantiﬁed.  The samples were subsequently sequenced on the Illumina HiScan SQ instrument using 50 cycles plus 7 index sequencing cycles.

treatment_protocol: The US Army Ranger Cadets (RASP cadets) where exposed to extreme battlefield-like stress for about eight weeks

tag: condition

value: post-stress


title: Ranger18Post_Stress

description:
Ranger18Post_Stress_CATTTT_L006
post-stress


title: Ranger21Post_Stress

description:
Ranger21Post_Stress_GTCCGC_L006_R1_001
post-stress


title: Ranger17Post_Stress

description:
Ranger17Post_Stress_CATGGC_L006
post-stress


title: RAF_DR_4 [H01819]

description:
H01819
mRNA


title: RAF_DRNM_5 [H01825]

description:
H01825
mRNA


title: Ranger15Pre_Stress

description:
Ranger15Pre_Stress_CACTCA_L006
pre-stress

value: pre-stress


title: RAF_NM_5 [H01815]

description:
H01815
mRNA

value: NM


title: RAF_DR_3 [H01818]

description:
H01818
mRNA


title: RAF_DR_2 [H01817]

description:
H01817
mRNA


title: Ranger16Post_Stress

description:
Ranger16Post_Stress_CAGGCG_L006_R1_001
post-stress


title: RAF_DR_1 [H01816]

description:
H01816
mRNA


title: Ranger14Pre_Stress

description:
Ranger14Pre_Stress_CACCGG_L006_R1_001
pre-stress


title: RAF_NM_3 [H01813]

description:
H01813
mRNA


title: RAF_DR_5 [H01820]

description:
H01820
mRNA


title: ctrl_NM_2 [H01812]

description:
H01812
mRNA

value: Control


title: Ranger19Post_Stress

description:
Ranger19Post_Stress_CCAACA_L006_R1_001
post-stress


title: Ranger13Pre_Stress

description:
Ranger13Pre_Stress_CAACTA_L006_R1_001
pre-stress


title: Ranger12Pre_Stress

description:
Ranger12Pre_Stress_ATTCCT_L006_R1_001
pre-stress


title: ASXL1-MT-KI3

city: Tokyo

first: Keita

last: Yamamoto

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy

country: Japan

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to the mouse reference genome (mm10) using HISAT2 (version 2.0.4).
To identify differential alternative splicing events, we applied rMATS (version 3.2.2.beta) with the following parameters: anchor length 2, unpaired analysis type, and "unstranded" librarytype.
Gene and transcript annotations were referred from "archive-2015-07-17-14-33-26" in the University of California Santa Cruz annotation archives.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
We extracted total RNA using the RNeasy Micro Kit (QIAGEN) from bone marrow LK cells derived from 8- to 12-week-old littermate wild-type and ASXL1-MT-KI mice.
The synthesis and ampliﬁcation of cDNA were performed with 200 ng RNA using the NEB Next Ultra RNA Library Prep Kit for Illumina (New ENGLAND BioLabs：E7530), followed by high-throughput sequencing on the HiSeq 2000 System (Illumina) with 124 bp paired-end reads.

value: Bone marrow Linage negative c-Kit positive cells


title: ASXL1-MT-KI1


title: ASXL1-MT-KI2


title: Wild-type2

value: wild type


title: Ranger11Pre_Stress

description:
Ranger11Pre_Stress_ACTGAT_L006_R1_001
pre-stress


title: Wild-type3


title: Ranger14Post_Stress

description:
Ranger14Post_Stress_CACGAT_L006
post-stress


title: Wild-type1


title: RAF_NM_4 [H01814]

description:
H01814
mRNA


title: Ranger11Post_Stress

description:
Ranger11Post_Stress_ATGAGC_L006_R1_001
post-stress


title: ROD1_13

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

description: iCLIP protocol is described in PMID: 20601959. Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. The RNA linker used was L34: P-AUAGAUCGGAAGAGCGGUUCAG-Puromycin; the RT CLIP primer used was RCLIP-D:  5-phosphate-NNNNACTAGATCGGAAGAGCGTCGTGGATCCTGAACCGCTC-3′; The 5' Barcode used for iCLIP demultiplexing and deduplication: AGT_0,NNNN

data_processing:
Raw sequence reads were trimmed with cutadapt.
Trimmed reads were mapped with STAR and the GRCm38 mouse genome.
Reads were de-duplicated using random barcodes included in the library preparation and xlink-binding sites for individual replicates were determined as described in PMID:20601959 with iCOUNT: https://icount.readthedocs.io/en/latest/cite.html. In the provided fastq files, the random barcodes for deduplication are tagged to the end of the header lines; these and the three nucleotides for demultiplexing have been removed from the reads themselves.
xlink-binding sites from the individual libraries were pooled together.
significant xlink binding sites (FDR<0.05) were identified with iCOUNT https://icount.readthedocs.io/en/latest/cite.html
Genome_build: GRCm38
Supplementary_files_format_and_content: PTBP3_groupTotal_grouped_cdna.bedgraph: bedgraph file with all the xlink-binding sites; PTBP3_groupTotal_grouped_cdna_peaks.bedgraph: significant xlink-binding sites (FDR<0.05)  identified with iCOUNT https://icount.readthedocs.io/en/latest/cite.html

source_name: Splenic B cells, LPS 48h

extract_protocol:
Cell extracts were prepared after UV crosslinging by lysing the cells in 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS lysis buffer
iCLIP libraries were carriead out as described in PMID: 20601959 and PMID: 29358707, with the primers included in the description of each sample and using the PTBP3 rabbit polyclonal (PTBP3-L2–3)  antibody ( PMID: 25940628)

tag: molecular weight (kda)

value: Splenic B cells


title: ROD1_12

description: iCLIP protocol is described in PMID: 20601959. Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. The RNA linker used was L34: P-AUAGAUCGGAAGAGCGGUUCAG-Puromycin; the RT CLIP primer used was RCLIP-C:  5-phosphate-NNNNATCAGATCGGAAGAGCGTCGTGGATCCTGAACCGCTC-3′; The 5' Barcode used for iCLIP demultiplexing and deduplication: GAT_0,NNNN


title: ROD1_11

description: iCLIP protocol is described in PMID: 20601959. Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h.  The RNA linker used was L34: P-AUAGAUCGGAAGAGCGGUUCAG-Puromycin; the RT CLIP primer used was RCLIP-B: 5-phosphate-NNNNGCCAGATCGGAAGAGCGTCGTGGATCCTGAACCGCTC-3′; the 5' Barcode used for iCLIP demultiplexing and deduplication is: GGC_0,NNNN


title: Ranger10Pre_Stress

description:
Ranger10Pre_Stress_CCGTCC_L006_R1_001
pre-stress


title: siCirc3

city: Shenzhen

first: Yue

last: Qi

address: Lianhua

institute: Peking University

description: N2a cells - si-circRtn4 transfected

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: N2a cells

growth_protocol: Mouse neuroblastoma cell line Neuro2A cells (N2a) were maintained in the growth medium composed of Minimum Essential Medium (MEM) with 10% Fetal Bovine Serum (FBS, Gibco, USA).

extract_protocol:
Total mRNA was extracted from cells with RNA-easy Isolation Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N2a cells was transfected with si-NC and si-circRtn4


title: M2c macrophages

type: RNA

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was normalized using quantile normalized by GenomeStudio software

label: biotin

source_name: monocytic cell line

label_protocol: cRNA were prepared with TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip

growth_protocol: THP-1 was grown with RPMI 1640 media supplemented with 2g/L Na2HCO3, 2g/L glucose, 2.38g/L HEPES, and 10% fetal bovine serum.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with NanoDrop.

treatment_protocol: Briefly, M0 macrophage was differentiated into M1, M2a and M2c by IFN-r/LPS, IL-4 and IL-10, respectively. Detail procedure was referred to“Opposite Effects of M1 and M2 Macrophage Subtypes on Lung Cancer Progression. Sci Rep 5, 14273”.

value: Acute monocytic leukemia

value: M2c macrophages


title: ctrl_DRNM_3 [H01808]

description:
H01808
mRNA


title: siCirc2

description: N2a cells - si-circRtn4 transfected

value: Mouse neuroblastoma cell line Neuro2A cells


title: ctrl_DRNM_4 [H01809]

description:
H01809
mRNA


title: M2a macrophages

value: M2a macrophages


title: siCirc1

description: N2a cells - si-circRtn4 transfected


title: siNC3

description: N2a cells - si-NC transfected


title: ctrl_DRNM_2 [H01807]

description:
H01807
mRNA


title: Ranger12Post_Stress

description:
Ranger12Post_Stress_CAAAAG_L006_R1_001
post-stress


title: ctrl_NM_1 [H01811]

description:
H01811
mRNA


title: siNC2

description: N2a cells - si-NC transfected


title: Ranger9Pre_Stress

description:
Ranger9Pre_Stress_AGTTCC_L003
pre-stress


title: ctrl_DRNM_1 [H01806]

description:
H01806
mRNA


title: siNC1

description: N2a cells - si-NC transfected


title: ctrl_DRNM_5 [H01810]

description:
H01810
mRNA


title: Ranger8Pre_Stress

description:
Ranger8Pre_Stress_CTTGTA_L003_R1_001
pre-stress


title: Ranger8Post_Stress

description:
Ranger8Post_Stress_AGTCAA_L003_R1_001
post-stress


title: ctrl_DR_5 [H01805]

description:
H01805
mRNA


title: ctrl_DR_4 [H01804]

description:
H01804
mRNA


title: M0 macrophages

value: M0 macrophages


title: Ranger7Pre_Stress

description:
Ranger7Pre_Stress_GGCTAC_L003_R1_001
pre-stress


title: Ranger6Pre_Stress

description:
Ranger6Pre_Stress_GATCAG_L003
pre-stress


title: ctrl_DR_3 [H01803]

description:
H01803
mRNA

value: Midguts


title: ctrl_DR_2 [H01802]

description:
H01802
mRNA


title: ctrl_NM_5 [H01800]

description:
H01800
mRNA


title: ctrl_DR_1 [H01801]

description:
H01801
mRNA


title: Ranger4Pre_Stress

description:
Ranger4Pre_Stress_CAGATC_L003_R1_001
pre-stress


title: Ranger5Pre_Stress

description:
Ranger5Pre_Stress_ACTTGA_L003
pre-stress


title: Ranger3Pre_Stress

description:
Ranger3Pre_Stress_ACAGTG_L003_R1_001
pre-stress


title: RAF_NM_4 [H01799]

description:
H01799
mRNA

value: Cancer


title: RAF_NM_3 [H01798]

description:
H01798
mRNA


title: Ranger3Post_Stress

description:
Ranger3Post_Stress_GCCAAT_L003_R1_001
post-stress


title: post-RASP Yersinia pestis infected dataset #2 sample 11

description: post-RASP Yersinia pestis infected samples 11 of 14

hyb_protocol: The slides were hybridized at 60ºC for 16 h (for cDNA microarrays and Trizol® isolated RNA)

scan_protocol: Hybridized slides were scanned and recorded using a GenePix® Pro 4000B (Axon Instruments Inc., Union City, CA) optical scanner, and the images were digitized using GenePix® 6.0 software (Axon Instruments Inc, Union City, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: pooled whole human tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., Waltham, MA) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: RASP trainees underwent extreme stressor condtions which simulated an intense battlefield scenario for more than 8 weeks.  Yersinia pestis treatment: leucocytes from whole blood were diluted with 1x balanced salt solution (BSS) without divalent cations (Invitrogen-Gibco, CA) & centrifuged at 350 x g, for 15 minutes.  A total of 2 ml culture fluid consisting of RPMI 1640 (Invitrogen-Gibco, CA) and 10 % human AB serum (Sigma) and was incubated with Y. pestis for 30 minutes, then diluted and centrifuged as before. Cells were re-suspended in 7 ml of culture media (RPMI 1640 and 10 % human AB serum) and plated in wells.  These were treated with Y. pestis to a final multiplicity of infection of 1 (MOI) or 1 bacterium per cell, and then incubated at 37 C and 5% CO2 for 4 hours.  Dengue virus treatment: isolated leukocytes were incubated with dengue virus serotype 2 (DENV-2) for 2 hours pre-plate incubation, and then 4 hours in plates to a final MOI of 1 (one viral particle per cell). Incubation was done in RPMI 1640 and 10 % human AB serum media at 37 ˚C and 5% CO2.  SEB exposure: SEB toxin was added to leukocytes to a final concentration of 100 ng/mL and incubated at 37 °C for 6 hours with 5% CO2.  At the end of the incubation period, treated leucocytes were centrifuged at 350 x g for 15 minutes. The pellets obtained from spinning of each well were treated with 2 ml TRIzolTM (Invitrogen, CA) reagent, and kept at –80 C for RNA isolation.

tag: sample type

value: Strategen universal reference RNA Cat. No. 740000

source_name: leukocytes

value: WBCs (leukocytes)


title: post-RASP Yersinia pestis infected dataset #2 sample 13

description: post-RASP Yersinia pestis infected samples 13 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 8

description: post-RASP Yersinia pestis infected samples 8 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 10

description: post-RASP Yersinia pestis infected samples 10 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 14

description: post-RASP Yersinia pestis infected samples 14 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 7

description: post-RASP Yersinia pestis infected samples 7 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 9

description: post-RASP Yersinia pestis infected samples 9 of 14


title: M1 macrophages

value: M1 macrophages


title: post-RASP Yersinia pestis infected dataset #2 sample 6

description: post-RASP Yersinia pestis infected samples 6 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 5

description: post-RASP Yersinia pestis infected samples 5 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 3

description: post-RASP Yersinia pestis infected samples 3 of 14


title: post-RASP Yersinia pestis infected dataset #2 sample 4

description: post-RASP Yersinia pestis infected samples 4 of 14


title: Ranger6Post_Stress

description:
Ranger6Post_Stress_TAGCTT_L003_R1_001
post-stress

value: post-stress


title: post-RASP Yersinia pestis infected dataset #2 sample 2

description: post-RASP Yersinia pestis infected samples 2 of 14


title: ctrl_NM_2 [H01797]

description:
H01797
mRNA

value: 13 days


title: post-RASP Yersinia pestis infected dataset #2 sample 1

description: post-RASP Yersinia pestis infected samples 1 of 14


title: Ranger9Post_Stress

description:
Ranger9Post_Stress_ATGTCA_L003
post-stress


title: Ranger2Pre_Stress

description:
Ranger2Pre_stress_TTAGGC_L003_R1_001
pre-stress

value: pre-stress


title: ctrl_NM_1 [H01796]

description:
H01796
mRNA

value: Control

value: NM


title: Ranger2Post_Stress

description:
Ranger2Post_Stress_TGACCA_L003
post-stress


title: post-RASP dengue virus infected dataset #2 sample 12

description: post-RASP dengue virus infected samples 12 of 13


title: post-RASP dengue virus infected dataset #2 sample 11

description: post-RASP dengue virus infected samples 11 of 13


title: Ranger1Post_Stress

description:
Ranger1Post_Stress_CGATGT_L003
post-stress


title: Ranger1Pre_Stress

description:
Ranger1Pre_Stress_ATCACG_L003
pre-stress


title: post-RASP dengue virus infected dataset #2 sample 10

description: post-RASP dengue virus infected samples 10 of 13


title: post-RASP dengue virus infected dataset #2 sample 9

description: post-RASP dengue virus infected samples 9 of 13


title: single-cell-derived clonal populations, collected 24h after mock treatment with DMSO

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description:
bulk transcriptome profiling by MARS-seq (following methodology described in Meir et al. 2020 and Meir, Aviezer et al., 2021) of PC-9 single cell derived clonal populations, 24 hours after those were subjected to mock treatment with DMSO
SBZM_PC9_DMSO

data_processing:
Preparaion of bulk cDNA library by MARS-seq:
.37 bases of Read-1 sequences were mapped to the hg19 genome assembly using Bowtie2 (default parameters). UMIs from replicate wells of 374,071 and 348,357 reads per clone PC9 single-cell-derived clones were aggregated prior to downstream analysis. Libraries were sequenced by paired end 150bp sequencing on Nextseq 500 to a mean depth of 374,071 and 348,357 reads per treated- and untreated clones, respectivelly.
.Demultiplexing and counts of UMIs per well (technical replicate) were based on 8bp of UMI and 7bp of cell-barcodes in Read-2 (see attached Readme table for further details), and performed with the pipeline described in Jaitin et al. 2014. UMIs obtained from the 4 wells that were assigned to the same clonal population in each plate were aggregated based on 1) conversion key of well-barcode to well-position. 2) plate design template, assigning each unique ID of a single-cell-derived clone to a well-position in that plate.
Genome_build: hg19
Supplementary_files_format_and_content: Tab sep table, containing UMI counts in each well (4 such wells serve as repicates from each clonal population)

source_name: Lung cancer cell-line derived from human adenocarcinoma

growth_protocol: # Any of the protocols below which are applicable to only a subset of Samples should be included as additional columns of the SAMPLES section instead.

extract_protocol:
Lysis of PC-9 clonal populations prior to transcriptome analysis: In order to process each clonal population to transcriptome analysis by MARS-seq, clones were washed with 150 µL PBS (Biological Industries, 02-023-1A) and detached by the addition of 30 µL trypsin b (Biological Industries, #03-052-1B) for 3 minutes at 37°C. 1um of Lysis buffer per 50cells was added. The lysis buffer contained 0.005% RNAse-Inhibitor (RNAsin plus, Promega, N2611) and 10% Triton X-100 (Sigma Aldrich, 9002-93-1).
Preparaion of bulk cDNA library by MARS-seq: In a similar assay to Meir et al. 2020, lysed clonal populations were manually transferred in four replicates of 1µL into MARS-Seq 384-well plates containing 2µL of barcoded RT primers (concentration of 8 nM in each well). Downstream library preparation was done according to Jaitin et al. 2014, and by using a randomized UMI sequence of 8 base-pairs (allowing a maximal count of ~65K UMIs per gene per well). Library preparation was identical to that used for single cells (Jaitin et al. 2014), with the only exception of extending the 95°C evaporation step before RT1 from 3 minutes to 4 minutes, in order to compensate for the higher volume.

treatment_protocol: Generation of single-cell-derived clones for parallel CTP and MARS-seq transcriptome analysis: GFP-labeled PC-9 lung cancer cells (0.5 cells/well in 50μl) were plated on a black clear-bottom 384-well plate (Corning #3712). 6-8 hours after plating, plates were imaged by the Operetta automated imaging system (PerkinElmer) at 2x magnification and wells containing one cell were selected. Cells were cultured for ~2-3 weeks and clonal populations that have reached to 80%-100% confluency by then were moved to Corning 96-well plate (Cat. Number 3595). After 48 hours clones were split into 6 replicates of same clonal populations in 96-well plates, and were cultured for an additional 24 hours. Then, two plates were used for measuring CTPgefitinib (as described in Jacob Et al 2021), two plates were used for measuring the population doubling time (as described in Jacob Et al 2021) and two plates were treated for 24 hours with either DMSO or 0.5µM gefitinib and were then used for trancriptiome analysis by MARS-seq. In order to process each clonal population to transcriptome analysis by MARS-seq, clones were washed with 150 µL PBS (Biological Industries, 02-023-1A) and detached by the addition of 30 µL trypsin b (Biological Industries, #03-052-1B) for 3 minutes at 37°C. 1um of Lysis buffer per 50cells was added. The lysis buffer contained 0.005% RNAse-Inhibitor (RNAsin plus, Promega, N2611) and 10% Triton X-100 (Sigma Aldrich, 9002-93-1). Lysed clonal population were manually transferred in four replicates of 1µL into MARS-Seq 384-well plates containing 2µL of barcoded RT primers (concentration of 8 nM in each well). Downstream library preparation was done according to Jaitin et al. 2014, and by using a randomized UMI sequence of 8 base-pairs (allowing a maximal count of ~65K UMIs per gene per well). Library preparation was identical to that used for single cells (Jaitin et al. 2014), with the only exception of extending the 95°C evaporation step before RT1 from 3 minutes to 4 minutes, in order to compensate for the higher volume.

tag: genotype/variation

value: Wild type


title: single-cell-derived clonal populations, collected 24h after  treatment with Gefitinib drug

description:
bulk transcriptome profiling by MARS-seq (following methodology described in Meir et al. 2020 and Meir, Aviezer et al., 2021) of PC-9 single cell derived clonal populations, 24 hours after those were subjected to Gefitinib drug treatment
SBZM_PC9_GEFITINIB


title: prime/boost challengecaLend14 dpc (SAMPLE 109)

type: genomic

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description: Fig 8 and 10

hyb_protocol: Serum, BALF and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing:
Spot and background intensities were measured using an annotated grid (.gal) file. Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis, A one-way ANOVA was performed. A P value below 0.05 was considered significant. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA).
The graphs generated in the publication associated to this document were done using the raw data. Therefore, there are no differences between the raw data and processed data.

molecule: other

source_name: BALF

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: caLen

tag: time point

value: d14 dpc

tag: mouse id

value: BALF


title: prime/boost challengecaLend14 dpc (SAMPLE 110)

description: Fig 8 and 10


title: E12_Limbs_Wt_CTCF-right

description: 4C material

data_processing:
All scripts are available at https://github.com/lldelisle/scriptsForWilleminEtAl2021. The analysis is a local version of what was done on htsstation.epfl.ch
De-multiplexing, mapping and 4C-analysis were performed as described in David F et al, 2014 (previously done on http://htsstation.epfl.ch). Reads were mapped to the TgN38-40 (custom genome based on mm10) with bowtie2 version 2.2.1 with parameters “--end-to-end --sensitive -k 20”. The segtofrag files were obtained after mapping the 4C data. Figures were made using a running mean algorithm with a window size of eleven fragments. Normalisation is done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample).
Genome_build: TgN3840 (custom genome based on mm10)
Supplementary_files_format_and_content: bedgraph: smooth 4C profile normalized to the +-5Mb region
Supplementary_files_format_and_content: bigwig: scores per fragment normalized to the number of reads mapped

source_name: Whole limbs

extract_protocol:
Cells were dissociated with collagenase type XI an d strained. Chromatin was crosslinked for 10 minutes at room temperature in 1X PBS/10% FCS containing 2% formaldehyde. Crosslinking was blocked by glycine addition. Following cell lysis, nuclei pellets were resuspended in 1.2X Cutsmart Buffer (NEB), followed by SDS addition to a final concentration of 0.29%. The samples were incubated while shaking for 10 minutes at 55°C and 50 minutes at 37°C. TritonX-100 was added in order to quench SDS. Crosslinked chromatin was primarily digested using NlaIII (NEB). Ligation was performed in the presence of T4 DNA Ligase in diluted conditions. Chromatin reverse crosslinking was carried out using proteinase K at 65°C. Proteinase K removal was achieved using phenol-chloroform DNA purification with ethanol precipitation. The purified DNA was diluted to a concentration of 100 ng/μL in 1X NEBuffer DpnII. Secondary restriction was performed using DpnII (4-cutter; NEB). Secondary ligation was carried out with T4 DNA Ligase in diluted conditions. Ligated DNA products were then extracted using phenol-chloroform with ethanol precipitation and purified.
4C-seq library preparation was achieved by inverse PCR using 100 ng template DNA (for 14 reactions in total), viewpoint-directed inverse PCR primers carrying Illumina Solexa sequencing adapters (listed in S2 Table, Willemin et al. 2021) and the Expand Long Template PCR System polymerase (Roche) with the provided Buffer 1, following the manufacturer’s protocol with 3 minutes extension time and annealing at 55°C.

tag: genotype

value: Wild-type

tag: strain

tag: embryonic day


title: prime/boost challengecaLend14 dpc (SAMPLE 111)

description: Fig 8 and 10


title: prime/boost challengecaLend14 dpc (SAMPLE 112)

description: Fig 8 and 10


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 108)

description: Fig 8 and 10


title: post-RASP dengue virus infected dataset #2 sample 5

description: post-RASP dengue virus infected samples 5 of 13

tag: cell type


title: post-RASP dengue virus infected dataset #2 sample 8

description: post-RASP dengue virus infected samples 8 of 13


title: post-RASP dengue virus infected dataset #2 sample 6

description: post-RASP dengue virus infected samples 6 of 13


title: post-RASP dengue virus infected dataset #2 sample 13

description: post-RASP dengue virus infected samples 13 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 13

description: pre-RASP Yersinia pestis infected samples 13 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 11

description: pre-RASP Yersinia pestis infected samples 11 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 12

description: pre-RASP Yersinia pestis infected samples 12 of 13


title: E12_Limbs_Wt_CTCF-left

description: 4C material


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 107)

description: Fig 8 and 10


title: post-RASP dengue virus infected dataset #2 sample 7

description: post-RASP dengue virus infected samples 7 of 13


title: post-RASP dengue virus infected dataset #2 sample 2

description: post-RASP dengue virus infected samples 2 of 13


title: post-RASP dengue virus infected dataset #2 sample 3

description: post-RASP dengue virus infected samples 3 of 13


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 106)

description: Fig 8 and 10


title: E12_Limbs_TgN3840_CTCF-right

description: 4C material


title: post-RASP dengue virus infected dataset #2 sample 4

description: post-RASP dengue virus infected samples 4 of 13


title: post-RASP dengue virus infected dataset #2 sample 1

description: post-RASP dengue virus infected samples 1 of 13


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 105)

description: Fig 8 and 10


title: pre-RASP Yersinia pestis infected dataset #2 sample 9

description: pre-RASP Yersinia pestis infected samples 9 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 8

description: pre-RASP Yersinia pestis infected samples 8 of 13


title: E12_Limbs_TgN3840_CS40

description: 4C material


title: pre-RASP Yersinia pestis infected dataset #2 sample 7

description: pre-RASP Yersinia pestis infected samples 7 of 13


title: prime/boost challengePBSd14 dpc (SAMPLE 103)

description: Fig 8 and 10

value: PBS


title: prime/boost challengePBSd14 dpc (SAMPLE 104)

description: Fig 8 and 10


title: pre-RASP Yersinia pestis infected dataset #2 sample 6

description: pre-RASP Yersinia pestis infected samples 6 of 13


title: E12_Limbs_TgN3840_CTCF-left

description: 4C material


title: nca_DRNM_10d_rep5 [H06501]

description:
H06501
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

data_processing:
Library strategy: 16S rRNA sequencing
16S rRNA: After assembling the reads using SeqPrep, subsequent identification of chimera with ChimeraSlayer and manual verification, chimera were removed from the data set. The sequences were further analyzes using QIIME 1.9.0.
RNA-Seq: After quality filtering (fastq_illumina_filter, prinseq-lite, cutadapt), sequencing reads were mapped against the Drosophila melanogaster reference BDGP6 using TopHat v2.1.0 with sensitive option. The read counts per transcript were calculated with the Python script HTSeq v0.6.1p1 using the mode ‘intersection-strict’.
Genome_build: Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files include read counts per gene for each sample.
Supplementary_files_format_and_content: otu_table_mc50_w_tax_wochimera_ctrl_50filtered.txt: Tab-delimited text file includes read counts per OTU for each sample.

organism: insect gut metagenome

source_name: midguts of 5 Drosophila melanogaster individuals

tag: tissue

value: Midguts

value: DRNM

value: 10 days


title: pre-RASP Yersinia pestis infected dataset #2 sample 4

description: pre-RASP Yersinia pestis infected samples 4 of 13

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: pre-RASP Yersinia pestis infected dataset #2 sample 2

description: pre-RASP Yersinia pestis infected samples 2 of 13


title: prime/boost challengePBSd14 dpc (SAMPLE 102)

description: Fig 8 and 10


title: pre-RASP Yersinia pestis infected dataset #2 sample 5

description: pre-RASP Yersinia pestis infected samples 5 of 13


title: E12_Limbs_TgN3840_CS38

description: 4C material


title: pre-RASP dengue virus infected dataset #2 sample 12

description: pre-RASP dengue virus infected samples 12 of 13


title: prime/boost challengePBSd14 dpc (SAMPLE 101)

description: Fig 8 and 10


title: pre-RASP dengue virus infected dataset #2 sample 11

description: pre-RASP dengue virus infected samples 11 of 13


title: nca_DRNM_10d_rep4 [H06500]

description:
H06500
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP dengue virus infected dataset #2 sample 13

description: pre-RASP dengue virus infected samples 13 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 1

description: pre-RASP Yersinia pestis infected samples 1 of 13


title: prime/boost challengecaLend14 dpc (SAMPLE 99)

description: Fig 8 and 10


title: pre-RASP Yersinia pestis infected dataset #2 sample 3

description: pre-RASP Yersinia pestis infected samples 3 of 13


title: prime/boost challengecaLend14 dpc (SAMPLE 100)

description: Fig 8 and 10


title: nca_DRNM_10d_rep3 [H06499]

description:
H06499
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_DRNM_10d_rep2 [H06498]

description:
H06498
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP dengue virus infected dataset #2 sample 10

description: pre-RASP dengue virus infected samples 10 of 13


title: pre-RASP Yersinia pestis infected dataset #2 sample 10

description: pre-RASP Yersinia pestis infected samples 10 of 13


title: prime/boost challengecaLend14 dpc (SAMPLE 98)

description: Fig 8 and 10


title: nca_DRNM_10d_rep1 [H06497]

description:
H06497
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP dengue virus infected dataset #2 sample 9

description: pre-RASP dengue virus infected samples 9 of 13


title: pre-RASP dengue virus infected dataset #2 sample 8

description: pre-RASP dengue virus infected samples 8 of 13


title: nca_DR_10d_rep5 [H06496]

description:
H06496
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: DR


title: pre-RASP dengue virus infected dataset #2 sample 6

description: pre-RASP dengue virus infected samples 6 of 13


title: pre-RASP dengue virus infected dataset #2 sample 7

description: pre-RASP dengue virus infected samples 7 of 13


title: pre-RASP dengue virus infected dataset #2 sample 5

description: pre-RASP dengue virus infected samples 5 of 13


title: nca_DR_10d_rep3 [H06494]

description:
H06494
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP dengue virus infected dataset #2 sample 2

description: pre-RASP dengue virus infected samples 2 of 13


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 95)

description: Fig 8 and 10


title: nca_DR_10d_rep4 [H06495]

description:
H06495
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 96)

description: Fig 8 and 10


title: pre-RASP dengue virus infected dataset #2 sample 3

description: pre-RASP dengue virus infected samples 3 of 13


title: pre-RASP dengue virus infected dataset #2 sample 4

description: pre-RASP dengue virus infected samples 4 of 13


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 94)

description: Fig 8 and 10


title: pre-RASP SEB exposed dataset #2 sample 8

description: pre-RASP SEB exposed samples 8 of 9


title: pre-RASP SEB exposed dataset #2 sample 7

description: pre-RASP SEB exposed samples 7 of 9


title: pre-RASP dengue virus infected dataset #2 sample 1

description: pre-RASP dengue virus infected samples 1 of 13


title: nca_DR_10d_rep1 [H06492]

description:
H06492
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP SEB exposed dataset #2 sample 9

description: pre-RASP SEB exposed samples 9 of 9


title: nca_DR_10d_rep2 [H06493]

description:
H06493
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP Yersinia pestis infected dataset #2 sample 12

description: post-RASP Yersinia pestis infected samples 12 of 14


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 93)

description: Fig 8 and 10


title: pre-RASP SEB exposed dataset #2 sample 6

description: pre-RASP SEB exposed samples 6 of 9


title: prime/boost challengePBSd14 dpc (SAMPLE 92)

description: Fig 8 and 10


title: nca_NM_10d_rep5 [H06491]

description:
H06491
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 97)

description: Fig 8 and 10


title: prime/boost challengePBSd14 dpc (SAMPLE 91)

description: Fig 8 and 10


title: nca_NM_10d_rep4 [H06490]

description:
H06490
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengePBSd14 dpc (SAMPLE 90)

description: Fig 8 and 10


title: pre-RASP SEB exposed dataset #2 sample 5

description: pre-RASP SEB exposed samples 5 of 9


title: nca_NM_10d_rep2 [H06488]

description:
H06488
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_NM_10d_rep3 [H06489]

description:
H06489
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_NM_10d_rep1 [H06487]

description:
H06487
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 88)

description: Fig 8 and 10

source_name: Nasal wash

value: Nasal wash


title: prime/boost challengePBSd14 dpc (SAMPLE 89)

description: Fig 8 and 10


title: pre-RASP SEB exposed dataset #2 sample 3

description: pre-RASP SEB exposed samples 3 of 9


title: pre-RASP SEB exposed dataset #2 sample 2

description: pre-RASP SEB exposed samples 2 of 9


title: prime/boost challengecaLend14 dpc (SAMPLE 86)

description: Fig 8 and 10


title: post-RASP SEB exposed dataset #2 sample 13

description: post-RASP SEB exposed samples 13 of 15


title: post-RASP SEB exposed dataset #2 sample 12

description: post-RASP SEB exposed samples 12 of 15


title: post-RASP SEB exposed dataset #2 sample 10

description: post-RASP SEB exposed samples 10 of 15


title: post-RASP SEB exposed dataset #2 sample 11

description: post-RASP SEB exposed samples 11 of 15


title: pre-RASP SEB exposed dataset #2 sample 4

description: pre-RASP SEB exposed samples 4 of 9


title: pre-RASP SEB exposed dataset #2 sample 1

description: pre-RASP SEB exposed samples 1 of 9


title: post-RASP SEB exposed dataset #2 sample 14

description: post-RASP SEB exposed samples 14 of 15


title: nca_DRNM_6d_rep4 [H06485]

description:
H06485
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: 6 days


title: post-RASP SEB exposed dataset #2 sample 9

description: post-RASP SEB exposed samples 9 of 15


title: post-RASP SEB exposed dataset #2 sample 3

description: post-RASP SEB exposed samples 3 of 15


title: post-RASP SEB exposed dataset #2 sample 5

description: post-RASP SEB exposed samples 5 of 15


title: post-RASP SEB exposed dataset #2 sample 6

description: post-RASP SEB exposed samples 6 of 15


title: post-RASP SEB exposed dataset #2 sample 15

description: post-RASP SEB exposed samples 15 of 15


title: post-RASP SEB exposed dataset #2 sample 4

description: post-RASP SEB exposed samples 4 of 15


title: post-RASP SEB exposed dataset #2 sample 8

description: post-RASP SEB exposed samples 8 of 15


title: post-RASP SEB exposed dataset #2 sample 7

description: post-RASP SEB exposed samples 7 of 15


title: nca_DRNM_6d_rep3 [H06484]

description:
H06484
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Control


title: prime/boost challengecaLend14 dpc (SAMPLE 87)

description: Fig 8 and 10


title: prime/boost challengecaLend14 dpc (SAMPLE 85)

description: Fig 8 and 10


title: post-RASP SEB exposed dataset #2 sample 2

description: post-RASP SEB exposed samples 2 of 15


title: nca_DRNM_6d_rep2 [H06483]

description:
H06483
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_DRNM_6d_rep5 [H06486]

description:
H06486
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 84)

description: Fig 8 and 10


title: nca_DRNM_6d_rep1 [H06482]

description:
H06482
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 83)

description: Fig 8 and 10


title: nca_DR_6d_rep5 [H06481]

description:
H06481
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 82)

description: Fig 8 and 10


title: post-RASP SEB exposed dataset #2 sample 1

description: post-RASP SEB exposed samples 1 of 15


title: pre-RASP control dataset #2 sample 35

description: pre-RASP control samples 35 of 36


title: pre-RASP control dataset #2 sample 36

description: pre-RASP control samples 36 of 36


title: pre-RASP control dataset #2 sample 32

description: pre-RASP control samples 32 of 36


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 81)

description: Fig 8 and 10


title: pre-RASP control dataset #2 sample 30

description: pre-RASP control samples 30 of 36


title: prime/boost challengePBSd14 dpc (SAMPLE 80)

description: Fig 8 and 10


title: nca_DR_6d_rep4 [H06480]

description:
H06480
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_DR_6d_rep2 [H06478]

description:
H06478
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 34

description: pre-RASP control samples 34 of 36


title: pre-RASP control dataset #2 sample 33

description: pre-RASP control samples 33 of 36


title: nca_DR_6d_rep1 [H06477]

description:
H06477
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 31

description: pre-RASP control samples 31 of 36


title: pre-RASP control dataset #2 sample 27

description: pre-RASP control samples 27 of 36


title: nca_DR_6d_rep3 [H06479]

description:
H06479
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 28

description: pre-RASP control samples 28 of 36


title: pre-RASP control dataset #2 sample 24

description: pre-RASP control samples 24 of 36


title: pre-RASP control dataset #2 sample 29

description: pre-RASP control samples 29 of 36


title: prime/boost challengePBSd14 dpc (SAMPLE 79)

description: Fig 8 and 10


title: pre-RASP control dataset #2 sample 25

description: pre-RASP control samples 25 of 36


title: pre-RASP control dataset #2 sample 23

description: pre-RASP control samples 23 of 36


title: nca_NM_6d_rep5 [H06476]

description:
H06476
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: NM


title: pre-RASP control dataset #2 sample 26

description: pre-RASP control samples 26 of 36


title: prime/boost challengePBSd14 dpc (SAMPLE 78)

description: Fig 8 and 10


title: prime/boost challengePBSd14 dpc (SAMPLE 77)

description: Fig 8 and 10


title: pre-RASP control dataset #2 sample 21

description: pre-RASP control samples 21 of 36


title: pre-RASP control dataset #2 sample 22

description: pre-RASP control samples 22 of 36


title: nca_NM_6d_rep2 [H06473]

description:
H06473
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_NM_6d_rep3 [H06474]

description:
H06474
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_DR_3d_rep4 [H06470]

description:
H06470
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: 3 days


title: nca_DR_3d_rep5 [H06471]

description:
H06471
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 73)

description: Fig 8 and 10

value: prime/boost challenge


title: prime/boost challengecaLend14 dpc (SAMPLE 74)

description: Fig 8 and 10

value: caLen


title: prime/boost challengecaLend14 dpc (SAMPLE 75)

description: Fig 8 and 10

value: d14 dpc


title: nca_DR_3d_rep3 [H06469]

description:
H06469
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 71)

description: Fig 8 and 10


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 72)

description: Fig 8 and 10


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 70)

description: Fig 8 and 10


title: prime/boost challengecaLend14 dpc (SAMPLE 76)

description: Fig 8 and 10


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 69)

description: Fig 8 and 10


title: pre-RASP control dataset #2 sample 16

description: pre-RASP control samples 16 of 36


title: pre-RASP control dataset #2 sample 19

description: pre-RASP control samples 19 of 36


title: pre-RASP control dataset #2 sample 18

description: pre-RASP control samples 18 of 36


title: pre-RASP control dataset #2 sample 13

description: pre-RASP control samples 13 of 36


title: pre-RASP control dataset #2 sample 17

description: pre-RASP control samples 17 of 36


title: pre-RASP control dataset #2 sample 9

description: pre-RASP control samples 9 of 36


title: pre-RASP control dataset #2 sample 20

description: pre-RASP control samples 20 of 36


title: pre-RASP control dataset #2 sample 11

description: pre-RASP control samples 11 of 36


title: pre-RASP control dataset #2 sample 12

description: pre-RASP control samples 12 of 36


title: nca_DR_3d_rep2 [H06468]

description:
H06468
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 7

description: pre-RASP control samples 7 of 36


title: nca_NM_6d_rep1 [H06472]

description:
H06472
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 10

description: pre-RASP control samples 10 of 36


title: nca_NM_6d_rep4 [H06475]

description:
H06475
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 14

description: pre-RASP control samples 14 of 36


title: prime/boost challengePBSd14 dpc (SAMPLE 68)

description: Fig 8 and 10


title: nca_NM_3d_rep5 [H06466]

description:
H06466
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: pre-RASP control dataset #2 sample 6

description: pre-RASP control samples 6 of 36


title: pre-RASP control dataset #2 sample 15

description: pre-RASP control samples 15 of 36


title: nca_DR_3d_rep1 [H06467]

description:
H06467
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: DM_48h_PFI3_B

city: Worcester

first: Tapan

last: Sharma

state: MA

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

data_processing:
Libraries were sequenced using the BGISEQ-500 platform and reads were filtered to remove adaptor-polluted, low quality and high content of unknown base reads.
About 99% of the raw reads were identified as clean reads (~65M). Of these about 70% reads were uniquely mapped to mouse reference genome mm10 using HISAT.
Transcripts were reconstructed using StringTie, and novel transcripts were identified using Cufflinks. All transcripts were then combined together and mapped to the mm10 reference transcriptome using Bowtie.
Gene expression levels were calculated using RSEM. DEseq2 and PoissonDis algorithms were used to detect differentially expressed genes (DEG).
Genome_build: mm10
Supplementary_files_format_and_content: Spreadsheet files in xls format containing FPKM values for each Sample.

source_name: Immortalized myoblast cell line

growth_protocol: C2C12 cells were grown at 37℃ in 5% CO2 and maintained at a confluency of 70% or less in Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). For induction of differentiation, cells were allowed to become 90% confluent and media was changed to Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 2% horse serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). Insulin was added freshly to a final concentration of (2ug/ml).

extract_protocol:
Cells were harvested after the required treatments at specified timepoints. RNA was extracted by Trizol-chloroform phase separation followed by iso-propanol precipitaion. RNA pellet was resuspended in nuclease-free water.
RNA libraries were prepared by BGI Americas according to their standard protocol.

treatment_protocol: Cells were pretreated with DMSO/PFI-3 for 12 hours before harvesting for proliferative condition (GM). Cells for DM 24h and DM 48h were also pretreated with DMSO/PFI-3 for 12 hours. DMSO/PFI-3 was also replenished in the differentiation media every 24 hours.

tag: cell line

value: Myoblasts

tag: Stage

value: 48h differentiated stage

tag: treatment

value: 50uM PFI-3


title: pre-RASP control dataset #2 sample 8

description: pre-RASP control samples 8 of 36


title: prime/boost challengePBSd14 dpc (SAMPLE 66)

description: Fig 8 and 10

value: PBS


title: prime/boost challengePBSd14 dpc (SAMPLE 67)

description: Fig 8 and 10


title: DM_48h_DMSO_B

value: DMSO


title: DM_24h_PFI3_B

value: 24h differentiated stage


title: nca_NM_3d_rep4 [H06465]

description:
H06465
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Midguts

tag: disease state

tag: diet

tag: feeding time


title: pre-RASP control dataset #2 sample 5

description: pre-RASP control samples 5 of 36

tag: sample type

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: DM_24h_DMSO_B


title: pre-RASP control dataset #2 sample 3

description: pre-RASP control samples 3 of 36


title: pre-RASP control dataset #2 sample 4

description: pre-RASP control samples 4 of 36


title: nca_NM_3d_rep2 [H06463]

description:
H06463
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: nca_NM_3d_rep3 [H06464]

description:
H06464
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 64)

description: Fig 7 and 9

source_name: Serum

value: Serum


title: prime/boost challengePBSd14 dpc (SAMPLE 65)

description: Fig 8 and 10

value: Nasal wash


title: prime/boost challengecaLend14 dpc (SAMPLE 63)

description: Fig 7 and 9


title: nca_NM_3d_rep1 [H06462]

description:
H06462
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Control


title: ca_DRNM_10d_rep5 [H06461]

description:
H06461
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Cancer

value: DRNM

value: 10 days


title: GM_DMSO_B

value: proliferative stage


title: pre-RASP control dataset #2 sample 2

description: pre-RASP control samples 2 of 36


title: DM_48h_PFI3_A


title: post-RASP stress dataset #2 sample 43

description: post-RASP stress samples 43  of 43


title: pre-RASP control dataset #2 sample 1

description: pre-RASP control samples 1 of 36


title: post-RASP stress dataset #2 sample 42

description: post-RASP stress samples 42  of 43


title: ca_DRNM_10d_rep4 [H06460]

description:
H06460
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: DM_48h_DMSO_A


title: DM_24h_PFI3_A


title: ca_DRNM_10d_rep3 [H06459]

description:
H06459
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP stress dataset #2 sample 41

description: post-RASP stress samples 41  of 43


title: prime/boost challengecaLend14 dpc (SAMPLE 60)

description: Fig 7 and 9

value: prime/boost challenge

value: caLen

value: d14 dpc


title: prime/boost challengecaLend14 dpc (SAMPLE 61)

description: Fig 7 and 9


title: prime/boost challengecaLend14 dpc (SAMPLE 59)

description: Fig 7 and 9


title: GM_PFI3_B

value: Myoblasts

value: 50uM PFI-3


title: DM_24h_DMSO_A

value: DMSO


title: ca_DRNM_10d_rep2 [H06458]

description:
H06458
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: ca_DRNM_10d_rep1 [H06457]

description:
H06457
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 62)

description: Fig 7 and 9


title: post-RASP stress dataset #2 sample 40

description: post-RASP stress samples 40  of 43


title: GM_PFI3_A


title: prime/boost challengecaLend14 dpc (SAMPLE 58)

description: Fig 7 and 9


title: post-RASP stress dataset #2 sample 39

description: post-RASP stress samples 39  of 43


title: ca_DR_10d_rep5 [H06456]

description:
H06456
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: DR


title: ca_DR_10d_rep4 [H06455]

description:
H06455
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Midguts


title: SPLASH delta382

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description: processed data file:

data_processing:
library strategy: SPLASH
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
PoreCupine samples were basecalled with  live basecalling and processed with minimap2, Python and R
SPLASH samples were mapped with bwa-mem (version 0.7.17); chimeric reads were detected using the pipelie from Aw et al (2016)
NmSeq: the adaptor were trimmed by cutadapt (version 1.8.1); duplicational reads were remove according to UMI; Nmseq samples were mapped with bwa-aln (version 0.7.17); the accumulation depth of 3' end of reads were normalized by the read counts of each gene, subtracted to the background of input control; the enrichment of 2'OM was calculated with Z-test with the conditions FDR <0.05, DOED >=10, DOED/Dinput > 1.5.
Genome_build: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_414378 (SARS-CoV-2 Delta382); ChlSab1.1.102
Supplementary_files_format_and_content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary_files_format_and_content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT & Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_03_Delta382_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_04_WT_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_05_PORECUPINE.csv: Pore-Cupine reactivity data
Supplementary_files_format_and_content: SUPPORTING_TABLE_06_Delta382_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_07_WT_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_08_NMseq_HOST_ALL.tsv: 2'O-methylation on host RNA
Supplementary_files_format_and_content: SUPPORTING_TABLE_09_NMseq_SARS-CoV-2.tsv: 2'O-methylation on virus RNA

organism: Chlorocebus

source_name: Vero cell infected with SARS COV2 EPI_ISL_414378 strain

growth_protocol: Vero E6 cells were infected with/without SARS-CoV viruses (WX56 wild-type and CA001 d382 mutant) at an multiplicity of infection (MOI) = 0.01 for 48 h.

extract_protocol:
SHAPE-MaP Structure probing: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
SHAPE-MaP libraries were made similar to the published protocol Smola et al. (2015)
SPLASH: The total RNA was extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
SPLASH libraries were made similarly to the published protocol in Aw et al.(2016)
NmSeq: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
NmSeq libraries were constructed and multiplexed following the published method in Hsu, P.J., et al. (2019).

treatment_protocol:
SHAPE-MaP Structure probing and PORE-cupine were performed by using 1:20 the volume of 1M NAI (03-310, Merck, 25 µl of NAI in 500 µl of infected cells) and incubated the reaction for 15 min at 37 °C for structure probing; we added 1:20 volume of dimethyl sulfoxide (DMSO) as negative control; aside a third portion of the virus as for the denaturing control in the downstream library preparation process.
We performed SPLASH libraries similarly to the published protocol in Aw et al.(2016). The cells were then incubated with 200 µM biotinylated psoralen and 0.01% digitonin in PBS for 10 min at 37 °C. The cells were spread onto a 10cm dish and irradiated at 365 nm of UV on ice for 20 min. the total RNA was extracted using E.Z.N.A. Total RNA Kit I (Omega bio-tek) according to the manufacturer’s instructions.
NmSeq was performed following the published method in Hsu, P.J., et al. (2019). In brief, 8 rounds of oxidation-elimination-dephosphorylation (OED) plus an extra oxidation-elimination step were performed to cause enrichment of the 3' read ends at the 2’OM sites. 10 ug of each samples were used following NmSeq protocol. For input control library without OED, 1ug of RNA were used. The libraries were constructed using NEBNext Small RNA library kit with customized adaptors as mentioned in the published protocol.

value: Vero cell


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 56)

description: Fig 7 and 9


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 55)

description: Fig 7 and 9


title: ca_DR_10d_rep3 [H06454]

description:
H06454
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: SPLASH wt

description: processed data file:

source_name: Vero cell infected with SARS COV2 EPI_ISL_407987 strain


title: post-RASP stress dataset #2 sample 36

description: post-RASP stress samples 36  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: post-RASP stress dataset #2 sample 35

description: post-RASP stress samples 35  of 43


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 54)

description: Fig 7 and 9

value: Serum


title: GM_DMSO_A


title: post-RASP stress dataset #2 sample 38

description: post-RASP stress samples 38  of 43


title: ca_DR_10d_rep1 [H06452]

description:
H06452
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP stress dataset #2 sample 34

description: post-RASP stress samples 34  of 43


title: ca_NM_10d_rep5 [H06451]

description:
H06451
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: NM


title: prime/boost challengecaLend14 dpc (SAMPLE 57)

description: Fig 7 and 9


title: PORE-cupine_delta_unmod

description:
processed data file:
SUPPORTING_TABLE_05_PORECUPINE.csv

data_processing:
library strategy: PORE-cupine
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
PoreCupine samples were basecalled with  live basecalling and processed with minimap2, Python and R
SPLASH samples were mapped with bwa-mem (version 0.7.17); chimeric reads were detected using the pipelie from Aw et al (2016)
NmSeq: the adaptor were trimmed by cutadapt (version 1.8.1); duplicational reads were remove according to UMI; Nmseq samples were mapped with bwa-aln (version 0.7.17); the accumulation depth of 3' end of reads were normalized by the read counts of each gene, subtracted to the background of input control; the enrichment of 2'OM was calculated with Z-test with the conditions FDR <0.05, DOED >=10, DOED/Dinput > 1.5.
Genome_build: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_414378 (SARS-CoV-2 Delta382); ChlSab1.1.102
Supplementary_files_format_and_content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary_files_format_and_content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT & Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_03_Delta382_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_04_WT_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_05_PORECUPINE.csv: Pore-Cupine reactivity data
Supplementary_files_format_and_content: SUPPORTING_TABLE_06_Delta382_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_07_WT_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_08_NMseq_HOST_ALL.tsv: 2'O-methylation on host RNA
Supplementary_files_format_and_content: SUPPORTING_TABLE_09_NMseq_SARS-CoV-2.tsv: 2'O-methylation on virus RNA

value: infected with SARS COV2 EPI_ISL_414378 strain


title: PORE-cupine_wt_unmod

value: infected with SARS COV2 EPI_ISL_407987 strain


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 52)

description: Fig 7 and 9


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 51)

description: Fig 7 and 9


title: post-RASP stress dataset #2 sample 37

description: post-RASP stress samples 37  of 43


title: ca_NM_10d_rep4 [H06450]

description:
H06450
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Cancer

value: 10 days


title: post-RASP stress dataset #2 sample 32

description: post-RASP stress samples 32  of 43


title: PORE-cupine_delta_mod


title: post-RASP stress dataset #2 sample 31

description: post-RASP stress samples 31  of 43


title: ca_DR_10d_rep2 [H06453]

description:
H06453
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP stress dataset #2 sample 30

description: post-RASP stress samples 30  of 43


title: ca_NM_10d_rep2 [H06448]

description:
H06448
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: ca_NM_10d_rep3 [H06449]

description:
H06449
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt