title: Ago2KO + FM-Ago1 Rep2

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1; subsequently all had 4N (from sequencing adapters) trimmed from 5p and 3p end using seqtk (v1.2-r101).
Trimmed reads were first aligned drosophila viral genomes to eliminate contaminants and then to dm6 using bowtie and intersected with the genome annotation r6.12 to determine the alignment identity using inhouse scripts.
The total count of reads after accounting for multimappers is reported in the read_annotation.tsv
The only conclusions and analysis we've made in our manuscript is based on the reads aligning to ncRNA and coding RNA regions. This data should be enclosed in the read_annotation.tsv file.
Genome_build: dm6
Supplementary_files_format_and_content: read_annotation.tsv: Read counts per annotation group, following a hierarchical strategy outlined above.

organism: Drosophila melanogaster

source_name: Schneider 2 (S2) cells

growth_protocol: Drosophila Schneider 2 (S2) cells were cultured in Schneider’s Drosophila Medium (Gibco) containing 10% FBS (Gibco), maintained at 25°C and passaged every 3 days.

extract_protocol:
Total RNA extraction with Trizol according to manufacturer's instructions followed by biochemical purification of Argonaute ribonucleoprotein complexes.
Libraries were performed using an in-house protocol: ligate 3p linker; size select ligation product; ligate 5p linker; size select ligation product; reverse transcription; qPCR library amplification. 3p and 5p adapters contain 4N at ligation interface (Jayaprakash et al, NAR, 2011)

treatment_protocol: Drosophila S2 cells either wild-type, tailorKO, wild-type + FM-Ago1, ago2KO, or ago2KO + FM-Ago1 directly lysed in Trizol® (Ambion)

tag: genotype

tag: overexpression

tag: flag-myc

value: Flag-myc


title: Ago2KO + FM-Ago1 Rep1

status: Public on Aug 06 2019

type: SRA

library_source: transcriptomic

molecule: total RNA


title: Ago2KO Rep2

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1; subsequently all had 4N (from sequencing adapters) trimmed from 5p and 3p end using seqtk (v1.2-r101).
Trimmed reads were first aligned drosophila viral genomes to eliminate contaminants and then to dm6 using bowtie and intersected with the genome annotation r6.12 to determine the alignment identity using inhouse scripts.
The only conclusions and analysis we've made in our manuscript is based on the reads aligning to ncRNA and coding RNA regions. This data should be enclosed in the read_annotation.tsv file.
The total count of reads after accounting for multimappers is reported in the read_annotation.tsv
Genome_build: dm6
Supplementary_files_format_and_content: read_annotation.tsv: Read counts per annotation group, following a hierarchical strategy outlined above.


title: Ago2KO Rep1


title: 1_Mock_Veh

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

country: Japan

institute: Tohoku University

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
Reads were mapped against mouse (mm9) genome using the TopHat v2.0.8b.
Differential gene analaysis was performed using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

organism: Mus musculus

growth_protocol: MEFs were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN).
Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).

treatment_protocol: MEFs were treated with 100µM Diethyl Maleate (DEM) or Vehcle for 12 hr.

tag: cell type

value: embryonic fibroblast

tag: genotype/variation

tag: treatment

value: Vehcle for 12 hrs


title: wild-type + FM-Ago1 Rep3

value: wt


title: eMZB_pos_3

city: Atlanta

first: Jeremy

middle: Matthew

last: Boss

state: Georgia

address: 1510 Clifton Rd NE, Room 3120

department: Microbiology and Immunology

country: USA

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the Bioconductor package GenomicAlignments.
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing FPKM for each sample.

source_name: ex vivo-derived marginal zone B cells

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
All RNA from 2,000 cells per sample was used as input for the Takara SMART-Seq v4 Ultra Low Input RNA Kit to generate cDNA. Libraries were generated with the Illumina Nextera XT DNA Library Prep Kit

treatment_protocol: Transitional B cells were magnetically enriched from the spleens of wild-type and LSD1-knockout mice. They were either FACS-purified or cultured for 3 days while subjected to BAFF and DL1 stimulated. After 3 days, culture-derived marginal zone B cells were FACS-purified

value: ex vivo-derived marginal zone B cells

tag: Sex

value: female

tag: sorting markers

tag: strain

tag: organ

value: culture

tag: stimulation

value: DL1 and BAFF

tag: lsd1 status

value: wild-type


title: eMZB_pos_2


title: wild-type + FM-Ago1 Rep2


title: eMZB_pos_1


title: wild-type + FM-Ago1 Rep1


title: TailorKO Rep2

value: tailorKO


title: S2 wild-type Rep3


title: S2 wild-type Rep2

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1; subsequently all had 4N (from sequencing adapters) trimmed from 5p and 3p end using seqtk (v1.2-r101).
Trimmed reads were first aligned drosophila viral genomes to eliminate contaminants and then to dm6 using bowtie and intersected with the genome annotation r6.12 to determine the alignment identity using inhouse scripts.
The total count of reads after accounting for multimappers is reported in the read_annotation.tsv
Genome_build: dm6
The only conclusions and analysis we've made in our manuscript is based on the reads aligning to ncRNA and coding RNA regions. This data should be enclosed in the read_annotation.tsv file.
Supplementary_files_format_and_content: read_annotation.tsv: Read counts per annotation group, following a hierarchical strategy outlined above.


title: TailorKO Rep1


title: ago2KO 5min s4U bound Rep3

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1; subsequently all reads were reverse complemented and 10 nucleotides were trimmed from the (new) 3p end using seqtk (v1.2-r101).
Trimmed reads were aligned using SLAMdunk v0.2.4: Reads were aligned to the full reference genome (dm6) using local alignment scoring. In the filtering step, alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped were retained. SNPs exceeding a coverage cutoff of 10x and a variant fraction cutoff of 0.2 were called using VarScan2.4.1 using default parameters. Non-SNP overlapping T>C mutations with a base quality of Phred score >26 were identified.
T>C containing reads and total reads aligning within the custom defined counting windows (pri-mir_transcripts.bed) were reported.
T>C conversion rate was determined for each position along the custom defined counting windows by normalizing to genomic T content and coverage of each position and averaged per UTR.
Genome_build: dm6
Supplementary_files_format_and_content: pri-mir_transcripts.bed: manually curated windows defining primary miRNA transcripts as a basis to quantify their specific expression and T>C conversions. *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

extract_protocol:
Total RNA was extracted from Ago2ko Drosophila S2 cells using TRIZOL as per manufacturers instructions.
Libraries were prepared combining TT-Seq (Schwalb et al, Science 2016) and SLAMseq. Isolated RNA was fragmented for 1 min at 94°C in NEBNext RNA Fragmentation buffer resulting in 1kb fragments and then was immediately placed on ice to stop the reaction by adding 2 µl Fragmentation stop solution. Fragmented RNA was biotinylated and after removing excess biotin denatured. Denatured RNA was mixed and incubated with µMACS streptavidin beads for 15 minutes. Labelled RNA was captured on µMACS column, washed 3 times and subsequently eluted. Now purified RNA was subjected to iodoacetamide treatment as previously described (Herzog et al, Nature Methods, 2017). The library was then prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s protocol, but the fragmentation time prior to first strand synthesis was shortened to 8 min due to the pre-fragmentation of RNA before biotinylation.

treatment_protocol: Drosophila S2 cells were incubated with standard medium, supplemented with 500µM s4U for the indicated time and then dirctly lysed in Trizol® (Ambion)

value: 5min s4U

tag: molecule

value: Biotin precipitated total RNA


title: TrB_pos_2

source_name: transitional B cells

value: transitional B cells

value: spleen

value: no stimulation


title: eMZB_del_3

value: knockout


title: eMZB_del_2


title: TrB_del_3


title: TrB_pos_1


title: TrB_pos_3


title: ago2KO 5min s4U bound Rep2


title: eMZB_del_1


title: TrB_del_1


title: ago2KO 5min s4U input Rep3


title: ago2KO 5min s4U input Rep2


title: TrB_del_2


title: FoB_pos_2 RNAseq

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the Bioconductor package GenomicAlignments.
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing mRNA/cell (FPKM normalized to ERCC spike-in transcripts) normalized read counts for each sample.

source_name: follicular B cells

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
All RNA from 50,000 cells per sample was used as input for the KAPA Biosystems Stranded mRNA-seq kit with polyA selection beads.

treatment_protocol: No treatment

value: follicular B cells


title: ago2KO 5min s4U bound Rep1


title: ago2KO 5min s4U input Rep1


title: FoB_del_3 RNAseq


title: FoB_pos_1 RNAseq


title: nbrKO + nbrCM-OE S2 cells smallRNAs Rep2

description:
nbr_smallRNAreads
filteredPositions.tsv
filteredLenDis.tsv

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1 and subsequently 4 nucleotides were trimmed from both ends using seqtk (v1.2-r101).
Trimmed reads were aligned to genome with bowtie v1.2.2, to determine total number of smallRNA locus drived reads.
Trimmed reads were aligned to pre-miRNA hairpins only, and analysed using smRNAseq nextflow pipeline, to determine length statistics
Genome_build: dm6
----
Supplementary_files_format_and_content -- nbr_smallRNAreads.tsv:
tab separated text file for libraries - Columns:
(idx) 5-digit sample id of each file; corresponds to number before "_" of file name
(sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint
(miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint
(time) required to partition files or replicates. random unique values are used for this column as the processing script would fail without it."
----
Supplementary_files_format_and_content -- filteredPositions.tsv:
tab separated text file - Columns:
(pos) hairpin-relative position of mapped 5' isoforms
(flybase_id) flybase gene name
(mir_name) mirbase mir name
(arm.name) 5p or 3p arm
(average.ppm) average reads over entire timecourse
(mir.type) mature or star
(seed) first 8nt
(UCount) Ts over position 1-18
(5p) mirbase annotated start of 5p miR
(loop) rough position of start/within hairpin loop; unused
(3p) mirbase annotated start of 3p miR
(read.type) totalReads or tcReads for a count of all or only tc reads aligning to same 5' position
(timepoint) 5-digit id of file; corresponds to number before "_" of file name, corresponds to idx in smallRNAreads.tsv
(time) time from smallRNAreads.tsv for corresponding idx (which is labelled as "timepoint" in this file)
(reads) reads in ppm, normalised to smallRNAs
----
Supplementary_files_format_and_content -- filteredLenDis.tsv:
tab separated text file - Columns:
(pos) hairpin-relative position of mapped 5' isoforms
(flybase_id) flybase gene name
(mir_name) mirbase mir name
(arm.name) 5p or 3p arm
(average.ppm) average reads over entire timecourse
(mir.type) mature or star
(seed) first 8nt
(UCount) Ts over position 1-18
(seqLen) length of sequences mapped to same 5' position; used for weighted average length
(5p) mirbase annotated start of 5p miR
(loop) rough position of start/within hairpin loop; unused
(3p) mirbase annotated start of 3p miR
(LD.type) totalLenDis or tcLenDis depending for all or TC only reads
(timepoint) 5-digit id of file; corresponds to number before "_" of file name, corresponds to idx in smallRNAreads.tsv
(time) time from smallRNAreads.tsv for corresponding idx (which is labelled as "timepoint" in this file)
(reads) reads in ppm, normalised to smallRNAs, at length specified in (seqLen), mapping to the same 5' position"

extract_protocol:
Cells are spun down and directly lysed in Trizol according to manufacturers instructions.
in-house protocol: size select 18-30nt RNA; deplete 2S rRNA; ligate 3p linker; size select ligation product; ligate 5p linker; size select ligation product; reverse transcription; qPCR library amplification. 3p and 5p adapters contain 4N at ligation interface (Jayaprakash et al, NAR, 2011)

treatment_protocol: Drosophila S2 cells either wild-type, nbrKO, nbrKO + nbrWT (wild-type), or nbrKO + nbrCM (catalytically inactive) cells.

value: nbr knock-out + nbr catalytic mutant overexpression

tag: size selection


title: ago2KO no s4U input

value: no s4U


title: FoB_del_2 RNAseq


title: FoB_del_1 RNAseq


title: S2 wild-type Rep1


title: nbrKO + nbrWT-OE S2 cells smallRNAs Rep2

value: nbr knock-out + nbr wt overexpression


title: MZB_pos_3 RNAseq

source_name: marginal zone B cells

value: marginal zone B cells


title: nbrKO + nbrWT-OE S2 cells smallRNAs Rep1


title: nbrKO + nbrCM-OE S2 cells smallRNAs Rep1


title: MZB_pos_1 RNAseq


title: MZB_pos_2 RNAseq


title: MZB_del_2 RNAseq


title: FoB_pos_3 ATACseq

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie-1.1.1
For each sample, peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Data were normalized to reads per peak per million as previously described (Scharer et al. Sci. Rep. 2016. PMID 27249108)

molecule: genomic DNA

extract_protocol: 10,000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).


title: nbrKO S2 cells smallRNAs Rep1

value: nbr knock-out


title: MZB_del_1 RNAseq

value: female


title: wt S2 cell smallRNAs Rep 2

value: wildtype


title: FoB_pos_2 ATACseq


title: FoB_del_3 ATACseq


title: FoB_del_2 ATACseq


title: wt S2 cell smallRNAs Rep 1


title: FoB_pos_1 ATACseq


title: ago2ko 6h s4U Rep2

description:
rep2_smallRNAreads.tsv
merged_smallRNAreads.tsv
rep2_filteredPositions.tsv
rep2_filteredLenDis.tsv
rep2_mirs.wAllMuts.tsv
merged_filteredPositions.tsv
merged_filteredLenDis.tsv
merged_mirs.wAllMuts.tsv

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1 and subsequently 4 nucleotides were trimmed from both ends using seqtk (v1.2-r101).
Trimmed reads from both replicates were merged to one file per time-point
Merged datasets were aligned to genome with bowtie v1.2.2, to determine total number of smallRNA locus drived reads.
Merged datasets were aligned to pre-miRNA hairpins only, and analysed using smRNAseq nextflow pipeline, to determine mutation rates, count T>C containing reads and length statistics
Genome_build: dm6
Supplementary_files_format_and_content: rep1_smallRNAreads.tsv - tab separated text file for replicate1 libraries - Columns:  (idx) 5-digit sample id of each file; corresponds to number before "_" of file name  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (time) s4U labelling time in minutes
Supplementary_files_format_and_content: rep2_smallRNAreads.tsv - tab separated text file for replicate2 libraries - Columns:  (idx) 5-digit sample id of each file; corresponds to number before "_" of file name  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (time) s4U labelling time in minutes
Supplementary_files_format_and_content: merged_smallRNAreads.tsv - tab separated text file for merged libraries - Columns:  (idx) 5-digit sample id of each file; corresponds to number before "_" of file name  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (time) s4U labelling time in minutes
Supplementary_files_format_and_content: filteredPositions.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped 5' isoforms  (flybase_id) flybase gene name  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (mir.type) mature or star  (seed) first 8nt  (UCount) Ts over position 1-18  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (read.type) totalReads or tcReads for a count of all or only tc reads aligning to same 5' position  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) time in minutes  (reads) reads in ppm, normalised to smallRNAs
Supplementary_files_format_and_content: filteredLenDis.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped 5' isoforms  (flybase_id) flybase gene name  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (mir.type) mature or star  (seed) first 8nt  (UCount) Ts over position 1-18  (seqLen) length of sequences mapped to same 5' position; used for weighted average length  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (LD.type) totalLenDis or tcLenDis depending for all or TC only reads  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) time in minutes  (reads) reads in ppm, normalised to smallRNAs, at length specified in (seqLen), mapping to the same 5' position
Supplementary_files_format_and_content: miRs.wAllMuts.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped nucleotide  (nucleotide) nucleotide identity  (count) raw count of mapped (nucleotides) at this position  (relPos) miRNA-relative position  (flybase_id) flybase gene name  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) time in minutes  (mir.type) mature or star  (start.pos) hairpin-relative position of mapped 5' isoforms; corresponds to (pos) in filteredLenDis and filteredPositions  (refNuc) reference nucleotide at this position  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (seed) first 8nt  (UCount) Ts over position 1-18  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (read.type) totalReads or tcReads for a count of all or only tc reads aligning to same 5' position  (totalReads) sum of all reads mapping to this miRNA at this (start.pos) in ppm  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (align) temporary file path; unused  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (full.seq) full sequence of this miRNA locus + 20nt downstream

extract_protocol:
total RNA extraction followed by IAA-derivatization where indicated
in-house protocol: size select 18-30nt RNA; deplete 2S rRNA; ligate 3p linker; size select ligation product; ligate 5p linker; size select ligation product; reverse transcription; qPCR library amplification. 3p and 5p adapters contain 4N at ligation interface (Jayaprakash et al, NAR, 2011)

tag: labelling

value: 6h s4U

tag: rna treatment

value: IAA


title: ago2ko 12h s4U Rep2

value: 12h s4U


title: ago2ko 3h s4U Rep2

value: 3h s4U


title: ago2ko 24h s4U Rep2

value: 24h s4U


title: FoB_del_1 ATACseq


title: ago2ko 30min s4U Rep2

value: 30min s4U


title: MZB_pos_3 ATACseq

value: spleen

value: wild-type


title: MZB_pos_2 ATACseq

value: no stimulation


title: ago2ko 15min s4U Rep2

value: 15min s4U


title: nbrKO S2 cells smallRNAs Rep2


title: MZB_pos_1 ATACseq


title: ago2ko no s4U Rep2

value: no IAA


title: MZB_del_3 ATACseq

value: knockout


title: MZB_del_2 ATACseq


title: ago2ko 24h s4U Rep1

description:
rep1_smallRNAreads.tsv
merged_smallRNAreads.tsv
rep1_filteredPositions.tsv
rep1_filteredLenDis.tsv
rep1_mirs.wAllMuts.tsv
merged_filteredPositions.tsv
merged_filteredLenDis.tsv
merged_mirs.wAllMuts.tsv


title: ago2ko 12h s4U Rep1


title: MZB_del_1 ATACseq


title: ago2ko 6h s4U Rep1


title: ago2ko 60min s4U Rep1

value: 60min s4U


title: ago2ko 30min s4U Rep1


title: ago2ko 15min s4U Rep1


title: ago2ko 5min s4U Rep1

value: 5min s4U


title: ago2ko 3h s4U Rep1


title: wt 12h s4U +ox

description:
ox_smallRNAreads.tsv
ox_filteredPositions.tsv
ox_filteredLenDis.tsv
ox_mirs.wAllMuts.tsv

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Barcoded libraries were demultiplexed using Picard Tools BamIndexDecoder v1.13 and converted to fastq using picard-tools SamToFastq v1.82
Sequencing adapters were trimmed with cutadapt v1.7.1 and subsequently 4 nucleotides were trimmed from both ends using seqtk (v1.2-r101).
Trimmed reads were aligned to genome with bowtie v1.2.2, to determine total number of smallRNA locus drived reads.
Trimmed reads were aligned to pre-miRNA hairpins only, and analysed using smRNAseq nextflow pipeline, to determine mutation rates, count T>C containing reads and length statistics
Genome_build: dm6
Supplementary_files_format_and_content: ox_smallRNAreads.tsv - tab separated text file for oxidised libraries - Columns:  (idx) 5-digit sample id of each file; corresponds to number before "_" of file name  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (time) s4U labelling time in minutes
Supplementary_files_format_and_content: unox_smallRNAreads.tsv - tab separated text file for unoxidised libraries - Columns:  (idx) 5-digit sample id of each file; corresponds to number before "_" of file name  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (time) s4U labelling time in minutes
Supplementary_files_format_and_content: filteredPositions.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped 5' isoforms  (flybase_id) flybase gene name  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (mir.type) mature or star  (seed) first 8nt  (UCount) Ts over position 1-18  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (read.type) totalReads or tcReads for a count of all or only tc reads aligning to same 5' position  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) s4U labelling time in minutes  (reads) reads in ppm, normalised to smallRNAs
Supplementary_files_format_and_content: filteredLenDis.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped 5' isoforms  (flybase_id) flybase gene name  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (mir.type) mature or star  (seed) first 8nt  (UCount) Ts over position 1-18  (seqLen) length of sequences mapped to same 5' position; used for weighted average length  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (LD.type) totalLenDis or tcLenDis depending for all or TC only reads  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) s4U labelling time in minutes  (reads) reads in ppm, normalised to smallRNAs, at length specified in (seqLen), mapping to the same 5' position
Supplementary_files_format_and_content: miRs.wAllMuts.tsv - tab separated text file - Columns:  (pos) hairpin-relative position of mapped nucleotide  (nucleotide) nucleotide identity  (count) raw count of mapped (nucleotides) at this position  (relPos) miRNA-relative position  (flybase_id) flybase gene name  (timepoint) 5-digit id of file; corresponds to number before "_" of file name  (time) s4U labelling time in minutes  (mir.type) mature or star  (start.pos) hairpin-relative position of mapped 5' isoforms; corresponds to (pos) in filteredLenDis and filteredPositions  (refNuc) reference nucleotide at this position  (mir_name) mirbase mir name  (arm.name) 5p or 3p arm  (average.ppm) average reads over entire timecourse  (seed) first 8nt  (UCount) Ts over position 1-18  (5p) mirbase annotated start of 5p miR  (loop) rough position of start/within hairpin loop; unused  (3p) mirbase annotated start of 3p miR  (read.type) totalReads or tcReads for a count of all or only tc reads aligning to same 5' position  (totalReads) sum of all reads mapping to this miRNA at this (start.pos) in ppm  (miRNAreads) absolute total number of reads mapping to miRNA loci throughout the genome for this timepoint  (align) temporary file path; unused  (sRNAreads) absolute total number of reads mapping to smallRNA loci throughout the genome for this timepoint  (full.seq) full sequence of this miRNA locus + 20nt downstream

extract_protocol:
total RNA extraction followed by IAA-derivatization where indicated
treated RNA was split; one sample being treated normally and the other undergoing oxidation by NaIO4  where indicated (Seizt et al, 2008)
in-house protocol: size select 18-30nt RNA; deplete 2S rRNA; ligate 3p linker; size select ligation product; ligate 5p linker; size select ligation product; reverse transcription; qPCR library amplification. 3p and 5p adapters contain 4N at ligation interface (Jayaprakash et al, NAR, 2011)

value: wild type

tag: rna oxidation

value: yes


title: ago2ko 60min s4U Rep2

tag: genotype


title: wt 3h s4U +ox


title: wt 24h s4U +ox


title: wt 6h s4U +ox


title: 0.5h s4U +ox


title: ago2ko 5min s4U Rep2


title: wt 1h s4U +ox

value: 1h s4U


title: 0.25h s4U +ox


title: wt 24h s4U

description:
unox_smallRNAreads.tsv
unox_filteredPositions.tsv
unox_filteredLenDis.tsv
unox_mirs.wAllMuts.tsv

value: no


title: wt 12h s4U

value: IAA


title: wt 3h s4U


title: IL-1-2

city: Bethesda

first: Devikala

last: Gurusamy

state: Maryland

address: Building 10, 3W-5816

department: Surgery Branch

institute: NCI - NIH

data_processing:
Illumina RTA v1.18.66.3 used for basecalling.
Use CCBR pipeliner installed in biowulf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalization values for each Sample

source_name: OT-I cells isolated from IL-1b-treated mice

growth_protocol: Naïve OT-I cells were transferred into a host, followed by LPS/OVA immunization

extract_protocol:
Qiagen RNeasy micro kit (following manufacturer instructions)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Host mice were treated with PBS or IL-1b for three days and OT-I cells were sorted from lymph nodes on day 4

tag: tissue

value: Lymph nodes

tag: in vivo treatment

value: OVA/LPS + IL-1b

value: Primary splenic OT-I CD8+ T cells


title: IL-1-1

tag: cell type


title: 0.5h s4U


title: Veh-3

source_name: OT-I cells isolated from vehicle-treated mice

value: OVA/LPS + PBS


title: wt 1h s4U


title: 0.25h s4U


title: wt no s4U

value: no s4U


title: ago2ko no s4U Rep1


title: Veh-1


title: Veh-2


title: wt no s4U no IAA


title: wt no s4U +ox


title: wt 6h s4U

value: 6h s4U


title: IL-1-3


title: 20180921_sample_8_L4_S154

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
raw sequencing data was converted to fastq files using Bcl2fastq (version 2.20)
reads were mapped against the genome (mm10) using STAR (version 2.4.2a)
gene expression levels were quantified using rpkmforgenes (Ramsköld 2009)
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrices gene-/sample-wise for raw counts and calculated RPKM values

source_name: Neocortex

extract_protocol:
The electrophysiological properties of the neurons were recorded by patch clamping. The cytosol of the cells were extracted and transferred into lysis buffer and converted to cDNA libraries for sequencing.
Patch-seq (Cadwell 2016 )

value: Neocortex

tag: region

tag: layer


title: 20180920_sample_3_L4_S145


title: 20180921_sample_6_L4_S152


title: 20180921_sample_5_L4_S150


title: 20180921_sample_1_L4_S142


title: 20180920_sample_5_L4_S149


title: 20180921_sample_2_L4_S144


title: 20180920_sample_9_L4_S155


title: 20180920_sample_2_L4_S143


title: 20180921_sample_3_L4_S146


title: 20180920_sample_7_L4_S153


title: 20180920_sample_4_L4_S147


title: 20180921_sample_4_L4_S148


title: 20180920_sample_1_L4_S141


title: 20180920_sample_6_L4_S151


title: 2h_28_A7351

type: RNA

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

label: biotin

source_name: bone-marrow derived macrophages

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: BMDM were prepared from 6-8 week old C57BL/6 mice by the following procedure. Bone marrow was plated at a density of 0.6-0.8 million cells/ml in non-tissue petri dishes and cells were cultured in complete DMEM supplemented with 60 ng/ml of recombinant mouse M-CSF (R&D, Minneapolis, MN, cat# 416-ML-050) for 6 days.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: BMDM were plated at a density of 1 million cells/ml in a 48-well dish (NUNC) in a total volume of 0.2 ml. 24 hr after plating, the cells were treated for 2 hours with the indicated concentration (nM) of single or dual TLR ligands, KDO2-Lipid A (KLA) and Pam3CSK4(P3C)

tag: rna sample id

tag: treatment

value: Pam3CSK4, 100

value: KDO2-Lipid A, 1000

tag: treatment time


title: 2h_26_A7349

tag: strain

value: Pam3CSK4, 0


title: 2h_27_A7350

value: Pam3CSK4, 10


title: 2h_22_A7345

value: KDO2-Lipid A, 100


title: 2h_23_A7346


title: 2h_24_A7347


title: 20180920_sample_12_L4_S160


title: 2h_29_A7352


title: 20180920_sample_11_L4_S159


title: 2h_18_A7341

value: KDO2-Lipid A, 10


title: 20180919_sample_8_L4_S114


title: 20180920_sample_10_L4_S157


title: 20180919_sample_9_L4_S116


title: 20180919_sample_7_L4_S112


title: 20180919_sample_6_L4_S110


title: 2h_19_A7342


title: 20180919_sample_4_L4_S108


title: 20180919_sample_25_L4_S139


title: 20180919_sample_3_L4_S106


title: 2h_16_A7339


title: 20180919_sample_23_L4_S140


title: 20180919_sample_2_L4_S104


title: 2h_25_A7348


title: 2h_13_A7336

value: KDO2-Lipid A, 1


title: 2h_20_A7343

description: 2h_20; Hyb input <1.5 ug; low signal


title: 2h_14_A7337


title: 20180919_sample_21_L4_S136


title: 20180919_sample_22_L4_S138


title: 2h_9_A7332

value: KDO2-Lipid A, 0.1


title: 2h_30_A7353


title: 20180919_sample_20_L4_S134


title: 2h_10_A7333


title: 2h_11_A7334


title: 2h_15_A7338


title: 2h_21_A7344


title: 2h_7_A7330


title: 2h_12_A7335


title: 20180919_sample_1_L4_S102


title: 20180919_sample_19_L4_S132


title: 20180919_sample_18_L4_S130


title: Ov/Ob Post 14

city: Shreveport

first: Tara

middle: M

last: Henagan

state: LA

address: 1501 Kings Hwy

department: Medical School

institute: Louisiana State University Health Sciences Center - Shreveport

data_processing:
Reads were trimmed for the adaptor sequence and aligned to the human (hg38) genome using Tophat version 2.1.0 allowing up to 2 nucleotide mismatches. On average, ~97% of sequenced reads aligned to genome.
Differential gene expression was determined using Cuffdiff version 2.2.1.3 (FDR: 0.05). The expression values for 56,891 transcripts, which represented 26,376 unique genes, were obtained to represent the transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: abular file generated using CuffDiff is formatted as follows: test_id (column 1), gene_id (column 2), gene (column 3), locus (column 4), sample_1 (column 5), sample_2 (column 6), status (column 7), value_1 (column 8), value_2 (column 9), log2(fold_change) (column 10), test_stat (column 11), p_value (column 12), q_value (column 13), significant (column 14)

organism: Homo sapiens

source_name: vastus lateralis

extract_protocol:
Skeletal muscle biopsies were obtained from the vastus lateralis muscle using the percutaneous muscle biopsy technique before (Pre) and immediately following (Post) the exercise testing trial. Briefly, 2.5 mL of a 1% lidocaine solution was injected into the thigh and a 6 mm Bergstrom biopsy needle (Pelomi Medical, Denmark) under suction was used collect the muscle sample. The collected sample was quickly rinsed in PBS and blotted to remove any blood prior to freezing. Pre biopsy samples were taken from the participant’s non-dominant leg, whereas Post biopsies were obtained from the dominant leg. Samples were then flash frozen in liquid nitrogen and stored at −80°C until further processing. Skeletal muscle samples (n=14 per group for lean Pre and lean Post and n=15 per group for Ov/Ob Pre and Ov/Ob Post) were homogenized (Polytron homogenizer, Kinematica AG, Lucerne, Switzerland) in Trizol reagent (Thermo Fisher Scientific, Waltham, MA) per the manufacturer’s protocol. Following phase separation, the aqueous layer was removed and column purified using the RNeasy kit (Qiagen, Germantown, MD).
RNA-seq sample preparation and sequencing was performed by the Genomics Core Facility at Purdue University. cDNA libraries were constructed using the TruSeq stranded mRNA library prep kit (Illumina, San Diego, CA), per the manufacturer’s protocol and were subjected to sequencing on the Illumina HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). 100 nucleotides long single-end reads were generated, with an average of ~42 million reads per treatment group.

treatment_protocol: 30 men, aged 19-30 years, were recruited and divided into two groups: lean (BMI<25, 18.5- 24.1 kg/m2, n=15) and Ov/Ob (BMI≥25, 25.5- 36.9 kg/m2, n=15). Participants were instructed to refrain from vigorous physical activity for 24 h prior to the exercise testing trial. Following an overnight fast, participants reported to the Purdue University Nutrition Science Bionutrition Core between 0700 and 1000 h where they sat quietly for 15 min prior to quadriceps muscle biopsy sampling (Pre samples). Participants then consumed a standardized, high carbohydrate meal (7 kcal/kg; 60% carbohydrate, 25% fat, 15% protein) under the supervision of a registered dietician. Following the meal, participants were asked to refrain from eating or drinking, with the exception of water, and to refrain from physical activity for the next 4 h, at which time they reported back to the laboratory for the exercise testing trial. For the exercise testing trail, each participant completing a 2 min warm up at a self-selected intensity not exceeding 100W on the stationery cycle ergometer. Participants then cycled at the workload equal to their previously measured 50% VO2 max. Between minutes 5-8 of the exercise testing trial, steady-state oxygen consumption was measured using the TrueOne 2400 Metabolic Measurement System (Parvo Medics, Utah, USA). Measured values were compared with the participant’s expected 50% VO2 max. Workload was adjusted as necessary to obtain the expected oxygen consumption necessary for the participants to expend 650 kcal upon completion of the exercise testing trial. Immediately following the exercise testing trial, a second quadriceps muscle biopsy were obtained from each participant (Post samples).

value: Vastus Lateralis Muscle

tag: Sex

value: male

tag: group

tag: time

value: biopsy immediately following exercise bout


title: Ov/Ob Post 13


title: Ov/Ob Post 15


title: 20180919_sample_15_L4_S124


title: Ov/Ob Post 12


title: 20180919_sample_13_L4_S119


title: 20180919_sample_16_L4_S126


title: 20180919_sample_11_L4_S120


title: 2h_6_A7329


title: 20180705_sample_9_L4_S177


title: 20180919_sample_10_L4_S118


title: Ov/Ob Post 7


title: 2h_2_A7325

value: KDO2-Lipid A, 0


title: 20180705_sample_8_L4_S176


title: Ov/Ob Post 9


title: Ov/Ob Post 11


title: Ov/Ob Post 8


title: 2h_3_A7326


title: 2h_5_A7328


title: 2h_8_A7331


title: Ov/Ob Post 5


title: Ov/Ob Post 6


title: 20180919_sample_17_L4_S128


title: 2h_4_A7327


title: 2h_NT_A7324


title: Ov/Ob Post 4


title: 20180705_sample_7_L4_S175


title: 20180919_sample_14_L4_S122


title: 2h_17_A7340


title: Ov/Ob Post 10


title: 20180705_sample_6_L4_S174


title: Ov/Ob Post 3


title: Ov/Ob Post 2


title: Ov/Ob Post 1


title: 20180705_sample_5_L4_S173


title: 20180705_sample_4_L4_S172


title: Lean Post 14


title: 20180705_sample_1_L4_S169


title: 20180705_sample_2_L4_S170


title: 20180703_sample_7_L4_S158


title: 20180705_sample_10_L4_S178


title: 20180703_sample_6_L4_S157


title: 20180703_sample_8_L4_S159


title: Lean Post 11


title: Lean Post 10


title: Lean Post 12


title: Lean Post 13


title: Lean Post 8


title: Lean Post 9


title: Lean Post 6


title: Lean Post 7


title: Lean Post 4


title: 20180703_sample_5_L4_S155


title: 20180703_sample_4_L4_S154


title: Lean Post 5


title: 20180705_sample_3_L4_S171


title: Lean Post 2


title: 20180703_sample_3_L4_S153


title: Lean Post 3


title: 20180703_sample_2_L4_S152


title: Lean Post 1


title: 20180703_sample_1_L4_S151


title: 20180703_sample_18_L4_S168


title: 20180703_sample_17_L4_S167


title: Ov/Ob Pre 15

value: biopsy prior to exercise bout


title: 20180703_sample_9_L4_S160


title: 20180703_sample_16_L4_S166


title: 20180703_sample_15_L4_S165


title: Ov/Ob Pre 13


title: Ov/Ob Pre 12


title: 20180703_sample_14_L4_S164


title: 20180703_sample_13_L4_S163


title: 20180703_sample_11_L4_S161


title: Ov/Ob Pre 10


title: 20180627_sample_8_L4_S143


title: 20180627_sample_9_L4_S145


title: 20180627_sample_7_L4_S142


title: Ov/Ob Pre 9


title: Ov/Ob Pre 8


title: 20180627_sample_6_L4_S141


title: 20180627_sample_1_L4_S137


title: Ov/Ob Pre 14


title: 20180627_sample_3_L4_S138


title: 20180627_sample_5_L4_S140


title: 20180627_sample_4_L4_S139


title: 20180627_sample_14_L4_S150


title: Ov/Ob Pre 1


title: Ov/Ob Pre 6


title: Ov/Ob Pre 2


title: Ov/Ob Pre 5


title: 20180627_sample_13_L4_S149


title: Ov/Ob Pre 3


title: Ov/Ob Pre 11


title: Lean Pre 12


title: 20180627_sample_12_L4_S148


title: 20180703_sample_12_L4_S162


title: Ov/Ob Pre 7


title: 20180627_sample_11_L4_S147


title: Lean Pre 10


title: Lean Pre 11


title: Ov/Ob Pre 4


title: 20180627_sample_10_L4_S146


title: Lean Pre 14


title: 20180626_sample_9_L4_S127


title: Lean Pre 9


title: Lean Pre 7


title: 20180626_sample_8_L4_S126


title: 20180626_sample_6_L4_S124


title: 20180626_sample_7_L4_S125


title: Lean Pre 5


title: Lean Pre 13


title: 20180626_sample_5_L4_S123


title: Lean Pre 4


title: Lean Pre 6


title: 20180626_sample_4_L4_S122


title: Lean Pre 2


title: 20180626_sample_1_L4_S118


title: 20180626_sample_18_L4_S136


title: Lean Pre 1


title: 20180626_sample_17_L4_S135


title: Lean Pre 8


title: RNA-seq RS4;11-Asn_rep1

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

data_processing:
The sequencing data was next assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK) and then mapped to the Human genome (GRCh38) using STAR RNA-seq aligner with default parameters.
Uniquely mapped sequencing reads were assigned to GRCh38 refGene genes using featureCounts (from subread) .
Genome_build: GRCh 38
Supplementary_files_format_and_content: tab-delimited cpm matrix file

source_name: ALL line

growth_protocol: Cells were maintained in lymphocyte culturing medium (DMEM:IMDM=1:1), with 10% FBS

extract_protocol:
RNA was extracted with standard Trizol protocol
library construction performed by Genewiz

treatment_protocol: Cells were centrifuged and cell pellets were resuspended in asparagine-free lymphocyte culturing medium with 10% dialyzed FBS

tag: cell line

value: ALL cell line


title: RNA-seq RS4;11-Asn_rep3


title: RNA-seq RS4;11-Asn_rep2


title: 20180626_sample_14_L4_S132


title: RNA-seq RS4;11+Asn_rep2


title: RNA-seq RS4;11+Asn_rep1


title: 20180626_sample_13_L4_S131


title: RNA-seq RS4;11+Asn_rep3


title: 20180626_sample_12_L4_S130


title: F9_C_1

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
smallRNA
ProcessedData_Quatified-Counts_JF14.xls

data_processing:
FASTQs were trimmed for adapters and quality score.
We used bowtie 1.01 to align reads against the human genome with the corresponding annotations (GRCh38/GENCODE-v26).
Mapped reads were quantified to GENCODE-v26 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table in Excel, Quantified read counts

source_name: Cerebrospinal fluid (CSF)

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit (Ambion) and the Plasma/Serum RNA Purification kit (Norgen), as detailed in the SAMPLES section
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: CSF samples were obtained via lumbar puncture, centrifuged to remove contaminant cells (500 xg for 10 min), aliquoted, and immediately stored at -80°C until their processing. Then, samples were thawed together at 4°C, mixed to generate a pool of samples, centrifuged to remove cell debris (3,000 xg for 15 min at 4°C), and aliquoted in a 200 µl format (cleared CSF). Before total RNA extraction some of them incorporated a EVs enrichment step, as detailed in SAMPLES section.

tag: evs enrichment method

value: Size exclusion chromatography (SEC)

tag: total rna extraction method

value: mirVana PARIS kit (Ambion)

value: Cerebrospinal fluid (CSF)


title: 20180626_sample_16_L4_S134

value: Neocortex


title: 20180626_sample_3_L4_S121


title: 20180626_sample_2_L4_S119


title: F3_B_1


title: F9_A_1


title: F3_C_1


title: 20180605_sample_7_L4_S106


title: 20180605_sample_6_L4_S105


title: 20180626_sample_11_L4_S129


title: Lean Pre 3


title: DIrC_1

value: No


title: DirB_1


title: F3_A_1


title: 20180605_sample_4_L4_S103


title: 20180605_sample_3_L4_S102


title: 20180626_sample_15_L4_S133


title: InvC_1

value: Total exosome isolation (Invitrogen)


title: DirA_1


title: 20180605_sample_2_L4_S101


title: 20180605_sample_20_L4_S117


title: F9_B_1


title: InvA_1


title: InvB_1


title: 20180626_sample_10_L4_S128


title: 20180605_sample_19_L4_S116


title: 20180605_sample_1_L4_S100


title: NorB_1

value: Plasma/Serum RNA Purification kit (Norgen)


title: 20180605_sample_18_L4_S115


title: 20180605_sample_16_L4_S113


title: NorA_1


title: 20180605_sample_15_L4_S112


title: 20180605_sample_13_L4_S110


title: NorC_1


title: RNA-seq of cultured RPE #1

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequencing reads were evaluated for their quality by FastQC followed by removal of adapter sequences.
The processed sequencing reads were aligned to the human reference genome (hg19) with TopHat2 (version 2.0.14)
Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012).
hg19
Genome_build: The sequence reads were mapped to human reference genome (hg19), with UCSC refSeq genes, downloaded on 25th April 2014.
Supplementary_files_format_and_content: The TSV file were generated using RPKMforgenes, and contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Cultured retinal pigment epithelum

growth_protocol: We cultured cells according to manufacturer's instructions.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN).
Sequencing libraries were generated using KAPA Stranded mRNA Kit. The initial amount of total RNA was 500 ng.

value: Epithelial cells derived from the outer layer of the embryonic optic cup, obtained from Lonza

tag: passage

tag: lot


title: RNA-seq of RPE obtained from eye tissue #2

source_name: Retinal pigment epithelum obtained from eye tissue

value: RPE derived from eye tissue


title: 20180605_sample_14_L4_S111

tag: tissue


title: 20180605_sample_17_L4_S114


title: 20180604_sample_3_L4_S99


title: 20180605_sample_5_L4_S104


title: RNA-seq of RPE obtained from eye tissue #1


title: 20180605_sample_11_L4_S107


title: Control_04

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
library strategy: Digital restriction enzyme analysis of methylation (DREAM)-seq
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let m be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and u be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(m+0.5)/(c*(m+0.5)+u+0.5)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text files

source_name: Normal peripheral blood cells

extract_protocol:
DNA isolation: Pretreated whole-blood genomic DNA was purified with the QIAamp DNA Blood mini Kit (Qiagen) and QIAcube automated sample preparation system (Qiagen).
Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 50 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 50 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments.
Ends of restriction fragments were repaired using Klenow exo- DNA polymerase. NEBNext adaptors for Illumina were ligated to the fragments. Size selected fragments were amplified with barcoded NEBNext oligos for Illumina.

value: Normal peripheral blood cells

tag: dna methylation type

value: Normal


title: Control_03

tag: cell type


title: Control_05


title: Control_02


title: 20180604_sample_1_L4_S97

tag: region


title: Control_01


title: 20180604_sample_2_L4_S98

tag: layer


title: 20180605_sample_12_L4_S109


title: rrAML570

source_name: AML patient peripheral blood cells

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

value: negative

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: Normal-like


title: rrAML569

tag: vital status

tag: overall survival days

value: M

value: Intermediate Risk

value: positive

tag: cell type

tag: dna methylation type

value: CIMP-like


title: RNA-seq of cultured RPE #2

tag: passage

tag: lot


title: rrAML568

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 6

city: Boston

first: Kee Wui

last: Huang

state: MA

address: 200 Longwood Ave, WAB 347

department: Neurobiology

institute: Harvard Medical School

description:
Contains libraries DRM4.6, DRF5.6, DRM5.1, DRF6.1. Please see README file containing library barcodes for demultiplexing.
DRN_3_6

data_processing:
All processing steps performed on sequencing fastq files to generate count matrices were performed using a custom pipeline for inDrops data analysis available at https://github.com/indrops/indrops (Klein et al., 2015).
Reads were filtered by expected structure and sorted by library index (see README file containing library information). Valid reads were then trimmed (Trimmomatic version 0.33; parameters: LEADING: "28" SLIDINGWINDOW: "4:20" MINLEN: "16") before demultiplexing and sorting by cell barcodes. Cell barcodes containing fewer than 250 total reads were discarded.
Remaining reads were aligned using Bowtie (version 1.2.2; parameters: m = 200, n = 1, l = 15, e = 100) to a custom-built reference transcriptome, which is based on GRCm38.87 with the addition of genes from SAD B19 rabies viruses and transgenes.
Aligned reads were quantified as UMI-filtered mapped read (UMIFM) counts. The UMIFM count matrix (counts per gene per cell) for a single library (e.g. DRM1.1) were exported as a gunzipped TSV file for downstream analysis.
Genome_build: GRCm38.87, modified to include sequences from G-deleted SAD B19 rabies viruses (B19N, B19P, B19M, B19L, EGFP, tdTomato, AmCyan1).
Supplementary_files_format_and_content: Processed files are compressed TSV files containing UMIFM count matrices from a single library.

molecule: polyA RNA

source_name: Microdissected brain tissue containing dorsal raphe nucleus

growth_protocol: Mice were pair-housed in standard 12:12 light-dark cycles (7:00 AM - 7:00 PM) with ad-libitum food and water.

extract_protocol:
Mice were transcardially perfused with an ice-cold choline cutting solution containing neuronal activity blockers (10 µM (R)-CPP, 1 µM tetrodotoxin). Brains were rapidly dissected out and sliced into 250 µm thick coronal sections on a vibratome in a chilled cutting chamber filled with choline cutting solution.
Coronal slices containing the DRN were then transferred to a chilled dissection dish containing a choline-based cutting solution for microdissection. Dissected tissue chunks were transferred to cold HBSS-based dissociation media with an inhibitor cocktail (0.9 mM kynurenic acid, 10 µM (R)-CPP, 1 µM tetrodotoxin, 10 µM triptolide, 5 µg/ml actinomycin D, 30 µg/ml anisomycin) and kept on ice.
Dissected tissue chunks for each sample were pooled into a single tube for dissociation. Tissue chunks were mixed with a digestion cocktail (dissociation media with 20 U/ml papain, 1 mg/ml pronase, 0.05 mg/mL DNAse I, 10 µM triptolide, 5 µg/ml actinomycin D, 30 µg/ml anisomycin) and incubated at 34 °C for 90 min with gentle rocking. Digestion was quenched by adding dissociation media with 0.2% BSA and 10 mg/ml ovomucoid inhibitor, and samples were kept chilled for the rest of the dissociation procedure.
Tissue chunks were then mechanically triturated using fine-tip plastic micropipette tips of progressively decreasing size. Triturated cell suspension was filtered in two stages using a 70 µm cell strainer and 40 µm pipette tip filter and washed in two repeated centrifugation (5 min, 300 g) and re-suspension steps to remove debris before a final re-suspension in dissociation media containing 0.04% BSA and 15% OptiPrep.
Cell density was calculated based on hemocytometer counts and adjusted to approximately 100,000 cells/ml. Single-cell encapsulation and RNA capture on the InDrop platform was performed at the Harvard Medical School ICCB Single Cell Core using v3 chemistry hydrogels based on previously described protocols (Zilionis et al., 2017).
Libraries were constructed following the protocols described in Zillionis et al. (2017) for inDrop v3 hydrogels. 4 libraries were pooled for sequencing (2 sequencing runs per set) and demultiplexed using library barcodes (see README file). R1 is the biological read, R2 is the first half of the hydrogel barcode, R3 is the library index, and R4 contains the second half of the hydrogel barcode, UMI, and fraction of the polyA tail.

treatment_protocol: None - control (uninjected).

tag: tissue

value: dorsal raphe nucleus

tag: strain

tag: age

value: 8-10 weeks

tag: condition

value: Control (uninjected)


title: rrAML565

value: CRp

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 5

description:
Contains libraries DRM4.5, DRF5.5, DRM5.2, DRF6.2. Please see README file containing library barcodes for demultiplexing.
DRN_3_5


title: rrAML563

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: cell type

tag: dna methylation type

value: Intemediate


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 4

description:
Contains libraries DRM4.4, DRF5.4, DRM5.3, DRF6.3. Please see README file containing library barcodes for demultiplexing.
DRN_3_4

tag: tissue

tag: strain

tag: age

tag: condition


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 1

description:
Contains libraries DRM4.1, DRF5.1, DRM5.6, DRF6.6. Please see README file containing library barcodes for demultiplexing.
DRN_3_1


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 3

description:
Contains libraries DRM4.3, DRF5.3, DRM5.4, DRF6.4. Please see README file containing library barcodes for demultiplexing.
DRN_3_3


title: Dorsal Raphe Nucleus, Control, Batch 2, Set 2

description:
Contains libraries DRM4.2, DRF5.2, DRM5.5, DRF6.5. Please see README file containing library barcodes for demultiplexing.
DRN_3_2


title: rrAML559

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 6

description:
Contains libraries DRM1.11, DRM1.12, DRF2.3, DRF2.4. Please see README file containing library barcodes for demultiplexing.
DRN_1_6


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 5

description:
Contains libraries DRM1.9, DRM1.10, DRF2.1, DRF2.2. Please see README file containing library barcodes for demultiplexing.
DRN_1_5


title: rrAML557

tag: vital status

value: Alive

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: rrAML558

value: Dead

tag: age (years)

tag: cytogenetic risk

tag: cell type

tag: dna methylation type


title: rrAML562

value: F

tag: best response

value: CRi

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 4

description:
Contains libraries DRM1.3, DRM1.6, DRF1.7, DRF1.8. Please see README file containing library barcodes for demultiplexing.
DRN_1_4

tag: tissue

tag: strain

tag: age

tag: condition


title: rrAML553

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: NR

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation


title: rrAML552

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

value: CR

value: negative

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

tag: dna methylation type


title: rrAML550

value: M

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

value: AML patient peripheral blood cells

value: Normal-like


title: Liat 945 (161-MAP)

city: Haifa

first: Michal (Miki)

middle: A.

last: Rahat

address: 7 Michal st.,

department: Immunology, Faculty of Medicine

country: Israel

institute: Carmel Medical Center & Technion-Israel Institute of Technology

data_processing:
Quality control was performed using FastQC (v0.11.2) and overrepresented sequences were removed using CUTADAPT tool (v 1.8)
The 75 paired-end reads were aligned to mouse reference genomeand annotation file (Mus_musculus.GRCm38 downloaed from ENSEMBL) using TopHat (v2.0.13), allowing 2 mismatches per read with options - very-sensitive and -GTF. The number of reads per genes was counted using HTseq (0.6.1).
Principal components analysis (PCA), samples' clustering, and differential expressed genes (DEGs), were calculated using Deseq2 (version 1.8.1).
DEGs were further investigated for function and pathway enrichment using Ingenuity Pathway Analysis (IPA) and functional gene and term networks from clustering of enrichment analysis using Bioconductor R package FGNet (V3.2.1).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and read counts.

source_name: CT26 cells

extract_protocol:
Total RNA was extrcted from tumors using the Qiacube (Qiagen) with the RNeasy kit (cat. no.  74106). Quality measurements of total RNA were performed using TapeStation (Agilent). RINe values were between 6.5-10.0
Six RNAseq libraries (NEBNext® Ultra™ RNA Library Prep Kit for Illumina, cat no. E7530) were produced according to the manufacturer protcol from 800 ng of total RNA.  mRNA pull-up was performed using Magnetic Isolation Module (NEB, cat no. E7490). The six libraries were mixed into a single tube with equal molarity of all samples.  The RNAseq data was generated on NextSeq500 mid-output (75bp pair-end reads) kit v2 (Illumina, FC-404-2005).

treatment_protocol: After CT26 cells were implanted s.c. (day 0), mice were vaccinatd with either Scr-MAP or 161-MAP (50 ug each, emulsified in Freund's adjuvants) at day 7, 14 and 21.

tag: cell line

tag: mouse strain

value: BALB/c

tag: tissue

value: s.c. tumor

tag: tumor extracted

value: 27 days after implantation


title: rrAML555

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

value: CIMP-like


title: rrAML566

source_name: AML patient whole blood cells

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

value: AML patient whole blood cells

tag: dna methylation type


title: NMU-O-P (single cell RNA-Seq)

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 12 nt)
*R2_001.fastq.gz: contains the 56 nt RNA sequence.
Reads were locally processed with Bcltofastq (bcl2fastq 2.19.0, Illumina). Cell Ranger version 3.0.2 software (10x Genomics) pipeline was then used to demultiplex and align reads to the GRCm38/mm10 transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger tab-delimited text files include raw counts expression matrices, features and barcodes.

source_name: Normal Mouse Urothelium organoids

extract_protocol:
NMU-o-P and NMU-o-D were enzymatically dissociated and cells were suspended in phosphate-buffered saline (PBS) with 0.04% bovine serum albumin (BSA, Ambion AM2616). 10,000 cells per condition were loaded onto a 10x Chromium Single Cell Controller chip B (10x Genomics) as described in the manufacturer's protocol (Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, PN-1000075).
Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean up, cDNA amplification and library construction were performed following the manufacturer's recommendations

tag: strain

tag: genotype

value: WT

tag: age

value: 8-10 week-old mice

tag: tissue

value: Normal Mouse Urothelium organoids

tag: differentiation stage

value: Proliferative (NMU-O-P)


title: NMU-O-D (single cell RNA-Seq)

value: Differentiated (NMU-O-D)


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 1

description:
Contains libraries DRM1.1, DRM1.2, DRF1.1, DRF1.2. Please see README file containing library barcodes for demultiplexing.
DRN_1_1

value: dorsal raphe nucleus

value: 8-10 weeks

tag: condition

value: Control (uninjected)


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 2

description:
Contains libraries DRM1.4, DRM1.5, DRF1.3, DRF1.4. Please see README file containing library barcodes for demultiplexing.
DRN_1_2


title: rrAML546

tag: vital status

value: Alive

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: best response

value: CR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

value: negative

value: positive

value: Intemediate


title: rrAML548

value: Dead

tag: age (years)

tag: cytogenetic risk

value: NR

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

value: AML patient peripheral blood cells

tag: dna methylation type

value: Normal-like


title: Liat-941 (161-MAP)

tag: cell line

tag: mouse strain

value: BALB/c

tag: tissue

value: s.c. tumor

tag: tumor extracted

value: 27 days after implantation


title: Liat 943 (161-MAP)


title: rrAML542

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: Intermediate Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)


title: Liat-126 (Scr-MAP)


title: rrAML545

value: F

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

value: CIMP-like


title: Dorsal Raphe Nucleus, Control, Batch 1, Set 3

description:
Contains libraries DRM1.7, DRM1.8, DRF1.5, DRF1.6. Please see README file containing library barcodes for demultiplexing.
DRN_1_3

tag: tissue

value: dorsal raphe nucleus

tag: strain

tag: age

value: 8-10 weeks

tag: condition

value: Control (uninjected)


title: rrAML543

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

value: negative

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

tag: dna methylation type


title: Liat-5 (Scr-MAP)

tag: cell line

tag: mouse strain

tag: tumor extracted


title: Liat-2 (Scr-MAP)


title: rrAML541

tag: age (years)

tag: cytogenetic risk

value: Unevaluable

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

value: positive


title: rrAML540

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: NR

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: pre_TIL_CD8_0009

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

data_processing:
Adapter sequences and low-quality reads were trimmed using cutadapt-v1.11 and PRINSEQ-0.20.4. Filtered reads were processed using “analyze amplicon” command of MiXCR-3.0.2 with following high-level options: -s = hsa, -starting-material = rna, -5-end = no-v-primers, -3-end = c-primers, -adapters = no-adapters, -receptor-type = trb, -region-of-interest = CDR3. In alignment to ImMunoGeneTics (IMGT) reference human TCR V/D/J sequences, we used the following parameters: -OvParameters.geneFeatureToAlign = VTranscript -OvjAlignmentOrder = JThenV. In assembling identical sequences into clones with PCR and sequencing error correlations, we used the following parameters: -ObadQualityThreshold=10, -OseparateByV=true. Only clones with productive CDR3 sequences were analyzed using VDJtools (ver 1.2.1.). Then, the sequencing coverage of samples, which was defined as the ratio of total reads to the starting number of T cells, was normalized to ×5 using the “DownSample” command in VDJtools. After coverage normalization, clones with lead count less than sequencing coverage were excluded as sequencing noise. Finally, for PBMC sample, we identified clones shared between CD4+ and CD8+ T cell repertoire as contamination, and separated these shared clones into CD4+ or CD8+ repertoire by their frequency in CD4+ or CD8+, because these shared clones were very few and their frequencies were biased to either CD4+ or CD8+ (Data not shown)
Genome_build: IMGT reference sequences of human TRB
Supplementary_files_format_and_content:  text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

source_name: CD8+ TILs collected from biopsy of gastric cancer

extract_protocol:
For bulk biopsy samples, total RNA was extracted using a RNA easy mini extraction kit (Qiagen) according to standard protocol, and diluted with Lysis buffer (100 mM Tris-HCl pH7.5, 500 mM LiCl, 10 mM EDTA, 5 mM DTT). For sorted CD4+ and CD8+ T cells, cells were collected directry into the Lysis buffer.
TCR sequencing libraries for next generation sequencing were prepared according to the previous report (Aoki, et al, GSE115425) with some modifications. PolyA RNAs were isolated and amplified from sorted T cells according to a previous report (Shichino, et al, GSE110711). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. The first PCR mixture comprised 0.4 μL of 10 μM primer mix (5′ WTA and Trbc_ex), 4.6 μL of template, and 5 μL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 58°C and extension for 30 sec at 72°C, followed by final extension at 72°C for 2 min. Next, 10 μL of the first-PCR products was used for purification with an Agencort AM Pure XP kit (Beckman Coulter) at a 0.7:1 ratio of beads to sample, and eluted with 12 μL of DW. The second PCR mixture consisted of 1.25 μL of 10 μM primer mix (5′ WTA and Trbc_in-Bio), 11.25 μL of template and 12.5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 13 cycles. Next, 25 μL of the second-PCR products were purified using Agencort AM Pure XP kit (Beckman-Coulter) at a 0.8:1 ratio of beads to sample, and eluted in 15 μL of DW. The purified PCR products were sheared randomly using NEBNext dsDNA fragmentase (New England Biolabs). The fragmentation reaction mix consisted of 6 μL of DW, 2 μL of 10X Fragmentase Reaction Buffer v2, 10 μL of PCR product, and 2 μL of fragmentase. The fragmentation reaction was incubated at 37°C for 30 min, and then 5 μL of 0.5 M EDTA was added to stop the reaction on ice. The sheared PCR product was then purified and subjected to size selection using the Agencort AM Pure XP kit (Beckman Coulter) at a 0.8:1 ratio of beads to sample to remove large fragments, a 0.8:1 ratio of beads to sample to remove the smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). To capture the TCR cDNA containing the end of Constant region, the purified PCR products were incubated with 10 μL of Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) for 30 min at room temperature (r.t.), washed 3 times with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0), and DW. The captured TCR cDNA was repaired using NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs). The repair reaction mix contained 1.2 μL of reaction buffer, 8.3 μL of beads re-suspended with DW, and 0.5 μL of enzyme mix. The repair reaction was incubated at 20°C for 30 min, then washed once with lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, 10 mM EDTA, and 5 mM DTT], 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The repaired TCR cDNA was attached to the sequencing adaptor using the DNA Ligation Kit ＜Mighty Mix＞ (TaKaRa Bio). The ligation reaction mix consisted of 1 μL of 10 μM P1 adaptor, 6.5 μL of beads re-suspended in Tris-HCl (pH 8.0), and 15 μL of enzyme mix. The ligation reaction was incubated at 16°C for 60 min using a thermal cycler with the cover open, washed once with lysis buffer, 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The third PCR were carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The third PCR mixture consisted of 0.35 μL of 10 μM trP1 primer, 1 μL of 3.5 μM IonA-BC-Trbc primer, 3.65 μL of beads resuspended in DW and 5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 12 cycles. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Beckman Coulter,) at a 0.75:1 ratio of beads to sample to remove large fragments, a 0.65:1 ratio of beads to sample to remove smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA Library Quantification Kit ((KAPA Biosystems) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific). Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion Hi-Q Chef kit, an Ion PI v3 Chip kit, and an Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions, except the input library concentration (100 pM) and flow number (550).

treatment_protocol: Patients with advanced solid tumors for whom no standard therapy was available, were treated with intravenous infusion of IT1208 at dose of 0.1 or 1.0 mg/kg. First patient in each cohort was treated as a single administration and other patients received two administrations of IT1208 on day 1 and 8 followed by safety and efficacy assessment with DLT evaluation period as 4 weeks.

tag: cell type

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: gastric

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: gastric cancer


title: post1_TIL_CD8_0009


title: pre_TIL_CD8_0008

source_name: CD8+ TILs collected from biopsy of gastro-esophageal cancer

value: gastro-esophageal

value: gastro-esophageal cancer


title: post1_TIL_CD8_0008


title: pre_TIL_CD8_0007


title: rrAML534

value: Alive

value: F

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

value: CRp

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

value: AML patient peripheral blood cells

tag: dna methylation type

value: CIMP-like


title: rrAML537

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: negative

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

value: Normal-like


title: rrAML538

value: Dead

value: M

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)

value: positive

value: Intemediate


title: rrAML532

value: NR

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)


title: rrAML539

tag: vital status

tag: overall survival days

tag: nras mutation

value: ND

tag: dna methylation type


title: rrAML536

tag: clinical trial (p1/p2)

tag: gender

value: CR

tag: kras mutation

tag: dnmt3a mutation


title: post1_TIL_CD8_0007

tag: cell type

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: gastro-esophageal

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: gastro-esophageal cancer


title: pre_TIL_CD8_0005

source_name: CD8+ TILs collected from biopsy of stomach

value: female

value: gastric

value: stomach with no cancer


title: rrAML530

value: Alive

value: F

tag: age (years)

tag: cytogenetic risk

value: Unevaluable

tag: best response

value: CRi

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: Normal-like


title: rrAML528

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: Poor Risk

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: cell type

tag: dna methylation type


title: post1_TIL_CD8_0004

source_name: CD8+ TILs collected from biopsy of bronchus metastasis of colorectal cancer

value: CD8+ CD4- T cells

tag: age

tag: Sex

tag: cancer type

value: colorectal

tag: dose level

tag: agent

tag: organ


title: rrAML525

value: M

tag: age (years)

tag: cytogenetic risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: CIMP-like


title: post1_TIL_CD8_0002

tag: cell type

value: male

value: gastric cancer


title: rrAML524

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

value: positive

tag: dna methylation type


title: pre_TIL_CD8_0002

tag: age

tag: Sex

tag: cancer type

value: gastric

tag: dose level

tag: agent

tag: organ


title: rrAML522

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: pre_TIL_CD4_0009

source_name: CD4+ TILs collected from biopsy of gastric cancer

tag: cell type

value: CD4+ CD8- T cells

value: 1.0 mg/kg


title: rrAML521

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: dna methylation type


title: rrAML519

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

tag: peripheral blasts (%)


title: post1_TIL_CD4_0009

tag: age

tag: Sex

tag: cancer type

tag: dose level

tag: agent

tag: organ


title: pre_TIL_CD4_0008

source_name: CD4+ TILs collected from biopsy of gastro-esophageal cancer

tag: cell type

value: gastro-esophageal

value: gastro-esophageal cancer


title: post1_TIL_CD4_0007


title: rrAML515

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: Normal-like


title: pre_TIL_CD4_0007

tag: age


title: pre_TIL_CD4_0005

source_name: CD4+ TILs collected from biopsy of stomach

tag: Sex

value: female

value: stomach with no cancer


title: pre_TIL_CD8_0004

value: CD8+ CD4- T cells

tag: cancer type

value: colorectal

value: bronchus metastasis of colorectal cancer


title: post1_TIL_CD4_0004

source_name: CD4+ TILs collected from biopsy of bronchus metastasis of colorectal cancer

tag: dose level


title: pre_TIL_CD4_0004

tag: agent


title: post1_TIL_CD4_0002

value: male

tag: organ


title: pre_Bulk_0011

source_name: biopsy of liver metastasis of pancreatic cancer

tag: cell type

value: bulk biopsy

value: colorectal and pancreas

value: liver metastasis of pancreatic cancer


title: rrAML506

tag: vital status

value: Dead

value: M

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: dna methylation type

value: CIMP-like


title: rrAML509

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: Intermediate Risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: Intemediate


title: rrAML507

tag: vital status

tag: age (years)

tag: cytogenetic risk

tag: cell type

value: AML patient peripheral blood cells


title: rrAML510

value: F

tag: best response

tag: peripheral blasts (%)

tag: hemoglobin in (g/dl)

tag: nras mutation

value: positive


title: rrAML502

tag: overall survival days

value: Unevaluable

tag: kras mutation

tag: dnmt3a mutation

value: ND

tag: dna methylation type

value: Normal-like


title: post1_Bulk_0011

value: bulk biopsy

tag: age

tag: Sex

value: male

tag: cancer type

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ


title: rrAML399

tag: vital status

value: Alive

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: rrAML503

value: Dead

tag: overall survival days

value: M

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: cell type

tag: dna methylation type


title: rrAML516

tag: vital status

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: CR


title: post1_TIL_CD4_0008

value: CD4+ CD8- T cells

tag: age

tag: Sex

tag: cancer type

value: gastro-esophageal

tag: dose level

tag: agent

tag: organ

value: gastro-esophageal cancer


title: post1_Bulk_0010

value: colorectal

value: liver metastasis of pancreatic cancer


title: rrAML392

tag: overall survival days

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: CIMP-like


title: pre_Bulk_0010

tag: cell type

value: bulk biopsy


title: pre_Bulk_0009

source_name: biopsy of gastric cancer

tag: age

value: male

value: gastric

value: gastric cancer


title: rrAML391

tag: vital status

value: Dead

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: Poor Risk

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: dna methylation type


title: rrAML395

value: Alive

tag: overall survival days

value: F

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

value: positive

value: Normal-like


title: rrAML508

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

value: ND

tag: npm1 mutation

value: Intemediate


title: pre_TIL_CD4_0002

tag: cell type

value: CD4+ CD8- T cells

tag: age

tag: Sex

tag: cancer type

tag: dose level

tag: agent

tag: organ


title: rrAML387

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: age (years)

value: NR

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: dna methylation type


title: rrAML382

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

value: AML patient peripheral blood cells


title: post1_Bulk_0008

source_name: biopsy of gastro-esophageal cancer

value: bulk biopsy

tag: age

tag: Sex

value: male

tag: cancer type

value: gastro-esophageal

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: gastro-esophageal cancer


title: pre_Bulk_0008


title: pre_Bulk_0007


title: post1_Bulk_0007


title: rrAML381

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: CRi

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: dna methylation type


title: post1_Bulk_0009

tag: cell type

value: gastric

value: gastric cancer


title: pre_Bulk_0006

source_name: biopsy of skin metastasis of colorectal cancer

tag: age

value: female

value: colorectal

value: skin metastasis of colorectal cancer


title: rrAML379

source_name: AML patient peripheral blood cells

value: M

tag: cytogenetic risk

value: Unevaluable

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: Normal-like


title: rrAML505

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

tag: age (years)

value: Poor Risk

value: NR

value: negative


title: rrAML378

value: Intermediate Risk

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

value: AML patient peripheral blood cells

tag: dna methylation type

value: CIMP-like


title: rrAML373

value: Alive

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

value: positive

tag: cell type


title: rrAML376

value: Dead

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: idh1 mutation

value: ND


title: post1_Bulk_0006

value: bulk biopsy

tag: age

tag: Sex

value: female

tag: cancer type

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ


title: rrAML374

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: age (years)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: idh2 mutation

tag: npm1 mutation


title: pre_Bulk_0004

source_name: biopsy of bronchus metastasis of colorectal cancer

tag: cell type

value: colorectal


title: pre_Bulk_0005

source_name: biopsy of stomach with no cancer

tag: age

value: gastric

value: stomach with no cancer


title: rrAML371

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: dnmt3a mutation

tag: idh1 mutation

tag: dna methylation type

value: Intemediate


title: pre_Bulk_0003

source_name: biopsy of esophagus with no cancer

tag: Sex

value: male

tag: cancer type

value: esophageal

tag: dose level

tag: agent

tag: organ

value: esophagus with no cancer


title: post1_Bulk_0004

value: bronchus metastasis of colorectal cancer


title: pre_Bulk_0002

value: gastric cancer


title: post1_Bulk_0003


title: post1_Bulk_0002


title: rrAML366

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

tag: age (years)

value: NR

tag: hemoglobin in (g/dl)

tag: nras mutation

value: negative

tag: kras mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: Normal-like


title: rrAML368

value: Alive

tag: cytogenetic risk

value: Unevaluable

tag: best response

value: CR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: dnmt3a mutation

tag: idh1 mutation

tag: cell type


title: rrAML365

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

value: positive

tag: dna methylation type


title: rrAML370

value: Dead

tag: gender

tag: age (years)

value: Intermediate Risk

tag: hemoglobin in (g/dl)

tag: nras mutation


title: rrAML364

value: M

tag: cytogenetic risk

value: CRi

tag: kras mutation

tag: idh2 mutation

tag: npm1 mutation

value: Intemediate


title: rrAML362

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

value: CIMP-like


title: pre_Bulk1_0001

tag: cell type

value: bulk biopsy

tag: age

tag: Sex

value: male

tag: cancer type

value: gastric

tag: dose level

tag: agent

tag: organ


title: rrAML363

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

tag: age (years)

value: Poor Risk

value: NR

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

tag: idh1 mutation

tag: dna methylation type


title: rrAML357

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: nras mutation

value: negative

tag: kras mutation

tag: idh2 mutation

tag: npm1 mutation

tag: cell type

value: AML patient peripheral blood cells


title: post2_Blood_CD8_0011

source_name: CD8+ peripheral blood T cells

value: CD8+ CD4- T cells

tag: age

tag: Sex

tag: cancer type

value: colorectal and pancreas

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: peripheral blood


title: post1_Blood_CD8_0011


title: post1_Bulk1_0001

value: gastric cancer


title: post2_Blood_CD8_0010

value: colorectal


title: pre_Blood_CD8_0011


title: post1_Blood_CD8_0010


title: rrAML355

tag: vital status

value: Alive

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: Intermediate Risk

value: CR

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

tag: idh1 mutation

tag: dna methylation type


title: rrAML351

value: Dead

value: M

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: nras mutation

tag: kras mutation

tag: idh2 mutation

value: positive

tag: npm1 mutation

tag: cell type

value: Intemediate


title: rrAML354

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: CIMP-like


title: rrAML350

value: F

tag: age (years)

value: Poor Risk

value: NR

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation


title: post2_Blood_CD8_0009

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: gastric

tag: dose level

tag: agent

tag: organ


title: pre_Blood_CD8_0010

value: 1.0 mg/kg

value: peripheral blood


title: rrAML347

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: nras mutation

value: negative

tag: kras mutation

tag: idh1 mutation

tag: idh2 mutation

value: AML patient peripheral blood cells

tag: dna methylation type


title: post1_Blood_CD8_0009

tag: cell type


title: rrAML346

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: Unevaluable

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

tag: npm1 mutation

value: Normal-like


title: rrAML343

value: Dead

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)


title: pre_Blood_CD8_0008

tag: age

tag: Sex

tag: cancer type

value: gastro-esophageal

tag: dose level

tag: agent

tag: organ


title: rrAML339

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

value: M

tag: platelets (x10^9/l)

tag: nras mutation

tag: kras mutation

tag: idh1 mutation

tag: idh2 mutation

tag: cell type

tag: dna methylation type


title: rrAML359

value: Alive

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

value: positive

tag: npm1 mutation


title: pre_Blood_CD8_0009

tag: age

tag: Sex

tag: cancer type

tag: dose level

tag: agent

tag: organ


title: post1_Blood_CD8_0008

tag: cell type


title: rrAML336

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: platelets (x10^9/l)

tag: nras mutation

tag: kras mutation

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type


title: rrAML356

value: F

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

tag: npm1 mutation


title: post1_Blood_CD8_0006

tag: cell type

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: female

tag: cancer type

value: colorectal

tag: dose level

tag: agent

tag: organ


title: rrAML332

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: NR

tag: platelets (x10^9/l)

tag: nras mutation

tag: kras mutation

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type

value: CIMP-like


title: pre_Blood_CD8_0006

tag: cell type

value: 1.0 mg/kg

value: peripheral blood


title: pre_Blood_CD8_0007

tag: age

value: male


title: pre_Blood_CD8_0005

tag: Sex

value: gastric


title: post1_Blood_CD8_0005

tag: cancer type


title: rrAML314

value: Dead

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

value: negative

tag: dnmt3a mutation

tag: npm1 mutation

value: AML patient peripheral blood cells

value: Intemediate


title: rrAML320

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: platelets (x10^9/l)

tag: nras mutation

tag: kras mutation


title: rrAML311

value: Intermediate Risk

tag: idh1 mutation

tag: idh2 mutation

value: positive

tag: cell type

tag: dna methylation type

value: Normal-like


title: rrAML309

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)


title: post1_Blood_CD8_0007

value: CD8+ CD4- T cells

tag: age

tag: Sex

tag: cancer type

value: gastro-esophageal

tag: dose level

tag: agent

tag: organ


title: rrAML308

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

value: NR

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: dnmt3a mutation

tag: npm1 mutation


title: post1_Blood_CD8_0004

tag: cell type

value: female

value: colorectal


title: pre_Blood_CD8_0004

tag: age

value: peripheral blood


title: post2_Blood_CD8_0003

tag: Sex

value: male

value: esophageal


title: rrAML307

value: Dead

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: peripheral blasts (%)

tag: nras mutation

tag: kras mutation

value: negative

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type


title: rrAML306

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

value: AML patient peripheral blood cells

value: CIMP-like


title: post1_Blood_CD8_0003

tag: cell type

tag: age

tag: cancer type

tag: dose level

tag: agent

tag: organ


title: post1_Blood_CD8_0002

tag: Sex

value: gastric


title: pre_Blood_CD8_0003


title: pre_Blood_CD8_0002


title: post1_Blood_CD8_0001


title: post2_Blood_CD8_0002


title: rrAML193

value: M

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

value: positive

tag: npm1 mutation


title: rrAML322

tag: vital status

value: Alive

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: cell type

tag: dna methylation type


title: rrAML194

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)

value: Intemediate


title: rrAML301

value: F

value: NR

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

value: Normal-like


title: rrAML319

tag: vital status

tag: overall survival days

tag: dnmt3a mutation

tag: npm1 mutation


title: post2_Blood_CD8_0004

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: female

tag: cancer type

value: colorectal

tag: dose level

tag: agent

tag: organ

value: peripheral blood


title: rrAML191

value: Dead

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

value: negative

tag: idh1 mutation

tag: idh2 mutation

value: ND

tag: cell type

tag: dna methylation type


title: rrAML186

tag: vital status

tag: overall survival days

tag: best response

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation

value: AML patient peripheral blood cells


title: pre_Blood_CD8_0001

tag: age

tag: Sex

value: male

tag: cancer type

value: gastric

tag: dose level

tag: agent

tag: organ


title: post1_Blood_CD4_0011

source_name: CD4+ peripheral blood T cells

tag: cell type

value: CD4+ CD8- T cells

value: colorectal and pancreas

value: 1.0 mg/kg


title: post2_Blood_CD4_0011


title: pre_Blood_CD4_0011


title: rrAML183

tag: vital status

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation

value: positive

tag: idh2 mutation

tag: dna methylation type


title: rrAML185

tag: overall survival days

value: F

value: Poor Risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation

value: CIMP-like


title: post2_Blood_CD4_0010

tag: cell type

tag: age

tag: Sex

tag: cancer type

value: colorectal

tag: dose level

tag: agent

tag: organ