title: WIN_4

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Bos Taurus reference genome (ARS-UCD1.2) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against bovine mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: ARS-UCD1.2
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Bos taurus

source_name: Follicular fluid

extract_protocol:
For EV isolation, follicular fluid samples were subjected to a series of centrifugations starting at 500 xg for 10 minutes to remove cells, followed by 3000 xg for 10 minutes to remove the cellular debris, and at 12,000 xg for 30 min to remove protein aggregates and large particles. All centrifugation steps were performed at 4 °C. The supernatant of FF samples was filtered through a 0.22 µM sterile filter to remove particles larger than 200 nm. For the EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 OC using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 xg for 70 min. Finally, EVs were resuspended in 500 µL of PBS and stored at −80 °C until further characterization and analysis. Total RNA including miRNAs was isolated from EVs using a Norgen Exosomal RNA Isolation kit (Norgen, Canada), according to the manufacturer’s instructions. On-column DNA digestion was performed to remove genomic DNA contaminants.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Follicular fluid

value: Extracellular Vesicles

tag: season

value: Winter


title: MBD2aR181C_r2

status: Public on May 23 2023

type: SRA

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

library_source: transcriptomic

data_processing:
reads were trimmed using trim_galore using standard parameters
reads were aligned to the mouse genome mm9 annotation using STAR with following parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000
counts per gene were obtained in R using quasr::qCount() with the following parameters: reportLevel="gene", orientation="opposite", based on gencode.mouse.v1.annotation.gtf
differential gene expression was calculated using edgeR in R
Assembly: mm9
Supplementary files format and content: gene matrix containing raw counts per gene (rows) for each sample (columns)

molecule: polyA RNA

organism: Mus musculus

source_name: Neuronal progenitor

extract_protocol: not provided

tag: cell type

value: ES-derived neural progenitor cells

tag: genotype

value: Mbd3-KO + Mbd2a_R181C


title: pCCL4-IFNγ

type: RNA

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

description: liver carcinoma cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done in Rstudio following Agilent's standardized method.

molecule: total RNA

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

growth_protocol: liver carcinoma cell lines were maintained at 5% CO2 and 37°C

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: IFNγ treated primary carcinoma cell lines (pCCL-IFNγ) were treated with 20ng/ml Interferon-γ for 20 hours, primary carcinoma cell lines (pCCL) and explanted primary carcinoma cell lines (pCCL-ex) remained untreated

tag: tissue

value: liver carcinoma cell line

value: HBsAg+, Trp53 -/-

tag: treatment


title: WIN_3

country: USA


title: Untag_FLAG_rep3

city: Los Angeles

first: Meghan

middle: V

last: Petrie

state: CA

address: 1050 Childs Way

department: Molecular Biology

institute: University of Southern California

library_source: genomic

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filtered reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup.
Binning: Sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: Binned.bed files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: ~100 mL of cells were grown per sample and harvested at OD ~ 1.0 in YEPD at 23 °C.

extract_protocol:
Chromatin was cross-linked with formaldehyde solution (1 % final concentration) for 15min. After quenching cells were lysed by bead-beating with FastPrep and chromatin sonicated using a S2 sonicator (Covaris). Then PCI extraction and ethanol precipitation.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: At OD ~0.5 when noted alpha-factor was added and cells were grown for an additional ~3.5hr to achieve G1 arrest.

tag: strain

value: WT

tag: chip antibody

value: anti-FLAG M2 (Sigma F1804)


title: pCCL3-IFNγ

description: liver carcinoma cell line

source_name: IFNγ treated primary carcinoma cell line


title: pCCL2-IFNγ

description: liver carcinoma cell line


title: pCCL3

description: liver carcinoma cell line

source_name: primary carcinoma cell line

value: pCCL


title: MBD2aR181C_r1


title: pCCL1-IFNγ

description: liver carcinoma cell line


title: pCCL4

description: liver carcinoma cell line


title: pCCL2

description: liver carcinoma cell line


title: WIN_2


title: MBD2a-GR_r3

value: Mbd3-KO + Mbd2a_delGR


title: Untag_FLAG_rep2


title: WIN_1


title: MBD2a-GR_r2


title: pCCL1

description: liver carcinoma cell line


title: Dsim_5seq_dcr2_mutant_replicate2

city: New Yor

first: Jeffrey

last: Vedanayagam

state: NY

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
RNA sequencing analysis. Paired-end RNA-seq reads from wild-type and mutant dcr-2 samples in Dmel and Dsim were mapped to dm6 (FlyBase) and Dsim PacBio assemblies (Chakraborty et al., 2021), respectively using hisat2 aligner (Kim et al., 2015; Pertea et al., 2016).The resulting alignments in SAM format was converted to BAM using SAMtools software (Li et al., 2009) for downstream analyses. Mapping quality and statistics were determined using the bam_stat.py script provided in the RSeQC software (Wang et al., 2012). Transcript abundance was determined using FeatureCounts software from the subread package (Liao et al., 2014), using Dmel gene annotations from FlyBase r6.25. For Dsim, we used both gene annotations from FlyBase and de novo transcript annotation using StringTie software (see details below) (Pertea et al., 2015). As FlyBase gene annotations for Dsim correspond to Dsim r2.02 assembly, we converted the FlyBase assembly annotations to Dsim PacBio coordinates using the UCSC liftover tool implemented in the KentUtils toolkit from UCSC (https://github.com/ENCODE-DCC/kentUtils). We combined FlyBase liftover and de novo annotations in Dsim to determine transcript abundance for RNA-seq analyses. The following description for differential gene expression (DFE) analysis is the same for Dmel and Dsim data. DFE comparing control and dcr-2 mutant data was performed using the DEseq2 package in R (Love et al., 2014). Genes with low read counts and/or high variability among technical or biological replicates can lead to log fold change differences that are not representative of true differences. Therefore, to minimize variance, we used the log fold change (LFC) shrinkage implemented in the DEseq2 package using the ‘normal’ method described in (Love et al., 2014). For visualization of mapped reads, the BAM alignment files were converted to bigwig format using bam2wig.py script from RSeQC (Wang et al., 2012) and the bigwig tracks were visualized on the IGV genome browser (Robinson et al., 2011).
Small RNA sequencing analysis. Adapters were trimmed from small RNA sequences using Cutadapt software (https://github.com/marcelm/cutadapt); then the 5’ and 3’ 4-nt linkers (total 8 bp) were removed using sRNA_linker_removal.sh script described in (Vedanayagam et al., 2021) (https://github.com/Lai-Lab-Sloan-Kettering/Dox_evolution). The adapter and linker removed sequences were then filtered to remove < 15 nt reads. We mapped > 15 nt reads from Dmel and Dsim genotypes to dm6 reference genome assembly and Dsim PacBio assembly, respectively, with Bowtie (Langmead et al., 2009) using the following mapping options: bowtie -q -p 4 -v 3 -k 20 --best –strata. The resulting BAM alignments from bowtie mapping were converted to bigwig for visualization using bam2wig.py script from the RSeQC software (Wang et al., 2012).
In addition to previously annotated transcripts/genes from the FlyBase annotation, we performed de novo annotation of our transcriptome data to identify additional, novel testis-expressed transcripts in D. melanogaster and D. simulans. The novel annotated transcripts were then supplemented with known annotations to make a combined set of 17285 transcripts in D. melanogaster and 15119 transcripts in D. simulans. We employed two independent, genome assembly guided transcript prediction algorithms, Cufflinks (Trapnell et al., 2012) and StringTie (Pertea et al., 2015). For both methods, de novo transcripts were predicted for each RNA-seq dataset, and a merged transcript model was generated encompassing the transcriptome from WT and mutant datasets. hpRNAs were predicted using the scheme shown in Supplementary Figure 2, and visualized using the Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013). The termini of primary hpRNA transcripts were refined using the 5'-seq and 3'-seq data.
Assembly: For D. melanogaster, we used the dm6 genome assembly (Flybase) and for D. simulans, we used Dsim PacBio genome assembly (Chakraborty et al. 2021)
Supplementary files format and content: The processed data files for IGV visualization are in bigiwg format

organism: Drosophila simulans

source_name: testis

extract_protocol:
For D. melanogaster testis dissections dcr-2 mutant testis were collected from wIR; dcr-2[L811fsx]/dcr-2[R416X] trans-heterozygotes and wIR; dcr-2[R416X]/+ heterozygous flies were used as controls. For D. simulans, we collected testis from dcr2[DsRed]/[white+] trans-heterozygous mutants, and used the parental strain w[XD1] as control. Briefly, testis from 3 days old flies were extracted in TRIzol (Invitrogen) in batches of 10 flies at a time and the testis samples were flash frozen in liquid nitrogen. RNA was extracted from 25-50 testis per genotype.
RNA extraction was performed as described in (Lin et al., 2018), and the quality of RNA samples were assessed with the Agilent Bioanalyzer. RNA samples with RIN >6.5 were used for library preparation using the Illumina TruSeq Total RNA library Prep Kit LT. Briefly, for RNA-seq libraries we used 650 ng of total RNA, and we used the Manufacturer’s protocol except for reducing the number of PCR cycles from 15 as recommended to 8, to minimize artifacts that may arise from PCR amplification. We prepared stranded RNA-seq libraries for D. simulans and unstranded libraries for D. melanogaster as RNA samples were extracted and processed in different time points. Samples were pooled using barcoded adapters provided by the manufacturer and the paired-end sequencing was performed at New York Genome Center using PE75 in the Illumina HiSeq2500 sequencer. We prepared small RNA libraries used ~20 μg total RNA, as previously described in Lin et al. 2018. To the total RNA pool, we added a set of 52 RNA spike-ins, spanning a range of concentrations (QIAseq miRNA Library Spike-In kit #800100). Briefly, small RNAs of size 18- to 29-nt-long small RNAs were purified by preparative PAGE. Next, the 3′ linker (containing four random nucleotides) was ligated overnight using T4 RNA ligase 2, truncated K227Q (NEB), after which the products were recovered by a second PAGE purification. 5′ RNA linkers with four terminal random nucleotides were then ligated to the small RNAs using T4 RNA ligase (NEB) followed by another round of PAGE purification. The cloned small RNAs were then reverse transcribed, PCR amplified and sequenced using P50 single-end sequencing on the Illumina HiSeq 2500 sequencer. We prepared small RNA libraries used ~20 μg total RNA, as previously described in Lin et al. 2018. To the total RNA pool, we added a set of 52 RNA spike-ins, spanning a range of concentrations (QIAseq miRNA Library Spike-In kit #800100). Briefly, small RNAs of size 18- to 29-nt-long small RNAs were purified by preparative PAGE. Next, the 3′ linker (containing four random nucleotides) was ligated overnight using T4 RNA ligase 2, truncated K227Q (NEB), after which the products were recovered by a second PAGE purification. 5′ RNA linkers with four terminal random nucleotides were then ligated to the small RNAs using T4 RNA ligase (NEB) followed by another round of PAGE purification. The cloned small RNAs were then reverse transcribed, PCR amplified and sequenced using P50 single-end sequencing on the Illumina HiSeq 2500 sequencer. To map 5' ends, we used the parallel analysis of RNA 5′ ends from low-input RNA (nanoPARE) strategy (Schon et al., 2018). For Dsim libraries, testis was extracted from <1-week males and total RNA was extracted using TRIzol. cDNA was prepared using Smart-seq2 (Picelli et al., 2013) and tagmented using the Illumina Nextera DNA library preparation kit, purified using the Zymo 5x DNA Clean and Concentrator kit (Zymo Research), and eluted with resuspension buffer. For 5’-end enrichment PCR, the purified reaction was split and amplified either Tn5.1/TSO or Tn5.2/TSO enrichment oligonucleotide primer sets. PCR reaction products with Tn5.1/TSO enrichment oligonucleotide and Tn5.2/TSO enrichment oligonucleotide primer sets were pooled and purified using AMPureXP DNA beads. Final libraries were checked for quality on an Agilent DNA HS Bioanalyzer chip. Libraries with size ranges between 150 and 800 bp were diluted and sequenced to 10–15 million single-end 50-bp reads per sample using a custom sequencing primer (TSO_Seq) and a custom P5/P7 index primer mix on an Illumina HiSeq 2500 instrument. To annotate 3' transcript termini, we used the QuantSeq 3’ mRNA-seq library preparation REV kit for Illumina (Lexogen) with a starting material of 50 ng total RNA from Dmel and Dsim control and dcr-2 mutant samples, according to manufacturer’s instructions. cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with single-end SE 50 mode.
RNA-sequencing was done with the paired-end sequencing mode, while the small RNA sequencing was peformed with the single-end sequencing protocol.

value: testis


title: Untag_FLAG_rep1


title: SUM_3

value: Summer


title: MBD2a-GR_r1


title: SUM_4


title: MBD2aFL_r3

value: Mbd3-KO + Mbd2a


title: MBD2aFL_r2


title: SUM_2


title: Dsim_5seq_dcr2_het_replicate1


title: SUM_1


title: Dsim_5seq_dcr2_het_replicate2


title: Dsim_5seq_dcr2_mutant_replicate1


title: Thin_Whole-UdECM treated 2

city: Sungnam

first: Danbi

last: Lee

address: sampyeongro 335, Seongnam-Si, Kyounggido, Republic of Korea

department: Department of biological sciences

country: South Korea

institute: CHA university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Uterus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: 95% EtOH was instilled into one uterus cavity (TS), and after 4 days,  Endo-UdECM (TE) or Whole-UdECM (TE) were treated.

value: Uterus


title: MBD2aFL_r1


title: MBD3a_r2

value: Mbd3-KO + Mbd3a


title: MBD3a_r3


title: Thin_Whole-UdECM treated 3


title: MBD3a_r1


title: Thin_Endo-UdECM treated 2


title: Thin_Endo-UdECM treated 3


title: Thin_Endo-UdECM treated 1


title: tDC_rep2

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

data_processing:
Trim adapters and low quality bases (Trimmomatic, v.0.36)
Align to reference genome (star, v.2.7.3a)
Determine the distribution of the bases within the transcripts and 5’/3’ biases (picard-tools, v.2.18.20)
Generate genes-samples counts matrix with featureCounts (subread, v.1.6.3)
Differential expression analysis (DESeq2)
Assembly: mm10
Supplementary files format and content: Gene read counts matrix in .txt format generated by featureCounts

source_name: sorted tDCs from spleen

extract_protocol:
RNA was extracted from immediately after sorting using the NucleoSpin RNA XS kit (Takara Bio) according to manufacturer’s instructions.
Clontech Smart-seq HT with Nxt HT

treatment_protocol: splenic DCs from 2 mice were CD135-enriched and counted. The sample was split in two: 30% was stained and DC subsets were sorted fresh; 70% was resuspended at 10x106/mL and stimulated with the LPRC adjuvant cocktail [LPS 100ng/mL, Poly(I:C) 25ug/mL, Resiquimod 2.5ug/mL and CpG-A (ODN 2216) 6ug/mL] for 3h before staining and sorting. RNA was extracted from immediately after sorting using the NucleoSpin RNA XS kit (Takara Bio) according to manufacturer’s instructions.

value: spleen

tag: cell

value: unstimulated


title: stimulated tDC_rep2

source_name: sorted pDCs from spleen

value: stimulated with LPRC cocktail


title: tDC_rep1


title: Thin_saline treated 2


title: Thin_saline treated 1


title: Thin_Whole-UdECM treated 1


title: pDC_rep1


title: stimulated tDC_rep1


title: stimulated pDC_rep1


title: colon, WT-11

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Differential expression calls (p values) were made in sleuth using a full linear model (genotype + cage) against a reduced model (cage only), to account for cage-to-cage variability.
Displayed differential expression ratios take into account only the global gene expression values and do not normalize per cage.
Assembly: mm10
Supplementary files format and content: Comma-separated file includes tpm levels of individual principal transcripts for each sample and results of differential expression testing.

source_name: colon

growth_protocol: Mutant (Nrg4-/-) and wildtype (WT) mice were co-housed to mix genotypes at 9 weeks of age. Animals were dissected at 11-12 weeks of age. Both male and female mice were included in the experiment.

extract_protocol:
Mice were euthanized and their colons dissected. Full-thickness distal colonic tissue was homogenized and lysed. RNA was prepared using OMEGA Bio-tek EZNA on-column isolation kit.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.

value: colon

tag: cage

value: B

tag: age

value: adult (11-12 wks-old)


title: cDC2_EYFP+_rep2

source_name: sorted cDC2s from spleen


title: colon, KO-9

value: Nrg4 KO


title: cDC2_EYFP+_rep1


title: stimulated cDC2_EYFP+_rep2


title: stimulated cDC2_EYFP+_rep1


title: colon, WT-7

value: A


title: colon, WT-6

value: WT

value: C


title: colon, WT-5


title: colon, KO-8


title: cDC2_EYFP-_rep2


title: colon, KO-4


title: Thin_saline treated 3


title: cDC2_EYFP-_rep1


title: stimulated cDC2_EYFP-_rep2


title: colon, KO-3


title: stimulated cDC2_EYFP-_rep1


title: cDC1_rep2

source_name: sorted cDC1s from spleen


title: H1299 cells, vector-2

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

data_processing:
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases (LEADING:20 TRAILING:13 SLIDINGWINDOW:5:20 MINLEN:30).
Trimmed reads were aligned to the reference genome sequence (GRCh38) using HISAT2 v2.1.0 to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Read count extraction and normalization were performed using StringTie v2.1.2.
Differential expression analysis was performed using DESeq (for non-replicate samples) R package v1.39.0 to test for differential expression for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Homo sapiens

source_name: lung cancer

extract_protocol:
RNA was harvested using Trizol method (Invitogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent SureSelect XT HS2 mRNA Library Prep Kit following manufacturer's protocols.

value: lung cancer

tag: cell line

value: Non-Small Cell Lung Cancer cell

value: EGFR WT

value: vector control


title: colon, WT-2


title: stimulated pDC_rep2


title: colon, WT-10


title: cDC1_rep1


title: stimulated cDC1_rep2


title: H1299 cells, overexpressed TMPRSS2-2

value: overexpressed TMPRSS2


title: stimulated cDC1_rep1


title: H1299 cells, vector-1


title: H1299 cells, overexpressed TMPRSS2-1


title: colon, KO-1


title: SEQTR_vs_RACE_Replicate3_bis

status: Public on May 22 2023

city: Epalinges

first: Raphael

last: Genolet

address: Biopole 3, Chemin des Boveresses 155

department: Departement d'oncologie UNIL-CHUV

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

data_processing:
Ad hoc perl script
MiXCR software from MiLaboratories
Assembly: TCR alignment was performed using the IMGT database
Supplementary files format and content: Text file with the list of TCRs
Library strategy: Targeted amplification

source_name: peripheral blood mononuclear cell (PBMC) donnoe 4

growth_protocol: PBMC were obtained from leukapheresis of healthy donor.

extract_protocol:
mRNA were extracted using the Dynabeads mRNA DIRECT purification kit
Custum protocol for TCR sequencing describe in the manuscript.
ImmunoSEQ commercially available kit for TCR amplification
SMARTer (Takara) commercially available kit for TCR amplification

value: PBMC

tag: repertoire

value: beta TCR repertoire


title: SEQTR_vs_RACE_Replicate2_bis


title: SEQTR_vs_RACE_Replicate1_bis


title: 13F_M_3036

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 13F_M_3052


title: 13F_M_3048


title: 13F_M_3039


title: 13F_M_3059


title: 13F_M_3041


title: 13F_M_3044


title: 13F_M_3051


title: 13F_M_3056


title: 13F_M_3037


title: 13F_M_3053


title: 13F_M_3054


title: 13F_M_3049


title: 13F_M_3057


title: 13F_M_3050


title: 13F_M_3055


title: 13F_M_3042


title: 13F_M_3047


title: 13F_M_3035


title: 13F_M_3034


title: 13F_M_3033


title: 13F_M_3045


title: 13F_M_3046


title: 13F_M_3040


title: 13F_M_3038


title: 13F_M_3043


title: 13F_M_3032


title: 13F_M_3058


title: 13F_M_3060


title: 13F_M_3029


title: 13F_M_3030


title: 13F_M_3026


title: 13F_M_3031


title: 13F_M_3015


title: 13F_M_3013


title: 13F_M_3027


title: 13F_M_3028


title: 13F_M_3023


title: 13F_M_3016


title: 13F_M_3021


title: 13F_M_3020


title: 13F_M_3018


title: 13F_M_3011


title: 13F_M_3019


title: 13F_M_3022


title: 13F_M_3024


title: 13F_M_3010


title: 13F_M_3007


title: 13F_M_3008


title: 13F_M_3017


title: 13F_M_3005


title: 13F_M_3006


title: 13F_M_3014


title: 13F_M_3004


title: 13F_M_3025


title: 13F_M_3012


title: 13F_M_3009


title: 13F_M_3000


title: 13F_M_3001


title: 13F_M_2932


title: 13F_M_2931


title: 13F_M_2928


title: 13F_M_2927


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title: 13F_M_1293


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title: 13F_M_1274


title: 13F_M_1276


title: 13F_M_1284


title: 13F_M_1282


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title: 13F_M_1270


title: 13F_M_1279


title: 13F_M_1268


title: 13F_M_1278


title: 13F_M_1277


title: 13F_M_1273


title: 13F_M_1272


title: 13F_M_1266


title: 13F_M_1267


title: 13F_M_1263


title: 13F_M_1261


title: 13F_M_1262


title: 13F_M_1265


title: 13F_M_1275


title: 13F_M_1259


title: 13F_M_1260


title: 13F_M_1264


title: 13F_M_1257


title: 13F_M_1258


title: 13F_M_1271


title: 13F_M_1255


title: 13F_M_1252


title: 13F_M_1253


title: 13F_M_1249


title: 13F_M_1250


title: 13F_M_1251


title: 13F_M_1245


title: 13F_M_1247


title: 13F_M_1246


title: 13F_M_1243


title: 13F_M_1244


title: 13F_M_1254


title: 13F_M_1256


title: 13F_M_1242


title: 13F_M_1240


title: 13F_M_1241


title: 13F_M_1233


title: 13F_M_1234


title: 13F_M_1232


title: 13F_M_1235


title: 13F_M_1236


title: 13F_M_1229


title: 13F_M_1230


title: 13F_M_1228


title: 13F_M_1248


title: 13F_M_1227


title: 13F_M_1226


title: 13F_M_1225


title: 13F_M_1224


title: 13F_M_1222


title: 13F_M_1239


title: 13F_M_1221


title: 13F_M_1219


title: 13F_M_1218


title: 13F_M_1238


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title: 13F_M_1231


title: 13F_M_1237


title: 13F_M_1213


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title: 13F_M_1212


title: 13F_M_1016


title: 13F_M_1223


title: 13F_M_1210


title: 13F_M_1017


title: 13F_M_1214


title: 13F_M_1014


title: 13F_M_1013


title: 13F_M_1015


title: 13F_M_1012


title: 13F_M_1008


title: 13F_M_1009


title: 13F_M_1010


title: 13F_M_1007


title: 13F_M_1006


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title: 13F_M_1003


title: 13F_M_1000


title: 13F_M_1002


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title: 13F_M_991


title: 13F_M_994


title: 13F_M_985


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title: 13F_M_986


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title: 13F_M_981


title: 13F_M_974


title: 13F_M_978


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title: 13F_M_982


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title: 13F_M_963


title: 13F_M_964


title: 13F_M_962


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title: 13F_M_954


title: 13F_M_949


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title: 13F_M_944


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title: 13F_M_937


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title: 13F_M_616


title: 13F_M_614


title: 13F_M_618


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title: 13F_M_620


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title: 13F_M_609


title: 13F_M_606


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title: 13F_M_611


title: 13F_M_604


title: 13F_M_603


title: OT-1 T cell Sample 3

city: Durham

first: Emily

middle: Claire

last: Lerner

email: emily.sherber@duke.edu, ecs74@duke.edu

state: North Carolina

address: 303 Research Drive

institute: Duke University School of Medicine

source_name: In vitro culture of splenocyte-derived primary OT-1 mouse T cells

growth_protocol:
OT-1 T-cells were isolated from OT-1 mice by culturing OT-1 splenocytes in T-cell media supplemented with 50IU/mL IL-2 and 1 μM OVA SIINFEKL peptide (Anaspec) for 48 h. Cells were purified for CD8 T-cells as described above and subsequently cultured in TCM with 50IU/mL IL-2, splitting every 24h for a total of 4 days. T-cell media: (RPMI supplemented with 10% FBS, l-glutamine, HEPES, sodium pyruvate, non-essential amino acids, and pen/strep)
Ly6Chi monocytes were purified from bone marrow (BM) were loaded with OVA antigen by adding 10 µM peptide dissolved in DMSO to the culture for 4 hr.  Bone marrow derived macrophages (BMDMs) were then washed twice with PBS to remove remaining antigen, separated from culture plates using non-enzymatic dissociation agent
Tumor cells were cultured in vitro in Dulbecco’s Modified Eagle Medium (DMEM) with 2mM l-glutamine and 4.5 mg/mL glucose (Gibco) containing 10% fetal bovine serum (FBS).

treatment_protocol: Indicated cell types were co-cultured at ratios indicated above in murine T cell media (RPMI supplemented with 10% FBS, l-glutamine, HEPES, sodium pyruvate, non-essential amino acids, and pen/strep) for 24 hours. After 24hrs, CD8 T cells from co-culture conditions were isolated with FACS sorting for CD8+ cells.

tag: co-culture conditions

tag: t cell to tumor ratio

tag: t cell to macrophage ratio


title: 13F_M_617


title: 13F_M_615


title: control4

city: Shanghai

first: Xiaoyu

state: Shanghai

address: 180 Yue-yang road

department: Department of Interventional Radiology

country: China

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

data_processing:
The raw fastq data was asessed and trimed using fastp software.
Then the trimed fastq datasets were mapped to murine genome (mm10) using hisat2 software.
The gene read counts were identified us HTseq-count software .
The differentailly expressed genes (DEGs) were perfomed using DEseq2 in R environmet.
Further downstream analysis were perfomed using custom script in Linux or R environment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts values (Htseq-count) for each Sample

source_name: pancreatic tumor

growth_protocol: The KPC and Panc02 murine panctireac cancer cell line was used to generate the orthotopic pancreatic tumors.

extract_protocol:
Total RNA was extracted from each sample using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The IRE group tumors were treated with irreversible electroporation, while the conrtol group were blank control without IRE treatment.

value: pancreatic tumor

value: KPC

value: murine pancreatic cancer

value: non-treated control


title: control3


title: control2


title: 13F_M_605


title: IRE1

value: murine pancreatic  cancer

value: IRE


title: IRE2


title: control1


title: SI Crypts_KO1 [Bisulfite-seq]

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

institute: DKFZ

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.39
Preprocessing, quality filtering: Trimmomatic 0.39
BS-mapping: BSMAP 2.5
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: mm9
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

source_name: Small Intestine

extract_protocol:
We followed a previously published protocol to isolate intestinal crypts [PMID: 23097115]. Briefly, the small intestine (Jejunum) was flushed with ice-cold PBS then cut open longitudinally. The Jejunum was minced into small pieces in cold PBS (2-5 mm) and then incubated for 30 min at 4 °C in PBS containing 2 mM EDTA. Intestinal fragments were then transferred into cold PBS and the villi fraction was mechanically isolated by shaking. Then the intestinal fragments were transferred into fresh cold PBS and the crypts fraction was mechanically isolated by vigorously shaking. This step was repeated further two times to recover the crypts. Crypts fractions were then combined and passed through a 70 µm cell strainer. The combined fractions of crypts were then washed in PBS, centrifuged at 300g for 3 min, and stored at -80°C for DNA extraction. Genomic DNA was extracted from intestinal epithelial crypts using DNA blood and tissue kit (cat. no. 69504, Qiagen), according to the manufacturer's instructions.
Accel-NGS Methyl-Seq DNA

value: Small intestine

value: 11 weeks


title: SI Crypts_WT3 [Bisulfite-seq]

value: wild type


title: SI Crypts_WT2 [Bisulfite-seq]


title: SI Crypts_KO3 [Bisulfite-seq]


title: SI Crypts_KO2 [Bisulfite-seq]


title: OT-1 T cell with OVA Macrophage Sample 1

value: OVA Macrophage

value: 5 to 1


title: OT-1 T cell Sample 2


title: OT-1 T cell with OVA Macrophage and CT2A-TRP2-B2mKO Tumor Sample 3

value: OVA Macrophage and CT2A-TRP2-B2mKO


title: OT-1 T cell with OVA Macrophage and CT2A-TRP2-B2mKO Tumor Sample 1


title: OT-1 T cell with OVA Macrophage and CT2A-TRP2-B2mKO Tumor Sample 2


title: 13F_M_602


title: 13F_M_601


title: 13F_M_599


title: 13F_M_598


title: 13F_M_600


title: 13F_M_596


title: OT-1 T cell Sample 1


title: OT-1 T cell with OVA Macrophage Sample 3


title: 13F_M_597


title: OT-1 T cell with OVA Macrophage Sample 2


title: IRE4

value: WT


title: IRE3


title: SI Crypts_WT1 [Bisulfite-seq]


title: 13F_M_593


title: 13F_M_592


title: 13F_M_595


title: 13F_M_591


title: 13F_M_594


title: 13F_M_584


title: 13F_M_589


title: 13F_M_586


title: 13F_M_588


title: 13F_M_585


title: 13F_M_581


title: 13F_M_583


title: 13F_M_579


title: 13F_M_582


title: 13F_M_587


title: 13F_M_580


title: 13F_M_576


title: 13F_M_578


title: 13F_M_577


title: 13F_M_575


title: 13F_M_574


title: 13F_M_569


title: 13F_M_571


title: 13F_M_570


title: 13F_M_572


title: 13F_M_568


title: 13F_M_567


title: 13F_M_573


title: 13F_M_566


title: 13F_M_590


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title: 13F_M_560


title: 13F_M_553


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title: 13F_M_551


title: 13F_M_550


title: 13F_M_554


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title: 13F_M_547


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title: 13F_M_542


title: 13F_M_545


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title: 13F_M_565


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title: 13F_M_561


title: 13F_M_534


title: 13F_M_533


title: 13F_M_555


title: 13F_M_559


title: 13F_M_535


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title: 13F_M_532


title: 13F_M_546


title: 13F_M_530


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title: 13F_M_528


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title: 13F_M_522


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title: 13F_M_514


title: 13F_M_523


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title: 13F_M_515


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title: 13F_M_81


title: 13F_M_82


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title: 13F_M_86


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