title: ChIPseq_RNAPolymeraseII_OPM2_2hours_BKM120

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1).
Genome_build: HG19
Supplementary_files_format_and_content: bigWig

source_name: Multiple myeloma

growth_protocol: Cells were grown in vitro under standard culture conditions.

extract_protocol:
Cells were washed once in ice-cold PBS prior to crosslinking. For crosslinking, 1/10th volume of fresh formaldehyde solution (11% formaldehyde, 0.05mM EGTA, 1mM EDTA, 100mM NaCl, 50mM Hepes-KOH pH 7.5) was added and incubated for 20 minutes at room temperature with rotation. Crosslinking was quenched by addition of 1/20th volume of 2.5M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in ice-cold nuclear extraction buffer (0.5% NP-40, 2mM EDTA, 10mM NaCl, 20mM Tris-HCl pH 8) and incubated for 5 minutes on ice. Following three sequential incubations in nuclear extraction buffer, cell nuclei were pelleted and resuspended in sonication buffer (0.3% SDS, 1% NP-40, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 7.5) at a concentration equivalent to 50e6 cells per mL. Samples were sonicated in 12x24mm Covaris tubes using the Covaris S2 instrument for 18 minutes using the following settings: 20% Duty Cycle, 1000 cycles/burst, and 10 Intensity. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in ChIP dilution buffer (1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8) and quantified using Qubit dsDNA HS assay kit. For ChIP-Rx, sheared Drosophila chromatin from S2 cells was spiked into immunoprecipitations at 1:40 ratio of Drosophila:human and processed as a single sample until ChIP-Rx normalization following DNA sequencing. Immunoprecipitations were performed overnight (12-16 hours, 4°C, with rotation) using Protein A and Protein G Dyna beads (Invitrogen) and the indicated antibody. Samples were washed once with ChIP dilution buffer, wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), wash buffer 2 (0.5% deoxycholate, 0.5% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and TE buffer (1mM EDTA, 10mM Tris-HCl pH 7.5) prior to incubation in reverse crosslinking buffer (200mM NaCl, 100mM NaHCO3, 1% SDS, 300μg/mL Proteinase-K) for 4 hours at 55°C with shaking. Finally, the supernatant was reverse-crosslinked overnight (12-16 hours) at 65°C prior to ChIP DNA isolation using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205).
Libraries were generated from ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) and sequenced on an Illumina NextSeq 500 with 75 b.p. single-end reads.

treatment_protocol: Cells were treated with JQ1, BKM120, 18DS, or DMSO vehicle control for 2 hours.

tag: timepoint

value: 2 hours

tag: treatment+dose

tag: chip-seq antibody

value: RNA Polymerase II (Millipore, 05-623)


title: TNF Advanced

status: Public on Aug 14 2023

type: SRA

city: Rochester

first: H. Mark

last: Kenney

state: New York

address: 601 Elmwood Ave, Box 665

department: Center for Musculoskeletal Research

country: USA

institute: University of Rochester Medical Center

library_source: transcriptomic single cell

data_processing:
Demultiplexing: cellranger 3.1 mkfastq --use-bases-mask y*,I8,y* --nopreflight
Counting: cellranger-3.1.0 count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=refdata-cellranger-mm10-3.0.0/ --project=${PROJECT} --indices=SI-GA-${INDEX} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
To evaluate changes in cell composition between Early and Advanced popliteal lymph nodes, we integrated these datasets and performed unsupervised clustering using the Seurat R package (v.4.0.3). We also performed cell interaction analysis using NicheNet (v1.0.0) between particular integrated clusters. Data was analyzed according to the instructions and vignettes of Seurat and NicheNet.
Assembly: mm10
Supplementary files format and content: cell barcodes (_barcodes.tsv), feature list (_features.tsv), and feature/barcode matrices (_matrix.mtx) are provided for each condition

molecule: total RNA

organism: Mus musculus

source_name: TNF PLNs with Advanced Arthritis

extract_protocol:
Evan's blue dye was administered intradermal into the mouse hindpaw to identify the  popliteal lymph nodes (PLNs) posterior to the knee. The PLNs were minced with a scalpel, and then enzymatically digested (Accumax; Innovative Cell Technologies Cat# AM-105) for 1h at room temperature, filtered with a 75um strainer, and single cell suspensions were sorted by fluorescence activated cell sorting based on Hoechst positive and Sytox Green negative live cells. Sorted cells were then submitted to the Genomics Research Center at the University of Rochester for library preparation and sequencing. All cells in each sample were loaded on a Chromium Single-Cell Insrument (10x Genomics) and single-cell Gel Bead-in-Emulsions were generated. The Chromium Single-Cell 3' Library & Gel Bead Kit (10x Genomics) was used to generate the library based on the manufacturer's instructions. Barcoded cDNA from the Gel Bead-in-Emulsions was purified with DynaBeads MyOne Silane Beads (ThermoFisher Scientific Cat# PN37002D) with PCR amplification for 3' cDNA library construction. NovaSeq 6000 Illumina sequencers generated the sequenced data.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: TNF-Tg model of inflammatory-erosive arthritis

tag: strain

value: C57BL/6 genetic background


title: BFD1KO4wks4

city: Pittsburgh

first: Jon

middle: P

last: Boyle

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
Data analyzed using CLC Genomics workbench
log-transformed normalized data generated usign "rlog" in DESeq2
Assembly: hg18
Supplementary files format and content: log2 transformed normalized counts per million reads mapped

organism:
Toxoplasma gondii
Mus musculus

source_name: Brain

extract_protocol:
Qiagen Rneasy
NEB Next Ultra II stranded mRNA seq
200 bp insert

treatment_protocol: Intraperitoneal infection

tag: tissue

value: Brain

value: Mouse CBA/J, T. gondii strain VEG

tag: treatment

value: 4 weeks post-infection


title: BFD1KO4wks3


title: pheochromocytoma and paraganglioma, group 2, sample 1

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description:
PPGL_g2_1
GAL6380_exon_featureCounts.raw.txt

data_processing:
perform quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
perform quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count)
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Canis lupus familiaris

source_name: pheochromocytoma and paraganglioma

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: group

value: pheochromocytoma and paraganglioma

tag: cell type

value: tumor cells arising from the chromaffin cells


title: ChIPseq_Input_OPM2_2hours_DMSO

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: DMSO


title: ChIPseq_RNAPolymeraseII_OPM2_2hours_DMSO


title: BFD1KO4wks2


title: ChIPseq_RNAPolymeraseII_OPM2_2hours_JQ1


title: TNF Early

source_name: TNF PLNs with Early Arthritis


title: FACS-sorted cKIT(+) spermatogonia, Cbx2[23KRA/23KRA], H3K27me3, rep2

city: Ithaca

first: Jongmin

last: Kim

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

description:
CUT&RUN library
CBX2KRA_H3K27me3_rep2

data_processing:
Paired-end fastq reads were quality trimmed (score 20), with stringency 1 using trim_galore (ver. 0.4.3). Trimmed reads were mapped to the mm10 genome using bowtie2 (ver. 2.3.1) with the end-to-end option.
Mapped reads were qualify-filtered with MAPQ higher than 10, and only properly-paired reads were retained using Samtools (ver. 1.4.1). Picard (ver. 2.17.1) was used to remove duplicate reads (http://broadinstitute.github.io/picard).
Alignment files (bam) were converted to bigwig files using Deeptools (ver. 2.2.4) by normalizing with RPKM and with binsize 10.
Peaks were identified by using MACS2 (ver. 2. 1) with the ‘--broad' option, by comparing CUT&RUN results using CBX2 antibodies (Experimental) to IgG (Control) or using HA antibodies applied to Cbx2HA/HA (Experimental) or Cbx2+/+ (Control) mice.
All analysis scripts are available at (github.com/jongminkmg/cbx2).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN-seq

source_name: Testes

growth_protocol: Mice were maintained in shoebox cages with standard chow diet.

extract_protocol:
FACS purified, >100,000 c-Kit(+) spermatogonia were attached to Poly-D-Lysine (R&D Systems, Cat# 3439-200-01) coated 24-well plates by 1 minute centrifugation at 80 × g (instead of binding to Concanavalin A beads). After the attachment, cells were fixed with 1% formaldehyde in PBS for 15 minutes. After two PBS washes and one PBST (0.05% Triton X-100 (v/v)) wash, cells were incubated with primary antibodies in PBST BSA (0.05% Triton X-100, 3% BSA) overnight at 4 ºC. Next day, cells were washed twice with PBST and finally washed with PBST EDTA (2 mM). Cells were then incubated with 500 ng/mL pA-MNase (protein A-MNase) in PBST BSA EDTA for more than 1 hour at 4 ºC. After pA-MNase binding, cells were washed with PBST EDTA twice, and the plate was placed on wet ice. Cells were then incubated in pre-chilled 200 µL PBST with 2 mM CaCl2 for 30 minutes. After MNase cutting, 200 µL stop solution (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/µL RNase A) was added, and the plate was placed in a 37 ºC oven for 15 minutes. Released cut fragments were de-crosslinked in 0.1% SDS and 125 µg/mL Proteinase K (Sigma-Aldrich, Cat# 03115828001) in a 65 ºC oven for >12 hours. DNA was extracted using phenol-chloroform phase separation and sodium acetate/ethanol precipitation. Resuspended DNA was further cleaned up by using 2.0X Solid Phase Reversible Immobilization (SPRI) beads to remove residual salts.
Illumina sequencing libraries were generated based on a published protocol (Bowman et al., 2013) with the following modifications. SPRI beads were used in 2.0X ratio following end-repair and A-tailings steps instead of 1.8X. Adapters used in 2 nM final concentration instead of 10 nM. PCR extension was done for 30 seconds instead of 45 seconds. Final PCR cycles were between 12 to 17. Number of PCR cycles were determined to be in the exponential phase by a pre-run of 10% of reaction with SYBR green dye in a real time PCR machine.

treatment_protocol: No specific treatments

value: Testes

value: cKIT(+) differentiating spermatogonia

tag: cut&run antibody

value: H3K27me3 (CST, clone C36B11, Cat# 9733)


title: BFD1KO4wks1


title: pheochromocytoma and paraganglioma, group 1, sample 7

description:
PPGL_g1_7
GAL6380_exon_featureCounts.raw.txt


title: ChIPseq_H3K27ac_OPM2_2hours_DMSO

value: H3K27ac (Abcam, ab4729)


title: FACS-sorted cKIT(+) spermatogonia, Cbx2[23KRA/23KRA], CBX2-856, rep2

description:
CUT&RUN library
CBX2KRA_CBX2-856_rep2

value: CBX2 (home-made, 856)


title: pheochromocytoma and paraganglioma, group 1, sample 6

description:
PPGL_g1_6
GAL6380_exon_featureCounts.raw.txt


title: ChIPseq_BRD4_OPM2_2hours_18DS


title: ChIPseq_RNAPolymeraseII_OPM2_2hours_18DS


title: ROCY1KO4wks5


title: FACS-sorted cKIT(+) spermatogonia, WT, H3K27me3, rep2

description:
CUT&RUN library
WT_H3K27me3_rep2

value: wild type


title: ROCY1KO4wks4


title: pheochromocytoma and paraganglioma, group 1, sample 4

description:
PPGL_g1_4
GAL6380_exon_featureCounts.raw.txt


title: ChIPseq_BRD4_OPM2_2hours_BKM120


title: FACS-sorted cKIT(+) spermatogonia, WT, CBX2-856, rep2

description:
CUT&RUN library
WT_CBX2-856_rep2


title: ChIPseq_BRD4_OPM2_2hours_JQ1


title: ROCY1KO4wks2


title: pheochromocytoma and paraganglioma, group 1, sample 3

description:
PPGL_g1_3
GAL6380_exon_featureCounts.raw.txt


title: FACS-sorted cKIT(+) spermatogonia, Cbx2[HA/HA], HA-C29F4

description:
CUT&RUN library
HACBX2_HA-C29F4

value: HA (CST, clone C29F4, Cat# 3724)


title: ChIPseq_BRD4_OPM2_2hours_DMSO

value: 2 hours


title: WildType4wks5


title: ROCY1KO4wks1


title: FACS-sorted cKIT(+) spermatogonia, WT, HA-C29F4 (neg. ctrl)

description:
CUT&RUN library
WT_HA-C29F4_NegCtrl


title: QuantSeq_OPM2_2hours_JQ1_Replicate2

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0).
SAM files were subsequently converted to BAM files, sorted, and indexed using samtools (v1.9).
Read counting across genomic features (exons) was performed using featureCounts (function of Subread) prior to differential gene expression analysis using Limma/Voom.
Genome_build: HG19
Supplementary_files_format_and_content: CSV of raw (non-normalized) counts

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions.
Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Samples were treated in biological triplicate in the presence of small molecule inhibitors, as indicated, for 2 hours prior to collection.

tag: rna library prep

value: QuantSeq 3'-RNA Seq


title: pheochromocytoma and paraganglioma, group 1, sample 2

description:
PPGL_g1_2
GAL6380_exon_featureCounts.raw.txt


title: pheochromocytoma and paraganglioma, group 1, sample 1

description:
PPGL_g1_1
GAL6380_exon_featureCounts.raw.txt


title: Prdx1(lox/lox);Alb-cre-MCD-5w-3

city: TIANJIN

first: Yin

last: Wen

state: TIANJIN

address: Address:No.6 North Huanrui Rd, Beichen District, Tianjin, P.R China

department: NHC Key Laboratory of Hormones and Development

country: China

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: liver

value: MCD-5 WEEKS


title: Prdx1(lox/lox);Alb-cre-MCD-5w-2


title: QuantSeq_OPM2_2hours_JQ1_Replicate1


title: WildType4wks3

value: Brain


title: normal adrenal medulla 8

description:
NAM8
GAL6380_exon_featureCounts.raw.txt

source_name: normal adrenal medulla

value: normal adrenal medulla

value: healthy adrenal medulla cells


title: normal adrenal medulla 9

description:
NAM9
GAL6380_exon_featureCounts.raw.txt


title: QuantSeq_OPM2_2hours_DMSO_Replicate3


title: Prdx1(lox/lox);Alb-cre-MCD-5w-1


title: normal adrenal medulla 7

description:
NAM7
GAL6380_exon_featureCounts.raw.txt


title: pheochromocytoma and paraganglioma, group 1, sample 5

description:
PPGL_g1_5
GAL6380_exon_featureCounts.raw.txt

value: pheochromocytoma and paraganglioma


title: Prdx1(lox/lox)-MCD-5w-3


title: QuantSeq_OPM2_2hours_DMSO_Replicate2


title: Prdx1(lox/lox)-MCD-5w-2


title: WildType4wks1

value: Mouse CBA/J, T. gondii strain VEG

value: 4 weeks post-infection


title: normal adrenal medulla 6

description:
NAM6
GAL6380_exon_featureCounts.raw.txt


title: normal adrenal medulla 5

description:
NAM5
GAL6380_exon_featureCounts.raw.txt


title: QuantSeq_OPM2_2hours_DMSO_Replicate1

value: DMSO


title: QuantSeq_OPM2_2hours_JQ1_Replicate3


title: Prdx1(lox/lox)-MCD-5w-1


title: QuantSeq_OPM2_2hours_BKM120_Replicate3


title: NaBu3

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

description:
feature_table_with_taxonomy.xlsx
16S_fasta.fasta

data_processing:
Paired-end reads generated from Illumina platforms were processed and merged using FLASH software (v1.2.7)
Quality filtering on the raw reads were then performed under specific filtering conditions to obtain the high-quality clean tags according to the Fqtrim software (v0.9.4). Chimeric sequences were filtered using VSEARCH software (v2.3.4)
Finally, the feature table and feature sequence were obtained after dereplication using DADA2 software (v1.10.1)
Assembly: The V3-V4 region of the prokaryotic small-subunit (16 S) rRNA gene was amplified with primers 341 F (5′-CCTACGGGNGGCWGCAG-3′) and 805 R (5′-GACTACHVGGGTATCTAATCC-3′)

organism: Capra hircus

source_name: ileal contents

extract_protocol:
Total microbial DNA from ileal contents sample of each goat was extracted using FastPure Bacteria DNA Isolation Mini Kit according to manufacturer ’s instructions for 16S rRNA sequencing
SMRTbell libraries were prepared using the Pacific Biosciences SMRTbellTM Template Prep kit

value: ileal contents

value: infusion of sodium butyrate

tag: time

value: Day 13


title: NaBu2


title: WildType4wks4


title: normal adrenal medulla 4

description:
NAM4
GAL6380_exon_featureCounts.raw.txt


title: QuantSeq_OPM2_2hours_BKM120_Replicate2


title: normal adrenal medulla 3

description:
NAM3
GAL6380_exon_featureCounts.raw.txt


title: NaPr3

value: infusion of sodium propionate


title: NaBu1


title: QuantSeq_OPM2_2hours_BKM120_Replicate1


title: Advanced 1

description:
n = 6 PLNs
Spatial transcriptomics

data_processing:
Demultiplexing: spaceranger-1.1.0/spaceranger mkfastq --run=. --samplesheet=spaceRanger.csv --output-dir ./spaceRanger --nopreflight --jobmode=slurm --localcores=24 --localmem=120 --qc
Counting: spaceranger-1.1.0/spaceranger count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --slide=${SLIDE} --area=${AREA} --image=${IMAGE}
The filtered feature matrices were analyzed using the Seurat package (v4.0.3) in Rstudio (v1.2.1335; R v4.1.1). The different samples were merged together, and unsupervised clustering was performed to evaluate changes in cell composition between the groups. Minimally supervised clustering was then used to combined associated clusters and evaluate gene expression changes within clusters that localized to the sinus regions of the PLNs. To assess unique clusters between the samples, the different conditions were also integrated using canonical correlation analysis. Shared nearest neighbor clustering was performed and clusters were visualized using a uniform manifold approximation and projection (UMAP).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Sequencing information: cell barcodes (_barcodes.tsv), feature list (_features.tsv), and feature/barcode matrices (_matrix.mtx) are provided for each condition. Image information: aligned fiducials (_fiducials.jpg), detected tissue image (_tissue_image.jpg), scale factors (scalefactors_json.json), high resolution tissue image (hires_image.png), low resolution tissue image (lowres_image.png), and tissue positions list (_list.csv) are provided for each condition.

source_name: 8.5-9-month-old TNF-Tg Popliteal Lymph Nodes

extract_protocol:
Evan's blue dye was administered intradermal into the mouse hindpaw to identify the PLNs. The PLNs were harvested, embedded in Optimal Cutting Temperature (OCT) compound (Cat#4583; Sakura, Osaka, Japan), frozen in liquid nitrogen, and stored at -80C. The lymph nodes were patterned to identify PLNs from individual limbs to relate with arthritic severity. A single 10um tissue section was placed on each capture area of a Gene Expression Slide (10X Genomics). Standard protocols for the Visium Methanol Fixation and H&E Staining were performed, and each capture area was then imaged using an Olympus VS120 slide scanner at 20X magnification. The tissue sections were then permeabilized for 12-minutes, and poly-adenylated mRNAs were captured by primers on the slide. The protocols of the Visium Spatial Gene Expression Kit were then followed to produce full-length cDNA, and the Visium Library Construction Kit (10X Genomics) was used to generate sequencing libraries according to the manufacturer's instructions. A NovaSeq 6000 Sequencer (Illumina) was used to sequence amplified libraries at approximately 50,000 reads per spot for each capture area covered by tissue based on the instructions of the Visium Spatial Gene Expression manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: TNF-Tg

tag: Sex

value: Male

tag: age

value: 8.5-9 months

value: Popliteal Lymph Nodes

tag: diagnosis

value: Advanced arthritis


title: Advanced 2

description:
n = 6 PLNs
Spatial transcriptomics


title: NaPr2


title: WildType4wks2


title: Early

description:
n = 6 PLNs
Spatial transcriptomics

source_name: 5.5-month-old TNF-Tg Popliteal Lymph Nodes

value: 5.5 months

value: Early arthritis


title: NaPr1


title: QuantSeq_OPM2_2hours_18DS_Replicate2

value: 2 hours

value: QuantSeq 3'-RNA Seq


title: QuantSeq_OPM2_2hours_18DS_Replicate3


title: Wild-Type PLN

description:
n = 10 PLNs
Spatial transcriptomics

source_name: 5.5-month-old WT Popliteal Lymph Nodes

value: Wild-type


title: QuantSeq_OPM2_2hours_18DS_Replicate1


title: NaAc3

value: infusion of sodium acetate


title: H. hammondi in vitro bradyzoite induction conditions 3

data_processing:
For H. hammondi vs. T. gondii comparisons, data were reduced to include only genes that could be matched between T. gondii and H. hammondi based on synteny.  "Species specific" genes are included in the counts file but not subject to further analysis
Assembly: T. gondii and H. hammondia verson 43
Supplementary files format and content: Counts files have raw counts for each transcripts
Supplementary files format and content: Analyzed files have statistical analyses and log-transformed data

molecule: polyA RNA

organism: Hammondia hammondi

source_name: freshly excysted sporozoites

growth_protocol: in vitro derived tachyzoites or in vitro derived sporozoites

extract_protocol:
Qiagen Rneasy
NEB Next or Illuina Tru Seq stranded mRNA
200 bp insert

treatment_protocol: control conditions or high pH, low C02, low serum conditions

value: freshly excysted sporozoites

value: sporozoites grown in vitro

value: high pH, low C02, low serum conditions


title: H. hammondi in vitro bradyzoite induction conditions 2


title: NaAc2

value: ileal contents


title: H. hammondi in vitro bradyzoite induction conditions 1


title: cSAM cells, Day7, SAHA

city: Tokyo

first: Tomohiro

last: Yabushita

address: 7-3-1, Hongou, Bunkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
For each sample, the number of reads mapped to each sgRNA in the library (relative to the total number of reads for that sample) was calculated.
This analysis was performed by pipeline scripts (https://github.com/mhorlbeck/ScreenProcessing).
Assembly: Mouse Genome-wide CRISPRa-v2 Libraries (Addgene #83396)
Supplementary files format and content: tab-delimited text file includes read counts for each sample.

source_name: hematopoietic

growth_protocol: cSAM cells were cultured in RPMI-1640 medium supplemented with 10% FBS 1% P/S, and 1 ng/mL murine IL-3.

extract_protocol:
We extracted genomic DNA from the cells at the beginning (day 0) and at the end of the screen (day 7) using Nucleospin XL (Macherey Nagel).
To enrich the sgRNA-containing genomic DNA fragments, size fractionation was performed by the Sbfl-HF (NEB #R3642) digestion overnight. These fractionated genomic DNAs were electrophoresed on agarose gels and excised at 500 base pairs. These gels were purified using Wizard SV Gel and PCR Clean-Up System (Promega). These purified gDNAs were then subjected to PCR reactions with custom indexed primers designed to amplify the barcode for de-multiplexing and to append Illumina 5’ and 3’ adapter sequences. The PCR products were purified with Wizard SV Gel and PCR Clean-Up System (Promega).
PCR for sgRNA amplicon enrichment and Illumina adapter ligation

treatment_protocol: Suntag-cSAM cells transduced with the CRISPRa-v2 library were then cultured with DMSO (control), DAC (50 nM), or SAHA (500 nM) for one week.

value: hematopoietic

value: cSAM

value: non-adherent

value: SAHA


title: Ctrl3

value: infusion of normal saline

value: Day 13


title: cSAM cells, Day7, DAC

value: DAC


title: cSAM cells, Day0

value: DMSO


title: normal adrenal medulla 2

description:
NAM2
GAL6380_exon_featureCounts.raw.txt

value: normal adrenal medulla

value: healthy adrenal medulla cells


title: normal adrenal medulla 10

description:
NAM10
GAL6380_exon_featureCounts.raw.txt


title: H. hammondi in vitro control conditions 3

value: control media conditions


title: Ctrl2


title: Dissociated cells from an adult testis, wild type

description:
Used Chromium Single Cell 3’ Library & Gel Bead Kit v2 by 10X genomics
AdultTestis

data_processing:
1) Wild-type adult testis profiling: Cellranger count (cellranger/2.0.0) was used to map fastq files to the mouse genome (refdata-cellranger=mm10-1.2.0).
2) Cbx2 inducible knock out & FACS-sorted cKIT(+) spermatogonia profiling : Cellranger count (cellranger/6.0) was used to map fastq files to the mouse genome (refdata-cellranger-mm10-3.0.0) and to obtain gene expression counts per cell. Cells were filtered by a) nFeature_RNA > 2000, b) mitochondrial RNA percentage < 7.5, c) percent occupied by the largest gene < 3, and d) RNA count and feature ratio < 5.5 (see scripts posted on https://github.com/jongminkmg/Cbx2). Two control and two inducible KO samples were integrated to align cell populations across all four samples. Integrated data were then scaled and processed with 30 principal components for clustering. Differential gene expression tests were performed by the FindMarkers function of Seurat using Wilcoxon rank sum test.
Cbx2 genotypes were assigned based on independent Cbx2 amplicon sequencing data using a custom Python script (https://github.com/jongminkmg/Cbx2).  The script identifies 'TGGCGCATCTGGTTCCTTGAGCTTGGAGCG' (WT, exon5 linked to exon4) or 'TGGCGCATCTGGTTCTTGGAGGACCAGCCG' (Mut, exon5 linked to exon2) from the read2 of the paired-end reads, and assigns the genotypes to the associated read1 (UMI-barcode). When an UMI is assigned to two different genotypes, likely due to PCR chimera formation, the genotype was left unassigned unless reads supporting one genotype are present 10 times more than the other genotype. A cell was assigned to be 'Mut' when all Cbx2 amplicon reads show recombination (exon5 linked to exon2), and otherwise assigned to be 'WTorHet'. Only the cells that have at least four UMIs linked to Cbx2 sequence were assigned genotypes. The metadata for their genotypes (WT/Het or Mut) were added to the Seurat object by the AddMetaData function.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
1) Wild-type adult testis profiling: dissociated cells were diluted to 1000 cells/µL, and total 5200 cells (5.2 µL) were loaded into the Chromium controller to obtain RNA-seq profiles of approximately 3000 cells.   2) Cbx2 inducible knock out & FACS-sorted cKIT(+) spermatogonia profiling : c-KIT(+) spermatogonia were FACS-sorted to concentration of  about 300~600 cells/µL, and a total ~8000 cells were loaded into the Chromium controller. We used 5' barcoding instead of 3' barcoding because deleted exons of Cbx2 were close to the 5' end of the gene. Single cell analysis with targeted genotyping was done by adapting 'Genotyping of Transcriptome (GoT)' (Nam et al., 2019, PMID: 31270458) and V(D)J region amplification of T or B-cell receptor protocol by the 10X Genomics. We aimed to make specific Cbx2 amplicons from cell-barcoded cDNA to amplify cDNA fragments and sequence Exon5 junctions to distinguish wild type (Exon4 spliced to Exon5) and mutant (Exon2 spliced to Exon5 after the deletion of Exon3, 4) for specific cell barcodes.
1) Wild-type adult testis profiling: we used Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics, Cat: 120267) for single cell RNA-seq from wild-type adult testes. After producing emulsions encapsulating gel beads and cells in the Chromium controller, reverse transcription and 12 cycles of PCR were performed to produce cell-barcoded amplified cDNA. Illumina sequencing-ready libraries were produced from 200 ng of the amplified cDNA based on the manufacturer’s protocol. 12 cycles of library amplification indexing PCR was performed.   2) Cbx2 inducible knock out & FACS-sorted cKIT(+) spermatogonia profiling : single cell barcoded cDNA was made with Chromium Next GEM Single Cell 5' Reagent Kits (10X Genomics, Cat#:1000265) based on the manufacturer's protocol with 14 PCR cycles of cDNA amplification. 50 ng of the amplified cDNA based on the manufacturer’s protocol. 14 cycles of library amplification indexing PCR was performed. To generate Cbx2 amplicons, we performed nested PCRs to amplify Cbx2-specific cDNAs with cell barcodes. In the second PCR step of the nested PCR, Cbx2-specific primer that has a partial Illumina read2 sequence was used. The Cbx2-specific second nested primer also contains 'stagger' sequences between the Cbx2-specific region and partial read2 to increase library complexity for accurate base calls during Illumina sequencing. We confirmed the amplification of the correct-sized bands corresponding to wild-type and deleted Cbx2 amplicons by agarose gel electrophoresis. The amplified bands were excised and gel purified. Index PCR was performed to make the final Illumina-compatible libraries with unique indices with 10X provided index-PCR primers. Cbx2 amplicon libraries were pooled with standard 10X single cell gene expression libraries to occupy ~2% of total reads. A total of 4 samples were sequenced in one P3 lane on a NextSeq 2000 (NextSeq 2000 P3 Reagents (100 Cycles) Cat:20040559).

treatment_protocol: Tamoxifen (Sigma-Aldrich, Cat# T5648) was dissolved in corn oil (Spectrum Chemical, Cat# CO136) to a final 20 mg/mL by incubating the mixture at 37 ºC overnight while rotating. Dissolved tamoxifen was filtered and aliquots for daily use were stored in sterile tubes and kept at 4 ºC for up to 4 days. For the Cbx2 amplicon single cell RNA-seq experiments, 150 µL of warmed-up tamoxifen-corn oil was injected intraperitoneally daily for 3 consecutive days. No treatment was applied for profiling cells from the wild-type adult testis experiment.

value: Testes

value: Dissociated cells from an adult testis

value: wild type


title: H. hammondi in vitro control conditions 1

value: freshly excysted sporozoites

value: sporozoites grown in vitro


title: cSAM cells, Day7, DMSO


title: NHDF Control

type: RNA

first: Ryuichi

last: Nakahara

address: 4-6-1 Komaba, Meguro

department: the Research Center of Advanced Science and Technology

institute: the University of Tokyo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ATCC

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Quick Amplification labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: THP-1 was cultured in RPMI1640+10%FBS and seeded at 2*105 cells/ml in 75 cm2 flask. HeLa was cultured in DMEM+10%FBS and seeded at 106 cells on a 10cm culture dish. NHDF was cultured in FBM(Lonza)+10%FBS and seeded at 105 cells on a 10cm culture dish.

extract_protocol: Total RNA was prepared using RNeasy extraction kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: All cells were cultured in control or hypoxic (1%O2) condition for 24 hours before extraction

value: Dermal Fibroblast

tag: gender

value: female


title: NHDF Hypoxia


title: NaAc1

value: ileal contents

value: infusion of sodium acetate


title: HeLa Control

value: Epithelial Cell


title: HeLa Hypoxia


title: THP-1 Control

value: Monocyte

value: male


title: IL-10 KO-1-100-500nt

status: Public on Aug 13 2023

city: Nanjing

first: chen

last: Wang

address: xianlin street num 163

institute: Nanjing University

description:
IL-10 KO-100-500nt-rpkm.txt
Control-VS-IL-10_KO-100-500nt.sRNADiffExp.txt

data_processing:
The image files generated by the sequencer were then processed to produce digital data.
The subsequent procedures included summarizing the data produced, evaluating the sequencing quality and depth, and filtering the contaminated reads.
Then, the protein-coding ability of each transcript was predicted using Coding Potential Calculator (CPC) as previously described
The potential sRNAs of B. acidifaciens were predicted by comparison with its genome
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw sRNA counts for every sRNA and every sample
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...

source_name: Stool

extract_protocol:
Total RNA from the fecal samples was prepared using TRIzol Reagent (Thermo Fisher Scientific). Solexa sequencing was used to identify differentially expressed sRNAs in IL-10 KO chronic colitis mice.
CDNA libraries (18-100 nt and 100-500 nt) were prepared with the TruSeq Small RNA Library Preparation Kit (Illumina, San Diego, CA, USA) and sequenced using an Illumina Genome Analyzer according to the manufacturer’s instructions.

tag: profile

value: Stool


title: H. hammondi in vitro control conditions 2


title: IL-10 KO-1-18-100nt

description:
IL-10 KO-18-100nt-rpkm.txt
Control-VS-IL-10_KO-18-100nt.sRNADiffExp.txt


title: Control (C57BL/6J)-18-100nt

description:
Control (C57BL/6J)-18-100nt-rpkm.txt
Control-VS-IL-10_KO-18-100nt.sRNADiffExp.txt


title: Control (C57BL/6J)-100-500nt

description:
Control (C57BL/6J)-100-500nt-rpkm.txt
Control-VS-IL-10_KO-100-500nt.sRNADiffExp.txt


title: normal adrenal medulla 1

description:
NAM1
GAL6380_exon_featureCounts.raw.txt


title: Ctrl1

value: infusion of normal saline

value: Day 13


title: CD45RB high-4

data_processing:
Library strategy: DNA-Seq
Sequences were then trimmed and classified with the QIIME toolkit.
Using the clustering program VSEARCH (1.9.6) against the Silva 119 database, operational taxonomical units (OTUs) were picked at 97% sequence identity.
Based on the OTU data, PCA analysis and microbiota composition analysis at the phylum, class, order, family, genus and species levels were performed.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw bacteria counts for every bacteria and every sample
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...

extract_protocol:
Fresh stool samples were collected from experimental mice, and the total DNA was obtained using the MO BIO PowerFecal DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA) according to the manufacturer’s instructions.
Next-generation sequencing library preparations and Illumina MiSeq sequencing were conducted at Beijing Genomics Institute (BGI, Shenzhen, China).

value: CD45RB high


title: CD45RB high-5


title: CD45RB high-3


title: MRC+L1

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
The low-quality reads and adapters were removed using Fastp, after which the reads were mapped to the mouse reference genome (GRCm39).
The gene expression matrix was then calculated using FeatureCounts.

source_name: 4T1 cells

growth_protocol: 4T1 cells were cultured by DMEM medium (regarded as PBS group), DMEM medium with MRC nanoparticles (regarded as MRC group), DMEM medium with MRC nanoparticles under 660 nm irradiation.

extract_protocol:
RNA from 4T1 cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was treated by fresh DMEM medium or MRC nanoparticles for 12 hours with or without 660 nm irradiation (3min, 180 mV/cm2)

value: BALB/c

value: mouse breast cancer cells

value: treated with MRC for 12 hours and irradiated with 660 nm laser for 3 minutes (180 mW/cm2)


title: MRC2

value: treated with MRC for 12 hours


title: MRC+L2


title: MRC3


title: MRC+L3


title: Biotinylated BA-sRNA-172

description: biotinylated BA-sRNA-172 were incubated with lysates of primary Mice CECs

data_processing:
For the data analysis, sequencing tags were aligned to the mouse genome using TopHat.
Cufflinks was used to calculate the fragments per kilobase of transcript sequence per millions of base pairs sequenced (FPKM).
Differentially expressed genes (p-value ≤ 0.005, absolute fold change ≥ 2) were clustered and visualized using a clustergram heatmap.
In addition, IntaRNA 2.0 was used to predict minimal energy profiles and perfect matches between BA-sRNA-172 and human/mouse mRNAs of the seven most promising candidates
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...

source_name: colon

growth_protocol: Biotin-labeled BA-sRNA-172 were transcribed in vitro from pCI-BA-sRNA-172 plasmids using the Biotin RNA Labeling Mix (Roche, Indianapolis, IN, USA) and T7 RNA polymerase (Thermo Fisher Scientific). After treatment with RNase-free DNase I (Thermo Fisher Scientific), the RNA was purified with G50 Sephadex Quick-Spin columns (Roche) to remove small RNA molecules (<72 nucleotides) and free nucleotides. Biotinylated RNA was first denatured (65 °C, 10 min) and then cooled slowly to 4 °C to allow proper secondary structure formation.

extract_protocol:
After purification by TRIzol, immunoprecipitated RNA was analyzed by RNA high-throughput sequencing.Briefly, mRNA extraction was performed using Dynabeads oligo (dT) (Thermo Fisher Scientific). Double-stranded complementary DNAs were synthesized using Superscript II Reverse Transcriptase (Thermo Fisher Scientific) and random hexamer primers.
RNA was subjected to fragmentation, library construction and sequenced with the HiSeq 2000 platform.

treatment_protocol: The primary mouse CECs were washed with PBS followed by a brief vortex and incubated in lysis buffer (20 mM Tris, pH 7.5; 200 mM NaCl; 2.5 mM MgCl2; 0.05% Igepal; 60 U/ml SUPERase-In (Thermo Fisher Scientific); 1 mM DTT; protease inhibitors (Roche)) on ice for 10 min. The lysates were precleared by centrifugation, and 50 μl of the sample was aliquoted for input. The remaining lysates were incubated with biotin-labeled BA-sRNA-172 (Biotin-BA-sRNA-172). To prevent nonspecific binding of RNA and protein complexes, the beads were preincubated with RNase-free BSA and yeast tRNA (Thermo Fisher Scientific). The beads were incubated at 4 °C for 3 h, washed twice with ice-cold lysis buffer, three times with low-salt buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0; and 150 mM NaCl) and once with high-salt buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0; and 500 mM NaCl). Complexes were isolated with streptavidin agarose beads (Thermo Fisher Scientific).

value: primary Mice CECs


title: HSC3_miR-NT 48H

city: Toon

first: Saika

last: Masato

state: Ehime

department: Department of Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: Hyb protocol was performed according to the manufacturer's instructions.

scan_protocol: Scanning was performed with the GeneAtlas Imaging Station (Affymetrix Inc.).

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

label: biotin

source_name: OSCC Cells_Frozen_5

label_protocol: 100 ng of total RNA was labeled using a GeneAtlas 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Used 4 types human OSCC cell lines(SAS-L1, HSC2, HSC3, Ca9-22).These cells were cultured in D-MEM (FUJIFILM Wako Chemical Corporation) medium containing 10% FBS (BioSource) and 1% Penicillin-Streptomycin solution (Wako) in a humidified atmosphere of 95% air and 5% CO2 incubator at 37℃. Experiments were performed within 3–8 passages after thawing the cells.

extract_protocol: Washed with PBS three times after 48 hours after the introduction of mimic into the cells.Total RNA was extracted with cell scraper and ISOGEN (Nippon gene) according to the manufacturer's protocol.

treatment_protocol: 300000 OSCC cells were seeded in a 60mm dish, and RNAiMAX (Thermo Fisher Scientific) and mimic of human mature miR-375 or miR-NT(Dharmacon Inc.) were introduced at 20 nM. The cells were transfected for 24 hours, washed with D-PBS(-) (Wako) and incubated for another 24 hours.

value: Reverce transfect with miR-NT

value: OSCC cell line


title: HSC3_miR-375 48H

source_name: OSCC Cells_Frozen_6

value: Reverce transfect with miR-375


title: Ca9-22_miR-375 48H

source_name: OSCC Cells_Frozen_8


title: SAS-L1_miR-375 48H

source_name: OSCC Cells_Frozen_2


title: HSC2_miR-NT 48H

source_name: OSCC Cells_Frozen_3


title: Ca9-22_miR-NT 48H

source_name: OSCC Cells_Frozen_7


title: CD45RB high-1


title: MRC1


title: HSC2_miR-375 48H

source_name: OSCC Cells_Frozen_4


title: SB5

description:
16S_taxonomy.xlsx
16S_feature_table.xlsx
16S_fasta_file.fasta

source_name: cecal digesta

extract_protocol:
Total microbial DNA from cecal digesta sample of each goat was extracted using FastPure Bacteria DNA Isolation Mini Kit (DC103, Vazyme Biotech Co., Ltd., Nanjing, China) according to manufacturer ’s instructions for 16S rRNA sequencing
SMRTbell libraries were prepared using the Pacific Biosciences SMRTbellTM Template Prep kit

value: cecal digesta

value: infusion of sodium butyrate


title: SB6


title: SAS-L1_miR-NT 48H

source_name: OSCC Cells_Frozen_1


title: CD45RB high-2


title: Control (C57BL/6 RAG KO)-3


title: Control (C57BL/6 RAG KO)-1


title: PBS3

value: untreated


title: Control (C57BL/6 RAG KO)-2


title: SB4


title: PBS1


title: PBS2


title: IL-10 KO-5


title: SB3

value: infusion of sodium propionate


title: IL-10 KO-3


title: IL-10 KO-2


title: Aorta Ctrl 8w Male 226

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

data_processing:
Data Filtering: 1) Remove reads with adapter contamination 2)Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). 3) Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Mapping software: hisat2 v2.0.5 (Default parameter)
Quantification software: featureCounts v1.5.0-p3
Differential analysis: DESeq2 1.20.0
Assembly: mm10
Supplementary files format and content: Excel-file with counts and analysis of differential expression

source_name: Aorta

growth_protocol: Animal were used after weaning at age of 5-7 weeks

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: To induce knockout, mice were injected intraperitoneally with tamoxifen (1 mg in ethanol/sunflower seed oil, 1:10, as vehicle) for five consecutive days at the age of 6-8 weeks. Mice that were negative for Itga8-CreERT2 but harbored floxed alleles for Yap1 and Wwtr1 were injected with tamoxifen at the age of 6-8 weeks and used as controls.

tag: condition

value: Aorta Control 8w Male

value: Aorta

value: Male


title: Control (C57BL/6 RAG KO)-5

value: Stool


title: IL-10 KO-1


title: Aorta Ctrl 8w Female 236

value: Aorta Control 8w Female

value: Female


title: Control (C57BL/6 RAG KO)-4


title: Control (C57BL/6J)-4

value: wild type


title: Control (C57BL/6J)-5


title: Aorta Ctrl 8w Female 234


title: SB1

value: Day 13


title: SP6

value: infusion of sodium acetate


title: Control (C57BL/6J)-3


title: Aorta Ctrl 8w Female 231


title: Control (C57BL/6J)-2


title: Aorta KO 8w Male 223

value: Aorta YAP/TAZ KO 8w Male

value: Itga8-Cre ERT2-Yap1fl/fl/Wwtr1fl/fl


title: Control (C57BL/6J)-1


title: SP4


title: IL-10 KO-4


title: SP3

value: infusion of normal saline


title: C57BL/6J, 131-week-old

city: Suita

first: Shota

last: Shimizu

state: Osaka

address: 3-1 Yamadaoka

department: Department of Signal Transduction

institute: Research Institute for Microbial Diseases, Osaka University

data_processing:
CASAVA 1.8.2 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequence (mm9) using TopHat v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKM) values were determined with Cuffnorm v.2.2.1.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values of all the samples

source_name: Liver

extract_protocol:
Liver endothelial cells (CD31+45-) were isolated with FACS. Total RNA was extracted from 50,000 endothelial cells using Rneasy Plus Micro Kits (Qiagen).
RNA libraries were prepared using the TruSeq Sample Prep v2 kit and sequenced on a HiSeq 2500 in 75-base single-end mode.

value: Liver

value: endothelial cell

value: WT


title: C57BL/6J, 136-week-old


title: Aorta KO 8w Female 229

value: Aorta YAP/TAZ KO 8w Female


title: SB2

value: cecal digesta

value: infusion of sodium propionate


title: THP-1 Hypoxia

value: Monocyte

value: male


title: visceral white adipose tissue

first: Xiaohong

last: Jiang

address: 163 Xianlin Rd.

description: visceral white adipose tissue from C57BL/6 mouse housed at room temperature

hyb_protocol: Biotin-labelled miRNAs were used for hybridization on each miRNA microarray chip containing probes in triplicate.

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were normalized to U6 and analysed using GenePix Pro 4.0 software

organism: Mus

source_name: visceral white adipose tissue

label_protocol: Procedures were performed as described on the web site of CapitalBio.

growth_protocol: 8-week-old male C57BL/6J mices are raised under room temperature

extract_protocol: Total RNA from each pooled sample was isolated using the TRIzol method for Affymetrix miRNA microarray analysis.

treatment_protocol: No treatment


title: subcutaneous white adipose tissue

description: subcutaneous white adipose tissue from C57BL/6 mouse housed at room temperature

source_name: subcutaneous white adipose tissue


title: Aorta KO 8w Female 228

value: Aorta


title: C57BL/6J, 127-week-old


title: C57BL/6J, 10-week-old, #2


title: C57BL/6J, 10-week-old, #3


title: C57BL/6J, 10-week-old, #1


title: Aorta Ctrl 2w Male 202

value: Aorta Control 2w Male

value: Male


title: SP1


title: SP5


title: Aorta Ctrl 2w Male 200


title: immature dendritic cells - CBDLPS - 20D40

city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

data_processing:
HISAT2 algorithm was used for alignment of raw sequencing reads to human reference genome version GRCh38.
StrandNGS software (www.strand-ngs.com) was used for further statistical analysis.
Aligned data were normalized by using DESeq algorithm, then differentially expressed genes were determined by moderated T-test. P value < 0.05 was considered to significant change.
Every alignment and genetic statement has also been manually checked using bowtie2 and samtools software packages against the GRCH38 P.13 human reference genome.
The genomic variants were listed and tested using Broad Institute's GATK4 and via scripts leveraging Python 3.8.X and Bioconda packages
Assembly: GRCH38 P.13 human reference genome
Supplementary files format and content: Tab-delimited text files for each sample containing gene IDs and read counts.

source_name: periphereal blood monocytes

growth_protocol: CD14+ monocytes were  cultured in RPMI 1640 medium containing 10% heat-inactivated FBS, 10% HEPES, 50 mM 2-mercaptoethanol, 1% penicillin. The cells were seeded in 12-well tissue-culture plates (1 000 000 per well) containing  media supplemented with GM-CSF (80 ng/ml) and IL-4 (20 ng/ml) for five days. CBD treatment was applied on days 0 and 3, LPS was applied on day 4.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: monocyte-derived dendritic cell

value: CBD and LPS treated moDC


title: SA5

value: infusion of sodium butyrate

value: Day 13


title: SB3 [RNA-seq]

data_processing:
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome . After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: Capra hircus reference genome ARS1.2
Supplementary files format and content: raw counts  for each sample

source_name: colonic epithelial tissue

extract_protocol:
Total RNA  was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: colonic epithelial tissue


title: immature dendritic cells - CBDLPS - 20D36


title: Aorta KO 8w Female 230

value: Female

value: Itga8-Cre ERT2-Yap1fl/fl/Wwtr1fl/fl


title: SA6


title: SB2 [RNA-seq]


title: immature dendritic cells - CBD - 20D40

value: CBD treated moDC


title: SA4


title: Aorta Ctrl 2w Female 198

value: Aorta Control 2w Female


title: SA3


title: immature dendritic cells - CBD - 20D39


title: SB1 [RNA-seq]


title: Aorta KO 2w Male 222

value: Aorta YAP/TAZ KO 2w Male


title: SA2

value: cecal digesta


title: immature dendritic cells - CBD - 20D36


title: SP3 [RNA-seq]

value: infusion of normal saline


title: SP2


title: Aorta KO 2w Male 218


title: Aorta KO 2w Female 205

value: Aorta YAP/TAZ KO 2w Female


title: immature dendritic cells - LPS - 20D40

value: LPS treated moDC


title: interscapular brown adipose tissue

description: interscapular brown adipose tissue from C57BL/6 mouse housed at room temperature

source_name: interscapular brown adipose tissue


title: SP2 [RNA-seq]


title: NC6

value: infusion of sodium acetate


title: SA1

value: infusion of sodium propionate


title: SP1 [RNA-seq]


title: immature dendritic cells - LPS - 20D36


title: Aorta Ctrl 2w Female 192

value: Aorta


title: Aorta KO 2w Female 195


title: SA2 [RNA-seq]


title: NC4


title: NC5


title: SA3 [RNA-seq]


title: immature dendritic cells - LPS - 20D34

value: monocyte-derived dendritic cell


title: immature dendritic cells - CBDLPS - 20D34

value: CBD and LPS treated moDC


title: KO_Ero1a

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
ScRNA-seq alignment process was completed by cellranger (v5.0.1)
Seurat V3 workflow
Assembly: mm10
Supplementary files format and content: txt files with gene counts for scRNA-seq and rds files with embedding and annotation inforamtion for scRNA-seq

extract_protocol:
Preparation: We collected tumour grafts from wild type mice (n=5) and Ero1a KO mice (n=5). The samples were washed with 2% (v/v) FBS-PBS. Filtration of   tumour lysates through a 100 μm filter to form single-cell suspensions. After quantifying the cell number, adjusting the concentration to 800-1200 cells/μl, and ensuring the cell activity > 85%, single-cell suspensions from these specimens were subjected, typically within an hour after the acquisition, to single-cell RNA sequencing (scRNA-seq) using the 10X genomics platform to construct the single-cell library of samples.
Follwed by v3 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

value: tumour graft

tag: replicates

value: Ero1a KO


title: WT_Ero1a

value: Ero1a WT


title: SA1 [RNA-seq]

value: colonic epithelial tissue

value: Day 13


title: NC3

data_processing:
Paired-end reads generated from Illumina platforms were processed and merged using FLASH software (v1.2.7)
Quality filtering on the raw reads were then performed under specific filtering conditions to obtain the high-quality clean tags according to the Fqtrim software (v0.9.4). Chimeric sequences were filtered using VSEARCH software (v2.3.4)
Finally, the feature table and feature sequence were obtained after dereplication using DADA2 software (v1.10.1)
Assembly: The V3-V4 region of the prokaryotic small-subunit (16 S) rRNA gene was amplified with primers 341 F (5′-CCTACGGGNGGCWGCAG-3′) and 805 R (5′-GACTACHVGGGTATCTAATCC-3′)


title: immature dendritic cells - CTRL - 20D39

value: Control moDC


title: Control

source_name: Control

extract_protocol:
Preparation: collect the lymph nodes from the control (n=3), RHOAG17V (n=1), and RHOAG17V; DNMT3AR882H AITL (n=1) group. The samples were washed with 2% (v/v) FBS-PBS. Filtration of ground lymph node tissue through a 100um filter to form a single-cell suspension.  After quantifying the cell number, adjusting the concentration to 800-1200 cells/μl, and ensuring the cell activity > 85%, single-cell suspensions from these specimens were subjected, typically within an hour after the acquisition, to single-cell RNA sequencing (scRNA-seq) using the 10X genomics platform to construct the single-cell library of samples.
Follwed by v3 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

tag: genotype

value: Control


title: NC3 [RNA-seq]


title: NC2


title: NC2 [RNA-seq]


title: NC1


title: immature dendritic cells - CTRL - 20D36


title: NC1 [RNA-seq]


title: immature dendritic cells - CTRL - 20D34


title: RHOAG17V-DNMT3AR882H


title: hd2bhd2c,rep2,sRNA-seq

status: Public on Aug 12 2023

city: Wuhan

first: Xiangsong

last: Chen

state: Hubei

address: Bayi Road

institute: Wuhan university

description: Single-end sRNA-seq data from hd2bhd2c from replicate 2

data_processing:
The adapter 'AGATCGGA ' was trimmed from the raw fastq file using Cutadapt (Martin, 2011)
The trimmed sequences were aligned to the TAIR10 genome with STAR (Dobin et al., 2013) requiring no mismathches and allowing ≤ 100 multiple end-to-end alignments
Resulting SAM files were then processed with the readmapIO.py script to re-assign multimappers with a “rich-get-richer” algorithm as previously described (Schon et al., 2018)
Output bedFiles were sorted, condensed and normalized for total genome-matching reads.
Assembly: TAIR10
Supplementary files format and content: Bed files contain tab-separated values of chromosomes (column 1), start (column 2) and stop (column 3) coordinates of smallRNAs followed by normalize RPM score (column 4), strand (column 5), sequence (column 6) and small RNA size (column 7)

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: A. thaliana plants were growth on 1/2X MS agar (0.6%) + 1% sucrose  at 22 degree under a 16-h-light/8-h-dark photoperiod.

extract_protocol:
RNA isolated with Trizol （ThermoFisher, 15596026),following the manufacturer’s instructions
sRNA library was construbuted by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,E7580L)

treatment_protocol: normal

value: whole seedling

value: hd2b hd2c knockout

value: normal


title: hd2bhd2c,rep1,sRNA-seq

description: Single-end sRNA-seq data from hd2bhd2c from replicate 1


title: RHOAG17V


title: WT,rep3,sRNA-seq

description: Single-end sRNA-seq data from Col-0 from replicate 3

value: WT


title: WT,rep1,sRNA-seq

description: Single-end sRNA-seq data from Col-0 from replicate 1


title: One-day old

city: Bunkyo-ku

first: Luis

middle: Augusto Eijy

last: Nagai

state: Tokyo

address: #201 Main building, Institute for Quantitative Biosciences, 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: BDGP6.32
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Adult midgut

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell v3.1 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Library was performed according to the manufacter’s instructions (single cell v3.1 protocol, 10x Genomics).

value: Adult midgut

value: Midgut epithelial cells

value: Canton S (wild type)

value: Female


title: human

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

data_processing:
Adaptor-polluted reads, low-quality reads, and reads with over 10% Ns were removed by fastp (ver.0.21.0).
Clean reads were mapped to reference genome (rn6, UCSC) by Bismark (ver. 2.2.3)
Cytosines were considered as methylated based on the binomial test followed by adjusting the false discovery rate (FDR < 0.01) using the Benjamini-Hochberg method
The R package MethylSeekR version 1.36.0 was used to identify PMDs, LMRs and UMRs with default parameters
Chromosome 12 in rat was used to train the HMM
Assembly: rn6, UCSC
Supplementary files format and content: tab-delimited text files include CpG information (chromosome, position, readC, readT,methylation_level) for each Sample

source_name: Planceta

extract_protocol:
Genomic DNA of these samples were extracted using an EasyPure® Genomic DNA Kit (TransGen Biotech Co., Ltd., Beijing, China)
The sequencing libraries of 6 placenta DNA samples were constructed using NEBNext Kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: The uterus was exteriorized and silver clips were placed on the abdominal aorta (above the kidneys) and branches of the ovarian arteries

value: Planceta


title: H05802-14-01 Tumor biopsy

city: Frankfurt am Main

first: Florian

last: Greten

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

country: Germany

institute: Georg-Speyer-Haus

description: posttherapeutic

data_processing:
Sequence reads trimmed by Trimmomatic Software v.0.36
Reads mapped by STAR aligner v.2.5.2b
Hit counts calculated by Subread packages v.1.5.2
Differential gene expression by DESeq2
GSEA software for enrichment analysis
Genome_build: Human NCBI genome build GRCh38
Supplementary_files_format_and_content: Raw counts in txt file format

source_name: Surgical Material

extract_protocol:
Qiagen Rneasy FFPE kit (Qiagen; #73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FFPE material of Patients with advanced rectal cancer treated with neoadjuvant chemoradiotherapy

value: Tumor

tag: disease state

value: Rectal cancer

tag: Stage


title: H08503-14 Tumor biopsy

description: posttherapeutic

tag: tissue


title: H06240-14 Tumor biopsy

description: posttherapeutic


title: H05373-17-01 Tumor biopsy

description: posttherapeutic


title: H19548-17-01 Tumor biopsy

description: posttherapeutic


title: H50888-2018 Tumor biopsy

description: posttherapeutic


title: NH12654-17-01 Tumor biopsy

description: posttherapeutic


title: Three-day old


title: H03410-18-01 Tumor biopsy

description: posttherapeutic


title: H02753-18 Tumor biopsy

description: posttherapeutic


title: ∆vtlR/lsrB, 24h, biol rep2

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätstraße 150

department: Microbial Biology

institute: Ruhr University Bochum

data_processing:
Adapter sequences were removed via cutadapt 1.18 with Python 3.7.9 (options: -j 4 -q 10)
Cleaned reads were mapped with bwa (0.7.17-r1188) mem on default settings.
Duplicate reads were removed with Samtools 1.10.
Differential gene expression was analyzed  with DESeq2. A maximal adjusted p value of 0.05 was used as threshold.
Assembly: NCBI ID: 13606; 671 small RNA genes were added from Wilms et al. (2012, DOI: 10.4161/rna.17212), Lee et al. (2013, DOI: 10.1371/journal.pone.0070720) and from Möller et al. (2014, DOI: 10.1371/journal.pone.0110427)
Supplementary files format and content: Files include the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Agrobacterium fabrum

source_name: bacteria

growth_protocol: Cells were grown at 30 °C in YEB medium. Samples were taken after 24h of incubation.

extract_protocol:
RNA was extracted via hot-phenol method as described in Wilms et al. (2012, DOI: 10.4161/rna.17212). Samples were treated with RNase-free DNase.
RNA libraries were prepared by Novogene using 1 µg of RNA and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Index codes were added to attribute sequences to each sample. The RNA was fragmented with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. Then, first strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand synthesis was performed with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activities. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system. The cDNA was then incubated at 37 °C for 15 minutes with 3 µl USER Enzyme and then at 95 °C for 5 minutes. The subsequent PCR was performed with Phusion High-Fidelity DNA polymerase, Universail PCR primers, and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.

tag: strain

value: bacteria

value: deltavtlR/lsrB (deltaatu2186)

tag: treatment

value: Grown for 24h in YEB medium at 30 °C.


title: ∆vtlR/lsrB, 24h, biol rep1

tag: cell type


title: GP-3_1

city: beijing

first: wenjuan

last: xu

address: Beijing University of Chinese Medicine, No.11 North 3rd Ring East Road, Chao-Yang District, Beijing

institute: Beijing University of Chinese Medicine

description: We performed RNA-seq on RNA samples of SW491 cell derived from colorectal adenocarcinoma

data_processing:
Raw reads were subjected to quality control
Sequence reads were pre-processed to remove adaptors and filter low-quality reads
high-quality reads were aligned to the mouse reference genome using Tophat
Statistic modeling was performed using the DESeq 1.32.0 package of Bioconductor
Supplementary_files_format_and_content: .xls, normalized counts generated by the DESeq package
Genome_build: geo_submission_Aug5
Supplementary_files_format_and_content: .xls, normalized counts generated by the DESeq package

source_name: human colon cancer cells

growth_protocol: SW480 cells were seeded in T75 flask within IMDM supplemented with 10% FBS for 12 h.

extract_protocol:
Total RNA was isolated from experimental groups using RIPA Buff Reagent, Retinas were removed, flash frozen on dry ice, Total RNA was obtained by QIAGEN kit (QIAGEN, Germany), the total RNA concentration and purity were determined by a microplate reader, and RNA (0.5 μg) was reverse transcribed using the QuantiTect Reverse Transcription Kit (Thermo Fisher Scientific, Loughborough, UK).
RNA libraries were prepared for sequencing using standard BGISEQ500

treatment_protocol: The administration groups (PUE, GLY, BER and WOG) and control group were mixed with fresh medium to continue incubator cells for 12 h.

tag: cell line

value: SW480 cells

tag: treament

value: treated with combination GLY and PUE for 12 hours


title: ∆vtlR/lsrB, 24h, biol rep3


title: GP-2_1

description: We performed RNA-seq on RNA samples of SW490 cell derived from colorectal adenocarcinoma


title: H02732-17 Tumor biopsy

description: posttherapeutic


title: H00263-12 Tumor biopsy

description: posttherapeutic


title: immature dendritic cells - CTRL - 20D40

value: monocyte-derived dendritic cell

value: Control moDC


title: GP-1_1

description: We performed RNA-seq on RNA samples of SW489 cell derived from colorectal adenocarcinoma


title: WT,rep2,sRNA-seq

description: Single-end sRNA-seq data from Col-0 from replicate 2

value: whole seedling


title: H00130-09 Tumor biopsy

description: posttherapeutic


title: G3-3_1

description: We performed RNA-seq on RNA samples of SW488 cell derived from colorectal adenocarcinoma

value: treated with GLY for 14 hours


title: Bl6_TMPRSS2_humanization_116kbACE2_cWZ519_D5

city: New York

first: Weimin

last: Zhang

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description:
Targeted (capture) genome-seq
FCH57FYBGXK

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, hg38
Supplementary files format and content: bigwig files mapping to genome references (hg38 and/or mm10)
Supplementary files format and content: txt files for UMI numbers

organism:
Homo sapiens
Mus musculus

source_name: mESCs

growth_protocol: All sequenced mESC clones were from the feeder-independent condiftion. Culture medium consisted of 80% of 2i basal medium supplement with 3 µM CHIR99021 and 1 µM PD0325901, 20% of feeder-dependent ES medium (85% (v/v) KnockOut DMEM (Fisher Scientific, 10829018), 15% (v/v) Fetal Bovine Serum (Hyclone, SH30070.03), 0.5 mg/ml Penicillin-Streptomycin-Glutamine (Gibco, 10378016), 7 μL 2-Mercaptoethanol (Sigma-Aldrich, M6250), 0.1 mM MEM Non-Essential Amino Acids (Gibco, 11140050) and 1 U/ml LIF (EMD Millipore, ESG1107)). Tissue culture treated plates were coated with 0.1% gelatin solution before use. All cells were grown in a humidified tissue culture incubator at 37°C supplied with 5% CO2. E. coli cells were grown in standard LB medium supplemented with 12.5 ug/ml chloramphenical, or 50 ug/ml kanamycin.

extract_protocol:
1-3 million of feeder-independent mESCs were harvested for genomic DNA extraction by using a QIAamp DNA Mini Kit (QIAGEN, 51306). Plasmid DNA were extracted by using a NucleoBond Xtra BAC kit (Takara, 740436.25)
Approximately 100 ng DNA was used for the library construction using the NEBNext Ultra II FS DNA library prep kit (E7805). AMPure XP beads (Beckman Coulter, A63881) were used for DNA purification on a magnetic stand. DNA libraries were loaded on a ZAG DNA analyzer (Agilent) for quality control.

value: mESCs

tag: genetic modifications

value: Male


title: Bl6_TMPRSS2_humanization_116kbACE2_cWZ525_G1

tag: Sex


title: Bl6_ACE2_humanization_180kbNeo_cWZ351_2F4

description:
Targeted (capture) genome-seq
FCH53JCBGXJ


title: WH054724-01 Tumor biopsy

description: pretherapeutic

source_name: Biopsy


title: hd2bhd2c,rep3,sRNA-seq

description: Single-end sRNA-seq data from hd2bhd2c from replicate 3

value: hd2b hd2c knockout

value: normal


title: U10819-16 Tumor biopsy

description: pretherapeutic


title: Bl6_ACE2_humanization_180kbNeo_cWZ370_2G2


title: G3-1_1

description: We performed RNA-seq on RNA samples of SW486 cell derived from colorectal adenocarcinoma

value: treated with GLY for 12 hours


title: P2-3_1

description: We performed RNA-seq on RNA samples of SW485 cell derived from colorectal adenocarcinoma

value: treated with PUE for 12 hours


title: U06312-17 Tumor biopsy

description: pretherapeutic

value: Tumor


title: Bl6_ACE2_humanization_116kb_cWZ248_F2


title: P2-2_1

description: We performed RNA-seq on RNA samples of SW484 cell derived from colorectal adenocarcinoma


title: Bl6_ACE2_humanization_116kb_cWZ249_E1


title: ACE2_humanization_180kb_pWZ638_DNA

description:
Assemblon BAC DNA  seq
FCH77W7BGXH

library_source: other

molecule: other

source_name: E. coli

value: E. coli


title: ACE2_humanization_116kb_pWZ622_DNA

description:
Assemblon BAC DNA  seq
FCH5VLJBGXH


title: N028954-17 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: N018968-14 Tumor biopsy

description: pretherapeutic


title: ACE2_humanization_180kb_pWZ639_DNA

description:
Assemblon BAC DNA  seq
FCH77W7BGXH


title: P2-1_1

description: We performed RNA-seq on RNA samples of SW483 cell derived from colorectal adenocarcinoma


title: KB-3_1

description: We performed RNA-seq on RNA samples of SW482 cell derived from colorectal adenocarcinoma

value: untreated


title: N012593-14 Tumor biopsy

description: pretherapeutic


title: cWZ391_C1_R270R279_2nd

description:
Amplicon seq
HL3FLDRX2


title: KB-2_1

description: We performed RNA-seq on RNA samples of SW481 cell derived from colorectal adenocarcinoma


title: ACE2_humanization_116kb_pWZ621_DNA

description:
Assemblon BAC DNA  seq
FCH5VLJBGXH


title: G3-2_1

description: We performed RNA-seq on RNA samples of SW487 cell derived from colorectal adenocarcinoma

value: treated with GLY for 13 hours


title: cWZ391_C1_R245R246_2nd

description:
Amplicon seq
HL3FLDRX2


title: N008391-12-01 Tumor biopsy

description: pretherapeutic


title: KB-1_1

description: We performed RNA-seq on RNA samples of SW480 cell derived from colorectal adenocarcinoma

value: SW480 cells


title: cWZ391_C1_R155R172_2nd

description:
Amplicon seq
HL3FLDRX2


title: Bl6_ACE2_humanization_180kbNeo_cWZ371_2G12


title: K02975-16 Tumor biopsy

description: pretherapeutic


title: cWZ162_MK6_R155R172_2nd

description:
Amplicon seq
HL3FLDRX2


title: NH31084-16-01 Tumor biopsy

description: pretherapeutic


title: ACE2_humanization_180kb_pWZ637_DNA

description:
Assemblon BAC DNA  seq
FCH77W7BGXH


title: cWZ162_MK6_R245R246_2nd

description:
Amplicon seq
HL3FLDRX2


title: K01484-17 Tumor biopsy

description: pretherapeutic


title: H85697-13 Tumor biopsy

description: pretherapeutic


title: ACE2_humanization_116kb_pWZ620_DNA

description:
Assemblon BAC DNA  seq
FCH5VLJBGXH


title: H83725-16 Tumor biopsy

description: pretherapeutic


title: H78587-11 Tumor biopsy

description: pretherapeutic


title: 22082R-05-20

city: Atlanta

first: Srikant

last: Rangaraju

state: GA

address: 615 Michael St

department: Neurology

institute: Emory University

data_processing:
RNA-seq analysis was conducted to identify genes exhibiting differential expression. The counts data provided information on the abundance of reads mapped to the reference genome or the number of fragments assigned to each gene. The primary objective was to identify systematic changes between the conditions of interest, specifically Control vs Treatment. The analysis utilized the Deseq2 package, developed by Michael I. Love, Simon Anders, and Wolfgang Huber (Package Authors). A Deseq2DataSetFromMatrix object was created, and the design parameter was set to ~Treatment, which captured the information on how the traits file was structured. For instance, in the case of n=4 Control vs n=4 LPS, the design matrix reflected these conditions.
To ensure data quality, the raw counts data were aligned to the traits file, following the documentation guidelines. Lowly expressed genes were filtered out based on the criterion of rowSums(counts(dds)) ≥ 30, meaning that only genes with 30 reads in total across all samples (5 X 6 samples = 30) were retained. This step was performed to remove genes with insufficient expression levels. Additionally, if required by the dataset, Ensembl IDs were converted to gene names for ease of downstream analysis. The control condition was designated as the reference for comparison, and genes exhibiting differential expression were identified using the criteria of adjusted p-value < 0.05 and log2 fold change (LFC > 0 for upregulated genes and LFC < 0 for downregulated genes).
It should be noted that in the comparison of Bulk RNA-seq on responder BV2 cells, the LPS samples were contrasted against the control (n = 4), deviating from the general protocol. Principal component analysis (PCA) was employed as an initial analysis step to identify patterns, relationships, and important variables in the high-dimensional dataset.
Assembly: Next generation sequencing
Supplementary files format and content: comma separated file includes raw counts for each sample

source_name: Extracellular Vesicles

extract_protocol:
Total RNA was extracted from BV2 cells and BV2 cell-derived extracellular vesicles using the Qiagen miRNeasy Mini Kit (Cat. No. 217004). 20 µL of EV fraction was resuspended in 700 µL of trizol lysis buffer. BV2 cell pellets were harvested in 700 μL of trizol lysis buffer. Added 140ul of chloroform was added to each sample and shook vigorously. Samples were then centrifuged for 15 min at 12,000 x g at 4°C. After centrifugation, the sample separated into 3 phases: an upper, colorless, aqueous phase containing RNA; a white interphase; and a lower, red, organic phase.
The top aqueous phase was carefully isolated without disturbing the other phases. The top aqueous phase was transferred to a new collection tube and 1.5 volumes of 100% ethanol was added and mixed by pipetting up and down. 700 μL of the sample was added to the provided spin column in collection tubes. Samples were spin at ≥8000 x g for 15 s at room temperature and the flow-through was discarded. This was repeated for the rest of the sample.
Bound RNA was washed 2 times using the included wash solution (Buffer RPE). Finally, a preheated elution solution (RNase-free water) was used to elute the RNA in 40 uL volume for cells and 20 uL for extracellular vesicles.
cDNA Libraries were prepared for small RNAs using the SMARTer smRNA-seq kit. A total of 18 cycles of PCR were carried out to obtain a good yield of cDNA from cells and EVs. Final library quality was verified with Qbit and bioanalyzer. Negative (no RNA) and positive controls provided expected results. Next-generation RNA sequencing was performed using a HiSeq X Illumina 2x150, 40M total reads per sample (20M each direction) at Admera Health.

treatment_protocol: BV2 cells were treated with either TGF-β (50 ng/mL), IL-10 (50 ng/mL), and LPS (100 ng/mL) for 72 hours

value: Extracellular Vesicles

value: BV2 Cells

value: Microglia


title: 22082R-05-22

value: TGFB


title: cWZ162_MK6_R270R279_2nd

description:
Amplicon seq
HL3FLDRX2


title: 22082R-05-23


title: H69414-18 Tumor biopsy

description: pretherapeutic


title: H74623-08 Tumor biopsy

description: pretherapeutic


title: 22082R-05-24


title: 22082R-05-21


title: 22082R-05-19


title: 22082R-05-18

value: LPS


title: H65166-2016 Tumor biopsy

description: pretherapeutic


title: Control_rep2

organism: Rattus norvegicus

source_name: Placenta

value: Placenta

value: control


title: Muscle-Rbx1&Sag-deficient rep2

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

hyb_protocol: Samples were hybridized to Clariom S Arrays, mouse (Affymetrix, 902931).

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

data_processing: Microarray data sets were analyzed with Applied Biosystems Expression Console Software 1.4.

source_name: peripheral lymph nodes and spleens of mice (8-12 weeks old)

label_protocol: RNA samples were reverse transcribed, amplified, labeled (Affymetrix GeneChip pico kit, 703308).

growth_protocol: Mice were maitain in SPF condition until they were killed.

extract_protocol: RNA samples were prepared with the miRNeasy Mini Kit (Qiagen, 21704).

treatment_protocol: Peripheral lymph nodes and spleens were harvested from mice with indicated genotypes, and grinded into single cells, followed by treatment with Dynabeads™ Untouched™ Mouse CD4 Cells Kit (Invitrogen, 11415D) to isolate the CD4+ T cells. The FACS sorting (SONY Cell Sorter, SH800S) was used to isolate the CD4+YFP+ Treg cells with purities > 99%.

value: peripheral lymph nodes and spleens

value: CD4+YFP+ Treg cells


title: Muscle-Ube2m&Ube2f-deficient-rep3


title: H59457-17 Tumor biopsy

description: pretherapeutic


title: Muscle-Rbx1&Sag-deficient rep3


title: Control_rep3


title: Muscle-control rep1


title: Muscle-control rep2


title: 22082R-05-17


title: 22082R-05-16


title: Theoretical CTCF_C (CTCF Core motif sequence) , CTCF-ChIP-seq, replicate 2

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Genome-wide library of ChIPed chromatin

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates;
Combining data from multiple replicates (custom scripts)
Assembly: mm10
Supplementary files format and content: BigWig

source_name: E14TG2a.IV mES derived Erythroid cells

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) at 1x10^4 cells in 10 cm dishes for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ChIP-Seq as in Hay D et al, Nature Genetics, 2016.
Cells were fixed with 1% Formaldehyde, lysed, sonicated and immunoprecipitated with CTCF antibody (Merck Millipore 07-729 at 5ug/ml). Libraries were prepared using the NEB Ultra II library preparation kit according to manufacturer’s instructions. Samples were sequenced using40 bp paired end reads on the NextSeq platform.
The strategy was to characterise the CTCF binding pattern in the CD71+ erythroid cells (WT and mutant) derived from mESC-EB in vitro differentitation system by isolating and analysing DNA regions bound by the antibodies of interest, genome-wide.

value: E14TG2a.IV mES derived Erythroid cells

value: CD71+ erythroid cells derived from differentiated mES cells


title: Muscle-Ube2m&Ube2f-deficient-rep1


title: Control_rep1


title: Muscle-Rbx1&Sag-deficient rep1


title: Muscle-control rep3


title: Muscle-control-rep2


title: Muscle-control-rep3


title: H59079-16 Tumor biopsy

description: pretherapeutic

value: Tumor


title: 22082R-05-15

value: Control


title: Theoretical CTCF_C (CTCF Core motif sequence) , CTCF-ChIP-seq, replicate 1

description: Genome-wide library of ChIPed chromatin


title: H51483-17 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: RUPP_rep3

value: reduced uterine perfusion pressure


title: RUPP_rep2


title: Theoretical CTCF_U+C (CTCF Upstream motif +Core motif sequence) , CTCF-ChIP-seq, replicate 2

description: Genome-wide library of ChIPed chromatin


title: Muscle-control-rep1


title: H48628-17 Tumor biopsy

description: pretherapeutic


title: 22082R-05-14


title: Muscle-Ube2m&Ube2f-deficient-rep2


title: RUPP_rep1


title: Theoretical CTCF_U+C (CTCF Upstream motif +Core motif sequence) , CTCF-ChIP-seq, replicate 1

description: Genome-wide library of ChIPed chromatin


title: H43163-15 Tumor biopsy

description: pretherapeutic


title: 22082R-05-13


title: 22082R-05-12

source_name: Cells

value: Cells


title: Farnesol (F) biol rep2

city: Suwon

first: Ju-Hyeon

last: Bae

state: Gyeonggi-do

address: Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 2066

department: school of medicine

country: South Korea

institute: Sungkyunkwan 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: Gastrocnemius muscle

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: Mice (26-month-old) were orally administrated with Vehicle (Veh, 5% DMSO diluted in normal saline containing 0.85% NaCl.) or farnesol (350mg/kg) for 30 days.

value: Gastrocnemius muscle

tag: age

value: C57/BL6J WT

value: Farnesol


title: hd2bhd2c,heat,BS-seq

data_processing:
Adapters were removed by TrimGalore v2.70
The clean reads were mapped to the TAIR10 using BSMAP v2.90 (Xi and Li, 2009)
The python script methratio.py were used to remove duplicate and extract methylation ratios from BSMAP mapping results
Assembly: TAIR10
Supplementary files format and content: BigWig files were generated using the UCSC bedGraphToBigWig converter tool
Supplementary files format and content: BigWig files were generated using the UCSC bedGraphToBigWig converter tool

source_name: above ground parts

growth_protocol: Arabidopsis plants were grown on soil at 22 degree under a 16-h-light/8-h-dark photoperiod

extract_protocol:
DNA was extracted via the Qiagen DNeasy DNA extraction kit (catalog # 69104).
the WGBS library was constructed  according to the EZ DNA Methylation-GoldTM Kit DNA Methylation Kit (Zymo,D5006) method

treatment_protocol: 21-days-old seedings  were treated at 37 degrees for 24 hours

value: above ground parts

value: hd2b hd2c knockout

value: 37 degrees for 24 hours


title: H36899-18 Tumor biopsy

description: pretherapeutic


title: 22082R-05-11

value: BV2 Cells

value: Microglia

value: TGFB


title: Farnesol (F) biol rep1


title: Farnesol (F) biol rep3


title: Vehicle (V) biol rep3

value: Vehicle


title: 22082R-05-09

value: IL10 Cells


title: 22082R-05-10


title: hd2b,normal,BS-seq

value: hd2b knockout

value: normal


title: H35383-18 Tumor biopsy

description: pretherapeutic

value: Tumor


title: Vehicle (V) biol rep2


title: 22082R-05-08


title: H34738-2018 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: 22082R-05-07


title: H34538-15 Tumor biopsy

description: pretherapeutic


title: Vehicle (V) biol rep1


title: WT,heat,BS-seq

value: WT


title: WT,normal,BS-seq


title: H43290-14 Tumor biopsy

description: pretherapeutic


title: H27913-18 Tumor biopsy

description: pretherapeutic


title: Bl6_Trp53_Secondswapin_75kbpiggyBAC_F3

description:
Targeted (capture) genome-seq
FCHKJWWBGXM

value: mESCs

value: Male


title: Sperm_Native_ChIP_H3K4me3_Untreated

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

data_processing:
Paired-end reads were trimmed using Trim Galore (version 0.4.5), followed by reads alignment to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 700 no-mixed no-discordant.
PCR duplicates were removed using “MarkDuplicates” from Picard Tools (version 2.8.0) (https://broadinstitute.github.io/picard/). Only non-PCR duplicates and uniquely aligned reads (alignment records without “XS” tag) were used for downstream analyses.
The RPKM values for each 100-bp bin were calculated following the formula “read counts/((bin_length/1000) × (total_reads/106))
Peak calling for H3K4me3 and H3K27me3 datasets were done by MACS2 with parameters: --nolambda --nomodel, and --broad-cutoff 0.1 ---nolambda --nomodel, respectively.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Sperm

extract_protocol:
Sperm were first fixed with 1% formaldehyde in PBS for 10 min at room temperature, followed by quenching with Glycine. Next, sperm were pre-treated with 50 mM DTT and 1 mg/ml heparin at 37°C for 2 hr. Sperm were then quenched with NEM and washed with PBS twice.  After lysing sperm in complete buffer containing detergent, equal volume of 2x RIPA buffer was supplied to make a 1x RIPA condition. Chromatin shearing was performed using Covaris S220 platform with parameters: peak power 140 W, duty factor 5% and 200 Cycles/burst for a total of 30 min. Sonicated sperm chromatin were directly subjected to immunoprecipitation with corresponding antibodies
Library preparation was carried out using NEBNext Ultra II DNA Library Prep kit (NEB E7645)

value: Untreated

value: Sperm

tag: chip antibody

value: H3K4me3:Diagenode, C15410003


title: 22082R-05-06

value: Cells

value: LPS


title: hd2bhd2c,normal,BS-seq

value: above ground parts

value: hd2b hd2c knockout


title: 22082R-05-05

value: BV2 Cells

value: Microglia


title: H27064 Tumor biopsy

description: pretherapeutic


title: hd2c,normal,BS-seq

value: hd2c knockout


title: H22037-18 Tumor biopsy

description: pretherapeutic


title: Bl6_Trp53_Secondswapin_75kbpiggyBAC_B5


title: H2160-2017 Tumor biopsy

description: pretherapeutic


title: Sperm_Native_ChIP_H3K4me3_DNaseDTT

value: DNaseDTT


title: 22082R-05-04


title: 22082R-05-03

value: Control


title: H21539-14 Tumor biopsy

description: pretherapeutic

value: Tumor


title: Trp53_Secondswapin_75kbpiggyBAC_pWZ808_DNA

description:
Assemblon BAC DNA  seq
FCHVTHKAFX3

value: E. coli


title: Sperm_Native_ChIP_H3K4me3_Dnase

value: Dnase

value: WT


title: Sperm_Native_ChIP_H3K27me3_DTT

value: DTT

value: H3K27me3:Diagenode, C15410195


title: 22082R-05-02


title: H21502-17 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: Tmprss2_RP23-204E8_RepoBAC

description:
BAC DNA seq
FCHNC3CBGXH


title: H15491-10 Tumor biopsy

description: pretherapeutic


title: 22082R-05-01


title: Ace2_RP23-75P20_RepoBAC

description:
BAC DNA seq
FCH2FMKBGXH


title: Sperm_Native_ChIP_H3K27me3_DNaseDTT

value: Sperm


title: Trp53_Secondswapin_pW559_115kbPL

description:
Assemblon BAC DNA  seq
FCHFMKWBGXF


title: Sperm_Native_ChIP_H3K4me3_DTT

value: H3K4me3:Diagenode, C15410003


title: H140997-17 Tumor biopsy

description: pretherapeutic


title: 22082R-05-24

extract_protocol:
Total RNA was extracted from BV2 cells and BV2 cell-derived extracellular vesicles using the Qiagen miRNeasy Mini Kit (Cat. No. 217004). 20 µL of EV fraction was resuspended in 700 µL of trizol lysis buffer. BV2 cell pellets were harvested in 700 μL of trizol lysis buffer. Added 140ul of chloroform was added to each sample and shook vigorously. Samples were then centrifuged for 15 min at 12,000 x g at 4°C. After centrifugation, the sample separated into 3 phases: an upper, colorless, aqueous phase containing RNA; a white interphase; and a lower, red, organic phase.
The top aqueous phase was carefully isolated without disturbing the other phases. The top aqueous phase was transferred to a new collection tube and 1.5 volumes of 100% ethanol was added and mixed by pipetting up and down. 700 μL of the sample was added to the provided spin column in collection tubes. Samples were spin at ≥8000 x g for 15 s at room temperature and the flow-through was discarded. This was repeated for the rest of the sample.
Bound RNA was washed 2 times using the included wash solution (Buffer RPE). Finally, a preheated elution solution (RNase-free water) was used to elute the RNA in 40 uL volume for cells and 20 uL for extracellular vesicles.
cDNA Libraries were prepared  using the SMART-Seq v4 and Nextera XT kit. A total of 18 cycles of PCR were carried out to obtain a good yield of cDNA from cells and EVs. Final library quality was verified with Qbit and bioanalyzer. Negative (no RNA) and positive controls provided expected results. Next-generation RNA sequencing was performed using a HiSeq X Illumina 2x150, 40M total reads per sample (20M each direction) at Admera Health.

value: Extracellular Vesicles

value: TGFB


title: Trp53_Secondswapin_75kbpiggyBAC_pWZ809_DNA

description:
Assemblon BAC DNA  seq
FCHVTHKAFX3


title: Trp53_Secondswapin_pWZ550_75kbPL

description:
Assemblon BAC DNA  seq
FCH5GW3BGXF


title: 22082R-05-23


title: H137877-17 Tumor biopsy

description: pretherapeutic


title: Sperm_ChIP_H3K27me3_DTT_rep2


title: Sperm_ChIP_H3K4me3_DNaseDTT_rep2


title: Trp53_Secondswapin_pWZ546_40kbPL

description:
Assemblon BAC DNA  seq
FCH5GW3BGXF


title: H13761-17 Tumor biopsy

description: pretherapeutic


title: 22082R-05-22


title: 22082R-05-21


title: Bl6_Trp53_p53EF1a_1Swapin_cWZ632_B7

description:
Targeted (capture) genome-seq
FCHYCLWBGXK

value: mESCs

value: Male


title: Sperm_ChIP_CTCF_DTT_rep2

value: CTCF:Millipore 07-792


title: H136484-17 Tumor biopsy

description: pretherapeutic


title: 22082R-05-20

value: BV2 Cells

value: Microglia


title: Sperm_ChIP_H3K4me3_DTT_rep2


title: Bl6_Trp53_p53EF1a_1Swapin_cWZ395_E3

description:
Targeted (capture) genome-seq
FCH577GBGXJ


title: Sperm_ChIP_CTCF_DNaseDTT_rep2

value: DNaseDTT


title: Bl6_Trp53_p53EF1a_1Swapin_cWZ387_A9


title: H132017-17 Tumor biopsy

description: pretherapeutic

value: Tumor


title: H123074-17 Tumor biopsy

description: pretherapeutic


title: H12861-17 Tumor biopsy

description: pretherapeutic


title: Sperm_MNase_supernatant

data_processing:
Paired-end ATAC-seq reads were adapter-trimmed and aligned to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. MACS2 (Zhang et al. 2008) was used for peak calling with parameters: --nolambda --nomodel.
Reads with insert size larger than 150 bp were separated and used for nucleosome positioning analysis.
TSS enrichment analysis was done using Homer annotatePeaks (Heinz et al. 2010)
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
About 100,000 sperm were on-ice lysed with hypotonic lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) for 10 min.
Sperm were then resuspended in Tagmentation buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.05% Digitonin) and tagmentation was conducted by adding Tn5 transposase (Diagenode, C01070012) at 1:20 and incubated at 37C for 30min. Reaction was stopped by SDS and proteinase K and incubated at 55°C  overnight. SDS was quenched by tween-20 and library amplification was done with 1x NEBNext High-Fidelity PCR Master Mix containing 0.5 mM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 3 min; and 14 cycles at 98°C for 15 s, 63°C for 30 s, and 72°C for 1 min.

value: Tn5 transposase (Diagenode, C01070012)


title: Bl6_Trp53_p53EF1a_1Swapin_cWZ106_C2

description:
Targeted (capture) genome-seq
FCHHJWJBGXH


title: 22082R-05-18

value: LPS


title: Sperm_ExoV_supernatant

value: WT


title: 22082R-05-17


title: Sperm_ChIP_H3K27me3_DNaseDTT_rep2


title: Sperm_DNase_supernatant


title: 22082R-05-16


title: Trp53_p53CGmut_p53mNGreen_pWZ456_DNA

description:
Assemblon BAC DNA  seq
FCHFC7TBGXB

value: E. coli