title: A549_4C_rep2

address: 天津市和平区气象台路22号天津医科大学

data_processing:
The reduced genome was generated by extracting the sequences flanking the HindIII restriction sites (30 bp on each strand from the HindIII restriction sites to downstream) using the hg38 reference human genome, called 4C frag-ends. Non-unique frag-ends are discarded in subsequent analysis.
Subsequently, the highest covered frag-end was removed from the dataset in the normalization process and data are read-depth normalized to 1 million aligned intrachromosomal reads.
A Bioconductor package ‘r3Cseq’ with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference.
Assembly: hg38

growth_protocol: A549(TC)cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
4C-seq was performed as previously described using EcoR I for the first digestion, and Csp6 I for the second digestion. In brief, cells were cross-linked in 2% formaldehyde for 10 min at room temperature, glycine (V900144, Sigma) was added to a final concentration of 0.2 M to quench the reaction. After crosslinking, cells were rinsed with cold PBS at room temperature twice and incubated in lysis buffer (50 mM Tris-Cl, pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.5% CA630, 0.1% Triton X-100 and protease inhibitor cocktail (04693132001, Roche)) while tumbling for 1 h at 4 ℃. Cells were then pelleted, washed, and resuspended in EcoR I buffer. SDS was added to a final concentration of 0.3% for 1 h in a thermomixer at 37 °C and 900 rpm. Triton X-100 was then added to a final concentration of 1.8% and incubated in a thermomixer at 37 °C and 900 rpm for 3 h. 200 units EcoR I enzyme (New England Biolabs, R3101M) were added for a 4 h incubation in a thermomixer at 37 °C and 900 rpm; another 200 units EcoR I were added for overnight incubation. EcoR I was heat inactivated by incubating at 65 °C for 20 min. Cells were suspended in ligation buffer while 4,000 units of T4 ligase (New England Biolabs, M0202M) were added and incubated more than 8 h at 16 °C and 300 rpm. After ligation, 300 μg Proteinase K were added for overnight incubation at 65 °C and 400 rpm. DNA was purified and digested with 90 units Csp6 I (New England Biolabs, R0639S) and incubated for 5 h in a thermomixer at 25 °C and 500 rpm, followed by heat inactivation of enzyme at 65 °C for 20 min. DNA were then diluted with ligation buffer and 100 units T4 ligase were added for ligation overnight at 16 °C and 300 rpm. The second ligation circularized DNA were purified and amplified using bait-specific inverse primers (29 bp downstream of the rs1663689 and 55bp downstream of the EcoR I site to identify the allele at SNP and unknown DNA sequences interacting with the bait). Primers were extended with dangling Illumina adaptor sequences. After amplification, PCR products were pooled and purified. Sequencing reads were demultiplexed and trimmed of the primer sequence using sabre tool (https://github.com/najoshi/sabre), mapped to the human reference genome (hg38) with Bowtie2 (version 2.2.1) and converted to restriction fragment space. Interactions were called on single 4C experiments with peakC, using a sliding window of 21 fragments.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
4Cseq

value: TC

tag: time


title: PKL-GFP-IP-Rep2

status: Public on May 10 2023

type: SRA

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.05, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
1 ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction.  Libraries were constructed by the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607), VAHTSTM DNA Adapters set3 - set6 for Illumina® (N805) and VAHTS® DNA Clean Beads (N411-02, Vazyme) according to the manufacturer’s protocol. protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

tag: genotype/variation

value: wild type

tag: develomental stage

tag: condition

value: LD (long day)

tag: antibody

value: GFP (ab290, abcam)


title: E17.5_ChIP_H3K4me3_wildtype_rep3

city: New Haven

first: James

middle: P.

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale University

data_processing:
For ChIP-seq: reads were mapped to either the wild type mouse genome (mm39), or a humanized version in which the mm39 genome was edited to contain the human sequence. Indexes for both genomes were generated from fasta files using bowtie2-build in Bowtie 2 (v2.4.2). ChIP-seq reads were aligned using Bowtie2 with --sensitive and --no-unal settings. Peaks were called using MACS2 (v2.2.7.1) with the default (narrow peak) setting for H3K27ac, H3K4me3, and CTCF, and the --broad setting for H3K27me3. Bigwig files were generated using bamCoverage from deepTools (v3.5.1) using the settings --effectiveGenomeSize 2309746861 --normalizeUsing CPM --binSize 10 --extendReads 300 --centerReads. Effective genome size was calculated using unique-kmers.py from deepTools. Signal in bigwig files represents counts per million (CPM) in 10 bp bins.
For RNA-seq: reads were mapped to mm39 using STAR (2.7.9a) using an index generated using --runMode genomeGenerate with gencode.vM31.basic.annotation.gtf. STAR was then run using --quantMode GeneCounts to output reads counts for each gene.
Assembly: For ChIP-seq: mm39 or hs754-humanized mm39; For RNA-seq: mm39
Supplementary files format and content: bigWig (.bw) files contain ChIP-seq signal data as counts per million in 10-bp bins; bed files (.bed.gz) contain peak coordinates for ChIP-seq experiments; gene count files output by STAR (.ReadsPerGene.out.tab.gz) contain counts per gene as annotated by Gencode (vM31 basic annotation). Counts in each column are unstranded, forward strand, reverse strand.

organism: Mus musculus

source_name: diencephalon

extract_protocol:
Crosslinked diencephalon tissue from E11.5 or E17.5 was used for nuclei isolation, sonication, and chromatin extraction. Each replicate consists of tissue from 3 (at E17.5) or 6 (at E11.5) pooled embryos from the same litter. Chromatin immunopecipitation was performed with H3K27ac (Active Motif #39133), H3K4me3 (Cell Signaling #9751S), H3K27me3 (Cell Signaling #9733S), or CTCF (Diagenode #C15410210-50) antibody-coated magnetic beads (Protein G Dynabeads, Invitrogen) as described in doi:10.1101/pdb.prot084848.
Libraries were prepared and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.

tag: developmental stage

tag: tissue

value: diencephalon

tag: genotype

tag: chip antibody

value: H3K4me3 (Cell Signaling #9751S)

tag: strain


title: KKG_57_HNSCC_tumor_HPV-negative

type: RNA

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

hyb_protocol: According to the manufacturer's protocol.

data_processing: Text files were imported into R using the AgiMicroRna Bioconductor package. After quality filtering using Agilent quality filters and removing non-human miRNAs from the data set scanned intensities were background corrected, quantile normalized. The resulting expressions were log2-transformed after averaging signals determining expression of the same miRNA.

molecule: total RNA

organism: Homo sapiens

source_name: head and neck tumor

growth_protocol: Formalin-fixed paraffin-embedded tumour specimens were derived from treatment-naive surgically resected tumour tissues. Haematoxylin-eosin-stained tissue sections were histopathologically reviewed by a pathologist (DKTK-ROG: KS; LMU-KKG: CW/AW), the tumour area was defined and micro-dissected whereby only samples with at least 60% tumour cells were included.

extract_protocol: Total RNA including the small RNA fraction was extracted using the Qiagen miRNeasy FFPE (DKTK-ROG) or the AllPrep DNA/RNA FFPE Kit (LMU-KKG) according to the manufacturer's protocols (Qiagen, Hilden, Germany).

treatment_protocol: not applicable

tag: hpv-status

value: negative


title: KKG_59_HNSCC_tumor_HPV-negative

scan_protocol: According to the manufacturer's protocol.


title: KKG_58_HNSCC_tumor_HPV-negative

label_protocol: According to the manufacturer's protocol.


title: A549_4C_rep1

city: 天津市

first: Xinyue

last: Lei

state: 天津市

address: 天津市和平区气象台路22号天津医科大学

institute: 天津医科大学

treatment_protocol: untreatment

tag: cell line

tag: cell type

value: lung cancer


title: E17.5_ChIP_H3K4me3_hs754-humanized_rep2


title: KKG_56_HNSCC_tumor_HPV-negative


title: PKL-GFP-IP-Rep1


title: KKG_55_HNSCC_tumor_HPV-negative


title: KKG_54_HNSCC_tumor_HPV-negative


title: KKG_53_HNSCC_tumor_HPV-negative


title: A549, LRPPRC, rep2

city: Beijing

first: yuxin

last: Liang

address: No.2 North Street, Zhongguancun, Haidian District, Beijing

institute: Institute of  chemistry，Chinese Academy of Science

library_source: transcriptomic

data_processing:
Adapter were removed from RNA-seq library with software cutadapt (version 1.18) with parameters -u 5 -m 10.
Mapping performed using software HISAT2 (version 2.1.0) against the Human GRCh38(hg38) to get sam files. Salient parameters for HISAT2 are --dta -p 6 --rna-strandness RF.
The Sam files were sorted by samtools view -F 4 -Su and samtools sort command to get sorted Bam files. The version of samtools is 1.6.
Gene expression level was quantified by using stringtie v1.3.3b to compare the sorted Bam files with human genes gff file (Ensembl release 101).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The cell lysates were incubated with a 2 μg anti-LRPPRC antibody (Abcam) or rabbit IgG control (Millipore). Then the cell lysates were incubated with protein A/G modified beads for 4 h at 4℃ in a rotator. co-immunoprecipitated RNAs were extracted by miRNeasy Mini Kit (QIAGEN, 217004) for RNA sequencing or PCR verification.
A total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit V2 (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: anti-LRPPRC

value: epithelial cell

value: WT


title: PKL-GFP-INPUT


title: KKG_60_HNSCC_tumor_HPV-negative


title: E17.5_ChIP_H3K4me3_wildtype_rep1


title: Sample group 38

city: Oxford

first: Sean

last: Wen

address: Headley Way

country: United Kingdom

institute: University of Oxford

description: TARGET-seq

data_processing:
For processing of gDNA reads, sequencing reads were first aligned to the human reference genome using Burrows-Wheeler Aligner (BWA). Next, gDNA reads were retrieved based on gDNA-specific primer coordinates using custom perl script. Reads names were assigned and duplicate reads were marked using Picard.
For processing of mRNA reads, sequencing reads were first aligned to the human reference genome using STAR aligner. Next, cDNA reads were retrieved based on cDNA-specific primer coordinates using custom perl script. Reads names were assigned and duplicate reads were marked using Picard. Additionally, splicing intervals encoded as N CIGAR string were hardclipped using GATK-SplitNCigarReads.
Variant calling was performed using Mutect2 for insertion and deletion (INDEL) detection whereas Samtools mpileup was used for single-nucleotide substitution (SNV) detection.
Finally, Coverage at variant sites were computed using bedtools.
Assembly: GRCh38
Supplementary files format and content: Sparse matrix containing normalised umi counts for each cell

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol: TARGET-seq (Rodriguez-Meira et al, 2019)

value: Peripheral blood

value: Mononuclear cells


title: E17.5_ChIP_input-for-H3K27ac_hs754-humanized_rep3

value: none (input control)


title: Sample group 34

description: TARGET-seq

value: CD34+ cells

value: preleukemic


title: Sample group 37

description: TARGET-seq

source_name: Bone marrow

value: Bone marrow


title: E17.5_ChIP_H3K4me3_hs754-humanized_rep1


title: A549, LRPPRC, rep1


title: E17.5_ChIP_H3K4me3_wildtype_rep2


title: EV_siBMPR2_Hypoxia_24h_biorep1_smallRNA

city: Palo Alto

first: Kevin

last: Van Bortle

state: CA

address: 3165 Porter Dr

institute: Stanford University

description: Extracellular Vesicle, siBMPR2, 24 hour hypoxia, biol rep 1

data_processing:
Biological replicates and experimental conditions (siControl, siBMPR2) were sequenced together on an Illumina NovaSeq 6000 (single-end, 100) for each experiment, and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed smallRNA sequencing reads were mapped to the GRCh38 genome using Bowtie v 2.2.4 with settings --sensitive
Assembly: GRCh38
Supplementary files format and content: Processed abundance files correpond to read counts extracted over a comprehensive RNAcentral database annotation of noncoding RNAs. Gene annotation set and corresponding GRCh38 coordinates were downloaded from the contemporaneous RNAcentral database [release version13: ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/13.0/genome_coordinates/bed/homo_sapiens.GRCh38.bed.gz.]. RNAcentral coordinate IDs were mapped to Ensembl, Gencode, GtRNAdb, HGNC, Lncbase, Lncbook, Lncipedia, Lndcrnadb, miRbase, noncode, Refseq, and Rfam. To remove duplicate coordinate gene entries derived from multiple databases, genes with start and end coordinates within 50 bp of each other were merged into singular coordinate entries. Gene-specific raw small RNA signal counts were extracted and include the flanking 25 bp for each RNAcentral gene coordinate entry

source_name: pulmonary arterial endothelial cell

growth_protocol: PAEC were cultured for 24 hours in EC media (ScienCell) with 5% exosome-depleted FBS (Thermo-Fischer).

extract_protocol:
Extracellular vesicle miRNA was isolated using the mirVana miRNA isolation kit according to instructions (AM1560, Invitrogen).
Small RNA libraries were generated using the NEBnext small RNA library kit according to instructions (E7580S, New England BioLabs).

treatment_protocol: After 24 hours hypoxia (0.5% O2) EV were collected by differential centrifugation.

value: pulmonary arterial endothelial cell

tag: treatment

value: 24 hours hypoxia


title: E17.5_ChIP_input-for-H3K27ac_wildtype_rep3

value: wild type


title: Sample group 33

description: TARGET-seq

source_name: Peripheral blood (mobilized)

value: Peripheral blood (mobilized)


title: EV_siBMPR2_Hypoxia_24h_biorep3_smallRNA

description: Extracellular Vesicle, siBMPR2, 24 hour hypoxia, biol rep 3


title: KKG_52_HNSCC_tumor_HPV-negative


title: E17.5_ChIP_input-for-H3K27ac_hs754-humanized_rep2

value: diencephalon


title: EV_siBMPR2_Hypoxia_24h_biorep2_smallRNA

description: Extracellular Vesicle, siBMPR2, 24 hour hypoxia, biol rep 2


title: KKG_51_HNSCC_tumor_HPV-negative


title: KKG_50_HNSCC_tumor_HPV-negative


title: EV_siControl_Hypoxia_24h_biorep3_smallRNA

description: Extracellular Vesicle, siControl, 24 hour hypoxia, biol rep 3

value: siControl


title: Sample group 31

description: TARGET-seq

source_name: Peripheral blood and bone marrow

value: Peripheral blood and bone marrow


title: EV_siControl_Hypoxia_24h_biorep2_smallRNA

description: Extracellular Vesicle, siControl, 24 hour hypoxia, biol rep 2


title: Sample group 28

description: TARGET-seq


title: E17.5_ChIP_input-for-H3K27ac_hs754-humanized_rep1


title: OB_H3K27ac

city: Shenzhen

first: Wenhui

last: Yu

address: Shennan middle road #3025

department: Department of Orthopedics

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw reads were filtered and trimmed to remove sequencing adaptors and low-quality reads
Clean reads were mapped to the human genome version hg38 using Bowtie2 (v2.5.1)
Peaks were called using MACS2 (v.2.1.1) and normalization (reads per kilobase per million or RPKM) of the ChIP-seq data and heatmap plotting were performed using deepTools (v2.3.6.0)
The normalized ChIP-seq data were visualized on Integrative Genomics Viewer (IGV)
Grch38
Genome_build: peaks txt files
Supplementary_files_format_and_content: bw files were generated by deepTools (v2.3.6.0)

growth_protocol: MSCs were seeded in 12-well plates at a density of 5×104/well and cultured with DMEM (1000 mg/L glucose) with 10% FBS

extract_protocol:
Cells were harvested and cross-linked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min. Cells were lysed in 1 mL lysis buffer and rotated for 30 min at 4°C. Cell lysates were centrifuged at 2,400 g for 10 min at 4°C to isolate the nuclei. Nuclei were resuspended in digestion buffer and subjected to enzymatic digestion to shear chromatin fragments to an average size between 200 bp and 500 bp by incubating the tube at 37°C for 10-15 min.  The shearing reaction was stopped, and the fragmented chromatin was centrifuged at 18000 g for 10 min at 4°C. The supernatant was transferred to a new Eppendorf tube, and the ChIP reaction mix containing protein A/G magnetic beads, ChIP IP buffer, antibody, and protease inhibitor cocktail was added and rotated at 4°C overnight. After overnight incubation, protein A/G magnetic beads were washed. The chromatin was eluted in reverse cross-linking buffer followed by incubation of the tube at 65°C for 3 h. Then, the ChIP DNA was treated with RNase A and protease K at 37°C for 30 min and purified using phenol chloroform.
ChIP DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Culture medium was changed to osteogenic medium (OM) to induce osteogenic differentiation, consisting of DMEM (glucose 1000 mg/L) with 10% FBS, 100 IU/mL penicillin, 100 IU/mL streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate, and 50 μM ascorbic acid (Sigma-Aldrich). The OM was changed every 3 days thereafter for 7 days

value: Mesenchymal stem cells

tag: group

value: Osteogenesis


title: KKG_48_HNSCC_tumor_HPV-negative

value: negative


title: OB_input

value: input


title: Sample group 30

description: TARGET-seq

value: Peripheral blood


title: E17.5_ChIP_input-for-H3K27ac_wildtype_rep2


title: NC_H3K27ac

value: Normal control


title: KKG_45_HNSCC_tumor_HPV-negative


title: KKG_47_HNSCC_tumor_HPV-negative


title: Sample group 29

description: TARGET-seq


title: NC_input


title: EV_siControl_Hypoxia_24h_biorep1_smallRNA

description: Extracellular Vesicle, siControl, 24 hour hypoxia, biol rep 1


title: E17.5_ChIP_input-for-H3K27ac_wildtype_rep1

value: none (input control)


title: KKG_49_HNSCC_tumor_HPV-negative


title: KKG_42_HNSCC_tumor_HPV-negative


title: Sample group 20

description: TARGET-seq

value: CD34+ cells


title: Sample group 27

description: TARGET-seq


title: Sample group 17

description: TARGET-seq

value: Mononuclear cells


title: E17.5_ChIP_H3K27ac_hs754-humanized_rep3

value: H3K27ac (Active Motif #91193)


title: KKG_46_HNSCC_tumor_HPV-negative


title: KKG_44_HNSCC_tumor_HPV-negative


title: E17.5_ChIP_H3K27ac_wildtype_rep3


title: KKG_43_HNSCC_tumor_HPV-positive

value: positive


title: E17.5_ChIP_H3K27ac_hs754-humanized_rep2


title: Nsp6 [12_Nsp6]

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

description:
12_Nsp6
Nsp6_Nsp8_M_featureCounts.matrix.tsv

data_processing:
Quality control for raw mRNA-seq data was generated by FastQC v0.11.5.
Illumina adapter sequences and low-quality bases were trimmed by Trim Galore v0.4.5.
High-quality paired-end reads was mapped to human genome (hg38) with the aligner STAR v2.7.2b.
bam-filter in ngsutilsj v0.4.8 (https://compgen.io/ngsutilsj) was used to keep only properly and uniquely mapped paired reads (MAPQ ≥ 10) for downstream analysis.
FeatureCounts from package subread v1.6.5 was employed for quantification of gene expression by summarizing mapped reads to corresponding genes according to GENECODE v31 annotation.
Analysis of differential expression genes (DEGs) was performed by edgeR v3.32.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Nsp6_Nsp8_M_featureCounts.matrix.tsv: Tab-delimited text file includes raw read counts for every gene and every sample by featureCounts.

source_name: cardiomyocytes

growth_protocol: All purified hESCs derived-cardiomyocytes are cultured in DMEM (no glucose) with 10% FBS.

extract_protocol:
Total RNAs are extracted by Qiagen RNeasy Mini Kit.
Purified mRNA by enriching the polyA RNA.
mRNA-seq by using ultra-low mRNA-seq protocol.

value: human pluripotent stem cell-derived cardiomyocytes


title: Sample group 6

description: TARGET-seq


title: M [9_M]

description:
9_M
Nsp6_Nsp8_M_featureCounts.matrix.tsv

value: M


title: M [14_M]

description:
14_M
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: E17.5_ChIP_H3K27ac_wildtype_rep2

value: wild type


title: Nsp8 [13_Nsp8]

description:
13_Nsp8
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: Sample group 3

description: TARGET-seq


title: E11.5_ChIP_input-for-H3K27me3_wildtype_rep2

value: diencephalon


title: Sample group 10

description: TARGET-seq


title: E17.5_ChIP_H3K27ac_hs754-humanized_rep1


title: KKG_41_HNSCC_tumor_HPV-negative


title: KKG_37_HNSCC_tumor_HPV-negative


title: KKG_40_HNSCC_tumor_HPV-negative


title: Sample group 9

description: TARGET-seq

value: unassigned


title: E11.5_ChIP_input-for-H3K27me3_wildtype_rep1


title: KKG_39_HNSCC_tumor_HPV-negative


title: KKG_36_HNSCC_tumor_HPV-negative


title: Sample group 23

description: TARGET-seq

value: Peripheral blood and bone marrow


title: RBM9-KO-3-G11

city: Lausanne

first: Christina

last: Ernst

state: Vaud

address: EPFL SV GHI LVG, AI 3147 (Bâtiment AI), Station 19

country: Switzerland

institute: EPFL

data_processing:
Sequencing libraries were aligned against hg19 using STAR v.2.7.3a and alternative splicing events were identified using rMATS.
Assembly: hg19
Supplementary files format and content:
txt file containing output from rMATS to detect skipped exons between WT and KO condition based on junction counts
AS_Event.MATS.JunctionCountOnly.txt evaluates splicing with only reads that span splicing junctions
IJC: inclusion junction counts, SJC: skipping junction counts, Sample_1: KO, Sample_2: WT

growth_protocol: Adherent 293T cells (ATCC® CRL-1573™) were grown to ~80% confluency in Dulbecco’s Modified Eagle Medium (Gibco, #41966-029) supplemented with 10% FCS (Sigma-Aldrich, #F9665-500ML, Lot #19A124) and 1% Penicillin-Streptomycin-L-Glutamine (MED30-009-CI).

extract_protocol:
RNA was extracted using Trizol following the manufacturer's instructions
Stranded total RNA-Seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L) after ribosomal RNA depletion (NEB, #E6310L)

treatment_protocol: Cells were transfected with PX459 and pgRGFP encoding guide RNAs targeting upstream and downstream of RBFOX2. Single cells were sorted and clones were expanded for 3 weeks when genotypes were determined by PCR.

value: Human embryonic kidney

value: RBFOX2 KO


title: E17.5_ChIP_H3K27ac_wildtype_rep1


title: E11.5_ChIP_input-for-H3K27me3_hs754-humanized_rep2


title: control [11_control]

description:
11_control
Nsp6_Nsp8_M_featureCounts.matrix.tsv

value: control


title: Sample group 5

description: TARGET-seq


title: M [4_M]

description:
4_M
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: Nsp8 [8_Nsp8]

description:
8_Nsp8
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: E11.5_ChIP_input-for-H3K27me3_hs754-humanized_rep1


title: KKG_38_HNSCC_tumor_HPV-negative

value: negative


title: Sample group 1

description: TARGET-seq

value: preleukemic


title: E11.5_ChIP_H3K27me3_wildtype_rep2

value: H3K27me3 (Cell Signaling #9733S)


title: RBM9-WT-3-D4

value: WT


title: E11.5_ChIP_H3K27me3_hs754-humanized_rep1


title: RBM9-KO-2-A4


title: KKG_35_HNSCC_tumor_HPV-negative


title: control [6_control]

description:
6_control
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: RBM9-WT-2-D5


title: KKG_34_HNSCC_tumor_HPV-negative


title: Nsp8 [3_Nsp8]

description:
3_Nsp8
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: Nsp6 [7_Nsp6]

description:
7_Nsp6
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: Nsp6 [2_Nsp6]

description:
2_Nsp6
Nsp6_Nsp8_M_featureCounts.matrix.tsv


title: E11.5_ChIP_H3K27me3_wildtype_rep1


title: KKG_32_HNSCC_tumor_HPV-negative


title: E11.5_ChIP_H3K27me3_hs754-humanized_rep2


title: E11.5_ChIP_input-for-H3K4me3_hs754-humanized_rep2

value: none (input control)


title: PROTAC_rep3_MDAMB436

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequence trimming was performed by Cutadapt version 2.4.
The tools Hisat2 and StringTie were used to perform sequence mapping and transcript assembling, respectively.
Read count information was obtained using the python script prepDE.py from StringTie.
For differential expression analysis, read counts were imported into the tool edgeR.
Assembly: GRCh38
Supplementary files format and content: Ensembl gene IDs and read counts are provided in tab-delimited text files as the processed data files.

source_name: Breast

growth_protocol: Cells cultured in DMEM with 10% FBS and 1% Pen/Strep at 37C with 5% CO2.

extract_protocol:
Total RNA isolated using TRIzol
GeneWiz (www.GENEWIZ.com) performed library preparation using the NEBNext Ultra II RNA Library Prep kit. The HiSeq 4000 platform was used to sequence the libraries and generate the RNA-seq profiles.

treatment_protocol: MDA-MB-231 and MDA-MB-436 cells expressing MDM2 shRNA or non-targeting control or treated with YX-2-30 (MDM2 PROTAC) or DMSO vehicle control (three replicates of each)

value: Breast

value: Epithelial

value: MDM2 PROTAC


title: Primary liver sinusoidal endothelial cells ( x23 )

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

data_processing:
Mapping of the reads were obtained using the STAR program against rattus norvegicus genome (Rn6) and the quantification of genes and transcripts were done with the RSEM program using Ensembl annotation reference v-91.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rattus norvegicus (v91)
Supplementary_files_format_and_content: RSEM expected counts

organism: Rattus norvegicus

extract_protocol:
Primary LSECs transcriptome profile under physiological or pathological hydrodynamic pressures was examined by mRNA sequencing. Briefly, mRNA was isolated using the RNeasy® Micro Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions.
The sequencing library was prepared using 25 ng of total RNA by a Universal Plus mRNA-Seq NuGEN (0508, 9133, 9134, Tekan, Leek, The Netherlands). Single-end mRNA-seq was performed in the Illumina platform HiSeq2500

value: LSEC pathological pressure


title: KKG_31_HNSCC_tumor_HPV-negative


title: PROTAC_rep2_MDAMB436


title: KKG_30_HNSCC_tumor_HPV-negative


title: Primary liver sinusoidal endothelial cells ( x9 )


title: E11.5_ChIP_input-for-H3K4me3_wildtype_rep2


title: PROTAC_rep1_MDAMB436


title: KKG_29_HNSCC_tumor_HPV-negative


title: Primary liver sinusoidal endothelial cells ( x3 )


title: DMSO_rep3_MDAMB436

value: DMSO


title: Primary liver sinusoidal endothelial cells ( x22 )

value: LSEC physiological pressure


title: E11.5_ChIP_input-for-H3K4me3_hs754-humanized_rep1

value: diencephalon


title: E11.5_ChIP_input-for-H3K4me3_wildtype_rep1

value: wild type


title: control [1_control]

description:
1_control
Nsp6_Nsp8_M_featureCounts.matrix.tsv

value: human pluripotent stem cell-derived cardiomyocytes


title: KKG_26_HNSCC_tumor_HPV-negative


title: DMSO_rep2_MDAMB436


title: DMSO_rep1_MDAMB436


title: Primary liver sinusoidal endothelial cells ( x11 )


title: E11.5_ChIP_H3K4me3_wildtype_rep2

value: H3K4me3 (Cell Signaling #9751S)


title: MDM2shRNA_rep3_MDAMB436

value: MDM2 shRNA


title: E11.5_ChIP_H3K4me3_hs754-humanized_rep1


title: 24h_1: rat NSPCs, PUCL@CNT1 platform, 24h, stemness maintaining medium

city: Cheonan

first: Yu

middle: Meng

last: Li

address: Pharmacy Bldg, Cheonan 31116, Republic of Korea

department: Department of Nanobiomedical Science

country: South Korea

institute: Institute of Tissue Regeneration Engineering (ITREN)

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 rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Neural stem/progenitor cells

growth_protocol: 1. rNSPCs were maintained in knockout DMEM/F12 supplemented with StemPro™ Neural Supplement and antibiotics; 2. Neural differentiation was induced by shifting medium to B-27™ Plus Neuronal Culture medium.

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: rNSPCs were cultured on PUCL or PUCL@CNT1 platforms in stemness maintaining media for 24h or continued cutured in the B-27™ Plus Neuronal Culture medium for another 1.5d.

value: Neural stem/progenitor cells

value: PUCL@CNT1, stemness maintaining medium


title: KKG_25_HNSCC_tumor_HPV-negative

value: negative


title: KKG_24_HNSCC_tumor_HPV-negative


title: KKG_28_HNSCC_tumor_HPV-negative


title: E11.5_ChIP_H3K4me3_wildtype_rep1


title: KKG_23_HNSCC_tumor_HPV-negative


title: 24h_0: rat NSPCs, PUCL platform, 24h, stemness maintaining medium

value: PUCL, stemness maintaining medium


title: MDM2shRNA_rep1_MDAMB436


title: KKG_22_HNSCC_tumor_HPV-negative


title: 1.5d_1: rat NSPCs, PUCL@CNT1 platform, Day1.5, differentiation medium

value: WT

value: PUCL@CNT1, Neural differentiation

value: Day 1.5


title: E11.5_ChIP_input-for-H3K27ac_hs754-humanized_rep2

value: none (input control)


title: KKG_27_HNSCC_tumor_HPV-negative


title: NTshRNA_rep3_MDAMB436

value: Breast

value: Epithelial

value: Non-targeting shRNA


title: E11.5_ChIP_input-for-H3K27ac_wildtype_rep2


title: E11.5_ChIP_H3K4me3_hs754-humanized_rep2


title: E11.5_ChIP_input-for-H3K27ac_hs754-humanized_rep1


title: NTshRNA_rep2_MDAMB436


title: 1.5d_0: rat NSPCs, PUCL platform, Day1.5,differentiation medium

value: PUCL, Neural differentiation


title: Primary liver sinusoidal endothelial cells ( x2 )

value: LSEC physiological pressure


title: KKG_21_HNSCC_tumor_HPV-negative


title: KKG_20_HNSCC_tumor_HPV-negative


title: E11.5_ChIP_input-for-H3K27ac_wildtype_rep1

value: diencephalon

value: wild type


title: NTshRNA_rep1_MDAMB436


title: KKG_19_HNSCC_tumor_HPV-negative


title: MDM2shRNA_rep2_MDAMB436


title: PROTAC_rep3_MDAMB231

value: MDM2 PROTAC


title: PROTAC_rep2_MDAMB231


title: E11.5_ChIP_H3K27ac_wildtype_rep2

value: H3K27ac (Active Motif #91193)


title: swi6Dmst2D 9me3 endogenous

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by reads per million.  normalized by reads per million
Supplementary files format and content: bigwig files

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: YEA, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

value: yeast cell

value: swi6Dmst2D, cenHD::10xteto-ade6+


title: swi6Dmst2Dset1D 9me3 endogenous

value: swi6Dmst2Dset1D, cenHD::10xteto-ade6+


title: swi6Dset1D 9me3 endogenous

value: swi6Dset1D, cenHD::10xteto-ade6+


title: KKG_18_HNSCC_tumor_HPV-negative

value: negative


title: swi6D 9me3 endogenous

value: swi6D, cenHD::10xteto-ade6+


title: KKG_17_HNSCC_tumor_HPV-negative


title: DMSO_rep3_MDAMB231

value: DMSO


title: KKG_16_HNSCC_tumor_HPV-negative


title: WT 9me3 endogenous

value: WT, cenHD::10xteto-ade6+


title: PROTAC_rep1_MDAMB231

value: Breast


title: E11.5_ChIP_H3K27ac_hs754-humanized_rep1


title: E11.5_ChIP_H3K27ac_wildtype_rep1


title: swi6Dmst2Dset1D 9me2 endogenous


title: DMSO_rep2_MDAMB231

value: Epithelial


title: DMSO_rep1_MDAMB231


title: E4

first: jinhua

last: jin

state: Beijing

address: 33 Ba-Da-Chu Road, Shi-Jing-Shan District

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: dorsal root ganglion cells

growth_protocol: Mice were killed under deep anesthesia with sevoflurane and placed under  ice and DRG were extraced with the aid of a microscope

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: dorsal root ganglion cells

value: female

value: Primary Cell

value: wt

value: ovariectomized+estrogen


title: KKG_15_HNSCC_tumor_HPV-negative


title: E3


title: swi6Dset1D 9me2 endogenous


title: swi6Dmst2D 9me2 endogenous


title: KKG_14_HNSCC_tumor_HPV-negative


title: E11.5_ChIP_H3K27ac_hs754-humanized_rep2

value: diencephalon


title: KKG_13_HNSCC_tumor_HPV-positive

value: positive


title: E2


title: KKG_12_HNSCC_tumor_HPV-negative


title: KKG_11_HNSCC_tumor_HPV-negative


title: swi6D 9me2 endogenous

value: yeast cell


title: KKG_10_HNSCC_tumor_HPV-negative


title: E1


title: WT 9me2 endogenous


title: NTshRNA_rep3_MDAMB231

value: Non-targeting shRNA


title: MDM2shRNA_rep2_MDAMB231

value: MDM2 shRNA


title: P3

value: ovariectomized+placebo


title: P4


title: KKG_09_HNSCC_tumor_HPV-negative

value: negative


title: set1Dmst2D 9me3 ectopic


title: KKG_07_HNSCC_tumor_HPV-negative


title: swi6Dmst2D 9me3 ectopic


title: KKG_08_HNSCC_tumor_HPV-positive


title: MDM2shRNA_rep3_MDAMB231


title: NTshRNA_rep2_MDAMB231


title: P2


title: swi6Dset1Dmst2D 9me3 ectopic


title: swi6Dset1D 9me3 ectopic


title: siRNA treatment 3

city: Shanghai

first: Yinghao

last: Shen

address: 180 Fenlin Road

institute: Zhongshan Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

growth_protocol: The human HepG2 Hepatocellular Carcinoma cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of HepG2 cells with different treatment was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The HepG2 liver cells were transfected with control siRNA or FTO siRNA.

value: human Hepatocellular Carcinoma cells

tag: passage

tag: transfection

value: FTO siRNA


title: KKG_06_HNSCC_tumor_HPV-negative


title: KKG_05_HNSCC_tumor_HPV-negative


title: siRNA treatment 2


title: clr4D 9me3 ectopic


title: MDM2shRNA_rep1_MDAMB231


title: siRNA treatment 1


title: KKG_03_HNSCC_tumor_HPV-negative


title: KKG_04_HNSCC_tumor_HPV-negative


title: WT 9me3 ectopic


title: set1Dmst2D 9me2 ectopic


title: Control 2

value: control


title: NTshRNA_rep1_MDAMB231

value: Breast


title: KKG_02_HNSCC_tumor_HPV-negative


title: KKG_01_HNSCC_tumor_HPV-negative


title: GCT cells from four-month-old DKO females (biol rep 3)

first: Kaixin

last: Cheng

state: 北京

address: Yuanmingyuan West Road 2#

department: State Key Laboratory of Agrobiotechnology, College of Biological Sciences

institute: China Agricultural University

data_processing:
The cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) was utilized to perform the clustering of index-coded samples.
After cluster generation, the Illumina Novaseq platform was used to sequence the library preparations and 150 bp paired-end reads were generated.
Differential expression analysis was conducted by using the DESeq2 R package (1.16.1).
The resulting P-values were adjusted for controlling the false discovery rate by using Benjamini and Hochberg’s approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: ovarian tumor

extract_protocol:
Total RNA samples of ovaries, GCT tissues, and GCT cells were extracted by TRIZOL Reagent (Thermo-Ambion, 15596018). Degradation and contamination of RNA samples were monitored on 1.5% agarose gel. RNA purity was analyzed by using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA). RNA integrity was detected by using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA sample preparations were conducted by using a total amount of 1 µg RNA per sample as input material. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used to generate sequencing libraries according to manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: ovarian tumor

value: ovarian GCT cell

value: Pten and P27 double knockout


title: Control 1


title: GCT cells from four-month-old DKO females (biol rep 1)


title: swi6Dmst2Dset1D 9me2 ectopic


title: mutant GCs from ovaries of PD23 DKO mice (MT-GCs) (biol rep 1)

source_name: ovary

value: ovary

value: ovarian granulosa cell


title: swi6Dset1D 9me2 ectopic


title: swi6D 9me3 ectopic


title: GCT cells from four-month-old DKO females (biol rep 2)


title: GCs from ovaries of PD23 control mice (WT-GCs) (biol rep 3)

value: wild type


title: mutant GCs from ovaries of PD23 DKO mice (MT-GCs) (biol rep 3)


title: swi6Dmst2D 9me2 ectopic


title: P1

value: dorsal root ganglion cells

value: female

value: Primary Cell

value: wt


title: GCs from ovaries of PD23 control mice (WT-GCs) (biol rep 2)


title: Control 3


title: mutant GCs from ovaries of PD23 DKO mice (MT-GCs) (biol rep 2)


title: clr4D 9me2 ectopic

value: yeast cell


title: WT 9me2 ectopic


title: GCs from ovaries of PD23 control mice (WT-GCs) (biol rep 1)


title: NHE1 CRISPR KO, day 3, rep 1

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

library_source: transcriptomic single cell

data_processing:
Cell Ranger pipeline 6.1.2 on 10X Genomics Cloud Analysis
Assembly: GRCm38 (mouse reference, mm10)
Supplementary files format and content: Filtered feature-barcode matrices, Market exchange format (MEX)

source_name: small intestine

extract_protocol:
Organoid cultures were first washed with the cold (4°C) advanced DMEM/F12 (Invitrogen, 12634-028) supplemented with 10 mM HEPES (Invitrogen, 15630-080), 1 mM N-acetylcysteine (Sigma-Aldrich, A7250), 1X glutaMAX (Invitrogen, 35050-061), and 1X pen/strep. After the washing, wells containing the organoids were incubated with 300 uL cold (4°C) Corning recovery solution (Corning, 354253) for 15 min to melt the Matrigel. Next, organoids were mechanically disrupted with the P1000 pipette tips first and then trypsinized with RT TrypLE Express (Gibco, 1952062) for up to 15 min to disassociate into single cells. Single cells were then suspended within a sorting buffer that contained Hanks’ balanced salt solution (HBSS) with 3% m/v FBS, 10 mM HEPES and 5 mM EDTA. After staining with Live/Dead (Invitrogen, L23105, 1:1000) in the sorting buffer, fluorescence-activated cell sorting (FACS) was performed on the BD FACSAira instrument to enrich either live cells (-/+ EIPA and -Dox conditions) or live GFP+ cells (+Dox condition). Around 100,000-150,000 cells per genotype/condition were collected and re-suspended in ~200 mL 1X PBS containing 0.04 % (w/v) BSA (Ambion, AM2616).
Approximately 20,000 cells per genotype/condition were loaded onto a 10X Genomics Chromium Next GEM chip to generate a single cell 3’ gene expression library using the 10X Chromium Next GEM Single Cell 3’ regent kits v3.1. Pooled libraries were sequenced (single indexing) on a Illuminar NovaSeq 6000 sequencer with a standard sequencing protocol (Read 1, 28 cycles; i7 Index, 8 cycles; i5 Index, 0 cycles; Read 2, 91 cycles).

value: small intestine

value: Dox


title: NHE1 CRISPR, day 3, rep 1


title: PR2

city: Bhubaneswar

first: Suraj

middle: Kumar

last: Tripathy

state: Odisha

address: Campus 11

department: Biotechnology

country: India

institute: KIIT-DU

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.9 and MultiQC v1.9 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.1 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Acinetobacter baumannii (ATCC® 19606™) reference genome using Bowtie2 aligner.
Gene level expression values were obtained as read counts using featureCounts software
Assembly: Assembly GCF_001077675.1
Supplementary files format and content: Expression counsts file in txt format

organism: Acinetobacter baumannii

source_name: Bacteria

growth_protocol: The bacteria were grown in nutrient broth at 37℃, 130 rpm.

extract_protocol:
TRIzol method was used for RNA extraction.
500µg of total RNA was taken for rRNA depletion using QIAseq FastSelect −5S/16S/23S Kit (Catalog: 335925,invitrogen) according to manufacturer’s protocol. This method offers selective depletion of bacterial 5S/16S/23S rRNA. In brief, the RNA sample was hybridized to the FastSelect 5S/16S/23S probe followed by the removal of this complex through QIAseq Beads included in the kit. Thus depleted RNA was eluted with NFW.

treatment_protocol: The bacteria were harvested in its log phase and then washed with normal saline solution. They were then inoculated in the reaction matrix and the setup was treated with Sono-Fenton for 90 minutes. For extraction, the treated sample was further grown in nutrient broth till log phase.

value: MTCC 9829

value: Treated with Sono-Fenton


title: WT, EIPA, day 3, rep 2

value: WT

value: EIPA


title: clpX::Tn_dark_3

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

description: Gene expression of D. shibae clpX::Tn under dark conditions cultivated, replicate 3

hyb_protocol: 300 ng of labeled RNA were pooled, fragmented and hybridized according to the “one-color microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing: Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). For analyses only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.

organism: Dinoroseobacter shibae

source_name: D. shibae, transposonmutant clpX::Tn, dark, replicate 3

label_protocol: 1 µg of isolated total cellular RNA was labeled with Cy3, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: For the  experiment Dinoroseobacter shibae DFL12T wild type and transposonmutant strain clpX::Tn were grown in artificial saltwater minimal medium (SWM). For cultivation 200 ml of cell culture was inoculated with a grown pre-culture to an OD578 nM of 0.05 in a baffled flasks shaking at 180 rpm at 30°C under light, dark or bluelight conditions. After reaching an OD578 nM of 0.5 cells were harvested.

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was analyzed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: Growth under light, dark or bluelight conditions.

tag: age

value: exponential phase

tag: light

value: dark


title: clpX::Tn_dark_4

description: Gene expression of D. shibae clpX::Tn under dark conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant clpX::Tn, dark, replicate 4


title: WT, EIPA, day 3, rep 1


title: clpX::Tn_dark_1

description: Gene expression of D. shibae clpX::Tn under dark conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant clpX::Tn, dark, replicate 1


title: clpX::Tn_dark_2

description: Gene expression of D. shibae clpX::Tn under dark conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant clpX::Tn, dark, replicate 2


title: clpX::Tn_blue_4

description: Gene expression of D. shibae clpX::Tn under bluelight conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant clpX::Tn, bluelight, replicate 4

value: blue


title: Brain, BCAS Replicate 3

city: Nanjing

first: Qian

last: Cao

address: 358 Zhongshan Road, Nanjing Drum Tower Hospital, Nanjing City, Jiangsu Province

department: Neurology

institute: Nanjing Drum Tower Hospital

description: Biological replicate 3 of 3. BCAS mice brain, surgery

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data.
Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: brain

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: gender

value: male

value: BCAS


title: swi6D 9me2 ectopic


title: Brain, BCAS Replicate 2

description: Biological replicate 2 of 3. BCAS mice brain, surgery


title: Brain, BCAS Replicate 1

description: Biological replicate 1 of 3. BCAS mice brain, surgery


title: Brain, Sham Replicate 2

description: Biological replicate 2 of 3. Sham mice brain, untreated

value: Sham


title: Brain, Sham Replicate 3

description: Biological replicate 3 of 3. Sham mice brain, untreated


title: Brain, Sham Replicate 1

description: Biological replicate 1 of 3. Sham mice brain, untreated


title: PR1

value: Untreated


title: Ppmta Sample 2

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

description:
RNA-seq_Ppmta_2
mettl3_2

data_processing:
Reads were adapter-trimmed with Trim-galore.
Mapping against the P. patens reference genome was done with Bowtie2.
Reads were PCR de-duplicated with PICARD tools.
Differential expression was performed with edgeR.
Assembly: Physcomitrium patens 318 v3
Supplementary files format and content: controlvsmettl3.txt: Normalized abundance with edgeR in tab-delimited text format.

organism: Physcomitrium patens

source_name: protonema 18 d

growth_protocol: Protoplasts were grown in PRMB for 4 d, and them moved to PPNH4 medium for 8 d.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen) for RNA-seq analysis.
RNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following manufacturer's protocols.

treatment_protocol: NAA 1uM, 5 d; kinetin 1 uM, 1d.

value: protonema 18 d

value: Grandsen

value: Protoplast

value: Ppmta

value: NAA 1uM, 5 d; kinetin 1 uM, 1d.


title: zebrafish embryo, 50% epiboly, NT, replicate A, scRNAseq

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: Drop-seq

data_processing:
Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in (Farrell et. al., Science, 2018), using Drop-seq tools v1.12.
Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment, original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described, then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop-seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files.
Assembly: GRCz11/102
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Drop-seq droplet encapsulation of cells.
Libraries were built according to the Drop-seq protocol version 3.1 (12/28/2015, available http://www.dropseq.org/) with the following modifications. Iodoacetamide (IAA, Sigma-Aldrich) was diluted in ethanol to a 100mM working concentration. Following breakage of droplets, beads were washed once with 300uL of 5x IAA buffer (250mM NaPO4 pH8), and incubated in IAA solution (50mM NaPO4 pH8, 10mM IAA, 20% DMSO, 6% Ficoll PM-400) for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction, and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction, and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.

treatment_protocol: 20mM 4sUTP injection at 1-cell stage

value: zebrafish embryo

value: 50% epiboly

value: AB/TL

value: NT


title: zebrafish embryo, 50% epiboly, IAA, replicate B, scRNAseq

description: Drop-seq

value: IAA


title: zebrafish embryo, 50% epiboly, NT, replicate B, scRNAseq

description: Drop-seq


title: WT, DMSO, day 3, rep 2

value: small intestine

value: WT

value: DMSO


title: Ppmta Sample 1

description:
RNA-seq_Ppmta_1
mettl3_1


title: WT, DMSO, day 3, rep 1


title: zebrafish embryo, 50% epiboly, IAA, replicate A, scRNAseq

description: Drop-seq


title: WT control 2

description:
RNA-seq_control_2
control_2


title: clpX::Tn_blue_2

description: Gene expression of D. shibae clpX::Tn under bluelight conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant clpX::Tn, bluelight, replicate 2

value: exponential phase

value: blue


title: WT control 1

description:
RNA-seq_control_1
control_1


title: clpX::Tn_blue_1

description: Gene expression of D. shibae clpX::Tn under bluelight conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant clpX::Tn, bluelight, replicate 1


title: Experiment4 NPC

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

data_processing:
RNA-Seq and CUT&RUN fastq files were trimmed for quality using TrimGalore v0.4.1
RNA and CUT&RUN trimmed reads were aligned with STAR with the following parameters: --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06. Genomic coverage in form of bigwig files was calculated using the genomecov tool from bedtools using 10000000 / number_of_mapped_reads as a scaling factor.
For RNA-Seq samples, the number of read counts per gene  was calculated using HTSeq-count. Differential expression analysis was performed with DESeq2. For further details see Enriquez-Gasca et al., 2022.
Assembly: mm10
Supplementary files format and content: Bigwig files for genomic coverage normalised to number of mapped reads. Excel spreadsheet with results of differential expression analysis.

source_name: NPC

growth_protocol: mESCs were cultured in N2B27 media: DMEM/F12 (Gibco, Thermo Fisher Scientific ), Neurobasal (Gibco, Thermo Fisher), N2 (Gibco, Thermo Fisher), B27 (Gibco, Thermo Fisher), 0.1mM 2-Mercaptoethanol (Life Technologies) and supplemented with 0.08% BSA and 100 U/ml penicillin/streptomycin (Pen-Strep, Life Technologies), under 2i/LIF culture conditions: 1,000units/ml Leukaemia inhibitory factor (LIF, Chemicon), 1μM PD0325901 (Merck, Sigma Aldrich) and 3μM CHIR99021 (Merck, Sigma Aldrich). Cells were grown at 5% CO2 at 37°C and split 1:4 every 2 days with Accutase.

extract_protocol:
Total RNA was extracted using an RNeasy micro kit (Qiagen) and treated with DNase (Ambrio, AM1907). cDNA was synthesised from 500ng of RNA with SuperScript II Reverse Transciptase (ThermoFisher Scientific) using random primers.
CUT&RUN was carried out according to the EpiCypher® CUTANA CUT&RUN Protocol (v1.6) (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol/). 100,000 ESCs or day 5 NPCs were collected per sample/antibody and washed twice with EpiCypher Wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine) plus protease inhibitors (cOmplete™, Mini, EDTAfree, Roche) before attachment to activated Concanavalin A coated magnetic beads. Beads and cells were resuspended in Antibody Buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x protease inhibitors, 0.01% w/v digitonin, 2mM EDTA) with antibodies (1ug of anti-H3K9me3, anti-H3K27me3 or IgG control; Supplementary Table 1) and incubated overnight at 4°C with gentle rocking.  The next day beads were washed twice in cold Digitonin Buffer (20 mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x Roche complete protease inhibitors, 0.01% digitonin) and then incubated with Digitonin Buffer plus 2.5μL pAG-MNase (CUTANA™, Epicypher) before addition of 2mM CaCl2 to activate cleavage at 4°C for 2h. The reaction was quenched by addition of 33μl Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml glycogen, 50μg/ml RNase A), vortexted and incubated at 37°C for 10minutes to enable the release of DNA fragments. Sample was cleaned using a magnetic rack and the supernatant containing DNA was purified with a MinElute PCR Purification Kit (Qiagen).
RNA-seq - 500 ng per sample was processed using KAPA’s stranded RNA HyperPrep RiboErase kit and sequenced on a NovoSeq instrument after pooling libraries in equimolar quantities, using a 2x 151 bp paired-end run, resulting in over 15 million reads per sample.
Libraries were prepared according to manufacturer’s instructions using the following kits: NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (New England BioLabs) and pooled in equimolar quantities. Sequencing was carried out on a Novaseq6000 with 150bp PE reads.

treatment_protocol: NPC differentiation. 46C ESCs (Ying et al., 2003) are a Sox1-GFP reporter cell line generated by gene targeting of E14Tg2a.IV ES cells which are derived from a 129/Ola mouse embryo (male) and were a gift from Prof. Austin Smith. ESCs were cultured in 2i/LIF conditions and then cultured for two passages without LIF; NPCs were generated from these cells as described in (Gouti et al., 2014), with some modifications: ESCs were plated on laminin-coated 6 well plates at a density of 65000 cells per well in N2B27 media (as above but with N2 Supplement-B from StemCell Technologies) supplemented with bFGF (10ng/uL bFGF (R&D)) and 1μg/mL laminin. Cells were cultured for 5 days with daily media changes (day 1-2 with bFGF, day 3-5 without bFGF) at 7% CO2 and at day 5, cells were collected and analysed by flow cytometry (ACEA Novocyte 3000) to measure GFP expression and used for downstream analyses.

value: NPC

value: NPC differentiated from 2i ESCs


title: zebrafish embryo, 30% epiboly, IAA, replicate B, scRNAseq

description: Drop-seq

value: 30% epiboly


title: zebrafish embryo, 30% epiboly, NT, replicate B, scRNAseq

description: Drop-seq


title: Experiment1 NPC


title: clpX::Tn_blue_3

description: Gene expression of D. shibae clpX::Tn under bluelight conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant clpX::Tn, bluelight, replicate 3


title: Experiment3 NPC


title: zebrafish embryo, 30% epiboly, IAA, replicate A, scRNAseq

description: Drop-seq


title: clpX::Tn_light_3

description: Gene expression of D. shibae clpX::Tn under light conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant clpX::Tn, light, replicate 3

value: light


title: Experiment2 NPC


title: clpX::Tn_light_4

description: Gene expression of D. shibae clpX::Tn under light conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant clpX::Tn, light, replicate 4


title: zebrafish embryo, Dome, IAA, replicate B, scRNAseq

description: Drop-seq

value: Dome


title: clpX::Tn_light_1

description: Gene expression of D. shibae clpX::Tn under light conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant clpX::Tn, light, replicate 1


title: Experiment4 ESC

source_name: mESC

value: mESC

value: N2B27/2i grown mESCs


title: zebrafish embryo, 6hpf, rep2

description:
paired-end sequencing was ribosomal depleted while single-end was polyA selected
S20

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt
Trimmed sequence reads were mapped to GRCz11 using STAR
Read count extraction and NTR calculation were performed using GRAND-SLAM
Assembly: GRCz11/102
Supplementary files format and content: tab-delimited text file includes readcount and NTR (%new RNA) for each Sample
Library strategy: SLAM-seq

source_name: whole embryo

extract_protocol:
Total RNA was isolated using tri reagent (Sigma T9424) and quantified using nanodrop
polyA+RNA: Indexed RNA-Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of 300 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer. total-RNA: indexed RNA-Seq libraries for each sample were generated from total RNA using the Illumina RiboZero(Human/Mouse/Rat) kit following the manufacturer’s instructions. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Libraries are then sequenced using an Illumina Novaseq sequencer.

treatment_protocol:
20mM 4sU injection at 1-cell stage
RNA was treated with Iodoacetamide to induce T to C conversions

value: whole embryo

value: 4sU injection

tag: time


title: Experiment2 ESC


title: clpX::Tn_light_2

description: Gene expression of D. shibae clpX::Tn under light conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant clpX::Tn, light, replicate 2


title: Experiment1 ESC


title: zebrafish embryo, 30% epiboly, NT, replicate A, scRNAseq

description: Drop-seq

value: zebrafish embryo

value: AB/TL


title: Sample group 42

city: Oxford

first: Sean

last: Wen

address: Headley Way

institute: University of Oxford

description: TARGET-seq

data_processing:
For processing of gDNA reads, sequencing reads were first aligned to the human reference genome using Burrows-Wheeler Aligner (BWA). Next, gDNA reads were retrieved based on gDNA-specific primer coordinates using custom perl script. Reads names were assigned and duplicate reads were marked using Picard.
For processing of mRNA reads, sequencing reads were first aligned to the human reference genome using STAR aligner. Next, cDNA reads were retrieved based on cDNA-specific primer coordinates using custom perl script. Reads names were assigned and duplicate reads were marked using Picard. Additionally, splicing intervals encoded as N CIGAR string were hardclipped using GATK-SplitNCigarReads.
Variant calling was performed using Mutect2 for insertion and deletion (INDEL) detection whereas Samtools mpileup was used for single-nucleotide substitution (SNV) detection.
Finally, Coverage at variant sites were computed using bedtools.
Assembly: GRCh38
Supplementary files format and content: Sparse matrix containing normalised umi counts for each cell

source_name: Peripheral blood

extract_protocol: TARGET-seq (Rodriguez-Meira et al, 2019)

value: Peripheral blood

value: Mononuclear cells


title: zebrafish embryo, 1hpf, rep2

description:
paired-end sequencing was ribosomal depleted while single-end was polyA selected
S19


title: Experiment3 ESC


title: NPC IgG rep2

data_processing:
RNA-Seq and CUT&RUN fastq files were trimmed for quality using TrimGalore v0.4.1
RNA and CUT&RUN trimmed reads were aligned with STAR with the following parameters: --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06. Genomic coverage in form of bigwig files was calculated using the genomecov tool from bedtools using 10000000 / number_of_mapped_reads as a scaling factor.
For RNA-Seq samples, the number of read counts per gene  was calculated using HTSeq-count. Differential expression analysis was performed with DESeq2. For further details see Enriquez-Gasca et al., 2022.
Assembly: mm10
Supplementary files format and content: Bigwig files for genomic coverage normalised to number of mapped reads. Excel spreadsheet with results of differential expression analysis.
Library strategy: CUT&RUN

tag: antibodies

value: IgG control Ab (Millipore, 12-370)


title: Sample group 39

description: TARGET-seq


title: zebrafish embryo, Dome, NT, replicate B, scRNAseq

description: Drop-seq

tag: developmental stage

value: NT


title: NPC IgG rep1


title: ESC IgG rep2


title: Sample group 41

description: TARGET-seq

source_name: Bone marrow

tag: tissue

value: Bone marrow


title: wt_dark_3

description: Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 3

source_name: D. shibae, wildtype, dark, replicate 3

value: WT

value: exponential phase

value: dark


title: ESC IgG rep1


title: Sample group 24

description: TARGET-seq

tag: genotype

value: preleukemic


title: wt_blue_4

description: Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 4

source_name: D. shibae, wildtype, bluelight, replicate 4

value: blue


title: wt_blue_3

description: Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 3

source_name: D. shibae, wildtype, bluelight, replicate 3


title: wt_dark_1

description: Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 1

source_name: D. shibae, wildtype, dark, replicate 1


title: wt_dark_4

description: Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 4

source_name: D. shibae, wildtype, dark, replicate 4


title: NPC H3K9me3 rep2

value: NPC

value: NPC differentiated from 2i ESCs

value: anti-H3K9me3 (Abcam, ab8898)


title: wt_blue_2

description: Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 2

source_name: D. shibae, wildtype, bluelight, replicate 2


title: wt_dark_2

description: Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 2

source_name: D. shibae, wildtype, dark, replicate 2


title: wt_light_4

description: Gene expression of D. shibae wildtype under light conditions cultivated, replicate 4

source_name: D. shibae, wildtype, light, replicate 4

value: light


title: Sample group 26

description: TARGET-seq


title: Sample group 22

description: TARGET-seq


title: wt_blue_1

description: Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 1

source_name: D. shibae, wildtype, bluelight, replicate 1


title: wt_light_3

description: Gene expression of D. shibae wildtype under light conditions cultivated, replicate 3

source_name: D. shibae, wildtype, light, replicate 3


title: wt_light_2

description: Gene expression of D. shibae wildtype under light conditions cultivated, replicate 2

source_name: D. shibae, wildtype, light, replicate 2


title: NPC H3K9me3 rep1

source_name: NPC


title: Sample group 12

description: TARGET-seq


title: ESC H3K9me3 rep2

source_name: mESC

value: mESC

value: N2B27/2i grown mESCs


title: Sample group 8

description: TARGET-seq

source_name: Peripheral blood (mobilized)

value: Peripheral blood (mobilized)


title: ESC H3K9me3 rep1


title: Sample group 2

description: TARGET-seq


title: wt_light_1

description: Gene expression of D. shibae wildtype under light conditions cultivated, replicate 1

source_name: D. shibae, wildtype, light, replicate 1


title: RMZM4_3

city: Haidian

first: Samina

last: Shabbir

address: Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu

department: Biomass Energy Technology Research Centre

institute: Graduate School of Chinese Academy of Agricultural Science,

data_processing:
Raw data (raw reads) were interpreted via in-house perl scripts and clean data was extracted by eliminating reads comprising adapters. Then, the clean data of Q20, Q30, and GC content were computed. Complete genome annotation files downloaded from the genome website Bowtie2-2.2.3 (ftp://ftp.ncbi.nlm.nih.gov/genomes/bacteria/Zymomonas_mobilis/) were used to construct a reference genome index and match clean reads to the reference genome [33]. Novel genes, operon and transcription start sites were identified by Rockhopper [22]. Then, extracted the 5’UTR (3’UTR) sequences. Then, RBS finder [34] and TransTermHP ([35] were used to predict SD sequences and terminator sequences, respectively. IntaRNA was used to predict the sRNA targets. And then we used RNAfold to predict RNA secondary structures [36, 37]. Mapping of clean reads to each gene was counted using HTSeq v0.6.1. The fragments per kilobase of exon per million fragments mapped (FPKM) reads of every single gene were determined as described earlie
The read counts were modified for each sequenced library by edger software package via one standardized scaling factor. Differentially expression genes (DEGs) analyses of two conditions were performed using the DESeq package in R (1.18.0) [39]. Then using Benjamini & Hochberg approach, the p-values were adjusted. Genes with fold change (FC) > 1.5 and a false discovery rate (FDR; < 0.05) were considered as DEGs. Gene Ontology (GO) and pathway enrichment analyses of the DEGs were implemented with GOseq package in R [40], respectively. GO terminologies with adjusted p-value less than 0.05 were identified as significantly enriched.
Genome_build: mm9
Supplementary_files_format_and_content:   fpkm.stat.xls: a statistical table of the number of genes in different expression level intervals, this table counts the number of genes at different expression levels and the expression level of a single gene
Supplementary_files_format_and_content: New transcript annotation results

organism: Zymomonas mobilis

source_name: Wild-type ZM4

extract_protocol:
Total RNAs were extracted using the RNA isolation kit from bacteria cells (2 strains × 2 conditions × 3 replications) cultured in RM and AF medium (Tiangen, China).
Highly qualified RNAs were used for construction and sequencing of cDNA libraries. The high-throughput sequencing was conducted by Illumina Hiseq 2000 platform after passing via a number of screening phases

value: Wild-type ZM4

value: Acetic acid and furfural

tag: medium

value: RM


title: LKR13KL MCT4KO, replicate 2, scRNAseq

city: Houston

first: John

last: Heymach

address: 1515 Holcombe blvd

institute: UT MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The raw scRNA-seq data were preprocessed using the Cell Ranger pipeline analysis provided by 10×Genomics. After data filtering, doublets removal, batch-effect evaluation and data normalization as described previously, “Seurat” R package (v3.1.5) was used to analyze the normalized gene-cell matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values matrix file

source_name: Subcutaneous tumor

extract_protocol:
tumors were harvested and dissociated into single cells suspension according to the protocol. Briefly, tumor tissues were mechanically disrupted and digested with Collagenase A, hyaluronidase, Dispase and DNase I. Then suspended cells were passed through a 40um strainer and treated with ammonium chloride to remove red blood cells for further processing.
Library was constructed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Subcutaneous tumor

value: LKR13KL MCT4KO

value: Kras/Stk11 MCT4KO

value: no


title: LKR13KL MCT4KO, replicate 1, scRNAseq

description: 10x Genomics


title: NPC H3K27me3 rep1

tag: strain

value: anti-H3K27me3 (Abcam, ab195477)


title: RMZM4_1


title: NPC H3K27me3 rep2


title: ESC H3K27me3 rep2


title: RM532_3


title: RM532_2


title: RMZM4_2


title: LKR13KL, replicate 1, scRNAseq

description: 10x Genomics


title: LKR13KL, replicate 2, scRNAseq

description: 10x Genomics


title: genomic DNA from Telomere Biology Disorder case 34

type: genomic

city: Umeå

first: Magnus

last: Hultdin

state: Vasterbotten

address: 6M-building, NUS, 2d floor

department: Department of Medical Biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC arrays using standard Illumina protocol

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

data_processing: Genome Studio software v2011.1 (Illumina) and R statistical software v4.0.4 (R Core Team)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from the TBD cases was extracted by standard protocols at the Department of Clinical Genetics, Umeå University Hospital, Sweden (n=19) or by clinical genetic laboratories outside of Umeå (n=16). Genomic DNA from the controls was extracted using the Gentra Puregene DNA extraction kit (Gentra Puregene DNA extraction kit, Qiagen, Hilden, DE).

tag: relative telomere length (rtl) group

value: extremely short RTL

tag: phenotype

value: non-hematological TBD

value: whole blood

value: leukocyte


title: LKR13K, replicate 1, scRNAseq

description: 10x Genomics

tag: cell line

value: Kras


title: PKD1 Het, NP-MTAza, Rep3

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Processed file columns are: chromosome, start, end, CpG ID, fraction of methylated reads, methylation percentage.

data_processing:
Quality and adapter trimming of raw fastq files was executed using Trim Galore (Version 0.4.4). 15 bp were removed from the 3’ end of read 1 and the 5’ end of read 2.
Trimmed reads were aligned to NCBI37/mm9 (July 2007) using Bowtie2 as part of Bismark (Version 0.20.1).
DNA methylation ratios were called using Bismark and were merged for neighboring CpGs on opposite sides of the strand.
Methylation ratios were filtered so that only CpGs that were captured in at least 2 of 3 samples in each experimental group (PBS, Aza, F-MTAza, and NP-MTAza) at a minimum read coverage of > 5x were used in DNA methylation analysis.
Assembly: mm9
Supplementary files format and content: BED file containing CpG methylation levels

source_name: proximal renal tubule epithelial cells

growth_protocol: Cells were cultured in DMEM/F-12 media, 2% FBS, 1x ITSG, and 2 nM of tri-ido-sodium salt. Cells were expanded at 37°C in a humidified incubator under 5% CO2. Cells at passage 3 were used for studies, and the media was changed every 2–3 days.

extract_protocol:
DNA was isolated from 500,000 PKD1 Het cells treated with one of the groups mentioned above using the Zymo Quick DNA Miniprep Plus Kit according to the manufacturer's instructions.
DNA was digested with MspI overnight. The digested products were size-selected using AMPure XP beads to remove anything above 300 bp for small fragment retention. 100 ng size-selected DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research). The eluted DNA was performed immediately using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences) according to the manufacturer’s instructions. Final libraries were generated from 10-12 PCR cycles. PCR products were cleaned up using SPRIselect beads (Beckman Coulter). Libraries were confirmed by an Agilent Bioanalyzer, and the yields were quantified by KAPA qPCR. Sequencing was performed at the UCI Genomics High Throughput Facility. 100 bp paired-end reads were sequenced using an Illumina NovaSeq 6000 sequencing system.

treatment_protocol: Cells were treated for 24 hours with 1) PBS, 2) free 50 µM Aza, 3) the combination of free 50 µM Aza, 300 µM metformin, and 10 µM tolvaptan, or 4) the combination of 50 µM Aza, 300 µM metformin, and 10 µM tolvaptan in micelle formulation.

tag: cell type

value: proximal renal tubule epithelial cells

value: Pkd1 heterozygous

tag: treatment

value: NP-MTAza


title: PKD1 Het, NP-MTAza, Rep1

description: Processed file columns are: chromosome, start, end, CpG ID, fraction of methylated reads, methylation percentage. Because 2 sets of barcodes were used for this sample, there are 2 sets of paired-end sequence files (4 files total) corresponding to the same sample. R1 refers to Read 1, R2 refers to Read 2.


title: genomic DNA from Telomere Biology Disorder case 35

value: short RTL

value: asymptomatic TBD


title: ESC H3K27me3 rep1

value: mESC

value: N2B27/2i grown mESCs


title: genomic DNA from Telomere Biology Disorder case 30


title: dKO4

city: Durham

first: Luke

last: Izzo

state: NC

address: 308 Research Drive

institute: Duke University

data_processing:
Illumina RNA-seq alignment software (version 2.0.1)
Transcripts per million (TPM) generation and differential expression analysis was performed on aligned reads to Mus musculus UCSC GRCm38/mm10 reference genome using Illumina RNA-seq differential expression software (DESeq2, v1.0.1)
Assembly: mm10
Supplementary files format and content: Excel files contain DESeq counts

growth_protocol: All liver cancer cells were maintained in DMEM/F12 supplemented with 10% calf serum at 37C and 5% CO2

extract_protocol:
Total RNA was extracted using Rneasy Plus Mini Kit (Qiagen #74134)
NEBNext poly(A) Magnetic Isolation Module (NEB #E7490L) followed by the NEBNext Ultra Directional RNA library preparation kit for Illumina (NEB #E7420L)

treatment_protocol: Liver cancer cells were cultured in DMEM supplemented with 10% calf serum fo 24 hours before extraction

value: liver cancer cell line

value: ACLY/ACSS2 double knockout (DKO1)


title: genomic DNA from Telomere Biology Disorder case 33


title: RM532_1

value: Acetic acid and furfural

value: RM


title: genomic DNA from Telomere Biology Disorder case 32


title: PKD1 Het, F-MTAza, Rep3

value: F-MTAza


title: PKD1 Het, NP-MTAza, Rep2


title: AFZM4_2

value: Wild-type ZM4

value: AF


title: genomic DNA from Telomere Biology Disorder case 28

value: hematological TBD

value: whole blood


title: AFZM4_3


title: dKO3


title: genomic DNA from Telomere Biology Disorder case 25

value: extremely short RTL

value: leukocyte


title: genomic DNA from Telomere Biology Disorder case 31

value: non-hematological TBD


title: LKR13K, replicate 2, scRNAseq

description: 10x Genomics

value: Subcutaneous tumor

value: Kras

value: no


title: AF532_2


title: AF532_1


title: PKD1 Het, F-MTAza, Rep2

value: proximal renal tubule epithelial cells

value: Pkd1 heterozygous


title: ACS2

value: liver cancer cell line

value: ACSS2 knockout (ACSS2 KO)


title: genomic DNA from Telomere Biology Disorder case 29

value: short RTL

value: asymptomatic TBD


title: genomic DNA from Telomere Biology Disorder case 20


title: dKO1

value: ACLY/ACSS2 double knockout (DKO1)


title: genomic DNA from Telomere Biology Disorder case 21


title: ACS4


title: genomic DNA from Telomere Biology Disorder case 27


title: genomic DNA from Telomere Biology Disorder case 22


title: genomic DNA from Telomere Biology Disorder case 24


title: PKD1 Het, F-MTAza, Rep1

value: F-MTAza


title: PKD1 Het, Aza, Rep3

value: Aza


title: AF532_3

value: Acetic acid and furfural

value: AF


title: PKD1 Het, Aza, Rep2


title: PKD1 Het, Aza, Rep1


title: YN8_SM-iGFP_2

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description: primary pig myoblasts with doxycycline inducible GFP transgene rep 2

data_processing:
Sequencing data was processed with Illumina Pipeline software (Casava version 1.9)
Raw reads were trimmed with trim_galore using default parameters and --nextseq polyG argument
Trimmed reads were aligned to genome using Rsubread v.2.10.0 with the following arguments: type = "rna", input_format = "gzFASTQ", output_format = "BAM",
Transcripts were counted from the aligned bam files using the Gencode V35 annotation file and featureCounts() from the Rsubread package, v2.10.0 with the following arguments: annot.ext = "sscrofa11.1_annotation_fixed.gtf", isGTFAnnotationFile = TRUE, useMetaFeatures = TRUE, isPairedEnd = TRUE,requireBothEndsMapped = TRUE)
Assembly: RefSeq Sus scrofa 11.1
Supplementary files format and content: csv with raw read counts

organism: Sus scrofa

growth_protocol: primary porcine myoblasts were cultured in F-10 media supplemented with 15% fetal bovine serum, 1x Gibco Antibiotic-Antimycotic, and 1% chicken embryo extract

extract_protocol:
RNA was isolated from cell lysates using Macherey-Nagel's Nucleospin RNA kit (p/n 740955.250)
Libraries were constructed using Illumina's TruSeq stranded mRNA kit (p/n 20020595)

treatment_protocol: Cells were induced with 1ug/mL doxycycline for 16 hours prior to harvest

value: primary Gottingen pig myoblasts

tag: passages

value: doxycycline inducible GFP transgene


title: genomic DNA from Telomere Biology Disorder case 19

value: extremely short RTL

value: non-hematological TBD

value: whole blood

value: leukocyte


title: ACL4

value: ACLY knockout (ACLY KO)


title: YN7_SM-iGFP_1

description: primary pig myoblasts with doxycycline inducible GFP transgene rep 1


title: ACL3


title: genomic DNA from Telomere Biology Disorder case 26


title: genomic DNA from Telomere Biology Disorder case 18


title: PKD1 Het, PBS, Rep3

value: proximal renal tubule epithelial cells

value: Pkd1 heterozygous

value: PBS


title: genomic DNA from Telomere Biology Disorder case 16


title: ACS1

value: liver cancer cell line

value: ACSS2 knockout (ACSS2 KO)


title: genomic DNA from Telomere Biology Disorder case 23

value: hematological TBD


title: genomic DNA from Telomere Biology Disorder case 17

value: asymptomatic TBD


title: WT4

value: wild-type (WT)


title: AFZM4_1

value: Wild-type ZM4

value: Acetic acid and furfural


title: 14DMI

city: Los Angeles

first: Reza

last: Ardehali

address: 675 Charles E Young Dr S

department: Internal Medicine, Division of Cardiology

institute: David Geffen School of Medicine at UCLA

data_processing:
CellRanger v2.2.0 was used to demultiplex each capture, process base-call files to fastq format, and perform 3’ gene counting for each individual cell barcode with mouse reference data set.
Assembly: mm10, v 2.1.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole heart - 14 days post MI

extract_protocol:
Hearts were extracted from mice, cannulated, and perfused with PBS. They were then perfused with 5mL of collagenase type II solution diluted in PBS. They were then minced into small pieces using a razor blade and re-suspended in 10mL of collagenase solution on a rotator at 37 degrees celsius for 1 hour with frequent pipetting to ensure complete digestion. Cells were then passed through a 40 micron filter and centrifuged at 350g for 10 minutes to isolate the cardiac pericytes. Debris was removed using Debris Removal Kit and cells were re-suspended in FACS buffer.
All cells were loaded to maximize the number of single cells acquired using the Chromium single Cell 3’ Reagent Kit. Libraries were prepared according to manufacturer’s instructions using the Chromium Single Cell 3’ Library and Gel Bead Kit v.3 (10x Genomics). Libraries were sequenced on a NovaSeq Sequencer (Illumina) and with an average of 150,000,000 million reads sequenced per sample.

treatment_protocol:
Mice were administered a 100mg/kg dose of tamoxifen for 4 days, followed by a 7 day washout period before Sham or LAD ligation.
Mice were given a Sham procedure, or an MI via LAD ligation. They were then sacrificed at 4 days, 7 days and 14 days post injury.

value: cardiac pericytes

value: Whole heart - 14 days post MI

value: C57BL/6J   Cspg4-CreER/+;Rosa26-tdT/+

value: 2-3 months


title: YN3_SM-iDUX4_3

description: primary pig myoblasts with doxycycline inducible human DUX4 transgene rep 3

value: primary Gottingen pig myoblasts


title: 7DMI

source_name: Whole heart - 7 days post MI

value: Whole heart - 7 days post MI


title: PKD1 Het, PBS, Rep2


title: PKD1 Het, PBS, Rep1


title: ACL1

value: ACLY knockout (ACLY KO)


title: ACL2


title: YN9_SM-iGFP_3

description: primary pig myoblasts with doxycycline inducible GFP transgene rep 3

value: doxycycline inducible GFP transgene


title: YN2_SM-iDUX4_2

description: primary pig myoblasts with doxycycline inducible human DUX4 transgene rep 2


title: 4DMI

source_name: Whole heart - 4 days post MI

value: Whole heart - 4 days post MI


title: genomic DNA from Telomere Biology Disorder case 14

value: extremely short RTL

value: non-hematological TBD

value: whole blood

value: leukocyte


title: genomic DNA from Telomere Biology Disorder case 15


title: YN1_SM-iDUX4_1

description: primary pig myoblasts with doxycycline inducible human DUX4 transgene rep 1


title: WT2

value: liver cancer cell line


title: YN5_SM-ipDUXC_2

description: primary pig myoblasts with doxycycline inducible pig DUXC transgene rep 2


title: WT1

value: wild-type (WT)


title: SHAM

source_name: Whole heart - SHAM

value: Whole heart - SHAM


title: WT3


title: YN6_SM-ipDUXC_3

description: primary pig myoblasts with doxycycline inducible pig DUXC transgene rep 3


title: B3xin: db/m mice 3, left ventricular, 16 week, control, miRNA-seq

city: chongqin

first: Yao

last: Yang

state: chongqin

address: Gaotanyan

institute: TMMU

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina NextSeq500 sequencing. Raw data with fastq format containing N, low quality, 5’ adapter contaminants, ploy A and low-quality reads were removed from the reads. Raw data without 3’adapter or the insert tag were also removed from the reads.
The small RNA tags from rRNA, tRNA, snRNA, and snoRNA were detected by mapping to the Rfam database and were mapped to reference genome mm10 by Bowtie software. The known miRNA was identified by mapping to the miRBase database with R package miRDeep2. MiRDeep2 was also used to count the reads numbers mapped to each miRNA. R package edgeR was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: left ventricular

growth_protocol: All the procedures were performed under the guidelines for the animal care, which is approved by the Animal Care and Ethics Committee of Southwest Jiaotong University. Two murine strains with C57BL/6 background including db/m and db/db mice are used as the spontaneous diabetic cardiomyopathy model and healthy control model, respectively. Three newborn healthy male db/m mice and three newborn healthy male db/db mice were purchased from Shanghai Nanfang Model Biotechnology Co. LTD (Shanghai, China).

extract_protocol:
miRNA was isolated from the left ventricular (3 db/db mice and 3 db/m mice).
The libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.).

treatment_protocol:
db/m mice were given ad libitum access to tap water and laboratory feed for 16w. db/db mice were fed with a high-fat diet for 16w.
The ultrasound system (VisualSonics, Toronto, ON, Canada) was used for echocardiographic measurements. After being anesthetized with avertin, the mice were shaved to expose the chest area and then fixed onto a flat plate. Left ventricular systolic diameter (LVDs), LV diastolic diameter (LVDd), LV ejection fraction (EF), and LV fractional shortening (FS) were determined and were the average of 6 consecutive cardiac cycles

value: left ventricular

value: db/m

value: laboratory feed


title: R3h_L2

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
The clean miRNA reads were obtained from raw reads after discarding sequences, adaptor-ligated contaminants, and reads shorter than 18 nt.
Clean reads were compared against small RNAs in Rfam database to identify and remove rRNA, scRNA, sonRNA, snRNA, and tRNA.
Known miRNAs were identified by aligning against the miRbase database (v.22), and unannotated reads were considered as novel miRNAs according to their genome positions and hairpin structures using Mireap_v0.2.
Assembly: miRbase database (v.22)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: wild-type

value: reoxygenation


title: KD3_H3K4me3_R2

city: Köln

first: Alicja

last: Pacholewska

address: Weyertal 115b

institute: Uniklinik Köln

description: KD biological replicate 3 technical replicate 2 treatment

data_processing:
ChIP-seq reads were aligned to the GRCm39 genome assembly using bowtie2 version 2.2.9 with the following configurations: --mm --threads  8 -x $REF  -U $SAMPLE
Bowtie2 output was converted into BAM format, sorted by coordinates with samtools v1.6 with the options: samtools view -Su /dev/stdin | samtools sort -@ 8 - -o BAM/${NAME}.bam
BAM files were filtered for the MAPQ > 30 with samtools v1.6 with the fillowing options: samtools view -bh -q 30
Peaks were called for WT and KD with macs2 v. 2.2.6 using all 6 treatment and all 6 input files (3 biological replicates x 2 technical replicates) with the following options: macs2 callpeak --bdg -g mm
Differential and common peaks were called using macs2 v.2.2.6 bdgdiff
For visualization, peak calling for WT and KD was redone using an additional --SPMR option to get normalized values and bdg files were converted to bigwig files using bedGraphToBigWig function of UCSC tools
Genome_build: GRCm39
Supplementary_files_format_and_content: bw files contain the signal per million reads normalized values for WT/KD condition
Supplementary_files_format_and_content: bed files contain common/WT-specific/KD-specific peaks called with macs2

source_name: CLL leukemic splenocytes

extract_protocol:
Splenocytes were isolated from leukemic mice. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq system

value: CLL leukemic splenocytes

value: KDM1A knockdown

tag: chip antibody


title: genomic DNA from Telomere Biology Disorder case 12

value: hematological TBD


title: R3h_L3


title: KD3_H3K4me3_R1

description: KD biological replicate 3 technical replicate 1 treatment


title: B2xin: db/m mice 2, left ventricular, 16 week, control, miRNA-seq


title: YN4_SM-ipDUXC_1

description: primary pig myoblasts with doxycycline inducible pig DUXC transgene rep 1

value: primary Gottingen pig myoblasts


title: R3h_L1


title: B1xin: db/m mice 1, left ventricular, 16 week, control, miRNA-seq


title: KD3_input_R1

description: KD biological replicate 3 technical replicate 1 input

value: No


title: E69xin: db/db mice 3, left ventricular, 16 week, DCM, miRNA-seq

value: db/db

value: high-fat diet


title: genomic DNA from Telomere Biology Disorder case 10

value: short RTL

value: whole blood

value: leukocyte


title: H24h_L2

value: hypoxia stress


title: KD3_input_R2

description: KD biological replicate 3 technical replicate 2 input


title: genomic DNA from Telomere Biology Disorder case 11


title: H24h_L1


title: genomic DNA from Telomere Biology Disorder case 9

value: asymptomatic TBD


title: E68xin: db/db mice 2, left ventricular, 16 week, DCM, miRNA-seq

value: left ventricular


title: genomic DNA from Telomere Biology Disorder case 8


title: genomic DNA from Telomere Biology Disorder case 13

value: extremely short RTL


title: H12h_L3

value: liver


title: KD2_input_R2

description: KD biological replicate 2 technical replicate 2 input


title: KD2_input_R1

description: KD biological replicate 2 technical replicate 1 input


title: Goat number 79 [C_079]

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

country: France

institute: INRAE

data_processing:
The vast majority of the data has a Q score greater than 30 (>99.9% correct)
Adapters were trimmed off. After, the read length distribution showed as expected main peak around 18-23 nt. representing microRNAs
Mapping was performed using bta and chi genome and annotation using miRBase 20
Assembly: bta and chi genome and annotation using miRBase 20
Supplementary files format and content: excel

organism: Capra hircus

source_name: Total RNA was extracted from milk EV of cows. There was 2 group of 5 cows and 4 goats

extract_protocol:
Milk-derived EVs were obtained by sucrose gradient ultracentrifugations. Then, total RNAs were isolated from EV samples by mirVana Total RNA Isolation Kit (Life Technologies) using Trizol LS Reagent (Ambion) in the firts step.
Small RNA-Seq librairies were generated from 100 ng of total RNA using NEBNext library generation kit (New England Biolabs INC.). Sequencing was performed using NewSeq 500 sequencing methodology (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified by 15 cycles to create cDNA constructs. Amplified cDNA constructs were size fractionated on a LabChip XT (Caliper Life Sciences) and a band representing adaptors and 15-40 bp insert excised using the manufacturer’s instructions. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis. the libraries were pooled in equimolar concentrations. The library pools were finally quantified again with qPCR and optimal concentration of the library pools used to generate the clusters on the surface of a flow cell before sequencing using NexSeq 500 sequencing methodology and reagents, according to the manufacturer instructions (Illumina).

tag: day in milk

value: milk-derived extracellular vesicle


title: E67xin: db/db mice 1, left ventricular, 16 week, DCM, miRNA-seq


title: KD2_H3K4me3_R1

description: KD biological replicate 2 technical replicate 1 treatment


title: Goat number 127 [C_127]


title: Goat number 44 [C_044]


title: H12h_L1

value: wild-type


title: genomic DNA from Telomere Biology Disorder case 7


title: KD1_H3K4me3_R1

description: KD biological replicate 1 technical replicate 1 treatment

value: CLL leukemic splenocytes


title: H3h_L3


title: H12h_L2


title: KD1_input_R2

description: KD biological replicate 1 technical replicate 2 input

value: KDM1A knockdown


title: HDM+Nafamostat_Replicate 3

city: Uppsala

first: Venkata Sita Rama Raju

middle: Sita Rama Raju

last: Allam

state: Sweden

address: Husargatan 3

department: IMBIM

institute: Biomedical Center Uppsala University

description:
is_164_015
Raw Counts_HDM+Nafamostat.xls

data_processing:
Generated data had read lengths with an average of 98-110 bp and high mapping (95% of aligned bases).
Normalized expression values generated by the Torrent Suite™ Software (version 5.10.1) were used for downstream differential gene expression analyses.
Assembly: mm10
Supplementary files format and content: Normalized expression values

source_name: Lung

extract_protocol:
RNA was extracted using the Qiagen RNeasy® plus mini kit
cDNA libraries were created and amplified using the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Life Technologies, Carlsbad, CA) following the protocol of the manufacturer

treatment_protocol: Mice were lightly anesthetized with isoflurane and the anesthetized mice were instilled with 10 mg of house dust mite (HDM) extract reconstituted in 30 ml PBS (Dermatophagoides pteronyssinus) intranasally twice a week for three weeks. Control mice received 30 ml PBS via the intranasal route. To investigate the efficacy of nafamostat on asthmatic features, nafamostat (20 mg/kg in 3% acetic acid in PBS) were administered thirty minutes before each PBS and/or HDM instillation via the intraperitoneal route

value: Lung

value: wildtype

value: House dust mite (HDM) + Nafamamostat 20 mg/kg


title: HDM+Nafamostat_Replicate 2

description:
is_164_014
Raw Counts_HDM+Nafamostat.xls


title: H3h_L1


title: KD1_H3K4me3_R2

description: KD biological replicate 1 technical replicate 2 treatment


title: Em3_H3K4me3_R2

description: WT biological replicate 3 technical replicate 2 treatment

value: no


title: KD2_H3K4me3_R2

description: KD biological replicate 2 technical replicate 2 treatment


title: Goat number 17 [C_017]


title: H24h_L3


title: HDM+Nafamostat_Replicate 1

description:
is_164_013
Raw Counts_HDM+Nafamostat.xls


title: N_L2

value: control


title: H3h_L2


title: genomic DNA from Telomere Biology Disorder case 4

value: hematological TBD


title: HDM_Replicate 3

description:
is_164_008
Raw Counts_HDM.xlsx

value: House dust mite (HDM)


title: genomic DNA from Telomere Biology Disorder case 2

value: whole blood

value: leukocyte


title: genomic DNA from control sample B045


title: N_L3


title: Em3_input_R2

description: WT biological replicate 3 technical replicate 2 input

value: No


title: Em3_H3K4me3_R1

description: WT biological replicate 3 technical replicate 1 treatment


title: HDM_Replicate 2

description:
is_164_007
Raw Counts_HDM.xlsx


title: HDM_Replicate 1

description:
is_164_006
Raw Counts_HDM.xlsx


title: Em3_input_R1

description: WT biological replicate 3 technical replicate 1 input


title: genomic DNA from control sample B047


title: genomic DNA from Telomere Biology Disorder case 1