title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep5 [small RNA-seq]

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing:
Raw data was collected by the Illumina HiSeq Control Software (version 2.2.58). Illumina Real-Time Analysis tool (version 1.18.64) was used for image analysis and base calling. The single-end sequence reads with 50 base pair read length were demultiplexed and FASTQ files were generated with CASAVA BCL2FASTQ Conversion Software (version 1.8.3).
Trim Galore (v0.0.4, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim reads of all analyzed data sets in two steps. In the first step, all adapters were removed and only reads shorter than the maximum sequencing length were kept. In the second step, reads were trimmed for a minimum quality threshold of 20.
We used STAR v2.5.2a to map the trimmed reads to the primary assembly of the human reference genome GRCh38. STAR was configured to match at least 16 nucleotides with a maximum of 5% mismatches over the mapped length having the splicing function switched off.
Normalization was done using DESeq2 v1.22.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with normalized counts for each sample.

source_name: Human skeletal muscle cells treated with TGF-β1 and the SB431542 inhibitor

growth_protocol: As described in the paper. Briefly, human satellite cells were obtained by percutaneous needle biopsies performed on vastus lateralis muscle. Cells were released by collagenase digestion and seeded on 15-cm dishes coated with GelTrex (thin layer protocol, 1:300, Life Technologies). After two rounds of proliferation in cloning medium (39% α-MEM, 39% Ham’s F-12, 20% FBS, 1% chicken extract, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.5 μg/ ml amphotericin B), CD56-positive myoblasts were enriched using MACS microbeads and LS-columns (Milteny Biotech) according to the manufacturer’s protocol, with 30 min incubation and stored in the gaseous phase of liquid nitrogen. For experiments, cells were seeded at 1000 cells/cm² in cloning medium on 6well plates. Myotube differentiation was initiated by either 2% FBS or FBS-free fusion medium (α-MEM, 100 U/ml penicillin, 50 μM palmitate, 50 μM oleate, 100 μM carnitine, 100 μg/ml streptomycin, 0.5 μg/ml amphotericin B) and continued for 5 days.

extract_protocol:
NucleoSpin miRNA kit (Macherey-Nagel).
Small RNA library preparation using NEBNext Small RNA Library Prep Set for Illumina (New England BioLabs).

treatment_protocol: As described in the paper. Briefly, stimulations with TGF-β1 were performed two days before initiation for 48 h, or during myotube differentiation for 96 h or 48 h as indicated. Human TGF-β1 (R&D Systems) was dissolved in 4 mM HCl 0.2% BSA while SB431542 (Milteny Biotech) was dissolved in DMSO.

value: Skeletal muscle cells

tag: treatment

value: TGF-beta1 + SB431542 inhibitor


title: 52-40-L

status: Public on Dec 07 2021

type: genomic

city: Lebanon

first: Meghan

middle: E.

last: Muse

state: NH

address: One Medical Center Drive, DHMC

department: Epidemiology

country: USA

institute: Geisel School of Medicine at Dartmouth

description: Subject 52 Naevus Tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Normalized using functional normalization (Fortin et. al. Genome Biology 2014)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: skin tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was performed either using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) or the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Hilden, Germany) according to manufacturer’s protocol

tag: subject

tag: age (years)

tag: Sex

value: F

tag: tissue

value: Naevus

tag: classification

value: Benign


title: 521_AGG_P_B14SH_2

type: SRA

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

library_source: transcriptomic

data_processing:
RNA-Seq analysis: RNA-Seq reads were filtered for rRNAs, tRNAs, microRNAs, and snoRNAs using STAR. The remaining reads were mapped to hg19 version of the human genome using STAR. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values
Genome_build: hg19
Supplementary_files_format_and_content: Samples' read counts and TPM values

molecule: total RNA

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in standard DMEM supplemented with 10% FBS, 1% Penicillin-Streptomycin in 37°C, 5% CO2 incubator.

extract_protocol: RNA was extracted from cells using RNeasy Mini kit (Qiagen, #74104).

treatment_protocol: Cells were transfected with either FUS-R521H-YFP or FUS-WT-YFP, together with either DNAJB14-FL, DNAJB14-short, or DsRed in 6 well plates. At 48 hours after transfection, cells were lifted from plates into standard DMEM supplemented with 10% FBS. FACS and sorting were performed on a BD FACSAria III sorter. Sorting cells into aggregate and diffused expressing populations was performed by the PulsA method. Tubes containing sorted cells were centrifuged for 7 minutes at 4 °C at 300 RCF, and the pelleted cell were flash-frozen in liquid nitrogen.

tag: cell type

value: Human embryonic kidney 293 cells

tag: transfection

tag: fus aggregation state

value: aggregate

tag: replicate


title: HUVECs treated with TNF replicate 2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: TNF treated HUVEC

data_processing:
Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg38) with HISAT2 v2.1.0
Gene counts were produced with StringTie v1.3.3b and the Python script “prepDE.py” provided in the package. StringTie was limited to reads matching the reference annotation GENCODE v27
DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tsv with Deseq2

source_name: Human umbilical vein endothelial cells, primary isolates

growth_protocol: Primary isolated from discard human umbilical cords from triplicate donors, cultured in EGM2MV (Lonza), passage 5 grown to 2 days post confluence and stimulated with 0.5 ng/mL TNF for 6 hours

extract_protocol:
Cell monolayers were washed with sterile phosphate buffered saline (PBS, Invitrogen) and total RNA was purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase treatment.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: Replicate cultures of HUVECs were maintained for 2 days post-confluence in a 12 well plate (Falcon) and stimulated with 0.5 ng/mL TNF (Invitrogen) for 6 hours or left untreated.

value: Umbilical vein

value: Endothelial cell

value: Tumor Necrosis factor


title: HUVECs treated with TNF replicate 3

description: TNF treated HUVEC


title: RNA neuron_f_12_4

city: Houston

first: Harry

last: MacKay

state: TX

address: 1100 Bates Ave

institute: Baylor College of Medicine

data_processing:
Fastq reads were quality trimmed using TrimGalore (v0.4.4) with a minimum quality score of 20 and a minimum read length of 50. Read quality was analyzed using fastqc (v0.11.5). WGBS: After trimming the reads were aligned to the mouse genome (mm10) using Bismark (v0.18.1) set to paired-end mode and using all other default settings. Read groups corresponding to each individual sample were added to these BAM alignments using Picard (v2.10.10) ‘AddOrReplaceReadGroups’ BAM files were query-name sorted using Picard ‘SortSam’, and then deduplicated using Picard ‘MarkDuplicates’. RNA-Seq: Quality-trimmed reads were aligned to the mouse genome (mm10) using Hisat2 (v2.1.0). Mapped reads were annotated and counted using featureCounts (v1.5.3) along with the gencode comprehensive gene annotation (gencode vM15 gff3 file). Differential expression testing was performed using DESeq2 (v1.16.1).
WGBS reads were also analyzed using PReLIM  and CluBCpG according to directions in (Scott, Duryea, et al., 2020)
Genome_build: mm10
Supplementary_files_format_and_content: Merged CpG coverage files, RNA-seq counts (.csv), CluBCpG clusters (.csv)

molecule: nuclear RNA

organism: Mus musculus

source_name: Microdissected ARH

extract_protocol:
Arcuate nuclei (ARH) were microdissected from coronal sections.  Nuclei were isolated by ultralcentrifugation, stained with Anti-NeuN (Millipore ABN78, 1:2000) and purified by FACS. DNA extracted by QIAGEN AllPrep Micro kit, RNA by RNA-STAT60
Tagmentation-based whole-genome bisulfite library preparation was performed on genomic DNA extracted from ARH NeuN+ and NeuN- nuclei as previously described (Wang et al., 2013).  Briefly, adaptors were pre-annealed and transposomes were assembled according to the protocol described in (Wang et al., 2013).  Next, 10-30 ng of mouse genomic DNA was tagmented by adding the assembled transposome and incubating at 55C for 8 min. Following purification using SPRI beads, ligonucelotide replacement and gap repair were performed using Ampligase and T4 DNA Polymerase. The product was purified using SRPI beads and followed by bisulfite treatment using the EZ DNA Methylation Gold kit (Zymo Research). Subsequently libraries were generated by PCR amplification using KAPA 2G robust hotstart ready mix. After purification using SPRI beads, libraries were diluted and loaded onto Illumina Hiseq2500 Sequencer for 100 bp paired-end sequencing. Libraries for RNA sequencing were prepared using the SMART-Seq v4 Ultra Low Input kit (Takara Clontech) according to the manufacturer’s instructions.  Briefly, purified RNA was incubated with lysis buffer for 5 minutes.  First strand cDNA synthesis was performed using the included 3-SMART-seq CDS primer II and V4 oligonucleotide.  cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (Beckman). Illumina libraries were prepared using Nextera XT DNA library preparation kit (Illumina), and sequenced on the Illumina Hiseq 2500 platform generating 100 bp paired-end reads.

value: neuron

tag: age

value: f


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep4 [small RNA-seq]

country: Germany


title: HUVECs treated with TNF replicate 1

description: TNF treated HUVEC


title: RNA glia_m_35_44

value: glia

value: m


title: 521_AGG_P_B14SH_1


title: 28-135-P

description: Subject 28 Skin Tissue

value: M

value: Skin


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep2 [small RNA-seq]


title: HUVECs treated with PBS replicate 3

description: PBS treated HUVEC

value: PBS


title: RNA neuron_f_12_7


title: RNA glia_m_35_42


title: 28-135-L

description: Subject 28 Naevus Tissue


title: 521_AGG_M_B14FL_2

value: diffused


title: HUVECs treated with PBS replicate 2

description: PBS treated HUVEC


title: HUVECs treated with PBS replicate 1

description: PBS treated HUVEC


title: Human_skeletal_muscle_cells_TGFB1_rep5 [small RNA-seq]

source_name: Human skeletal muscle cells treated with TGF-β1

value: Skeletal muscle cells


title: Human_skeletal_muscle_cells_TGFB1_rep4 [small RNA-seq]


title: RNA glia_m_35_40


title: RNA neuron_f_12_6


title: 158-4-L

description: Subject 158 Naevus Tissue


title: 521_AGG_M_DS_2


title: 521_AGG_M_DS_1


title: RNA glia_m_12_34


title: RNA glia_m_35_41


title: RNA neuron_f_12_2


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep3 [small RNA-seq]

value: TGF-beta1 + SB431542 inhibitor


title: 521_AGG_M_B14SH_1


title: RNA glia_m_35_43


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep1 [small RNA-seq]


title: sgZNF507 rep1

city: Worcester

first: Kevin

last: Creamer

state: MA

address: 55 Lake Ave N

institute: UMMS

description:
znf507-1
Raw_gene_counts_matrix.txt

data_processing:
RNA alignments were generated using TopHat2 software with --library-type fr-firststrand --no-coverage-search parameters and Ensembl (ver82) gene model annotations.
Count matrix generated using featureCounts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts.

source_name: embryonic kidney cells

growth_protocol: Cells were grown in DMEM supplemented with antibiotics.

extract_protocol:
RNA was isolated from cells disrupted with CRISPR/Cas9 in biological duplicate using Trizol RNA extraction reagent. RNA was treated with TURBO DNase (Thermo Fisher) to remove contaminating DNA and cleaned up using RNeasy Mini (Qiagen) kits according to manufacturer recommendations.
RNA sequencing libraries were prepared using a stand specific kit RNA-seq kit with ribosome depletion (KAPA Biosystems) and NEBNext Adapters and Multiplex Oligos for Illumina. Paired-end 50 bp sequencing was performed on the Illumina HiSeq 2000 platform (UMMS Core Facilities).

treatment_protocol: HEK293 cells were transiently transfected with equal amounts of Cas9 and sgRNA expressing plasmids (PX459) targeting either ZNF146, ZNF507 or an equivalent amount of empty vector control plasmid (Ran et al., 2013). Target sequences used for ZNF146 were 5’-ACTGAGCATGAGCATTTTC-3’, 5’-ACATGTACAATAAGTGATG-3’, 5’-ACTGTAAATTCTCTGCTGGC-3’, and 5’-TGAAGGTTTTTCCACACTC-3’. Target sequences used for ZNF507 were 5’-TGGGCTTCAAGTTCCTCC-3’, 5’-ATTGTTTCCGGACAAACTT-3’, 5’-CTGGCTTCTAGATGTAATA-3’, and 5’-AGGTTGGCTCTTGTCAACTC-3’. The day after transfection cells were selected for 36 hours using puromycin before outgrowth for a total of two weeks prior to analysis.

tag: cell line


title: RNA glia_m_12_33


title: 521_AGG_M_B14FL_1


title: Human_skeletal_muscle_cells_TGFB1_rep2 [small RNA-seq]


title: 1557-3-P

description: Subject 1557 Skin Tissue

value: F


title: 1564-34-L

description: Subject 1564 Naevus Tissue

value: Naevus

value: Benign


title: sgZNF507 rep2

description:
znf507-2
Raw_gene_counts_matrix.txt


title: Human_skeletal_muscle_cells_TGFB1_rep1 [small RNA-seq]


title: RNA glia_m_12_32


title: EV control rep2

description:
wt-2
Raw_gene_counts_matrix.txt


title: Human_skeletal_muscle_cells_TGFB1_rep3 [small RNA-seq]


title: EV control rep1

description:
wt-1
Raw_gene_counts_matrix.txt


title: 521_AGG_M_B14SH_2

value: Human embryonic kidney 293 cells


title: Human_skeletal_muscle_cells_rep5 [small RNA-seq]

source_name: Human skeletal muscle cells control

value: Control


title: Human_skeletal_muscle_cells_rep4 [small RNA-seq]


title: RNA glia_f_35_24


title: RNA glia_m_12_30


title: RNA glia_m_12_31


title: Human_skeletal_muscle_cells_rep3 [small RNA-seq]


title: Human_skeletal_muscle_cells_rep2 [small RNA-seq]


title: 1546-19-P

description: Subject 1546 Skin Tissue


title: Human_skeletal_muscle_cells_rep1 [small RNA-seq]


title: RNA glia_f_35_22


title: HTT134Q_agg_plus_rep1

description:
processed data file:
RNA_Seq_HTT_rsem.genes.expected_count.txt.gz
RNA_Seq_HTT_rsem.genes.tpm.txt.gz
RNA_Seq_HTT_rsem.isoforms.expected_count.txt.gz
RNA_Seq_HTT_rsem.isoforms.tpm.txt.gz

data_processing:
RNA-Seq analysis: RNA-Seq reads were filtered for rRNAs, tRNAs, microRNAs, and snoRNAs using STAR. The remaining reads were mapped to hg19 version of the human genome using STAR. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files with read count and TPM data for genes and isoforms, produced by RSEM.

molecule: polyA RNA

growth_protocol: HEK293T cells were grown in standard DMEM supplemented with 10% FBS.

extract_protocol:
48 hours after transfection, cells were harvested from plates using Trypsin EDTA (Biological Industries Israel, #03-052-1A), into ice-cold standard DMEM supplemented with 10% FBS, with 100μg/ml CHX. FACS and sorting was performed on a BD FACSAria III sorter. Sorting cells into aggregate and diffused expressing  populations by the PulsA method was done essentially as described in Ramdzan et al. (2012). Sorted cells were collected directly into tubes containing ice-cold DMEM with 100μg/ml CHX. Each plate was harvested and sorted separately, and sorting time was limited to minimize toxic effects of exposure to cycloheximide. After 12 minutes of PulsA sorting, tubes containing sorted cells were centrifuged for 7 minutes at 4 °C at 300 RCF, media was removed, and the cell pellets were immediately flash-frozen in liquid nitrogen. In total, 7e6 cells were collected for each sample.
Transcriptome library preparation was performed using the Truseq RNA Library Preparation (Illumina), according to the manufacturer’s instruction.

treatment_protocol: HEK293T cells (2.5*10 6 cells per plate) were seeded on gelatin-coated 10cm plates and transfected using Lipofectamine 2000 reagent on the next day, according to the manufacturer instruction, using 24μl Lipofectamine reagent and 12μg plasmid DNA. Cells were harvested 48 hours after the transfection, when they were at approximately 70% cell confluence.

value: Human embryonic kidney 293T

tag: over-expression

tag: population

value: Aggregate expression


title: sgZNF146 rep1

description:
znf146-1
Raw_gene_counts_matrix.txt


title: HTT134Q_agg_minus_rep1

value: Diffused expression


title: HTT19Q_agg_minus_rep1


title: RNA glia_f_35_23

value: f


title: 1564-34-P

description: Subject 1564 Skin Tissue


title: sgZNF146 rep2

description:
znf146-2
Raw_gene_counts_matrix.txt


title: 158-4-P

description: Subject 158 Skin Tissue


title: AC2191

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

data_processing:
Illumina HiSeq2000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapienS.GRCh38 using STAR program (version 2.5.2a) and quantification was done using RSEM program (1.2.28)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a DESeq2.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin biopsy

extract_protocol:
Skin RNA was extracted for RNA sequencing with RNeasy Mini Kit (Qiagen, Hilden, Germany).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: Post thalidomide

tag: disease state

value: Treated

tag: disease

value: Cutaneous Lupus


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep5 [RNA-seq]

data_processing:
Fastq files were generated with CASAVA BCL2FASTQ Conversion Software.
TrimGalore (v0.6.6, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Read mapping with STAR v2.7.6a.
Normalization was done using DESeq2 v1.32.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with normalized counts for each sample.

extract_protocol:
NucleoSpin miRNA kit (Macherey-Nagel).
Ovation RNA-Seq System V2 for cDNA synthesis, amplification and purification. Libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina.

value: TGF-beta1 + SB431542


title: RNA glia_f_35_21

value: glia


title: 521_AGG_M_B14FL_3

value: diffused


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep4 [RNA-seq]

value: Skeletal muscle cells


title: AC2189


title: RNA glia_f_12_9


title: RNA glia_f_12_14


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep2 [RNA-seq]


title: 1511-2-P

description: Subject 1511 Skin Tissue

value: M

value: Skin


title: 1546-2-L

description: Subject 1546 Naevus Tissue

value: Naevus

value: Dysplastic


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep1 [RNA-seq]


title: AC2187

value: Pre thalidomide

value: Active


title: RNA glia_f_12_13


title: AC2186


title: AC2190


title: RNA glia_f_12_12


title: Human_skeletal_muscle_cells_TGFB1_rep5 [RNA-seq]


title: AC2178


title: Human_skeletal_muscle_cells_TGFB1_rep4 [RNA-seq]


title: RNA glia_f_35_20


title: Human_skeletal_muscle_cells_TGFB1_rep3 [RNA-seq]


title: 1546-19-L

description: Subject 1546 Naevus Tissue


title: Human_skeletal_muscle_cells_TGFB1_rep2 [RNA-seq]


title: 1557-3-L

description: Subject 1557 Naevus Tissue

value: F

value: Benign


title: RNA glia_f_12_11

value: f


title: AC2179

value: skin


title: 1546-2-P

description: Subject 1546 Skin Tissue


title: Human_skeletal_muscle_cells_TGFB1_rep1 [RNA-seq]


title: BS neuron_m_35_37

library_source: genomic

value: neuron

value: m


title: 1510-3-P

description: Subject 1510 Skin Tissue


title: BS neuron_m_35_38


title: 1511-2-L

description: Subject 1511 Naevus Tissue


title: 1510-3-L

description: Subject 1510 Naevus Tissue


title: 1504-3-L

description: Subject 1504 Naevus Tissue


title: Human_skeletal_muscle_cells_rep5 [RNA-seq]

value: Control


title: 1427-RC-L

description: Subject 1427 Naevus Tissue


title: Human_skeletal_muscle_cells_TGFB1_SB431542_rep3 [RNA-seq]

value: TGF-beta1 + SB431542


title: AC2176

value: Post thalidomide

value: Treated

value: Cutaneous Lupus


title: AC2177


title: BS neuron_m_35_36


title: Human_skeletal_muscle_cells_rep4 [RNA-seq]

value: Skeletal muscle cells


title: BS neuron_m_35_35


title: AC2169


title: BS neuron_m_35_39


title: AC2180


title: AC2185


title: 1501-1-P

description: Subject 1501 Skin Tissue

value: M

value: Skin


title: BS neuron_m_12_29


title: BS neuron_m_12_28


title: Human_skeletal_muscle_cells_rep2 [RNA-seq]


title: AC2184


title: AC2183


title: Human_skeletal_muscle_cells_rep3 [RNA-seq]


title: Human_skeletal_muscle_cells_rep1 [RNA-seq]


title: AC2172


title: 1504-3-P

description: Subject 1504 Skin Tissue


title: ERRBS TKO CP

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

country: China

institute: Peking University Third Hospital

description:
ERRBS
TKO_D8

data_processing:
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format

source_name: human stem cell differentiated CP

growth_protocol: For cardiac differentiation, a chemically defined monolayer differentiation protocol was used as previously described (Lian et al., 2012). Briefly, hESCs at 40% confluence were incubated with differentiation basal medium comprising RPMI 1640 medium (Invitrogen) and B27 supplement minus insulin (Invitrogen). 6uM CHIR99021 was added to the differentiation basal medium. On day 2, medium was removed and replaced with differentiation basal medium minus CHIR99021. On day 3, 5uM IWP2, the Wnt antagonist, was added to the medium.On day 5, medium was removed and replaced with differentiation basal medium without any inhibitors. On day 7, the cells were incubated with complete CM medium consisting of RPMI 1640 medium and B27 supplement plus insulin (Invitrogen). The medium was changed every 2 days. At day 9 cells were incubated with cardiac enrichment medium (RPMI 1640 without glucose (Life technologies) + 4 mM sodium L-lactate (Sigma-Aldrich). Cells were kept in enrichment medium for 3 days. After enrichment phase medium was switched back to complete CM medium (RPMI + B27).

extract_protocol:
For RRBS genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines.
Genomic DNA was submitted to the Weill Cornell Medicine Epigenomics core for eRRBS. The WCM Computational Genomics core facility supported alignment and methylation extraction for eRRBS data as described (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: No treatments were applied prior to genomic DNA extraction

tag: genotype

value: TET1/2/3 KO

tag: developmental stage

value: cardiac progenitor


title: BS neuron_m_12_27


title: BS neuron_m_12_26


title: AC2171

tag: treatment

value: Pre thalidomide

value: Active


title: AC2175


title: ERRBS TKO CME

description:
ERRBS
TKO_D3

source_name: human stem cell differentiated CME

value: cardiac mesoderm


title: BS neuron_m_12_25


title: ERRBS TKO SC

description:
ERRBS
TKO_SC

source_name: human stem cell

value: stem cell


title: ERRBS WT CM

description:
ERRBS
WT_D15

value: WT

value: cardiomyocyte


title: AC2174

value: skin


title: AC2173


title: BS neuron_f_35_19

value: neuron

value: m


title: ERRBS WT CP

description:
ERRBS
WT_D8


title: ERRBS WT CME

description:
ERRBS
WT_D3-2_BS


title: 1501-1-L

description: Subject 1501 Naevus Tissue

tag: subject

tag: age (years)

value: Naevus

value: Dysplastic


title: BS neuron_f_35_18

tag: Sex


title: BS neuron_f_35_16

value: f


title: 1427-RA-L

description: Subject 1427 Naevus Tissue

tag: tissue

tag: classification


title: 1427-RCH-P

description: Subject 1427 Skin Tissue


title: ERRBS WT SC

description:
ERRBS
WT_SC_BS


title: AC2170

value: Post thalidomide

value: Treated

value: Cutaneous Lupus


title: 1294-20-P

description: Subject 1294 Skin Tissue

value: F

value: Skin


title: 1427-RA-P

description: Subject 1427 Skin Tissue

value: M


title: USC_DK023

city: Bethesda

first: Jeffrey

middle: B

last: Kopp

state: Maryland

address: 10 Center Drive, 3N116

department: NIDDK - KDB

institute: National Institutes of Health

description: FACS-sorted for viable cells

data_processing:
Basecalling was using Illumina RTA v2.4.11
Demultiplex was using BCL2FASTQ v2.17 and allowing I mismatch in barcodes.
Alignment  initial gene and transcript counting and clustering analysis were done using Cellranger v2.2.0
Seurat v2.3.4 was used for initial data filtering  normalization and clustering  analysis.
Genome_build: hg-38
Supplementary_files_format_and_content: unfiltered Cellranger raw_gene_bc_matrices (barcodes.tsv  genes.tsv  matrix.mtx)

source_name: urine

growth_protocol: Whole urine (50 to 100 ml) samples were filtered (70 µm) and then sedimented for 10 to 15 min at 300 x g at 4 ˚C. The sediment was washed twice with ice-cold 0.04% bovine serum albumin in Dulbecco’s phosphate buffered saline and then either subjected to FACS sorting or to immediate cell capture using the 10x Genomics platform.

extract_protocol:
Extraction protocol per the manufacturer guidelines (10X Genomics  Pleasanton  CA)
10x Genomics Chromium Single Cell 5' v2 Dual Index Gene Expression

treatment_protocol: For FACS sorting  urine cells were buffer exchanged into Flow Cytometry Staining Buffer (eBioscience  Invitrogen  Carlsbad  CA)  filtered through a 40 µm filter  combined with 7AAD and HOECHST and sorted for debris-free  nucleated live cells on a BDFASC Fusion (BD Biosciences  San Jose  CA) with a 70 µm nozzle size at 70 psi sheath pressure. HOECHST7AAD-positive cells were sorted into DPBS with 10% FBS and then subjected to immediate cell capture. Urine cells were captured using the scRNA-seq using Chromium Single Cell 3’ Library & Gel Bead Kit  v2 (10x Genomics  Pleasanton  CA) and processed following exactly the supplier provided protocol.

tag: cell type

value: urine cells

tag: biopsy diagnosis

value: FSGS


title: Hi-C G2

city: Ann Arbor

first: Indika

last: Rajapakse

state: Michigan

address: 500 S State St

institute: University of Michigan

data_processing:
Library strategy: Hi-C
For RNA-seq and Bru-seq, reads were aligned using Tophat and Bowtie after checking quality with FastQC. Cufflinks/Cuffdiff was used for expression quantification. SAMtools was used to quantify SNVs.
For Hi-C, low quality ends were trimmed from raw reads by Trimmomatic. Reads were aligned using BWA, and realigned by GATK. Juicer was applied to intra-haplotype reads and normalized through the Knight-Ruiz method of matrix balancing.  HaploHiC generated inter-haplotype reads and separated the maternal and paternal reads.
Genome_build: hg19
Supplementary_files_format_and_content: csv files for RNA-seq and Bru-seq generated as described in data processing step, hic files generated using Juicer Tools and HaploHiC

source_name: Cell line

growth_protocol: We grew GM12878 cells in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For RNA-seq and Bru-seq, live cells were stained with Hoechst 33342 (Cat #B2261, Sigma-Aldrich), and then sorted by fluorescence-activated cell sorting (FACS) to obtain cell fractions at the corresponding cell cycle phases G1, S, and G2/M. For cells used in construction of Hi-C libraries, cells were crosslinked with 1% formaldehyde, the reaction was neutralized with 0.125 M glycine, then cells were stained with Hoechst and sorted into G1, S, and G2/M fractions. Cross-linked chromatin was digested with the restriction enzyme MboI for 12 hours. The restriction enzyme fragment ends were tagged with biotin-dATP and ligated in situ. After ligation, the chromatins were de-cross-linked, and DNA was isolated for fragmentation. DNA fragments tagged by biotin-dATP, in the size range of 300-500 bp, were pulled down for sequencing adaptor ligation and polymerase chain reaction (PCR).
RNA-seq library construction was carried out in the University of Michigan DNA Sequencing Core facilities facility, and sequence reads of 50-base in length were generated on an Illumina HiSeq 2500 station. We converted the Bru-labeled transcripts from the different samples into cDNA libraries and they were deep-sequenced at 50-base length on an Illumina HiSeq2500 station. The Hi-C PCR products were sequenced on an Illumina HiSeq2500 station generating reads of 125-base in length, paired-end.

value: Blood

value: B-Lymphocyte


title: 111-3-L

description: Subject 111 Naevus Tissue

value: Benign


title: BS neuron_f_12_7


title: BS neuron_f_35_15


title: BS neuron_f_35_17


title: USC_DK022

description: FACS-sorted for viable cells


title: 1325-9-P

description: Subject 1325 Skin Tissue


title: 1078-47-P

description: Subject 1078 Skin Tissue


title: USC_DK024

description: FACS-sorted for viable cells


title: 1294-20-L

description: Subject 1294 Naevus Tissue


title: 111-3-P

description: Subject 111 Skin Tissue


title: 1325-9-L

description: Subject 1325 Naevus Tissue


title: Hi-C S


title: 111-21-P

description: Subject 111 Skin Tissue


title: 111-21-L

description: Subject 111 Naevus Tissue


title: BS neuron_f_12_6


title: USC_DK021

description: FACS-sorted for viable cells


title: OVOL2 gene knockout MCF7 cells replicate 1

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MCF7 cells

extract_protocol:
Total RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MCF7 cells

tag: strain

value: Breast cancer tissue

value: OVOL2 gene knockout MCF7 cells


title: BS neuron_f_12_5

value: neuron

tag: age


title: OVOL2 gene knockout MCF7 cells replicate 2


title: USC_DK020

description: FACS-sorted for viable cells


title: 1078-100-P

description: Subject 1078 Skin Tissue


title: 1062-76-L

description: Subject 1062 Naevus Tissue

value: Naevus

value: Dysplastic


title: 1078-100-L

description: Subject 1078 Naevus Tissue


title: Bru-seq Rep 3 G2

data_processing:
Library strategy: Bru-seq
For RNA-seq and Bru-seq, reads were aligned using Tophat and Bowtie after checking quality with FastQC. Cufflinks/Cuffdiff was used for expression quantification. SAMtools was used to quantify SNVs.
For Hi-C, low quality ends were trimmed from raw reads by Trimmomatic. Reads were aligned using BWA, and realigned by GATK. Juicer was applied to intra-haplotype reads and normalized through the Knight-Ruiz method of matrix balancing.  HaploHiC generated inter-haplotype reads and separated the maternal and paternal reads.
Genome_build: hg19
Supplementary_files_format_and_content: csv files for RNA-seq and Bru-seq generated as described in data processing step, hic files generated using Juicer Tools and HaploHiC

tag: cell line


title: USC_DK015


title: wild-type MCF7 cells replicate 2

value: wild-type MCF7 cells


title: 1078-47-L

description: Subject 1078 Naevus Tissue


title: USC_DK019

description: FACS-sorted for viable cells


title: 1048-RA-P

description: Subject 1048 Skin Tissue


title: BS glia_m_35_42

value: f


title: 1062-76-P

description: Subject 1062 Skin Tissue


title: 1048-RA-L

description: Subject 1048 Naevus Tissue


title: USC_DK013


title: BS glia_m_35_41

value: glia

value: m


title: 007-155-L

description: Subject 007 Naevus Tissue


title: Bru-seq Rep 2 G2


title: Bru-seq Rep 3 G1


title: BS glia_m_35_40


title: USC_DK016

description: FACS-sorted for viable cells


title: BS glia_m_35_43


title: USC_DK012

value: Arterio-nephrosclerosis


title: Hi-C G1


title: Bru-seq Rep 2 S


title: BS glia_m_12_34


title: USC_DK014


title: Bru-seq Rep 2 G1


title: BS neuron_f_12_2


title: Bru-seq Rep 1 S


title: Bru-seq Rep 3 S


title: USC_DK010


title: USC_DK011

description: methanol-fixed


title: RNA seq TKO CP 2

description: RNA-seq

data_processing:
RNA-seq data were aligned to the hg19 reference genome. RNA seq alignment, differential gene expression analysis and GSEA were performed as described (Anelli et al., 2017). Differentially expressed genes were defined by log2 fold change greater than 2 or less than −2 and an adjusted p value < 0.01.
Genome_build: hg19

extract_protocol:
For RNA seq, total RNA was isolated with the RNeasy Mini Kit.
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: No treatments were applied prior to RNA extraction

value: TET1/2/3 KO


title: 007-152-L

description: Subject 007 Naevus Tissue

value: M


title: RNA seq TKO CP 1

description: RNA-seq


title: RNA seq WT CP 2

description: RNA-seq

value: WT


title: BS glia_m_12_33


title: RNA seq WT CP 1

description: RNA-seq


title: 007-152-P

description: Subject 007 Skin Tissue

value: Skin


title: 007-155-P

description: Subject 007 Skin Tissue


title: USC_DK009

value: urine cells

value: FSGS


title: BS glia_m_12_31


title: BS glia_m_12_32


title: RNA-seq Rep 3 G2

data_processing:
For RNA-seq and Bru-seq, reads were aligned using Tophat and Bowtie after checking quality with FastQC. Cufflinks/Cuffdiff was used for expression quantification. SAMtools was used to quantify SNVs.
For Hi-C, low quality ends were trimmed from raw reads by Trimmomatic. Reads were aligned using BWA, and realigned by GATK. Juicer was applied to intra-haplotype reads and normalized through the Knight-Ruiz method of matrix balancing.  HaploHiC generated inter-haplotype reads and separated the maternal and paternal reads.
Genome_build: hg19
Supplementary_files_format_and_content: csv files for RNA-seq and Bru-seq generated as described in data processing step, hic files generated using Juicer Tools and HaploHiC

value: Blood

value: B-Lymphocyte


title: RNA-seq Rep 3 G1


title: BS glia_m_12_30


title: BS glia_m_35_44


title: USC_DK007

value: MCD


title: Bru-seq Rep 1 G1


title: BS neuron_f_12_4

value: neuron


title: USC_DK018

description: FACS-sorted for viable cells


title: U87 cells, Rutaecarpin group 3

first: Yiyun

last: Liu

address: 18 Shuangqing Road, Haidian District, Beijing

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

data_processing:
Sequences of resulting DNA products were probed through Illumina NovaSeq 6000 by Majorbio Ltd.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Essentially, differential expression analysis was performed using the DESeq2/DEGseq/EdgeR with Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value ≤ 0.05 (DESeq2 or EdgeR) /Q value ≤ 0.001 (DEGseq) were considered to be significantly different expressed genes)
Gene ontology (GO) functional analysis was completed by Fisher's exact test using GOatools Software, and P value was adjusted by four tests (Bonferroni, Holm, Sidak and false discovery rate) to control false positive rate, when corrected P value (p_fdr) ≤ 0.05 was considered to be significant for GO enrichment.
Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway was analysed by Fisher's exact test using KOBAS software. The corrected P ≤ 0.05 was considered to be significant for KEGG enrichment.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Glioblastoma

growth_protocol: The human glioblastoma cell line U87 (purchased from Cell Resource Center, IBMS, CAMS/PUMC, Beijing, China) was cultured in Minimum Essential Medium (MEM; Gibco, Paisley, Scotland, UK), supplemented with 10% fetal bovine serum (FBS; Corning, NY, USA) and 1% penicillin–streptomycin (Gibco, Paisley, Scotland, UK). Cells were incubated at 37°C in 95% air, 5% CO2.

extract_protocol:
In order to find out the regulation of rutaecarpine on migration related genes of glioblastoma, total mRNA of U87 cells was extracted by GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to the instruction manual.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rutecarpine (10^-1 M) was dissolved in dimethyl sulfoxide (DMSO) before treatment, which were then 1000 times diluted in the serum-free medium for dosing (10-4 M). The cells incubated with 0.1% DMSO served as a control.

value: Glioblastoma cell line U87

value: Exposure to rutaecarpin for 48 hours

tag: tumor stage

value: WHO IV


title: BS glia_f_35_24


title: USC_DK006

value: Single functioning kidney with no biopsy


title: RNA-seq Rep 3 S


title: USC_DK005

description: methanol-fixed


title: USC_DK008


title: U87 cells, Rutaecarpin group 2


title: BS glia_f_35_23

value: glia

value: f


title: RNA-seq Rep 2 G1


title: USC_DK004


title: USC_DK003


title: RNA-seq Rep 1 G2


title: RNA-seq Rep 2 S


title: BS glia_f_35_21


title: BS glia_f_35_20


title: BS glia_f_12_9


title: RNA-seq Rep 1 G1


title: BS glia_f_35_22


title: RNA-seq Rep 1 S


title: U87 cells, Solvent control group 1

value: Exposure to DMSO for 48 hours


title: USC_DK001


title: RNA-seq Rep 2 G2


title: Bru-seq Rep 1 G2


title: BS glia_f_12_14


title: USC_DK002


title: FUS_wt_rep3_agg_minus

description:
processed data file:
RNA_Seq_FUS_rsem.genes.expected_count.txt.gz
RNA_Seq_FUS_rsem.genes.tpm.txt.gz
RNA_Seq_FUS_rsem.isoforms.expected_count.txt.gz
RNA_Seq_FUS_rsem.isoforms.tpm.txt.gz

value: Human embryonic kidney 293T

tag: over-expression

value: wt FUS

tag: population

value: Diffused expression


title: U87 cells, Rutaecarpin group 1


title: elav-Gal4>UAS-Chd1_2

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

data_processing:
The whole workflow was performed according to "RNA-seq workflow: gene-level exploratory analysis and differential expression"; https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
Transcript abundances were estimated using Salmon with the Drosophila melanogaster   GCF_000001215.4_Release_6_plus_ISO1_MT_rna.fna.gz transcriptome downloaded from NCBI.
Estimates were imported into R using the package tximport.
DEseq2 was used to estimate differential expression between the sample groups.
Genome_build: Release 6 plus ISO1 MT
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: excel spreadsheet ".xlsx" file contains DEseq2 results for contrasts Chd1[-/-] vs Chd1[WT/WT] and Chd1[-/-] vs elav-Gal4>UAS-Chd1.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Virgin female flies were selected and kept at 25°, 60% humidity, 12/12 hour day/night cycle on standard cornmeal food until 10 days old

extract_protocol:
Total RNA was extracted from snap frozen samples with TRI reagent following the manufacturer's protocol
Sequencing library construction was performed by BGI Corp for sequencing with the DNA nanoballs (DNB)  system.

treatment_protocol: Flies were snap frozen and decapitated. Heads were used for RNA isolation

value: Chd1-rescued, elavGal4>UAS-Chd1

value: head

value: female


title: elav-Gal4>UAS-Chd1_3


title: U87 cells, Solvent control group 3


title: U87 cells, Solvent control group 2


title: FUS_wt_rep2_agg_minus


title: TH284

city: Shenzhen

first: Xingzheng

last: Li

state: Guangdong

address: Pengfei campus

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

data_processing:
Raw reads were preprocessed by fastp for quality control
Mapping to the duck (Anas platyrhynchos) reference genome assembly CAU_duck1.0 using HISAT2
Aligned reads were assembled and transcript abundances were quantified by StringTie
Raw transcript counts were extracted by python script prepDE.py
Genome_build: CAU_duck1.0
Supplementary_files_format_and_content: Matrix table with raw transcript counts for every transcript and every sample

organism: Anas platyrhynchos

source_name: Liver

extract_protocol:
Total RNA was isolated from the right liver tissue using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific)
The libraries were sequenced on an Illumina HiSeq2000 platform generating 2×150 bp paired-end reads

value: Jingjiang duck

value: liver

value: 72 wks

value: 4000 mg/kg choline chloride

tag: tma


title: BS glia_f_12_13


title: elav-Gal4>UAS-Chd1_1

tag: genotype


title: FUS_521_agg_plus_rep3

value: Aggregate expression


title: wild-type MCF7 cells replicate 1

value: MCF7 cells

value: Breast cancer tissue

value: wild-type MCF7 cells


title: TH072


title: TH116


title: BS glia_f_12_11

value: glia


title: BS glia_f_12_12

value: f


title: FUS_521_agg_minus_rep3


title: FUS_521_agg_plus_rep1


title: TH004


title: Chd1[-/-]_1


title: FUS_521_agg_minus_rep1


title: Chd1[-/-]_3


title: Chd1[-/-]_2


title: Glast-CreERT2;Ptbp1-HET;Sun1-GFP, Retina

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: 10x Genomics V3.1

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq count matrix

source_name: scRNA-Seq - HET

extract_protocol: scRNA-Seq following 10x V3.1 guideline

value: Retina

value: 2 months old

value: Female


title: TH283


title: Chd1[WT/WT]_3

value: wildtype


title: CL210


title: Glast-CreERT2;Ptbp1-WT;Sun1-GFP, Retina

description: 10x Genomics V3.1

source_name: scRNA-Seq - WT


title: Glast-CreERT2;Ptbp1-HOM;Sun1-GFP, Retina

description: 10x Genomics V3.1

source_name: scRNA-Seq - KO


title: CL209


title: TH024


title: Chd1[WT/WT]_2


title: FUS_518_agg_plus_rep1

value: Human embryonic kidney 293T


title: CL177


title: Chd1[WT/WT]_1

value: head


title: FUS_518_agg_plus_rep2


title: FUS_518_agg_minus_rep2

value: Diffused expression


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Substantia Nigra

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKD4

value: Substantia Nigra


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Substantia Nigra

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKD3


title: FUS_518_agg_minus_rep1


title: HTT134Q_agg_plus_rep2


title: HTT19Q_agg_minus_rep2


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Substantia Nigra

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKD2


title: Rv1_Des2

first: Jin-Tang

middle: and

last: Dong

address: 1088 Xueyuan Blvd., Research Building 2B

institute: Southern University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and gene countsfor each Sample ...

source_name: prostate cancer

extract_protocol:
Remove the supernatant and wash with PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

value: prostate cancer cells

value: treated with deslanoside for 48 hours


title: CL001

value: Jingjiang duck

value: liver

value: 72 wks

value: 4000 mg/kg choline chloride


title: TH296


title: CL021


title: HTT134Q_agg_minus_rep2


title: TH294


title: Rv1_C3

value: untreated


title: Rv1_C2


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Substantia Nigra -tech replicate

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKD4a


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Striatum

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKC8

value: Striatum


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Striatum

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKC9


title: hACE2 + SARS-CoV-2 rep2

city: Jerusalem

first: Lior

last: Nissim

address: Hadassah Medical School, Hadassah Ein-Kerem

department: Biochemistry and Molecular Biology

institute: The Hebrew University of Jerusalem

data_processing:
Quality and adapter trimming with cutadapt, v2.10, using parameters -q 32,32 -O 1 --match-read-wildcards -m 15.
Filtering low quality reads with fastq_quality_filter (FASTX package, v0.0.14), using parameters -q 20 -p 90.
Alignment with TopHat, v2.1.1, using parameters -G genes.gtf (from Ensembl release 99) -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 18 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-firststrand.
Counts per gene with htseq-count, v0.12.4, using parameters -s 'reverse' and genes from Ensembl release 99, including the viral and exogenous genes.
Genes with less than 6 reads were discarded prior to normalization with DESeq2, v1.22.2. Differential expression (with DESeq2) was done with default parameters except setting independentFiltering=F. Two models were used, either dividing samples to w/wo SARS-CoV-2 (the exposure model), or further dividing samples with SARS-CoV-2 to ones with the hACE2 gene and ones without it (the infection model).
Genome_build: GRCm38, supplemented with SARS-CoV-2 and two genes from lenti vectors
Supplementary_files_format_and_content: DESeq2_res.txt, a tab-delimited text file with a header line, followed by data (one line per gene) for mouse genes, SARS-Cov-2 genes, and the introduced genes of control and hACE2 lentiviruses. First 9 columns have general details; next 7 columns have raw counts; 7 columns after that have normalized counts; then a column for the mean expression; followed by 6 columns of DESeq2 results for each comparison.

source_name: Lung

extract_protocol:
RNA-sequencing  Mice lungs were stored at -70oC in RNALater (Sigma Aldrich) then total RNA was isolated using RNeasy preparation kit (Qiagen) according to the manufacturer protocol. RNA was stored frozen (-70oC) until used.   RNA quality was evaluated in TapeStation, using RNA ScreenTape kit (Agilent Technologies), and quantified in Qubit apparatus (Qubit® DNA HS Assay kit, Invitrogen). Libraries for RNA-sequencing were prepared using the ribosomal depletion method, due to low RNA integrated number (RIN) that was between 6 and 7. Libraries were prepared from 10 ng RNA using SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian according to manufacturer’s recommendations. The libraries were barcoded and pooled for multiplex sequencing (1.5 pM total including 1.5% PhiX control library). The pooled DNA was loaded on NextSeq 500 High Output v2 kit (75 cycles) cartridge (Illumina) and sequenced on Illumina NextSeq 500 System, using sequencing conditions of 75 cycles, single-read and sequencing at least 35 million reads per sample.   Reads were aligned to the mouse genome, GRCm38, supplemented with the human ACE2 sequence (NM_021804.3), the mKate2 sequence (from Addgene), and the SARS-CoV-2 sequence (EPI_ISL_406862).   Differential expression analysis was performed using the DESeq2 package. Normalized counts were used for several quality control assays, such as counts distributions and principal component analysis, which were calculated and visualized in R. Those assays showed sample Lenti-hACE2_1 to be an outlier and it was thus removed from the analysis.   Pair-wise comparisons were tested with default parameters, but not using the independent filtering algorithm, with two different models: (1) The exposure model (divided into two groups), and (2) The infection model (divided into 3 groups), as described in the tables below:   The exposure model  Sample Group Lentiviral Transgene SARS-  CoV-2 Productive  SARS-CoV-2  Replication Manuscript  Annotation  Lenti-control_1 1 mKate2  (RFP) - - Lenti-control  Lenti-control _2 1 mKate2  (RFP) - - Lenti-control  Lenti-hACE2_2 1 hACE2 - - Lenti-hACE2  Lenti-control/SARS-CoV-2(dpi 2) 2 mKate2  (RFP) + - Lenti-control/SARS-CoV-2  Lenti-control/SARS-CoV-2(dpi 4) 2 mKate2  (RFP) + - Lenti-control/SARS-CoV-2  Lenti-hACE2/SARS-CoV-2(dpi 2) 2 hACE2 + + Lenti-hACE2/SARS-CoV-2  Lenti-hACE2/SARS-CoV-2(dpi 4) 2 hACE2 + + Lenti-hACE2/SARS-CoV-2    The infection model  Sample Group Lentiviral Transgene SARS-CoV-2 SARS-CoV-2  Replication Manuscript  Annotation  Lenti-control_1 1 mKate2  (RFP) - - Lenti-control  Lenti-control_2  1 mKate2  (RFP) - - Lenti-control  Lenti-hACE2_2 1 hACE2 - - Lenti-hACE2  Lenti-control/SARS-CoV-2(dpi 2) 2 mKate2  (RFP) + - Lenti-control/SARS-CoV-2  Lenti-control/SARS-CoV-2(dpi 4) 2 mKate2  (RFP) + - Lenti-control/SARS-CoV-2  Lenti-hACE2/SARS-CoV-2(dpi 2) 3 hACE2 + + Lenti-hACE2/SARS-CoV-2   Lenti- hACE2/SARS-CoV-2(dpi 4) 3 hACE2 + + Lenti-hACE2/SARS-CoV-2    For each pair-wise comparison, genes were defined as significant if their adjusted p-value (padj) was less than 0.1 (DESeq2's default), their mean expression was above 5, and their absolute fold-change was large enough, in a mean expression-dependent manner (|log2FoldChange| > 5/sqrt(baseMean) + 0.3). The latter condition gave weight to the expression levels of the genes, so that highly expressed genes required a fold-change of at least 1.2, while genes with a very low expression level would need a 5.8-fold change to pass the filtering.  All the differential expression data were subjected to gene set enrichment analysis using GSEA (https://pubmed.ncbi.nlm.nih.gov/16199517/). GSEA uses all differential expression data (cutoff independent) to determine whether a priori defined sets of genes show statistically significant, concordant differences between two biological states. We used the following gene sets collections: Hallmark, Gene Ontology (GO), and REACTOME, all taken from the molecular signatures database MSigDB (v7.2 September 2020). In addition, we used a collection of cell type markers, extracted from the following databases: PanglaoDB (https://panglaodb.se/index.html); CIBERSORT (https://cibersort.stanford.edu/); and ImmGen (https://www.immgen.org/).
Ribosomal RNA depletion, followed by SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian according to manufacturer’s recommendations.

treatment_protocol: SARS-CoV-2  SARS-CoV-2 (GISAID accession EPI_ISL_406862) was kindly provided by Bundeswehr Institute of Microbiology, Munich, Germany. Virus stocks were propagated (four passages) on Vero E6 cells (Yahalom-Ronen et al., 2020). Handling and working with SARS-CoV-2 virus was conducted in a BSL3 facility in accordance with the biosafety guidelines of the Israel Institute for Biological, Chemical and Environmental Sciences (IIBR).  For titration of SARS-CoV-2, Vero E6 cells were seeded in 12-well plates (5×105 cells/well) and grown overnight in growth medium. Serial dilutions of SARS-CoV-2 were prepared in infection medium (MEM containing 2% FBS with NEAA, glutamine, and P/S/N), and used to infect Vero E6 monolayers in triplicates (200 µl/well). Plates were incubated for 1 h at 37°C to allow viral adsorption. Then, 2 ml/well of overlay [MEM containing 2% FBS and 0.4% tragacanth (Merck, Israel)] was added to each well, and plates were incubated at 37°C, 5% CO2 for 72 h. The media were then aspirated, and the cells were ﬁxed and stained with 1 ml/well of crystal violet solution (Biological Industries, Israel). The number of plaques in each well was determined, and the SARS-CoV-2 titer was calculated.    Mouse experiments  The animal model for SARS-CoV-2 was established by intranasal (i.n.) instillation of the lentiviruses (hACE2 or control) and three days later were similarly infected by i.n. instillation with SARS-CoV-2. Instillations were performed on anesthetized [intraperitoneal ketamine (160 mg/kg) with xylazine (6 mg/kg)] 12-14-week-old IFNAR1-/- female mice (The Jackson Laboratory). SARS-CoV-2 was diluted in PBS supplemented with 2% FBS (PBF) (Biological Industries, Israel). Mice body weight was monitored daily. All animal experiments involving SARS-CoV-2 were conducted in a BSL3 facility in accordance with the guidelines of the IIBR Institutional Animal Care and Use Committee (M-67-20). Lungs were harvested 5 dpi and stored at −80°C for viral load determination. For RNA-seq. analyses, lungs were excised and incubated in RNALater (Sigma-Aldrich) for 5 days at -70oC before RNA preparation. For viral load determination, lungs were processed as described (Israely et al., 2012), and infectious virus quantitation was performed by plaque assay. Viral load, as well as LOD, were calculated based on volume of cell infection, dilution factor, and tissue processing volume, and presented as pfu/organ.

value: IFNAR1-/-female mice (The Jackson Laboratory)

value: SARS-CoV-2(dpi 4)

tag: lentivirus


title: CL114

tag: treatment


title: TH293


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Cortex

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKC7

value: Cerebral cortex

value: 2 months old


title: Rv1_C1


title: Rv1_Des3


title: TH292


title: hACE2 + SARS-CoV-2 rep1

value: SARS-CoV-2(dpi 2)


title: PC3_Des3


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Cortex

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKC6

value: Female


title: PC3_Des2


title: TH286


title: Control + SARS-CoV-2 rep2

value: control


title: Rv1_Des1


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Striatum

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKD1


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Cortex

description: 10x Genomics V3.1

source_name: scRNA-Seq - TKC5


title: Control + SARS-CoV-2 rep1


title: PC3_Des1


title: hACE2 no SARS-CoV-2 rep1

value: No


title: PC3_C2


title: CL105


title: PC3_C1


title: Control no SARS-CoV-2 rep1


title: CL030


title: TRV_empty rep2

city: Manhattan

first: David

middle: E

last: Cook

state: KS

address: 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center

department: Plant Pathology

institute: Kansas State University

data_processing:
Reads were trimmed for sequencing adapters and quality filtered , then aligned to the Nicotiana benthamiana genome (version1.0.1, custom modified) using STAR.
Note, a custom version of the genome was used for alignment, in which a paralog of the PDS coding sequence (contig Niben101Scf14708, position 12885-21779, gene23) was masked. Also, the Cas13 coding sequence was added a an additional contig.
Reads uniqley mapping to the PDS transcript (contig Niben101Scf01283, position 197129-205076, gene 2002) were extracted using samtools and bedtools, and summarized per sample.
Per base read counts were normalized by the number of uniqley mapping reads per library as: (number of reads mapped at a nucleotide position) * (1 / number of uniquely mapped reads in library) * 1M
Genome_build: Nicotiana benthamiana, version 1.0.1, with following modifications- contigs smaller than 70K nt were removed, PDS paralog at contig Niben101Scf14708, position 12885-21779, gene23 was masked, and a contig was added corresponding to the Lbu Cas13a coding sequence. 7385 contigs in total.
Supplementary_files_format_and_content: CSV file with the per-base level sRNA mapping counts over the PDS exon

organism: Nicotiana benthamiana

source_name: TRV infected young upper leaves

extract_protocol:
Leaf tissue from agroinfiltrated area were collected and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol protocol.
DNBseq Small RNA Library, BGI Tech Solutions. Breifly, total RNA is size seperated (18-30nt) using PAGE and size selection. Adapters are ligated and first strand synthesis following BGI protocol. Libraries were PCR amplified, size selected and sequenced using the DNBseq platform.

value: Upper leaves following systemic TRV infection

value: two-weeks following TRV infiltration

tag: replicate

value: TRV alone control

tag: group

value: vector control


title: Basophil papain6

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

source_name: Basophil of papain treated mice's lung

extract_protocol:
Lung were removed, stained  ILC2 cells, epithlial cells, or basophils were sorted using flow cytometer, and RNA was harvested using Trizol reagent. Lexogen 3'mRNA-seq library prep kit (Cat#015) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen 3'QuantSeq standard protocols

treatment_protocol: Mice were intraperitoneally injected with FK506 (Cayman Chemical, Ann Arbor, MI, USA) for 3 consecutive days (0.2 mg in 100 µL of methyl cellulose/head/day). Two days after the last FK506 administration, the mice were intraperitoneally administered FK506 for another 3 consecutive days (0.2 mg/head/day) and intranasally administered papain (50 µg in 40 µL of PBS/head/day; Sigma-Aldrich, St. Louis, MO, USA).

value: Lung

value: 8 weeks

value: WT

value: papain


title: Basophil papain + FK506-7

source_name: Basophil of papain + FK506 treated mice's lung

value: papain + FK506


title: Basophil papain + FK506-8


title: PBS-ST naïve CD4 3

city: Boston

first: Eunha

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

data_processing:
ATAC-seq: after removal of adaptors by NGmerge (6), sequencing reads were aligned to the Mus musculus 10 (mm10, downloaded from ENSEMBL), using bowtie2 (v2.3.4.3) (7) using --very-sensitive parameter. PCR duplicates were removed using Picard (v2.8.0). Reads mapped to mitochondrial DNA were excluded by removeChrom.py, and non-uniquely mapped reads were also removed by mapping quality score < 10 with samtools (v1.9). Peaks were identified using the MACS peak caller.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq: Narrowpeak file from MACS2

source_name: Naïve CD4+ T cells

extract_protocol: ATACseq: naïve CD4+ T cells were isolated from spleen and lymph nodes by FACS

value: CD4 T cells

tag: tissue origin

value: Spleen and lymphnoids originated

value: naive CD4 T cells


title: Basophil papain5

tag: tissue


title: TRV_empty rep1


title: CL020

source_name: Liver

value: Jingjiang duck

value: liver

value: 72 wks

value: 4000 mg/kg choline chloride


title: Basophil control1,2

source_name: Basophil of untreated mice's lung

value: untreated


title: CL015


title: PC3_C3

value: prostate cancer cells


title: TH253


title: TRV_non-targeting(NT)-guide rep2

value: Upper leaves following systemic TRV infection

value: two-weeks following TRV infiltration

value: NT-guide guide-alone silencing control

value: guide-alone control


title: CL014


title: TH130


title: Basophil papain4

value: Lung

value: 8 weeks


title: PBS-ST naïve CD4 1


title: TH211


title: TRV_non-targeting(NT)-guide rep1


title: hACE2 no SARS-CoV-2 rep2

value: IFNAR1-/-female mice (The Jackson Laboratory)

value: No


title: Control no SARS-CoV-2 rep2

value: control


title: MIA-ST naïve CD4 3

value: CD4 T cells

value: Spleen and lymphnoids originated


title: Basophil papain + FK506-9

value: WT

value: papain + FK506


title: CL006

value: Jingjiang duck

value: liver

value: 72 wks


title: TRV_multi-guide 1 (PDS) rep2

value: multi-guide1 guide-alone silencing for PDS

value: guide-alone


title: MIA-ST naïve CD4 2

value: naive CD4 T cells


title: CL005

value: 4000 mg/kg choline chloride


title: ILC2 of papain + FK506 treated mice's lung2


title: CL003


title: ILC2 of papain + FK506 treated mice's lung1


title: TRV_mutli-guide 1 (PDS) rep1

value: Upper leaves following systemic TRV infection

value: two-weeks following TRV infiltration


title: MIA-ST naïve CD4 1


title: TRV_multi-guide 2 (PDS) rep2

value: multi-guide2 guide-alone silencing for PDS


title: PBS-ST naïve CD4 2


title: ILC2 of papain treated mice's lung3

source_name: ILC2 of papain treated mice's lung

value: Lung

value: 8 weeks

value: papain


title: TRV_mutli-guide 2 (PDS) rep1


title: 001179_S3

city: West lafayette

first: Michael

last: Scharf

state: IN

address: 901 W State St

department: Entomology

institute: Purdue University

description: Whole body mRNA, control line, rep 3

data_processing:
Sequencing reads were filtered using Phred quality scores and other parameters, and de novo transcriptome assembly performed from all six pooled replicate samples (3 selected and 3 control) using Trinity (Grabherr et al 2011).
Paired reads for individual replicate samples were then mapped to the de novo transcriptome using Bowtie2 (Langmead & Salzberg 2012), which provided read counts used for differential expression analyses
Genome_build: German_cockroach_Trinity.fasta
Supplementary_files_format_and_content: transcriptome assembly fasta file and gene expression counts Excel file

organism: Blattella germanica

source_name: AP strain - inbred control

growth_protocol: Insects were reared under standard laboratory conditions on a diet of Harlan-Teklad 7409 rodent chow, unlimited water, 12:12 light:dark, 25 degrees C and ~65% RH.

extract_protocol:
Total RNA was isolated from three independent biological replicate samples of 10 whole adult male cockroaches from each of F6-selected and control lines. A two-step process was used that included the Promega SV Total RNA Isolation Kit (Madison, WI, USA) followed by the Bioline TRIsure kit (Tuanton, MA, USA). DNase treatment was included as the final step for the first kit only.  The use of two kits ensured the RNA samples were free of excess protein. Total RNA yields ranged from 5.8–18.6 µg with A260/280 and 260/230 ratios in the range of 1.8–2.1. Sample quality was further assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) which verified above yields and provided acceptable RIN scores of 7.20-7.76.
RNA samples were enhanced for messenger RNA (mRNA) using the Agilent Tru-Seq RNA prep kit before bar-coded sequencing libraries were made. Sequencing was done on the Illumina HiSeq 2000 platform by the Purdue University Genomics Core (West Lafayette, IN, USA).

treatment_protocol: Treatment of the selected lines consisted of 60-80% selection of 4-5th instar nymphs over 5 generations with indoxacarb in bait matrix

value: 6th generation

value: whole body

value: inbred control


title: CD45.2 MIA CD4 4

data_processing:
RNA-seq: Quantification of gene expression was done by a lightweight alignment tool, Salmon (Patro, Rob, et al. “Salmon provides fast and bias-aware quantification of transcript expression.” Nature Methods (2017)) with kmer 31
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Salmon quantification files (Patro, Rob, et al. “Salmon provides fast and bias-aware quantification of transcript expression.” Nature Methods (2017));

source_name: Retrived CD4+, TCRb+ cells from mesenteric lymph nodes

extract_protocol:
Cells extracted from mesenteric lymph nodes and sort for CD4 and TCRb + followed by ULI-RNA seq protocol at Immgen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD4 T cells

value: Mesenteric lymph nodes retrieved transferred CD4 T cells


title: ILC2 of papain + FK506 treated mice's lung3

value: WT

value: papain + FK506


title: CD45.2 MIA CD4 2


title: ILC2 of papain treated mice's lung1


title: TRV_antiSense_PDS rep2

value: anti-sense fragment to PDS transcript

value: RNAi


title: CD45.2 MIA CD4 3


title: TRV_antiSense_PDS rep1


title: 001178_S2

description: Whole body mRNA, control line, rep 2


title: TRV_single-guide 1 (PDS) rep2

value: single-guide guide-alone silencing for PDS

value: guide-alone


title: 001176_P3

description: Whole body mRNA, selected line, rep 3

source_name: AP strain - indoxacarb selected

value: indoxacarb selected


title: CD45.1 PBS CD4 4


title: ILC2 of untreated mice's lung2

source_name: ILC2 of untreated mice's lung

value: untreated


title: 001177_S1

description: Whole body mRNA, control line, rep 1


title: ILC2 of untreated mice's lung3


title: CD45.2 MIA CD4 1


title: TRV_single-guide 1 (PDS) rep1

value: Upper leaves following systemic TRV infection

value: two-weeks following TRV infiltration


title: ILC2 of untreated mice's lung1

value: Lung

value: 8 weeks


title: CD45.1 PBS CD4 3


title: Cas13a plus non-targeting(NT)-guide rep2

source_name: agroinfiltrated leaf

value: agrobacterium infiltrated leaf tissue

value: five days post infiltration

value: Cas13 protein and non-targeting-guide

value: protein control


title: AEC1 of papain + FK506 treated mice's lung2


title: CD45.1 PBS CD4 2

value: CD4 T cells

value: Mesenteric lymph nodes retrieved transferred CD4 T cells


title: 001174_P1

description: Whole body mRNA, selected line, rep 1

value: 6th generation

value: whole body


title: Cas13a plus non-targeting(NT)-guide rep1


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water 3

type: RNA

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description: Gene expression data of hippocampus microvessels from male WT mice fed with high glycemic diet (HGD) with sEHI treated water

hyb_protocol: Following fragmentation and labeling, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on the Mouse Gene 2.0 ST Array using Affymetrix WT array hybridization protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Analyses of gene expression levels were performed with Transcriptome Analysis Console software version 4.0.2.

label: biotin

source_name: Male Mice brain hippocampus microvessels

label_protocol: 122 pg of total RNA was used to prepare cRNA according to Affymetrix's GeneChip® WT Pico Kit protocol. Biotinylated sscDNA (5.5 ug) were prepared from 20 ug of cRNA.

growth_protocol: Male mice were housed in single cages in a temperature- and humidity-controlled environment with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from the laser-captured hippocampal brain microvessels from each of the four experimental groups using an Arcturus PicoPure™ RNA Isolation Kit according to the manufacturer’s instructions.

treatment_protocol: 20 week old wild type male mice were fed a low glycemic diet (LGD), or a high glycemic diet (HGD) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks.

tag: agent

value: high glycemic diet (HGD)

tag: diet

value: sEHI


title: AEC1 of papain + FK506 treated mice's lung1

value: WT

value: papain + FK506


title: ILC2 of papain treated mice's lung2

value: papain


title: AEC1 of papain treated mice's lung2

source_name: AEC1 of papain treated mice's lung


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water 1


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water 2


title: CD45.1 PBS CD4 1

tag: cell type


title: PBS naïve CD4 3

tag: strain

value: Spleen and lymphnoids originated naïve CD4 T cells


title: Hairpin against PDS rep1

tag: age

value: Hairpin targeting PDS

value: RNAi


title: Hairpin against PDS rep2


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water 3

description: Gene expression data of hippocampus microvessels from male WT mice fed with low glycemic diet (LGD) with sEHI treated water

value: low glycemic diet (LGD)


title: MIA naïve CD4 3


title: empty plus multi-guide 2 (PDS) rep2

value: agrobacterium infiltrated leaf tissue

value: multi-guide 2 targeting PDS

value: guide-alone


title: AEC1 of papain treated mice's lung1

value: Lung

value: 8 weeks


title: 001175_P2

description: Whole body mRNA, selected line, rep 2

value: indoxacarb selected


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water 2


title: AEC1 of untreated mice's lung2

source_name: AEC1 of untreated mice's lung

value: untreated


title: empty plus multi-guide 2 (PDS) rep1

value: five days post infiltration


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water 1


title: MIA naïve CD4 2

value: CD4 T cells


title: PBS naïve CD4 2


title: AEC1 of untreated mice's lung1


title: Cas13a plus multi-guide 2 (PDS) rep2

value: Cas13 protein and multi-guide 2 targeting PDS

value: protein plus guide


title: AEC2 of papain + FK506 treated mice's lung2

value: WT

value: papain + FK506


title: WT mice fed with high glycemic diet (HGD) 3

description: Gene expression data of hippocampus microvessels from male WT mice fed with high glycemic diet (HGD)

value: high glycemic diet (HGD)


title: KO rep2

city: St. Louis

first: Wei-Le

last: Wang

state: MO

address: BJCIH, 8th Floor, Room 8107, 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University

data_processing:
Illumina Casava software was used for basecalling.
Sequence reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using HISAT aligner.
Normalized counts per million of library size (CPM) per gene were measured using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.

source_name: Treg cells

growth_protocol: Total RNA was extracted from primary murine Treg cells

extract_protocol:
Total RNA was isolated using miRNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sorted Treg cells were subjected to RNA extraction without treatment

tag: organ

value: Spleen

value: Treg

tag: gender

value: Female

value: miR-142 KO


title: empty plus single-guide 1 (PDS) rep2

value: agrobacterium infiltrated leaf tissue

value: single guide 1 targeting PDS


title: AEC2 of papain treated mice's lung2

source_name: AEC2 of papain treated mice's lung

value: Lung

value: papain


title: Cas13a plus multi-guide 2 (PDS) rep1


title: KO rep3


title: WT mice fed with high glycemic diet (HGD) 2


title: KO rep1


title: AEC2 of papain + FK506 treated mice's lung1

value: 8 weeks


title: WT mice fed with high glycemic diet (HGD) 1


title: WT mice fed with low glycemic diet (LGD) 3

description: Gene expression data of hippocampus microvessels from male WT mice fed with low glycemic diet (LGD)

value: low glycemic diet (LGD)


title: AEC2 of papain treated mice's lung1


title: WT rep3


title: AEC2 of untreated mice's lung2

source_name: AEC2 of untreated mice's lung

value: untreated


title: empty plus single-guide 1 (PDS) rep1

value: five days post infiltration

value: guide-alone


title: WT rep2


title: WT mice fed with low glycemic diet (LGD) 1


title: WT rep1


title: m-z-Dppa4_2C_polyA_3

status: Public on Dec 06 2021

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description:
Dppa4_mzKO_single28hpf2C_6_polyARNA_S4
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt

data_processing:
Both total RNA-seq and polyA RNA-seq reads were trimmed using Trimgalor (v. 0.4.5). For total RNA-seq, reads that were mapped to rRNA/tRNA were also removed.
Cleaned RNA-seq reads were aligned to mouse mm10 using Hisat2 (v. 2.1.0) (--sp 1000, 1000 --no-mixed --no-discordant --known-splicesite-infile mm10.splice.site.txt)
Stringtie (v. 1.3.3b) was used to gnereate FPKM values for each gene in the samples.
For total RNA-seq, "--rna-strandness RF" option was used for Hisat2 and  "--rf" option was used for Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: tab-deliminated txt files of FPKM values

source_name: embryo

extract_protocol:
Embryos were lysised and the lysates were used as input for RNA-seq library constructions.
The total RNA-seq libraries were prepared using the SMARTer-Seq Stranded kit (Takara). For polyA RNA-seq, cDNA was synthesized using the SMARTer Ultra low Input RNA cDNA preparation kit (Takara) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

tag: developmental stage

value: late 2-cell (28hpf)

tag: library type

value: non-stranded poly-A RNA


title: m-z-Dppa4_2C_polyA_1

description:
Dppa4_mzKO_single28hpf2C_10_polyARNA_S5
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa4_2C_polyA_1

description:
Dppa4_Het_single28hpf2C_1_polyARNA_S1
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa4_2C_polyA_3

description:
Dppa4_Het_single28hpf2C_5_polyARNA_S3
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: WT mice fed with low glycemic diet (LGD) 2


title: Cas13a plus single-guide 1 (PDS) rep1

value: Cas13 protein and single-guide 1 targeting PDS

value: protein plus guide


title: m-z-Dppa2_2C_polyA_3

description:
Dppa2_mzKO_single28hpf2C_5_polyARNA_S4
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt

value: B6/DBA mixed background


title: m-z-Dppa4_2C_polyA_2

description:
Dppa4_mzKO_single28hpf2C_11_polyARNA_S6
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa2_2C_polyA_3

description:
Dppa2_Het_single28hpf2C_9_polyARNA_S6
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z-Dppa2_2C_polyA_2

description:
Dppa2_mzKO_single28hpf2C_4_polyARNA_S3
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa4_2C_polyA_2

description:
Dppa4_Het_single28hpf2C_2_polyARNA_S2
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa4_2C_totalRNA_2

description:
Dppa4_mKO_late2C_28hpf_totalRNA_rep2_S12
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt

value: reverse-stranded total RNA


title: m-z+Dppa4_1C_totalRNA_1

description:
Dppa4_mKO_late1C_12hpf_totalRNA_rep1_S10
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt

value: late 1-cell (12hpf)


title: m-z-Dppa2_2C_polyA_1

description:
Dppa2_mzKO_single28hpf2C_2_polyARNA_S2
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa4_1C_totalRNA_2

description:
Dppa4_mKO_late1C_12hpf_totalRNA_rep2_S2
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: WT_1C_polyA_1

description:
Dppa4_CTR_single12hpf1C_2_polyARNA_S12
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: Cas13a plus single-guide 1 (PDS) rep2


title: AEC2 of untreated mice's lung1

value: WT


title: m-z+Dppa4_2C_totalRNA_1

description:
Dppa4_mKO_late2C_28hpf_totalRNA_rep1_S4
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa4_1C_totalRNA_2

description:
Dppa4_CTR_late1C_12hpf_totalRNA_rep2_S1
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: WT_2C_polyA_2

description:
Dppa4_CTR_single28hpf2C_2_polyARNA_S14
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa2_2C_polyA_2

description:
Dppa2_Het_single28hpf2C_7_polyARNA_S5
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m+z+Dppa4_1C_totalRNA_1

description:
Dppa4_CTR_late1C_12hpf_totalRNA_rep1_S9
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: WT_1C_polyA_2

description:
Dppa4_CTR_single12hpf1C_3_polyARNA_S11
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa2_2C_totalRNA_2

description:
Dppa2_mKO_late2C_28hpf_totalRNA_rep2_S20
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m-z+Dppa2_2C_polyA_1

description:
Dppa2_Het_single28hpf2C_1_polyARNA_S1
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: m-z+Dppa2_2C_totalRNA_1

description:
Dppa2_mKO_late2C_28hpf_totalRNA_rep1_S2
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa4_2C_totalRNA_2

description:
Dppa4_CTR_late2C_28hpf_totalRNA_rep2_S11
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa4_2C_totalRNA_1

description:
Dppa4_CTR_late2C_28hpf_totalRNA_rep1_S3
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m-z+Dppa2_1C_totalRNA_1

description:
Dppa2_mKO_late1C_12hpf_totalRNA_rep1_S17
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa2_2C_totalRNA_2

description:
Dppa2_CTR_late2C_28hpf_totalRNA_rep2_S19
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m-z+Dppa2_1C_totalRNA_2

description:
Dppa2_mKO_late1C_12hpf_totalRNA_rep2_S18
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa2_2C_totalRNA_1

description:
Dppa2_CTR_late2C_28hpf_totalRNA_rep1_S1
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa2_1C_totalRNA_1

description:
Dppa2_CTR_late1C_12hpf_totalRNA_rep1_S15
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: m+z+Dppa2_1C_totalRNA_2

description:
Dppa2_CTR_late1C_12hpf_totalRNA_rep2_S16
processed data file: Dppa2_Dppa4_totalRNAseqFPKM.txt


title: WT_2C_polyA_1

description:
Dppa4_CTR_single28hpf2C_1_polyARNA_S13
processed data file: Dppa2_Dppa4_PolyARNAseqFPKM.txt


title: Gcn4 G-SELEX Round 3 Replicate 1

first: Christopher

last: Coey

state: MD

address: 6 Center Drive Bldg 6A 2A02

institute: National Institute of Child Health and Human Development

description: 20180702 replicate of yeast DNA fragments incubated for 3 rounds in the presence of recombinant Gcn4

data_processing:
Library strategy: G-SELEX
Reads trimmed using cutadapt 3.4 python module to remove Illumina adapter sequences
Reads aligned to sacCer3 reference genome with Bowtie2 2.4.4
Reads in ChrXII ribosomal DNA region (nt 451000 - nt 469000) are removed due to repetitive elements, using R 4.0.0
Coverage (Gcn4 occupancy) is normalized to the chromosomal average (set at 1) using an R 4.0.0 script.
bigWig files for viewing in IGV were generated from normalized coverage using an R 4.0.0 script
Genome_build: sacCer3
Supplementary_files_format_and_content: The data in the bigWig files represent normalized base coverage at each nucleotide (Gcn4 occupancy). Normalized to the chromosome average (set at 1).

organism: Saccharomyces cerevisiae

source_name: Log-phase Saccharomyces cerevisiae cells in synthetic complete medium

growth_protocol: Grown in SC medium to log-phase (optical density at 600 nm of 0.5 - 1.0)

extract_protocol:
The sonicated DNA was gel purified to isolate fragments < 200 base pairs in length
Gel-purified DNA fragments were ligated to the Illumina paired-end adaptor and amplified with InPE 1.0 and InPE 2.0 (Illumina) primers as described in kits from New England Biolabs.
G-SELEX - incubation with protein of interest, followed by washing and elution of DNA bound to protein.  Bound DNA is PCR amplified and subjected to 2 subsequent incubation rounds (3 total) before Illumina paired-end sequencing

treatment_protocol: Cells were cross-linked with formaldehyde, lysed, sonicated, and washed before cross-linking was reversed and DNA was extracted.

value: YDC 111 strain

tag: growth phase

value: Log-phase

value: Incubated with recombinant Gcn4 bound to HisPur Ni-NTA magnetic beads for 3 rounds


title: YDC 111 Input DNA Mock control

description: Genomic DNA incubated with empty magnetic beads for 3 rounds

value: Incubated with washed HisPur Ni-NTA magnetic beads (no protein) for 3 rounds


title: Gcn4 G-SELEX Round 3 Replicate 2

description: 20180711 replicate of DNA incubated for 3 rounds in the presence of recombinant Gcn4


title: YDC 111 Input DNA

description: Fragmented genomic DNA used as input for G-SELEX experiments

value: Input for SELEX


title: MCF10A ATAC-seq Redmedium

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description:
ATAC-seq MCF10A Redn Medium
merged MCF10A Red ATAC-seq alltags.bigwig
merged MCF10A Red ATAC-seq poissP.bigwig

data_processing:
ChIP-seq and ATAC-seq Peak Calling Analysis of sequence data was carried out as previously described (Ferrari et al, 2020)  with minor modifications. Reads were aligned to the hg38 human genome reference  sequence (GRCh38) using Bowtie (Langmead et al, 2009) and aligning parameters of  uniqueness (-S –m1 –v2 –t –q). p values for the significance of ChIP-seq counts  compared to input DNA were calculated as described (Pellegrini & Ferrari, 2012) using  a threshold of 10-8 and a false discovery rate (FDR) < 1%.
HiCHIP experiments were performed as described (Mumbach et al., 2016) using PR  specific antibody (Santa Cruz, H190). Analysis was performed using dovetail HiChIP  pipeline (https://hichip.readthedocs.io/en/latest/).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig or bed

source_name: ATAC-seq MCF10A Redn Medium

growth_protocol: T47D breast cancer cells were routinely grown in RPMI 1640 medium supplemented with  10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin.  For the experiments, cells were plated in RPMI medium without phenol red  supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later  medium was replaced by fresh medium without serum.  MCF10A cells were routinely grown in DMEM/F12 medium with 5% Horse Serum, 20  ng/ml EGF, 100 U/ml penicillin and 100mg/ml streptomycin, 0.5 mg/mL Hydrocortisone,  100 ng/ml Cholera Toxin and 10 mg/ml Insulin.  T47Dwhite cells  were routinely grown in RPMI medium without phenol red supplemented with 10%  dextran-coated charcoal treated FBS (DCC/FBS).

extract_protocol:
RNA was extracted from cells treated or not for 6hs with 50pM or 10nM  R5020 and submitted to massive sequencing using the Solexa Genome Analyzer.
RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and  dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer  and RNA subjected to Bioanalyzer for quality control. Libraries were prepared using 1 μg of polyA+ RNA by PCR amplification of cDNA with bar-coded primers using the Illumina  TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-  2500 to obtain pair-ended (PE) 100-base-long reads.
ChIP assays were performed as described (Strutt and Paro, 1999)

treatment_protocol: After 24h in serum-free  conditions, cells were incubated with R5020 or Progesterone at different concentrations  ranging from 0.01, 0.05, 0.5, 0.1, 1 and 10nM for different times at 37 C.

tag: cell line


title: ATAC-seq 005nM T30 alltags

description:
ATAC-seq 005nM T30
ATAC-seq 005nM T30 alltags.bigwig
ATAC-seq 005nM T30 poissP.bigwig

source_name: ATAC-seq 005nM T30


title: RNA-seq T47D T30 10nM Rep2

description:
RNA-seq T47D T30 10nM Rep2
sn 013 02 01 rnaseq unique strand1 rpm.bw
sn 013 02 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T30 10nM Rep2


title: RNA-seq T47D T30 10nM Rep1

description:
RNA-seq T47D T30 10nM Rep1
sn 013 01 01 rnaseq unique strand1 rpm.bw
sn 013 01 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T30 10nM Rep1


title: ATAC-seq T47D white REP2

description:
ATAC-seq White Medium T47D
ATAC-seq white 2D merged alltags.bigwig
ATAC-seq white 2D merged poissP.bigwig

source_name: ATAC-seq White Medium T47D


title: HF crossbred_ Infected_182

city: Bengaluru

first: Suresh

middle: H

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

country: India

institute: Indian Veterinary Research Institute

data_processing:
Tophat-2.0.13
DESeq2
Genome_build: ARS UCD 1.2
Supplementary_files_format_and_content: Txt files with raw counts

organism: Bos taurus

source_name: Ventral soft palate

growth_protocol: Cattle calves were experimentally infected with FMDV serotype ‘O’ by intradermolingual inoculation. Ventral soft palate tissue biopsy was collected at 48 hours post infection. Transcript profile from the tissue biopsies  were analysed for differential gene expression.

extract_protocol:
RNA was isolated from tissue samples using RNAeasy kit (Qiagen, USA). The total RNA was used to enrich mRNA using NEB Magnetic mRNA Isolation Kit.
The transcriptome library was prepared using NEB ultraII RNA library prep kit and sequenced using Illumina HiSeq (151 nt, paired-end), technology

treatment_protocol: Experimental infection of 6-9 month old cattle calves with Foot and mouth Disease Virus serotype ‘O’ by intradermolingual inoculation.

tag: breed

value: Holstein Friesian Crossbred

value: FMDV infected

value: Ventral soft palate

value: Epithelial


title: HF crossbred_ Infected_185

tag: treatment


title: HF crossbred_ Mock control_187

value: Uninfected


title: HF crossbred_ Mock control_183


title: RNA-seq T47D T30 005nM Rep2

description:
RNA-seq T47D T30 005nM Rep2
sn 012 02 01 rnaseq unique strand1 rpm.bw
sn 012 02 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T30 005nM Rep2


title: T47D T30 10nM R5020 ChIP PR

description:
ChIP-seq PR T30 R5020 10 nm R5020 rep2
T47D T30 10nM R5020 PGRmerged alltags.bigwig
T47D T30 10nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 10 nm R5020 rep2


title: RNA-seq T47D T30 005nM Rep1

description:
RNA-seq T47D T30 005nM Rep1
sn 012 01 01 rnaseq unique strand1 rpm.bw
sn 012 01 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T30 005nM Rep1


title: T47D T0 ChIP PR rep2

description:
ChIP-seq PR T0 rep2
T47D T0 PRGmerged alltags.bigwig
T47D T0 R5020 merged poissP.bigwig

source_name: ChIP-seq PR T0 rep2


title: RNA-seq T47D T0 Rep2

description:
RNA-seq T47D T0 Rep2
sn 011 02 01 rnaseq unique strand1 rpm.bw
sn 011 02 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T0 Rep2


title: HF crossbred_ Infected_184


title: T47D T30 0,5nM R5020 ChIP PR

description:
ChIP-seq PR T30 R5020 0.5 nm R5020 rep2
T47D T30 005nM R5020 PGRmerged alltags.bigwig
T47D T30 05nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 0.5 nm R5020 rep2


title: ATAC-seq T47D white REP1


title: T47D T30 1nM R5020 ChIP PR

description:
ChIP-seq PR T30 R5020 1 nm R5020 rep2
T47D T30 1nM R5020 PGRmerged alltags.bigwig
T47D T30 1nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 1 nm R5020 rep2


title: T47D T30 0,1nM R5020 ChIP PR

description:
ChIP-seq PR T30 R5020 0.1 nm R5020 rep2
T47D T30 01nM R5020 PGRmerged alltags.bigwig
T47D T30 01nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 0.1 nm R5020 rep2


title: T47D T30 0,05nM R5020 ChIP PR

description:
ChIP-seq PR T30 R5020 0.05 nm R5020 rep2
T47D T30 005nM R5020 PGRmerged alltags.bigwig
T47D T30 005nM R5020 merged poissP.bigwig


title: T47D T30 R5020 0,5 nM ChIP PR

description:
ChIP-seq PR T30 R5020 0.5 nm R5020 rep1
T47D T30 05nM R5020 PGRmerged alltags.bigwig
T47D T30 05nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 0.5 nm R5020 rep1


title: T47D T30 R5020 0,1 nM ChIP PR

description:
ChIP-seq PR T30 R5020 1 nm R5020 rep1
T47D T30 1nM R5020 PGRmerged alltags.bigwig
T47D T30 1nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 1 nm R5020 rep1


title: Gcn4 G-SELEX Round 3 Replicate 3

description: 20180808 replicate of DNA incubated for 3 rounds in the presence of recombinant Gcn4

source_name: Log-phase Saccharomyces cerevisiae cells in synthetic complete medium


title: T47D T30 R5020 0,05nM ChIP PR

description:
ChIP-seq PR T30 R5020 0.05 nm R5020 rep1
T47D T30 005nM R5020 PGRmerged alltags.bigwig
T47D T30 005nM R5020 merged poissP.bigwig


title: RNA-seq T47D T0 Rep1

description:
RNA-seq T47D T0 Rep1
sn 011 01 01 rnaseq unique strand1 rpm.bw
sn 011 01 01 rnaseq unique strand2 rpm.bw

source_name: RNA-seq T47D T0 Rep1


title: T47D T30 R5020 0,1nM ChIP PR

description:
ChIP-seq PR T30 R5020 0.1 nm R5020 rep1
T47D T30 01nM R5020 PGRmerged alltags.bigwig
T47D T30 01nM R5020 merged poissP.bigwig

source_name: ChIP-seq PR T30 R5020 0.1 nm R5020 rep1


title: T47D T0 ChIP PR rep1

description:
ChIP-seq PR T0 rep1
T47D T0 PRGmerged alltags.bigwig
T47D T0 R5020 merged poissP.bigwig

source_name: ChIP-seq PR T0 rep1


title: Input DNA

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

department: Biology

institute: Indian Institute of Science, Education and Research, Pune

data_processing:
Libraries were sequenced on the Illumina Hi-seq 2500 platform using 101 bp pair-end sequencing.
Quality control for all Illumina sequence reads was performed using a FastQC tool (Version 0.72) on GALAXY ChIP-seq analysis platform
All quality-controlled reads were mapped against reference Human genome (hg19) using Bowtie2 (Version 2.2.6) on Galaxy server. Default parameters for pair-end reads were used. Correlation between two biological replicates of ChIP-seq was determined using multiBamSummary and plotCorelation tool on GALAXY server.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm  veersion 1.4.2 2012035
The wig files were generated by a moving window of size 200bp
Genome_build: hg19
Supplementary_files_format_and_content: wig files and peaks.bed file

source_name: Input DNA

growth_protocol: Colorectal adenocarcinoma cell line - DLD1 were cultured in RPMI media (Invitrogen, 11875), supplemented with 10% fetal bovine serum (FBS, Invitrogen, 6140-079, Carlsbad, USA), 100 U/ml penicillin/100 μg/ml of streptomycin (Gibco, 15070-063) at 37°C with 5% CO2.

extract_protocol:
Crosslinking 1% paraformaldehyde for 10 min, nuclear purification with 0.5% NP40, DNA solubilization and sonication in 1% SDS using Covaris sonicator, followed by Immunoprecipitation with following antibodies 1.Anti-Nup93 antibody (sc-292099)- 2µg/ 100µg of chromatin, 2. Normal Rabbit IgG (Millipore 12-370). Arpoximately 20-30 ng of DNA was used for library preparation.
ChIP-Seq libraries for sequencing were constructed according to the NEXTflex™ ChIP-Seq library protocol outlined in NEXTflex™ ChIP-Seq Kit - 5143-01. Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends, phosphorylate the fragments, add a single nucleotide A overhang and ligate adaptors (NEXTflex ChIP Barcodes-48 kit). The libraries are enriched using PCR (5 cycles), fragments were size selected using a 2 % Low melting agarose gel and purified using MinElute Gel Extraction Kit (QIAGEN). The libraries were further enriched using PCR (14 cycles), post PCR cleanup was performed using Agencourt AMPURE XP beads (Beckman Coulter #A63881). The prepared libraries were quantified using Qubit fluorometer and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).

value: Colorectal cancer cells

tag: chip antibody


title: Nup93_ChIPSeq_rep1

value: Anti-Nup93 antibody (sc-292099)


title: TCP3

city: Shanghai

first: Ce

last: Ji

address: 197 Ruijin 2nd Road, Shanghai

institute: Shanghai Jiaotong University

description: one sample from rat hindlimb bone

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co Ltd  ( China) Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy N and the low quality reads were removed to obtain the clean reads Then the  clean reads were mapped to reference genome using hisat 2
FPKM value of each gene was calculated using cufflinks  and the read counts of each gene  were obtained by htseq count  DEGs were identified using the DESeq  2012 R package  functions estimateSizeFactors and nbinomTest Pvalue< 0 05 and foldChange> 2 or  foldChange< 0 5 was set as the threshold for significantly differential expression Hierarchical  cluster analysis of DEGs was performed to explore genes expression pattern GO enrichment  and KEGG  pathway enrichment analysis of DEGs were respectively performed using R  based on the hypergeometric distribution
If it was transcript level quantification, FPKM  and read counts value of each transcript  protein_coding was calculated using bowtie  and eXpress  DEGs were identified using  the DESeq 2012 functions estimateSizeFactors and nbinomTest P value<0 05 and  foldChange>2  or foldChange <0.5  was set as the threshold for significantly differential  expression Hierarchical cluster analysis of DEGs was performed to explore transcripts  expression pattern GO enrichment and KEGG  pathway enrichment analysis of DEGs were  respectively performed using R based on the hypergeometric distribution
The reads were reassembled using StringTie  Then gene structure extension and novel  transcripts identification were performed by comparing the reference genome and the known  annotated genes using cuffcompare software
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with FPKM for every gene

organism: Rattus norvegicus

source_name: TCP group

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

tag: time

value: 2 weeks after defect

value: bone