title: Treatment miR-146b inhibitor replicate 2

data_processing:
Quality trimming and adapter removal,        trim_galore --length 25 -a "AGATCGGAAGAGC -a A{{{10}}} "  --three_prime_clip_R1  --output_dir <out_dir> <in.fastq.gz>
Mapping reads with STAR, STAR --genomeDir <genome_dir> --readFilesIn <trimmed.fastq.gz> --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outFileNamePrefix star/<sample_name> --quantMode TranscriptomeSAM
Samtools sort, samtools sort -o <out_sorted.bam> <star.bam>
deduplication of the UMIs, umi_tools dedup -I <bam>
prefix} --log={log} -S {output}
Samtools sort on name, samtools sort-n -o <out.bam> <in.bam>
Quantify with rsem, rsem-calculate-expression --forward-prob 1 --no-bam-output --bam <in.bam> <index_rsem>
Genome_build: Bos_taurus.ARS-UCD1.2 release 95 Ensembl
Supplementary_files_format_and_content: normalized_counts_deseq2.txt, normalized counts with DESeq2's standard method

source_name: Bovine Blastocysts

growth_protocol: Routine in vitro methods were used for bovine embryo production, as described previously by (Wydooghe, et al. 2014), during the embryo culture the persumed zygote were cultured group of 25 in 50-µL droplets. covered with Paraffin oil (SAGE oil for tissue culture, ART-4008-5P, Cooper Surgical Company), at 38 °C in 5% CO2, 5% O2, and 90% N2.

extract_protocol:
Seven groups of blastocysts were collected on 8 dpi (control, NC mimic, NC inhibitor, miR-378 mimic, miR-378 inhibitor, miR-146b mimic, and miR-146b inhibitor). For each group, total RNA was isolated from three replicates of 10 blastocysts using the RNeasy Micro kit (Qiagen) according to the manufacturer's protocol. The quality and concentration of the RNA samples were examined using an RNA 6000 Pico Chip (Agilent Technologies) and a Quant-iT RiboGreen RNA Assay kit (Life Technologies), respectively.
Transcriptome library preparation was done by Qiaseq UPX 3' transcriptome kit (Qiagen)

treatment_protocol: In vitro embryo culture was performed in two treatments (mimic and inhibitor). For the mimic treatment, the presumed zygotes (n = 715, eight replicates) were allocated to three different groups (control, NC mimic, miR-378 mimic, and miR-146b mimic). Similarly, for the inhibitor treatment, the presumed zygotes (n = 765, eight replicates) were allocated to four different groups (control, NC inhibitor, miR-378 inhibitor, and miR-146b inhibitor). Culture medium was prepared in groups, as described above, by culturing 25 embryos in 50-µL droplets of SOF+ITS+BSA, covered with mineral oil at 38.5 °C in 5% CO2, 5% O2, and 90% N2. Embryo development was evaluated on 7 and 8 dpi, while embryo quality was assessed by differential staining on 8 dpi. All blastocysts (8 dpi) were collected for differential apoptotic staining and transcriptomic analysis.

tag: embryos collected


title: Treatment miR-378 inhibitor replicate 2

status: Public on Mar 10 2022

type: SRA

city: Merelbeke

first: Krishna Chaitanya

last: Pavani

state: Gent

address: Salisburylaan 133, Merelbeke, Belgium

country: Belgium

institute: Ghent Univeristy

library_source: transcriptomic

molecule: total RNA

organism: Bos taurus

tag: treatment

value: 8 days post insemination


title: Cortex_P5_Chd8_WT_Oil_control_Male_b1-2_RNA_Rep2

status: Public on Apr 01 2022

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

country: USA

institute: Dana-Farber Cancer Institute

description: Jimenez_Chd8_DM_PND5_12month_RNAseq_VST.xlsx

data_processing:
Reads were filtered for a quality score of 20 or more in at least 90% of all bases using fastq_quality_filter in the FASTX toolkit 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Sequencing adapters were trimmed using cutadapt 1.12 {Martin, 2011 #224}
Reads were then aligned to the mm10 reference genome using STAR 2.5.2b {Dobin, 2013 #37}
Transcript abundance was then estimated using salmon, and differential expression was detected using DESeq2 using a model that corrected for batch and/or sex/litter effects and a threshold of adjusted p-value < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression provided as VST-normalized values from DESeq2

molecule: polyA RNA

organism: Mus musculus

source_name: Cerebral cortex

growth_protocol: All data presented in this study are from mice obtained by breeding Chd8V986*/+ male mice {Jiménez, 2020 #182} with C57BL/6J wild-type (WT) females. This breeding scheme was used because pup survival was reduced when raised by Chd8V986*/+ females {Jiménez, 2020 #182}. Upon confirmation of a vaginal plug, embryonic day 0 (E0), females were fed the first dose of oil control or DM (3 mg/kg) (ChemService, N-11579) mixed into peanut butter (Skippy, Hormel Foods), and were then fed DM or oil every 3 days up until weaning at postnatal day (PND) 22, to replicate work by Richardson et al {Richardson, 2015 #72}. To rigorously control for litter effects {Jiménez, 2021 #227}, only one animal of each sex and genotype were used per litter. Mice were raised in a facility with a 12:12-light:dark cycle with ad libitum access to food (Teklad 2020X, Envigo, Huntingdon, UK) and water. Animal protocols in this study were approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

extract_protocol:
The brains were removed, and the cerebral cortex (one hemisphere) was dissected and stored at −80°C until RNA extraction. Samples were processed in 4 batches, including meticulous planning to ensure that equal numbers of each genotype and time point were centrifuged together, to minimize batch effects associated with any part of processing, handling, RNA isolation, or RNA-sequencing library preparation. To lyse the samples, 350 μl of Qiagen RLT Plus buffer (with 20 μL DTT per mL buffer) per 20 mg tissue was added. A hand-held motorized homogenizer was used to immediately homogenize the samples. The lysate (350 μL) was processed through a RNeasy Plus Mini Kit for RNA extraction following the manufacturer protocol (Qiagen, 74136). RNA concentration was measured using Qubit RNA Broad-Range Assay and stored at −80°C (Thermo Fisher Scientific, Q10211).
PolyA RNA-stranded libraries were prepared (TruSeq mRNA stranded, Illumina) and sequencing was performed at the New York Genome Center (NYGC). Sequencing was conducted on an Illumina NovaSeq with stranded paired-end 100 bp reads

treatment_protocol: WT and Chd8V986*/+ mice exposed to vehicle control or DM from E0 to PND 22 were sacrificed at PND 5 or at 12 months of age by decapitation. A separate cohort of unexposed WT and Chd8V986*/+ mice were sacrificed at 18 months of age by decapitation.

tag: genotype

tag: age

tag: Sex

value: Male

tag: litter

value: E

tag: dissection

value: Eric

tag: batch


title: Treatment miR-378 inhibitor replicate 1


title: Treatment miR-378 inhibitor replicate 3


title: Treatment miR-146b inhibitor replicate 3


title: Treatment miR-146b inhibitor replicate 1


title: Negative inhibitor control replicate 3


title: Negative inhibitor control replicate 1


title: Control-2 replicate 3


title: Control-2 replicate 1


title: Negative inhibitor control replicate 2


title: Control-2 replicate 2


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b1-6_RNA_Rep2

value: Q

value: Jess


title: Treatment miR-378 mimic replicate 2


title: Treatment miR-378 mimic replicate 1


title: Treatment miR-146b mimic replicate 3


title: Treatment miR-378 mimic replicate 3


title: Treatment miR-146b mimic replicate 2


title: Treatment miR-146b mimic replicate 1


title: Negative mimic control replicate 2


title: Negative mimic control replicate 3


title: Negative mimic control replicate 1


title: Control replicate 1


title: Control replicate 3


title: Control replicate 2


title: W1

status: Public on Dec 31 2021

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing: For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step

organism: Homo sapiens

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin (Invitrogen).

extract_protocol:
After 72h RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transient transfection was performed using Rotifect (Carl Roth) according to the manufacturer’s instructions.

value: si C9orf78 + C9ORF78WT


title: W2


title: M1

value: si C9orf78 + C9ORF78MUT


title: S1

value: si C9orf78 + empty vector


title: C2

value: si CTRL + empty vector


title: S2


title: HEK293T cells, si3

data_processing:
For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step
Genome_build: hg19
Supplementary_files_format_and_content: gene TPMs

tag: cell line

value: si C9orf78


title: C3


title: HEK293T cells, si1


title: HEK293T cells, C3

value: si CTRL


title: HEK293T cells, si2


title: HEK293T cells, C2


title: CAR T cells scTCRseq

status: Public on Dec 15 2021

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

description: CAR-T scTCR

data_processing:
Library strategy: TCR-seq
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using the cellranger count (10X Genomics, version 6.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. We obtained a total of 6,206 cells with on average 63,895 reads per cell and a median of 1,958 genes per cell.
The scTCR-seq reads were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10X Genomics, version 6.0.0). The resultant clonotype and filtered contig annotation data were used for downstream analyses. The clonotype and contig data were then added to the scRNA data by matching the cell barcodes. The frequency of each clonotype in each sample were recalculated based on those successfully matched to the corresponding scRNA data. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions of  a productive TCRα chain paired with a productive TCRβ chain.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered expression matrix for scRNA
Supplementary_files_format_and_content: filtered clonotype and contigs for scTCR

extract_protocol:
Cryopreserved patient biospecimens were thawed in warm RPMI+10% FBS. Cells were first washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Next, Fc receptors were blocked by incubation with Human TruStain FcX (BioLegend, 422301) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-anti-CD3E (clone SK7) and Alexa Fluor 647-labeled antigen-tetramers at 3 nM final concentration for CAR-detection. Subsequently, cells were incubated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) diluted 1:1000 in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media before fluorescence-activated cell sorting. To draw sorting gates based on a biological control, cells from a healthy donor were similar stained and analyzed
12,000 sorted endogenous CAR- T cells and 7,853 sorted CAR+ T cells were  separately partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). From the resulting barcoded nucleic acids, TCR-seq libraries were prepared via the Chromium Single-Cell Human TCR Amplification Kit (10x Genomics, 1000252). Sequencing libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via a high-sensitivity D5000 screentape (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq-6000).

tag: disease state

value: Diffuse Large B-Cell Lymphoma

tag: tissue

value: Blood PBMCs

tag: cell type

value: CAR T cell


title: Endogenous T cells scTCRseq

description: Endo-T scTCR

value: Endogenous T cell


title: CAR T cells scRNAseq

description: CAR-T scRNA

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using the cellranger count (10X Genomics, version 6.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. We obtained a total of 6,206 cells with on average 63,895 reads per cell and a median of 1,958 genes per cell.
The scTCR-seq reads were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10X Genomics, version 6.0.0). The resultant clonotype and filtered contig annotation data were used for downstream analyses. The clonotype and contig data were then added to the scRNA data by matching the cell barcodes. The frequency of each clonotype in each sample were recalculated based on those successfully matched to the corresponding scRNA data. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions of  a productive TCRα chain paired with a productive TCRβ chain.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered expression matrix for scRNA
Supplementary_files_format_and_content: filtered clonotype and contigs for scTCR


title: miRNA F. nucleatum 1

status: Public on Dec 13 2021

city: Chengdu

first: Jieyu

last: Zhou

address: No. 14, section 3, Renmin South Road

department: Department of Periodontics

country: China

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
mRNAs, lncRNAs and circRNAs, Quality control of the sequencing raw data was conducted by Fast QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), including raw data filtering, sequencing error rate check and GC content distribution check.
mRNAs, lncRNAs and circRNAs, trimmomatic was applied to remove reads including adapter and low-quality reads from raw data and discard the sequences with N base before alignment
mRNAs, lncRNAs and circRNAs, Q20, Q30, and GC contents of the clean data were calculated.
The clean reads of mRNA were aligned to OryCun2.0 with HISAT2 program, and the mapped reads were assembled by using StringTie
mRNAs, lncRNAs and circRNAs, the cuffmerge software was used to merge and filter the transcripts, the criteria as follows: (a) The transcript does not have the coding potential (Software: cpc2, Pfam, CNCI); (b) the length of the transcript ≥ 200 bp; (c) exon number ≥ 2, filtering a large number of single exon transcripts with low expression level and low confidence in the splicing result of the transcriptome; (d) the transcripts are not indicated in the existing database as protein-coding transcripts
For miRNAs, library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on the Illumina Novaseq 6000  platform.
For miRNA reads, alignment was performed with Bowtie. Meantime, miREvo and miRDeep2 was used to find novel miRNA with default parameters
All miRNAs were counted and normalized with TPM, and the correlation analysis of gene expression among samples was conducted
The aberrantly-expressed miRNAs between experimental and control groups were analyzed by DESeq2
Genome_build: reference genomes from NCBI for human
Supplementary_files_format_and_content: mRNAs, lncRNAs and circRNAs, tab-delimited text files include RPKM values for each Sample. For miRNAs, tab-delimited text files include TPM values for each Sample ...

source_name: THP-1 derived macrophages

growth_protocol: human monocyte cell line THP-1 (TIB-202) cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium, with 10%foetal bovine serum (FBS; HyClone,UT, USA) under 5% CO2 at 37°C.THP-1 monocytes were differentiated into macrophages (THP-1 derived macrophages, dTHP1) by treatment with 100nM PMA (phorbol 12-myristate 13-acetate, Sigma-Aldrich) for 48h.

extract_protocol:
Total RNA was extracted, and the RNA purity and concentration was inspected with a Nanodrop, and RNA integrity was measured with an Agilent 2100 bioanalyzer. Specific library (including lncRNA, mRNA and circRNA) was constructed by removing ribosomal RNA,Small RNA library was constructed by Small RNA Sample Pre-Kit following the manufacturer’s procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols.Using the special structure of 3 'and 5' ends of small RNA, we directly added the two ends of small RNA with connectors, and then reverse transcribed into cDNA. After PCR amplification, the target DNA fragment was separated by PAGE gel electrophoresis, and then the products recovered by gel cutting were small RNA library.

treatment_protocol: Macrophages were infected with live F.nucleatum at a multiplicity of infection (MOI) of 100. Infected Cells were harvested after 24h.

value: F. nucleatum-infected


title: HEK293T cells, C1


title: Input_myoblasts

status: Public on Dec 01 2021

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

library_source: genomic

data_processing:
Reads were trimmed from adapter sequences and low quality sections using fastp.
Reads were aligned on the mouse genome using STAR, specifying maximum intron size of 1 and using a genome index made without a transcript GTF file. Only reads with mapq score of at least 40 were retained
Duplicate reads were marked using Picard markDuplicates
Genome-wide coverage was computed using deepTools bamCoverage, disregarding duplicates, in bins of 10 bp and normalizing by RPKM
The difference between anti-Six1 and Input read densities was calculated using SeqMonks in bins of 25 bp separated by 25 bp (start-to-start)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format with normalized genome coverage; bigWig format with difference in normalized genome coverage.
Supplementary_files_format_and_content: Table_S1.Six1_1MB_peaks.mm9.bed: Six1 binding peaks identified in primary myoblasts. MACS2 was used with default parameters in BED mode and using fragment size estimated using SSP. Peaks were refined by splitting large, compound peaks into individual ones using PeakSplitter with a cut-off of 70 reads and a valley of 0.8. Six1 peaks were further refined by eliminating those that overlap peaks discovered by MACS2 using the input sample, peaks discovered using the IgG against the input control, and mm9 genome blacklisted regions.
Supplementary_files_format_and_content: Table_S2.Six1_1MT_peaks.mm9.bed: Six1 binding peaks identified in primary myotubes. MACS2 was used with default parameters in BED mode and using fragment size estimated using SSP. Peaks were refined by splitting large, compound peaks into individual ones using PeakSplitter with a cut-off of 70 reads and a valley of 0.8. Six1 peaks were further refined by eliminating those that overlap peaks discovered by MACS2 using the input sample, peaks discovered using the IgG against the input control, and mm9 genome blacklisted regions.

molecule: genomic DNA

source_name: Primary myoblast culture

growth_protocol:
Primary mouse myoblasts were isolated and grown as described in PMID 23840772. Cells were kept subconfluent and in growth medium
Primary mouse myoblasts were isolated and grown as described in PMID 23840772.

extract_protocol:
Cells were fixed with 1% formaldehyde and chromatin was extracted as described in PMID 26229056.
TruSeq gDNA library construction

tag: differentiation stage

value: Myoblasts


title: Six1_myotubes_ChIP

source_name: Primary myotubes culture

growth_protocol:
Primary mouse myoblasts were isolated and grown as described in PMID 23840772. Cells were grown to confluence and switched to differentiation medium for 48 hours
Primary mouse myoblasts were isolated and grown as described in PMID 23840772.

value: Myotubes


title: Endogenous T cells scRNAseq

description: Endo-T scRNA


title: M2


title: Rabbit_IgG_myoblasts_ChIP


title: M3


title: S3


title: W3


title: Six1_myoblasts_ChIP


title: LAPLo rep2

status: Public on Nov 24 2021

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

data_processing:
Drop-seq tools 1.12 /STAR 2.5.3a
Seurat v3.0
binomial Generalized Linear Model in R
Genome_build: GRCm38
Supplementary_files_format_and_content: Text format matrix of gene expression counts. Each gene is a row, and each cell is a column.

source_name: Tumor tissue

extract_protocol: Seq-well library preparation protocol

tag: strain

value: BALB/c

value: young adult

value: CT26 Tumor

value: myeloid cells

value: wild-type

tag: lap status

value: low


title: C1


title: LAPHi rep3

value: High


title: LAPLo rep3


title: LAPHi rep4


title: LAPHi rep2


title: Totalinput_HA-ParB(R95A)_Myxococcus_xanthus_SA4269+pMO161_Sample1+2(AIYT-267)

status: Public on Sep 24 2021

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

description:
ParB depletion strain
(AIYT-267)

data_processing:
Base calling: NextSeq Control Software 4.0.1.41, RTA2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.72), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.2+galaxy0)
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.40.0 (Braham Bionformatics Institute)
Genome_build: Myxococcus xanthus DK1622 : CP000113.1
Supplementary_files_format_and_content: The xlsx file reporting ParB ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature Type; column 5: Feature Name; column 6: Description; column 7 to 20: ParB ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Myxococcus xanthus DK 1622

growth_protocol: M. xanthus strains carrying the endogenous parB gene under the control of a Cu2+-inducible promoter and HA-parB (MO81), HA-parBQ52A (MO82), HA-parBE93A (MO83) and HA-parBR95A (MO84) under the control of a vanillate-inducible promoter were grown overnight in the presence of CuSO4. The cells were washed three times in CTT medium and cultivated for an additional 24 h in 80 ml CTT medium supplemented with vanillate to deplete wild-type ParB and induce the synthesis of the HA-tagged ParB variants.

extract_protocol:
After resuspension in TES buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA), the cells were incubated for 10 min at 37°C in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) according to the manufacturer's instructions. The lysates were then sonicated (Bioruptor® Pico, Diagenode) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.2-0.5 kbp and cleared by centrifugation for 2 min at 14,000 rpm and 4°C. The volume of the lysates was adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (16.7 mM Tris/HCl pH 8.1, 167 mM NaCl, 0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche) and 100 μg BSA. 2% of each pre-cleared lysate were reserved as total input (negative control) samples. The pre-cleared lysates were then incubated overnight at 4°C with monoclonal rabbit Anti-HA Tag anti¬bodies (Millipore, clone 114-2C-7) at a 1:400 dilutions. Immunocomplexes were captured by incubation with Protein-A agarose beads (pre-saturated with BSA) for 4 h at 4°C. After collection by centrifugation, the beads were washed with low-salt washing buffer (20 mM Tris/HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), with high-salt washing buffer (20 mM Tris/HCl pH 8.1, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), with LiCl washing buffer (10 mM Tris/HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholate,) and finally twice with TE buffer (10 mM Tris/HCl pH 8.1, 1 mM EDTA). The immunocomplexes were eluted from the Protein-A agarose beads with two times 250 μL elution buffer (0.1 M NaHCO3, 1% SDS; freshly prepared) and, in parallel to the total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris/HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse-free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Single-end runs with 50 cycles were performed on an NextSeq High (Illumina) next-generation DNA sequencing instrument.

treatment_protocol: At an OD550 of 0.5, the cultures were supplemented with 10 µM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at room temperature for 10 min to achieve crosslinking. After incubation for an additional 30 min on ice and three washes in phosphate-buffered saline (PBS, pH 7.4), the cells were harvested by centrifugation and stored at -80°C until further use.

tag: plasmid

tag: antibody

tag: genotype/variation

value: HA-ParB(mutR)


title: Totalinput_HA-ParB(Q52A)_Myxococcus_xanthus_SA4269+pMO159_Sample1+2(AIYT-265)

description:
ParB depletion strain
(AIYT-265)

value: HA-ParB(mutQ)


title: LAPHi rep1


title: Totalinput_HA-ParB(WT)_Myxococcus_xanthus_SA4269+pMO158_Sample1+2(AIYT-264)

description:
ParB depletion strain
(AIYT-264)

value: HA-ParB(WT)


title: LAPLo rep4


title: ChIP-Seq_HA-ParB(R95A)_Myxococcus_xanthus_SA4269+pMO161_Sample1(AIYT-262)

description:
ParB depletion strain
(AIYT-262)

value: monoclonal rabbit Anti-HA Tag  (Millipore, clone 114-2C-7)


title: Totalinput_HA-ParB(E93A)_Myxococcus_xanthus_SA4269+pMO160_Sample1+2(AIYT-266)

description:
ParB depletion strain
(AIYT-266)

value: HA-ParB(mutE)


title: ChIP-Seq_HA-ParB(E93A)_Myxococcus_xanthus_SA4269+pMO160_Sample2(AIYT-261)

description:
ParB depletion strain
(AIYT-261)


title: ChIP-Seq_HA-ParB(WT)_Myxococcus_xanthus_SA4269+pMO158_Sample1(AIYT-256)

description:
ParB depletion strain
(AIYT-256)


title: ChIP-Seq_HA-ParB(WT)_Myxococcus_xanthus_SA4269+pMO158_Sample2(AIYT-257)

description:
ParB depletion strain
(AIYT-257)


title: ChIP-Seq_HA-ParB(Q52A)_Myxococcus_xanthus_SA4269+pMO159_Sample1(AIYT-258)

description:
ParB depletion strain
(AIYT-258)


title: ChIP-Seq_ParB(WT)_Myxococcus_xanthus_SA4269(ParB_depletion-strain)_Sample2(AIYT-255)

description:
ParB depletion strain
(AIYT-255)

value: ParB(WT)


title: ChIP-Seq_HA-ParB(Q52A)_Myxococcus_xanthus_SA4269+pMO159_Sample2(AIYT-259)

description:
ParB depletion strain
(AIYT-259)


title: Patient 63_Cov_D4_21

status: Public on Jul 03 2021

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

data_processing:
Basecalling was performed usin the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Reads were loaded in R using the tximport library
Genome_build: hg38
Supplementary_files_format_and_content: the raw count csv file was generated based on the txi matrix imported in R.

source_name: peripheral blood on day 4 after ICU admission

extract_protocol:
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Amplification of known human transcripts; Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)

tag: subject id

value: Patient 63

value: TT

tag: corticosteroids treatment

value: blood


title: Liver metastasis

status: Public on Aug 25 2021

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: LiM

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files, which were subsequently used to generate feature-barcode matrices using Cell Ranger RNA v3.1 (10x Genomics). PM sample was run through the Single cell RNA-seq app on BaseSpace. Briefly, reads were aligned against a reference genome using Spliced Transcripts Alignment to a Reference (STAR), followed by barcode tagging and BAM indexing. Count file was generated using gene UMI counter and with cells passing quality filter based on cells above background and passing knee filter.
Initial single-cell analysis was performed using Seurat v3.1.0 (2). Cells containing less than 200 genes were removed, and log-normalized expression of 2,000 variable genes were used to reduce the data into two-dimensional space.
Cells from all 9 biopsies were combined using FindIntegrationAnchors and IntegrateData functions. Cell identities were manually assigned using highly expressed genes. To retain the highest number of cells for subsequent analyses, no additional filters were initially applied.
Genome_build: hg19
Supplementary_files_format_and_content: filtered_feature_bc_matrix, UMI count file in CSV format

source_name: Liver

growth_protocol: Organoids were maintained in growth factor-reduced matrigel and grow in progenitor tumor organoid media (PaTOM)

extract_protocol:
Biopsies were minced with sterile surgical scalpels to 0.5-1 mm fragments in approximately 1 ml of media. After centrifugation for 5 minutes at 125 g, cells were resuspended in DMEM with 0.5 mg/ml Liberase TH (Sigma-Aldrich) and 1% penicillin-streptomycin (Corning) and incubated in an orbital shaker for 15 min at 37°C. Liberase was quenched with equal volume of 1% BSA in DMEM followed by centrifugation for 5 minutes at 125 g. Cells were resuspended in 2 ml Accutase (Sigma-Aldrich) and incubated in an orbital shaker for 15 minutes at 37°C. Organoids were dissociated by incubating with TrypLE Express (Thermo Fisher) for 5-15 minutes at 37°C followed by manual disruption. Dissociated cells were passed through a 40 μm strainer and centrifuged for 5 minutes at 125 g. Isolated cells were resuspended in 0.04% BSA in phosphate buffered saline (Corning) for subsequent viability analysis and counting.
Single-cell transcriptomic amplification and library preparation was performed using the 5’ or 3’ Library Construction Kit (10x Genomics) following the manufacturer’s recommendations. Amplification and library prep of the PM sample was performed using the SureCell WTA 3’ Library Prep Kit for the ddSEQ System following the manufacturer’s recommendations (Illumina, Cat# 20014279).
single cell RNA sequencing

value: Liver


title: Fine needle aspiration - P2

source_name: Pancreas

value: Pancreas


title: Patient 61_Cov_D4_19

value: Patient 61


title: Patient 62_Cov_D4_20

value: Patient 62

value: CC


title: Patient 60_Cov_D4_18

value: Patient 60


title: LAPLo rep1

value: BALB/c

tag: age

value: young adult

value: CT26 Tumor

value: myeloid cells

tag: genotype

value: wild-type

value: low


title: ChIP-Seq_HA-ParB(R95A)_Myxococcus_xanthus_SA4269+pMO161_Sample2(AIYT-263)

description:
ParB depletion strain
(AIYT-263)

value: monoclonal rabbit Anti-HA Tag  (Millipore, clone 114-2C-7)

value: HA-ParB(mutR)


title: Patient 58_Cov_D4_16

value: Patient 58


title: Patient 57_Cov_D4_15

value: Patient 57


title: Patient 55_Cov_D4_13

value: Patient 55

value: TT

value: blood


title: Patient 54_Cov_D4_12

value: Patient 54

value: CT


title: Patient 53_Cov_D4_11

value: Patient 53


title: Patient 52_Cov_D4_10

value: Patient 52


title: Patient 56_Cov_D4_14

value: Patient 56

value: CC


title: ChIP-Seq_HA-ParB(E93A)_Myxococcus_xanthus_SA4269+pMO160_Sample1(AIYT-260)

description:
ParB depletion strain
(AIYT-260)

value: HA-ParB(mutE)


title: Patient 51_Cov_D4_9

value: Patient 51


title: Patient 49_Cov_D4_7

value: Patient 49


title: ChIP-Seq_ParB(WT)_Myxococcus_xanthus_SA4269(ParB_depletion_strain)_Sample1(AIYT-254)

description:
ParB depletion strain
(AIYT-254)

value: ParB(WT)


title: Patient 50_Cov_D4_8

value: Patient 50


title: Patient 48_Cov_D4_6

value: Patient 48


title: Patient 47_Cov_D4_5

value: Patient 47


title: Patient 46_Cov_D4_4

value: Patient 46


title: Patient 45_Cov_D4_3

value: Patient 45


title: Patient 59_Cov_D4_17

value: Patient 59


title: Patient 44_Cov_D4_2

value: Patient 44

value: TT

value: blood


title: Patient 43_Cov_D4_1

value: Patient 43

value: CT


title: Patient 39

description:
RNA.PAC / Cov042
Ion Torrent S5 Plus
counts_IFIH1.csv

data_processing:
Basecalling was performed using the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Reads were loaded in R using the tximport library
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: counts_IFIH1.csv: Comma-separated text file was generated based on the txi matrix imported in R. Raw counts.

source_name: blood sample

extract_protocol:
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogenized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Transcriptome Human Gene Expression Kit (Ion Torrent).
Amplification of known human transcripts.


title: Patient 41

description:
RNA.PAC / Cov045
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 37

description:
RNA.PAC / Cov039
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 38

description:
RNA.PAC / Cov040
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 36

description:
RNA.PAC / Cov037
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 32

description:
RNA.PAC / Cov33
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 35

description:
RNA.PAC / Cov036
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 42

description:
RNA.PAC / Cov048
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 34

description:
RNA.PAC / Cov035
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 28

description:
RNA.PAC / Cov29
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 27

description:
RNA.PAC / Cov28
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 30

description:
RNA.PAC / Cov31
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 33

description:
RNA.PAC / Cov034
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 24

description:
RNA.PAC / Cov25
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 25

description:
RNA.PAC / Cov26
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 22

description:
RNA.PAC / Cov23
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 29

description:
RNA.PAC / Cov30
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 40

description:
RNA.PAC / Cov043
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 26

description:
RNA.PAC / Cov27
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 21

description:
RNA.PAC / Cov22
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 23

description:
RNA.PAC / Cov24
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 20

description:
RNA.PAC / Cov21
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 14

description:
RNA.PAC / Cov15
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 19

description:
RNA.PAC / Cov20
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 31

description:
RNA.PAC / Cov32
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 15

description:
RNA.PAC / Cov16
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 7

description:
RNA.PAC / Cov8
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 8

description:
RNA.PAC / Cov9
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 9

description:
RNA.PAC / Cov10
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 12

description:
RNA.PAC / Cov13
Ion Torrent S5 Plus
counts_IFIH1.csv


title: P14 CD5hi Ly6C- donor

status: Public on Jun 19 2021

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

data_processing:
Library preparation was carried out with TruSeq Stranded mRNA Sample Preparation Kit (RS-122-2101~2, Illumina) according to the manufacturer’s protocol.
RNA sequencing was carried out with NextSeq 500 Sequencing System (SY-415-1001, Illumina) using NextSeq 500 HighOutput kit (150 cycles) Reagent Cartridge (15057931, Illumina).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lymph nodes

extract_protocol:
Spleen were harvested from the host mice. Single cells from the spleens were stained with fluorochrome conjugated antibodies, followed by FACS-purification of the donor cells. The purified cells were used to prepare RNA using NucleoZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lymph nodes were harvested from 8~12 week old P14 Rag1-/- Ly5.1 mice. Single cells from the lymph nodes were stained with fluorochrome conjugated antibodies, followed by FACS-purification of naive P14 CD8+ T cell subsets (CD5lo, CD5hi Ly6C-, and CD5hi Ly6C+). Each subsets were adobptively transferred to WT B6 mice. After a day, LCMV armstrong were infected to the host mice. The infected mice were sacrificed at DPI 7.

value: P14 (B6.Cg-Tcratm1MomTg(TcrLCMV)327Sdz/TacMmjax) Rag1-/- (B6.129S7-Rag1tm1Mom/J) Ly5.1 (B6.SJL-PtprcaPepcb/BoyJ) C56BL/6

tag: infection

value: LCMV DPI 7

value: Lymph nodes

value: Effector CD8 T cells

tag: cell subset

value: CD5hi Ly6C-


title: Patient 18

description:
RNA.PAC / Cov19
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 16

description:
RNA.PAC / Cov17
Ion Torrent S5 Plus
counts_IFIH1.csv


title: CD5hi Ly6C+

extract_protocol:
Lymph nodes were harvested from 8~12 week old C57BL/6 mice. Single cells from the lymph nodes were stained with fluorochrome conjugated antibodies, followed by FACS-purification of naive CD8+ T cell subsets (CD5lo, CD5hi Ly6C-, and CD5hi Ly6C+). The purified cells were used to prepare RNA using NucleoZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: state

value: ex vivo

value: Naive CD8 T cells

value: CD5hi Ly6C+


title: Patient 10

description:
RNA.PAC / Cov11
Ion Torrent S5 Plus
counts_IFIH1.csv


title: CD5hi Ly6C-


title: Patient 6

description:
RNA.PAC / Cov7
Ion Torrent S5 Plus
counts_IFIH1.csv


title: CD4_Batch_1_A12_S12

status: Public on Jun 02 2021

data_processing:
Raw sequencing data was demultiplexed and aligned to the Hg19 genome using publicly available scripts on Terra (scCloud/dropseq_workflow, version 11, https://app.terra.bio/)
UMI-collapsed digital gene expression matrices were used as input to Seurat (v3) for further analyses in R (v3.6.2)
Bulk CD4 sequencing data were processed as described in GSE163256.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain digital gene expression (dge) matrices for each scRNA-seq sample and a single txt file containing FPKM values for bulk RNA-seq samples.

source_name: blood

extract_protocol:
Hematoma effluent and blood samples were collected and scRNA-seq was performed using the Seq-Well protocol (Gierahn et al., 2017). Briefly, cells were loaded onto arrays with polyA capture beads (ChemGenes), sealed with a membrane, and subject to cell lysis. RNA was captured, beads were collected, and reverse transcription with Maxima H Minus (ThermoFisher) was performed. Whole transcriptome amplification product was purified and used as input for library construction. Bulk RNAseq for CD4 sorted cells was performed as described in GSE163256.
Sequencing libraries were prepared using Nextera XT (Illumina).

tag: donor

value: PT

tag: hours

tag: bulk or scrna-seq

value: bulk RNA-seq

value: Nextseq

tag: use for merged analysis


title: Patient 4

description:
RNA.PAC / Cov4
Ion Torrent S5 Plus
counts_IFIH1.csv

tag: tissue


title: Patient 17

description:
RNA.PAC / Cov18
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 3

description:
RNA.PAC / Cov3
Ion Torrent S5 Plus
counts_IFIH1.csv

value: CC


title: CD5lo

tag: strain

tag: cell type


title: P14 CD5hi Ly6C+ donor


title: CD4_Batch_1_A11_S11


title: CD4_Batch_1_A05_S5

source_name: hematoma


title: Patient 2

description:
RNA.PAC / Cov2
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 1

description:
RNA.PAC / Cov1
Ion Torrent S5 Plus
counts_IFIH1.csv


title: CD4_Batch_1_A01_S1


title: CD4_Batch_1_A03_S3


title: CD4_Batch_1_A10_S10


title: CD4_Batch_1_A07_S7


title: CD4_Batch_1_A09_S9


title: Patient 13

description:
RNA.PAC / Cov14
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 5

description:
RNA.PAC / Cov6
Ion Torrent S5 Plus
counts_IFIH1.csv


title: Patient 11

description:
RNA.PAC / Cov12
Ion Torrent S5 Plus
counts_IFIH1.csv


title: P14 CD5lo donor


title: Day3_089_BLD_R1_Next

value: scRNA-seq


title: Day2_073_HEF_R2_Nova

source_name: hematoma effluent

value: Novaseq


title: Day5_137_BLD_R1_Next


title: Day5_137_HEF_R1_Next


title: Day4_112_BLD_R1_Next


title: Day3_089_HEF_R1_Next


title: Day4_112_HEF_R1_Next


title: Day2_066_HEF_R1_Next


title: Day2_073_BLD_R1_Next


title: Day3_089_HEF_R2_Next


title: Day2_066_BLD_R1_Next


title: Day2_073_HEF_R1_Next


title: Day3_089_BLD_R2_Next


title: Day1_050_BLD_R1_Next


title: Day1_050_HEF_R1_Next


title: DayF_500_BLD_00_Nova


title: DayF_500_BLD_01_Nova


title: Day4_112_HEF_R2_Nova


title: Day4_112_HEF_R1_Nova


title: DayF_500_BLD_02_Nova


title: Day4_112_BLD_R1_Nova


title: Day2_066_HEF_R1_Nova


title: Day4_112_BLD_R2_Nova


title: DayF_500_BLD_03_Nova


title: DayF_500_BLD_PT_Nova

value: followup


title: Day2_066_BLD_R1_Nova


title: Day5_137_HEF_R2_Nova


title: Day1_050_BLD_R1_Nova


title: Day1_050_HEF_R1_Nova


title: GD7.5_C57BL6J_Vehicle_Rep6

status: Public on Jun 01 2021

data_processing:
Reads were quality-ﬁltered by requiring at least 90% of bases to have a quality score greater than 20 using fastq_quality_ﬁlter in FASTX 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Adapter sequences were removed using cutadapt 1.12 (Martin, 2011)
Reads were then aligned to the mm9 reference genome using STAR 2.5.2b (Dobin et al., 2013)
Transcript abundance was measured using salmon (77), and differential expression tests were performed using DESeq2 1.22.2
Genome_build: mm9
Supplementary_files_format_and_content: VST normalized expression values from DESeq2

source_name: Whole embryo

growth_protocol: Male and female adult C57BL/6J (Jackson Labs, Bar Harbor, ME; Stock #: 000664) and C57BL/6NHsd mice (Envigo, Indianapolis, IN) were obtained. Males were housed singly and females were housed in groups up to five in standard polycarbonate cages with cob bedding, shelter, and nesting material. Mice had ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water and were maintained on a 12:12 hr light/dark cycle. Up to two female mice were placed into the cage of a male for each 2 hr mating session. Upon discovery of a vaginal plug, E0 was defined as the beginning of the mating session (Fig 1). All experimental procedures were approved by the Animal Care and Use Committee at UNC-Chapel Hill in accordance with NIH Guidelines. On E7.0, dams were weighed and pregnant dams were either dissected immediately or assigned to one of the experimental treatment groups.

extract_protocol:
RNA was collected from embryos either before alcohol administration (E7.0) or 6 or 12 hr after the first alcohol injection (E7.25 or E7.5) (Fig 1). Dams were sacrificed via CO2 followed by cervical dislocation and embryos were dissected from the placenta and stage-matched based on morphological assessment (Theiler Stages 10-11; representative image in Fig 2A). A total of 6 embryos per group were used, with no more than two embryos collected per litter to minimize litter effects. Sex was not considered as a biological variable as all time points occur prior to sexual differentiation. The embryo was dissected from the extraembryonic tissue and RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Germantown, MD). RNA concentrations and purity were assessed using a NanoDrop 2000 and Qubit 3.0 Fluorimeter (Thermofisher Scientific, Waltham, MA). A separate group of samples was collected at the E7.0 time point and isolated for validation of gene expression using qRT-PCR. Expression of Wdfy1, Entpd4, and Efcab7 was analyzed in each strain and found to validate the RNA-seq results from this time point (Supp Fig 9). All samples were run in triplicate (n = 6/strain).
Libraries for RNA sequencing (RNA-seq) were prepared using the SMARTr Ultra Low Input RNA (Clontech, Mountainview, CA) and Nextera XT DNA (Illumina, San Diego, CA) kits by the UNC High Throughput Sequencing Facility. Paired-end (50bp) sequencing was performed (Illumina HiSeq 4000). Samples from each time point were run and analyzed separately.

treatment_protocol: On E7.0, dams were administered two doses of 2.9 g/kg ethanol (25% vol/vol; Pharmaco-Aaper, Brookfield, CT) in Lactated Ringer’s solution 4 hr apart via i.p. injection (Fig 1). This dose and pattern of alcohol exposure results in maternal blood alcohol concentrations of ~400 mg/dl (76). Control mice were administered an equal volume of Lactated Ringer’s solution (1.5 ml/100 g body weight).

tag: treatment

value: Vehicle


title: GD7.5_C57BL6J_Vehicle_Rep5


title: GD7.5_C57BL6J_Vehicle_Rep2


title: GD7.5_C57BL6J_Vehicle_Rep4


title: GD7.5_C57BL6J_Vehicle_Rep3


title: GD7.5_C57BL6J_PAE_Rep6

value: PAE


title: GD7.5_C57BL6J_PAE_Rep4


title: GD7.5_C57BL6J_PAE_Rep5


title: GD7.5_C57BL6J_PAE_Rep1


title: GD7.5_C57BL6N_Vehicle_Rep6


title: GD7.5_C57BL6N_Vehicle_Rep5


title: GD7.5_C57BL6N_Vehicle_Rep2


title: GD7.5_C57BL6N_Vehicle_Rep4


title: GD7.5_C57BL6J_PAE_Rep2


title: GD7.5_C57BL6N_PAE_Rep4


title: GD7.5_C57BL6N_Vehicle_Rep1


title: GD7.25_C57BL6N_Vehicle_Rep6


title: GD7.25_C57BL6N_Vehicle_Rep5


title: GD7.5_C57BL6N_PAE_Rep1


title: GD7.5_C57BL6N_PAE_Rep3


title: GD7.5_C57BL6N_PAE_Rep2


title: GD7.25_C57BL6N_Vehicle_Rep4


title: GD7.25_C57BL6N_Vehicle_Rep3


title: GD7.25_C57BL6N_PAE_Rep6


title: GD7.25_C57BL6N_PAE_Rep5


title: GD7.25_C57BL6N_Vehicle_Rep2


title: GD7.25_C57BL6N_Vehicle_Rep1


title: GD7.5_C57BL6J_PAE_Rep3


title: GD7.25_C57BL6N_PAE_Rep4


title: GD7.5_C57BL6N_Vehicle_Rep3


title: GD7.25_C57BL6N_PAE_Rep3


title: GD7.25_C57BL6N_PAE_Rep2


title: GD7.25_C57BL6N_PAE_Rep1


title: GD7.25_C57BL6J_Vehicle_Rep5


title: GD7.25_C57BL6J_Vehicle_Rep6


title: GD7.25_C57BL6J_Vehicle_Rep3


title: GD7.25_C57BL6J_Vehicle_Rep2


title: GD7.25_C57BL6J_Vehicle_Rep4


title: GD7.25_C57BL6J_Vehicle_Rep1


title: GD7.25_C57BL6J_PAE_Rep6


title: GD7.25_C57BL6J_PAE_Rep5


title: GD7.25_C57BL6J_PAE_Rep3


title: GD7.25_C57BL6J_PAE_Rep4


title: GD7.25_C57BL6J_PAE_Rep2


title: GD7.25_C57BL6J_PAE_Rep1


title: GD7_C57BL6J_Rep6

value: Control


title: GD7_C57BL6J_Rep4


title: GD7_C57BL6J_Rep3


title: GD7_C57BL6N_Rep5


title: GD7_C57BL6J_Rep2


title: GD7_C57BL6N_Rep4


title: GD7_C57BL6N_Rep3


title: GD7_C57BL6J_Rep1


title: GD7_C57BL6J_Rep5


title: GD7_C57BL6N_Rep2


title: GD7_C57BL6N_Rep1


title: GD7_C57BL6N_Rep6


title: validation cohort patient 30

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: Minfi R package standard protocol.

label: Cy5 and Cy3

source_name: NSCLC biopsy

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Total DNA was isolated by standard procedures.

tag: disease status

value: non-small-cell lung cancer (NSCLC)

value: lung

tag: cohort

value: validation


title: validation cohort patient 36


title: validation cohort patient 41


title: validation cohort patient 38


title: validation cohort patient 46


title: validation cohort patient 39


title: validation cohort patient 23


title: validation cohort patient 31


title: validation cohort patient 35


title: validation cohort patient 43


title: validation cohort patient 29


title: validation cohort patient 44


title: validation cohort patient 25


title: validation cohort patient 34


title: validation cohort patient 28


title: validation cohort patient 19


title: validation cohort patient 24


title: validation cohort patient 32


title: validation cohort patient 47


title: validation cohort patient 27


title: validation cohort patient 42


title: validation cohort patient 18


title: validation cohort patient 40


title: validation cohort patient 21


title: validation cohort patient 22


title: validation cohort patient 37


title: validation cohort patient 26


title: validation cohort patient 33


title: validation cohort patient 20


title: validation cohort patient 45


title: validation cohort patient 17


title: validation cohort patient 15


title: validation cohort patient 14


title: validation cohort patient 16


title: validation cohort patient 7


title: validation cohort patient 10


title: validation cohort patient 11


title: validation cohort patient 12


title: validation cohort patient 9


title: validation cohort patient 8


title: validation cohort patient 5


title: discovery cohort patient 25

value: discovery


title: discovery cohort patient 32


title: validation cohort patient 2


title: validation cohort patient 13


title: validation cohort patient 1


title: discovery cohort patient 28


title: discovery cohort patient 26


title: validation cohort patient 3


title: discovery cohort patient 24


title: discovery cohort patient 31


title: discovery cohort patient 22


title: discovery cohort patient 33


title: discovery cohort patient 29


title: discovery cohort patient 30


title: discovery cohort patient 23


title: discovery cohort patient 27


title: HMEC2 rep5

status: Public on May 31 2021

description: small RNA

data_processing:
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation.  Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed genes to obseerve sample relationship and to detect outliers.
Paired end assembly by pear/0.9.10
RNA-Seq mapping against mirBase HomoSapiens mature miRNA
Gene expression was quantified using AQRNAseq pipeline
Genome_build: ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz
Supplementary_files_format_and_content: Excel format matrix of  raw gene counts or raw sequence counts. Each gene/sequence is a row, and each sample is a column.

source_name: Human Mammary Epithelial Cells

growth_protocol: Lonza MEGM BulletKit media

extract_protocol:
Trizol
AQRNA-Seq

treatment_protocol: Tamoxifen

tag: description

value: Intermediate transformed cells

value: Cell line


title: discovery cohort patient 34


title: HMEC1 rep5

description: small RNA

value: hTERT

value: Normal cells


title: HMEC3 rep4

description: small RNA

value: Fully Transformed cells


title: HMEC3 rep5

description: small RNA


title: HMEC2 rep4

description: small RNA


title: HMEC3 rep3

description: small RNA


title: HMEC1 rep4

description: small RNA


title: HMEC2 rep3

description: small RNA


title: HMEC1 rep3

description: small RNA


title: HMEC3 rep2

description: small RNA


title: validation cohort patient 6


title: HMEC1 rep2

description: small RNA


title: HMEC3 rep1

description: small RNA


title: HMEC1 rep1

description: small RNA


title: ZHX2-sh45 Rep2

status: Public on May 25 2021

data_processing:
Reads were filtered for adapter contamination using cutadapt (37) and filtered such that at least 90% of bases of each read had a quality score >20
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments (38). Reads overlapping blacklisted regions of the genome were then removed
Transcript abundance was then estimated using salmon (39), and differential expression was detected using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression provided as VST-normalized values from DESeq2
Supplementary_files_format_and_content: bigWig files for ChIP and input control have been normalized to the total number of aligned reads

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (GIBCO 11965118) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Pen Strep)

extract_protocol:
Total RNA from triplicates was extracted from MDA-MB-231 cells infected with control or ZHX2 shRNAs by using RNeasy kit with on column DNase digestion (Qiagen).
Library preparation and sequencing were performed by BGI as paired-end 50bp reads

treatment_protocol: Lentiviral ZHX2 shRNAs were obtained from Broad Institute TRC shRNA library. Target sequences were as follows:   Control shRNA: AACAGTCGCGTTTGCGACTGG   ZHX2 shRNA (43): CCCACTAAATACTACCAAATA    ZHX2 shRNA (45): CCGTAGCAAGGAAAGCAACAA.


title: ZHX2-sh45 Rep1


title: validation cohort patient 4


title: discovery cohort patient 21


title: ZHX2-sh43 Rep3


title: HMEC2 rep2

description: small RNA


title: ZHX2-sh45 Rep3


title: ZHX2-sh43 Rep1


title: ZHX2-sh43 Rep2


title: discovery cohort patient 19


title: shCtl-2 Rep3

value: shCtl


title: HMEC2 rep1

description: small RNA


title: discovery cohort patient 18


title: shCtl-2 Rep1


title: shCtl-2 Rep2


title: shCtl-1 Rep1


title: discovery cohort patient 15


title: ZHX2 ChIP input

data_processing:
Reads were filtered for adaptor contamination using Cutadapt and filtered such that at least 90% of bases of each read had a quality score > 20. Duplicated sequences were then capped at a maximum of 5 occurrences
Reads were aligned to the reference genome (hg19) using STAR (42) version 2.5.2b retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed. Reads were then extended in silico to a fragment size of 250 bp
Regions of significant enrichment relative to input control were identified using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression provided as VST-normalized values from DESeq2
Supplementary_files_format_and_content: bigWig files for ChIP and input control have been normalized to the total number of aligned reads

extract_protocol:
ChIP was performed with HA tag (Cell Signaling, 3724)
The ChIP-Seq library was prepared using a ChIP-Seq DNA sample preparation kit (Illumina) according to manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500 with single-end 76 bp reads

treatment_protocol: MDA-MB-231 cells were infected by HA-ZHX2 which is resistant to ZHX2 sh45, and then infected by ZHX2 sh45

tag: ip

value: input control


title: ZHX2 ChIP Rep2


title: discovery cohort patient 12


title: shCtl-1 Rep2


title: COL1A1-GFP+ cells from mouse CCA model induced by YAP/AKT

status: Public on Apr 28 2021

city: NEW YORK

first: Robert

middle: F

last: Schwabe

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description: scRNA-seq (10x) on fresh isolated cancer-associated-fibroblasts from mouse YAP/AKT-induced ICC

data_processing:
10x genomics' cellranger pipeline was used to process the data (RS013 v2.1.1; RS030 and AJ064 v3.1.0; RS037, RS038 v4.0.0).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse) or hg38 (human).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in MatrixMarket (mtx) format

source_name: liver

extract_protocol:
HSC,CAF and whole tumor specipments were obtained perfusing and digesting the liver, followed by FACS sorting.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 (RS013) and v3 (RS030, AJ064, RS037, RS038) Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina HiSeq instrument (NovaSeq 6000 for AJ064) at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Biliary liver fibrosis was induced in eight-week-old mice subjected to ligation of the common bile duct and mice were sacrificed 14 days after. Cholestatic liver fibrosis was induced in mice treated with diet containing 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for three weeks. CCA was induced by co-injection of YAP/AKT/SB13 or KRAS/sg-p19/SB13 plasmids hydrodinamic tail vein injection and mice were sacrificed 6weeks after.

value: C57BL/6, LratCre+, TdTom+, Col1a1-GFP

tag: liver damage

value: CCA model induced by hydrodynamic tail vein injection of YAP/AKT/SB13 plasmids, isolation 6 weeks later

value: COL1A1-GFP+CAF-enriched cell fraction


title: RS030_Cells from tumor digested CCA mouse model induced by KRAS/sg-p19 enriched for COL1A1-GFP+ cells

description: scRNA-seq (10x) on fresh isolated cancer-associated-fibroblasts and tumor from mouse KRAS/P19-induced ICC

data_processing:
bulk RNA-seq:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested using DESeq2. Normalization was done internally using DESeq2's specialized algorithm and normalization to compare across samples, was performed using the TPM (transcripts per million) method
scRNA-seq:
10x genomics' cellranger pipeline was used to process the data (RS013 v2.1.1; RS030 and AJ064 v3.1.0).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse) or hg38 (human).
Genome_build: mm10; hg38
Supplementary_files_format_and_content: text files includeTPM values for each Sample; raw counts in MatrixMarket (mtx) format

extract_protocol:
HSC,CAF and whole tumor specipments were obtained perfusing and digesting the liver, followed by FACS sorting.
BULK RNA Seq: Constructed libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.
scRNA-seq: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 (RS013) and v3 (RS030, AJ064) Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina NovaSeq 6000 at the JP Sulzberger Columbia Genome Center.

tag: strain background

tag: genotype/variation

value: LratCre+, TdTom+, Col1a1-GFP

value: liver

value: CCA model induced by hydrodynamic tail vein injection of KRAS/sg-p19/SB13 plasmids, isolation 6 weeks later

value: COL1A1+GFP+CAF, tumor cells and tumor microenvironment cells


title: RSB86_Mouse HSC-derived CAF from CCA model induced by KRAS/sg-p19

description:
CAF from mouse KRAS/P19-induced ICC
processed data file: tpm_values_genes_kallisto RSB85-86-87.txt

value: HSC-CAF


title: ZHX2 ChIP Rep1


title: discovery cohort patient 17

value: non-small-cell lung cancer (NSCLC)

value: lung


title: RSB46_Mouse HSC-derived CAF from CCA model induced by YAP/AKT

description:
CAF from mouse YAP/AKT-induced ICC
processed data file: tpm_values_genes_kallisto RSB19-26 32-36 43-46.txt


title: RSB44_Mouse HSC-derived CAF from CCA model induced by YAP/AKT


title: discovery cohort patient 13

value: discovery


title: discovery cohort patient 14


title: Cells from tumor digested CCA mouse model induced by YAP/AKT enriched for COL1A1-GFP+ cells

description: scRNA-seq (10x) on fresh isolated cancer-associated-fibroblasts and tumor from mouse YAP-AKT-induced ICC


title: RS013_COL1A1-GFP+ cells from mouse CCA model induced by YAP/AKT


title: RSB34_Mouse HSC from 3 week DDC diet biliary fibrosis model

description:
ultra-pure HSC
processed data file: tpm_values_genes_kallisto RSB19-26 32-36 43-46.txt

value: LratCre+, TdTom+

value: DDC 3 weeks

value: HSC


title: RSB87_Mouse HSC-derived CAF from CCA model induced by KRAS/sg-p19


title: RSB85_Mouse HSC-derived CAF from CCA model induced by KRAS/sg-p19


title: RSB45_Mouse HSC-derived CAF from CCA model induced by YAP/AKT


title: RSB43_Mouse HSC-derived CAF from CCA model induced by YAP/AKT


title: RSB26_ouse HSC from 14 day BDL biliary fibrosis model

value: BDL 14 days


title: RSB25_ouse HSC from 14 day BDL biliary fibrosis model


title: RSB35_Mouse HSC from 3 week DDC diet biliary fibrosis model


title: discovery cohort patient 9


title: discovery cohort patient 10


title: RSB23_ouse HSC from 14 day BDL biliary fibrosis model


title: RSB32_Mouse HSC from 3 week DDC diet biliary fibrosis model


title: RSB21_quiescent mouse HSC

source_name: quiescent mouse HSC


title: AJ064_Human hilar cholangiocarcinoma

description: scRNA-seq (10x) on fresh surgical tissue

source_name: Human hilar cholangiocarcinoma

tag: subject status

value: Patient with hilar cholangiocarcinoma

value: Cell fraction containing tumor cells and other cells from the tumor microenvironment


title: RSB20_quiescent mouse HSC


title: RSB24_ouse HSC from 14 day BDL biliary fibrosis model


title: discovery cohort patient 11


title: discovery cohort patient 7


title: RSB22_quiescent mouse HSC


title: RSB19_quiescent mouse HSC


title: discovery cohort patient 16


title: Pre-procurement liver sample [PP]

status: Public on Apr 07 2021

city: Guangzhou

first: Zhiyong

last: Guo

state: Guangdong

address: 58. Zhongshan 2 Road, Guangzhou, China

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
CellRanger (version 3.0.1) was used to count to align the sequence to the human reference genome (hg38) and calculate the gene expression matrix. The original gene expression matrix in the "filtered_feature_bc_matrix" folder generated by CellRanger software was used for further analysis.
Data filtering, normalizing, dimensionality reduction and clustering for cells were performed using R software (version 3.6.1; https://www.r-project.org) and Seurat package (version 3.1.2; https://satijalab.org/seurat).
Genome_build: hg38
Supplementary_files_format_and_content: Text file of matrix with raw gene counts for every gene and every sample

extract_protocol:
The tissues were cut into 3 mm pieces, incubated with 1 mM EGTA Sigma-Aldrich, Cat. no. E0396-10G) and rotate at 37°C, 50 rpm for 10 minutes. After washing away the EGTA, the tissues were treated in the digestion solution (1 mg/ml Collagenase II + 1 mg/ml Collagenase IV + 50 ug/ml DNase I) at 100 rpm and 37 °C for 30 minutes. The cell suspension was passed through a 70 mm nylon cell strainer (BD, Cat. No. 352350, USA), and then centrifuged at 50×g for 3 minutes to collect the cell pellet, and then the remaining suspension centrifuged at 300×g for 5 minutes to collect the remaining cell pellet. Each tissue was resuspended to a concentration of 50-500 million cells per milliliter with resuspension buffer. Then used LIVE/DEAD Viability/Cytotoxicity Kit (Invitrogen, Cat. no. L3224, USA) to stained cells, and only AM+EH- cells were collected by FACS for each tissue
Single-cell cDNA libraries were constructed using the standard procedure of GemCode technology (10X Genomics, USA)

value: Pre-procurement donor liver tisseue in liver transplatation


title: Post-reperfusion liver sample [PR]

value: Post-reperfusion donor liver in liver transplatation


title: discovery cohort patient 6


title: Cortex_miR29WT_Rep2

data_processing:
Reads were then trimmed and filtered of adapter sequencing using cutadapt, and required to have at least 90% of bases with quality scores exceeding 20
Reads were then aligned to the reference human genome (hg19) using STAR, and transcript abundance was estimated using Salmon
Differential expression between each genetic model and wild-type control was analyzed using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Normalized abundance matrix

source_name: Cortex

growth_protocol: Mice were housed 2-5 per cage in a 12 h light, 12 h dark cycle. Food and water were provided ad libitum. All animal handling and experiments were carried out in accordance with the National Institutes of Health Guide for Care and Use of Laboratory Animals and as approved by the Animal Care and Use Committee of the University of North Carolina (UNC).

extract_protocol:
For miR-29Nestin mice, total RNA were extracted from the cortex of P40 mice using RNeasy Mini Kit (Qiagen). For Dnmt3ami5 mice, total RNA were extracted from the cortex of 4.5 months old mice using Direct-Zol RNA mini-prep kit (Zymo Research, #R2051).
For mirR-29Nestin mice, stranded mRNA libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina). For Dnmt3ami5 mice, stranded mRNA libraries were prepared using the KAPA stranded mRNAseq kit (KAPA Biosystems)
Paired end sequencing (50 cycles) was performed on an Illumina HiSeq 2500 v4 (high output) or Illumina HiSeq 4000 (high output)

treatment_protocol: The miR-29ab1 and miR-29b2c floxed alleles were generated by the Duke Transgenic Mouse Facility by homologous recombination and genomic targeting. An 827 bp or an 817 bp genomic segment containing respectively, miR-29a and miR-29b1, or miR-29b2 and miR-29c, were amplified from 129/SvEv mice genomic DNA. To amplify the long arm (LA) and short arm (SA), a BAC clone (RP24-248C11 for miR-29ab1 and RP23-465H4 for miR-29b2c) was used as PCR template. miR-29ab1 or miR-29b2c gene segments and their corresponding LA and SA were cloned into the PGKneoF2L2DTA targeting vector. After verification for the absence of mutation, targeting vectors were linearized by SacII (New England BioLabs) restriction enzyme digestion and were used for microinjection of ES cells from 129/SvEv-B6 mice. ES cells were positively selected in neomycin-containing medium, and successful genomic targeting was confirmed by PCR. Animals were bred and maintained in the SPF facility managed by Duke University Division of Laboratory Animal Research. All animal procedures were approved by the Duke University Institutional Animal Care and Use Committee.   The above mice were bred to generate mice floxed at both genomic loci (miR-29abf/f, miR-29bcf/f mice). Deletion of miR-29 was carried out by crossing the above mice with various Cre recombinase lines including CMV-Cre and Nestin-Cre (Jackson Laboratories, #006054 and #003771) to obtain miR-29CMV and miR-29Nestin knockout mice.  The knockin mouse with five miR-29 binding sites mutated in Dnmt3a 3' UTR (Dnmt3ami5 mice) was generated by the UNC Animal Models Core Facility by CRISPR/Cas9 nuclease technology. CRISPR guide RNAs were designed to cut at miR-29 binding site 1 and miR-29 binding site 5 (target sequence miR-29-1: ACATCCCGACTTCATAA; target sequence miR-29-5: GAGGAATTAGCACCAGCT). A donor vector with approximately 1 kb homology arms flanking the 2909 bp region encompassing the 5 miR-29 binding sites, all mutated from TGGTGCT to CACGGCT, was generated. Guide RNAs, Cas9 protein and donor vector were injected into C57BL/6J mouse embryos. Founders were screened for homologous integration of the five mutated miR-29 binding sites.

tag: genotype

tag: age

value: Cortex


title: End of preservation liver sample [EP]

value: End of preservation donor liver in liver transplatation


title: Cortex_miR29WT_Rep1


title: Cortex_miR29Nestin_Rep1


title: RSB33_Mouse HSC from 3 week DDC diet biliary fibrosis model

value: liver


title: discovery cohort patient 8


title: Cortex_miR29Nestin_Rep3


title: Cortex_miR29Nestin_Rep2


title: Cortex_Dnmt3a-WT_Rep3

value: 4.5 months


title: Cortex_Dnmt3a-WT_Rep1


title: Cortex_Dnmt3a-mi5_Rep3


title: Cortex_Dnmt3a-mi5_Rep2


title: Cortex_Dnmt3a-WT_Rep2


title: discovery cohort patient 20


title: Cortex_Dnmt3a-WT_Rep4


title: Stroma population from Patient 0030

status: Public on Mar 19 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 500. At least 20 million 75 bp paired-end reads were obtained for each sample.
Reads were aligned to the human genome hg38 by Rsubread version 1.5.3
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted.
Total RNA (100 ng) was used to generate libraries for whole transcriptome analysis following the Illumina’s TruSeq RNA v2 sample preparation protocol.

tag: patient

tag: cell population

value: Stroma

value: Fresh


title: LP population from Patient 0030

value: LP


title: Cortex_Dnmt3a-mi5_Rep4


title: ML population from Patient 0030

value: ML


title: Cortex_miR29WT_Rep3


title: Cortex_Dnmt3a-mi5_Rep1


title: discovery cohort patient 1

value: non-small-cell lung cancer (NSCLC)

value: lung

value: discovery


title: ML population from Patient 0408


title: Basal population from Patient 0030

value: Basal


title: discovery cohort patient 2


title: discovery cohort patient 4


title: discovery cohort patient 3


title: Basal population from Patient 0408


title: Stroma population from Patient 0408


title: LP population from Patient 0408


title: LP population from Patient 0165


title: discovery cohort patient 5


title: ML population from Patient 0218


title: ML population from Patient 0165


title: LP population from Patient 0218


title: Basal population from Patient 0218


title: Basal population from Patient 0507 Left Breast


title: ML population from Patient 0507 Left Breast


title: LP population from Patient 0507 Right Breast


title: Stroma population from Patient 0507 Left Breast


title: LP population from Patient 0507 Left Breast


title: ML population from Patient 0507 Right Breast


title: Basal population from Patient 0507 Right Breast


title: Stroma population from Patient 0507 Right Breast


title: Basal population from Patient 0165


title: ML population from Patient 1105 sample 1

value: Frozen


title: Basal population from Patient 1105


title: Stroma population from Patient 0232


title: ML population from Patient 0233


title: shCtl-1 Rep3

value: shCtl


title: LP population from Patient 0232


title: ML population from Patient 0232


title: LP population from Patient 0233


title: Basal population from Patient 0232


title: Shell-Female-3

status: Public on Mar 10 2021

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

institute: Douglas Mental Health University Institute

description:
Messenger RNA
premrna_shell_aggr_barcodes.tsv.gz
premrna_shell_aggr_features.tsv.gz
premrna_shell_aggr_matrix.mtx.gz

data_processing:
Data processed with Cell Ranger (10X Genomics)
rn6 pre-mRNA reference made with cellranger mkref
Reads aligned and counted with cellranger count
Assembly: Rattus norvegicus rn6
Supplementary files format and content: Feature-barcode matrix, consisting of barcodes and features in TSV format and matrix in MTX format

organism: Rattus norvegicus

source_name: Nucleus Accumbens shell

growth_protocol: Long-Evans rats were bred and offspring were weaned on postnatal day 22. Animals were pair housed in groups of the same sex until 90 to 100 days old.

extract_protocol:
Adult rat's brain were rapidly removed, flash frozen using cold isopentane, stored at -80°C. Brain was sliced coronally at 200 µm thickness. Nucleus accumbens shell and core was punched. 50 mg frozen tissue of NAc shell or NAc core from 4 animals of the same sex were pooled.
Tissues were homogenized and nuclei were obtained as reported by Nagy et al., 2020. Gel beads in emulsion was made by using 10X Genomics chromium controller and barcoding using chromium NEXT GEM single cell 3' reagent kits v3.1 and chromium Next GEM Chip G single cell kit.
GEMs were incubated at 53°C to break emulsions, cDNA was then bulk amplified for 11 cycles and standard Illumina libraries were prepared.

value: Long-Evans

value: Adult

value: Brain

tag: brain region

value: Nucleus Accumbens shell

tag: Sex

value: Female


title: Stroma population from Patient 0233

tag: tissue


title: ML population from Patient 1105 sample 2


title: Shell-Male-1

tag: strain

value: Male


title: RNA-Seq_Caulobacter_crescentus_NA1000 (flbDTn)_rep2

status: Public on Feb 18 2021

data_processing:
Base calling: NextSeq Control Software 2.2.0.4, RTA 2.4.11, bcl2fastq2.17 v2.17.1.14
Read sequencing quality control: FastQC, Galaxy Version 0.72
Alignment: Bowtie2, Galaxy Version 2.3.4.3
Raw counts: htseq-count, Galaxy Version 0.9.1
Normalized counts and differential expression analysis: DESeq2, Galaxy Version 2.11.40.6
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xlsx file reporting the RNA-Seq analysis (Raw counts, Normalized counts and differential expression analysis) is organized as follows: Raw_counts: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(flbD::Tn)_rep1; column 5: NA1000(flbD::Tn)_rep2; column 6: NA1000(ΔmadA)_rep1; column 7: NA1000(ΔmadA)_rep2; Normalized_counts: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(flbD::Tn)_rep1; column 5: NA1000(flbD::Tn)_rep2; column 6: NA1000(ΔmadA)_rep1; column 7: NA1000(ΔmadA)_rep2; Diff_expression_analysis : column 1: Start; column 2: End; column 3: Orientation; column 4: Gene ID; column 5: Name;column 6: Description; column 7: Mean normalised counts; column 8: Log2(Fold change); column 9: SEM Log2(Fold change); column 10: p-value; column 11: -Log10(p-value); column 12: Mean normalised counts; column 13: Log2(Fold change); column 14: SEM Log2(Fold change);column 15: p-value; column 16: -Log10(p-value).

organism: Caulobacter vibrioides

source_name: RNA-Seq_C. crescentus_NA1000 (flbDTn)

growth_protocol: Overnight cultures in PYE of C. crescentus NA1000(WT), flbD::Tn and ΔmadA (two independent biological replicates) were freshly restarted in 10ml of PYE (starting O.D.660nm~0.05) and incubated at 30°C under agitation to reach an O.D.660nm~0,5.

extract_protocol:
Cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer’s instructions and lysates were homogenized through QiaShredder columns (Qiagen, Switzerland). The RNeasy Mini Kit (Qiagen, Switzerland) was used for total RNA extraction according to the manufacturer’s protocol which included a first DNase treatment using the On-column DNase I digestion kit (Qiagen, Switzerland). Extracted total RNA was subjected to a second DNase treatment using Promega RQ1 at 1 unit/μg of RNA. Another total RNA cleanup was performed after the DNase treatment. The RNA concentration was measured using a Nanodrop 1000 spectrophotometer (ThermoScientific, USA) and RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies, USA).
RNA-Seq library preparation and sequencing was performed at Fasteris SA (Geneva, Switzerland). Bacterial rRNA were removed from each total RNA samples and RNA-Seq libraries were prepared using the Ovation Complete Prokaryotic RNA-Seq library system kit according to the manufacturer’s instructions. Single-end runs were performed on an Illumina NextSeq 500 instrument (50 cycles), yielding several million reads (stored as fastq files). Using the web-based analysis platform Galaxy (https://usegalaxy.org), the single-end sequenced reads quality was checked (FastQC, Galaxy Version 0.72), and reads were mapped (Bowtie2, Galaxy Version 2.3.4.3) to the C. crescentus NA1000 genome (NC_011916.1). The tables of counts with the number of reads mapping to each gene feature were prepared using the htseq-count software, Galaxy Version 0.9.1. For each experimental series, the counts normalization and the statistical differential expression analysis was performed using the DESeq2 software, Galaxy Version 2.11.40.6.

treatment_protocol: To provide immediate stabilization of RNA, each cell cultures (4ml) are treated with 2 volumes of RNA Protect Bacteria reagent (Qiagen, Switzerland) according to the manufacturer’s protocol.


title: RNA-Seq_Caulobacter_crescentus_NA1000 (madA)_rep1

source_name: RNA-Seq_C. crescentus_NA1000 (ΔmadA)

value: {delta}madA


title: RNA-Seq_Caulobacter_crescentus_NA1000 (WT)_rep1

source_name: RNA-Seq_C. crescentus_NA1000 (WT)

value: Wild type


title: RNA-Seq_Caulobacter_crescentus_NA1000 (WT)_rep2


title: 38C_CHX_2

status: Public on Nov 01 2020

data_processing:
For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step
Supplementary_files_format_and_content: tpm

source_name: primary hepatocytes

growth_protocol: Hepatocytes were cultured in DMEM High glucose (Biowest) containing 10% FCS (Biochrom) and 1% Penicillin/Streptomycin (Biowest).

extract_protocol:
RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated hepatocytes were pre-entrained to 34°C or 38°C for 12 hours. Cells were shiftet and after 4 hours DMSO or CHX was added for 4 further hours (or maintained at 39°C); RNA was extracted and analyzed by RNA-Seq.

tag: treatment

value: CHX

tag: temperature

tag: cell type

value: primary hepatocytes


title: LP population from Patient 1105

value: LP


title: RNA-Seq_Caulobacter_crescentus_NA1000 (madA)_rep2


title: 34C_CHX_2


title: MDA-MB-468_shBBOX1_ctl_Rep1

status: Public on Dec 02 2020

data_processing:
Reads were then filtered for adapter contamination using cutadapt (DOI:10.14806/ej.17.1.200) and filtered such that at least 90% of bases of each read had a quality score >20.
Reads were aligned to the reference genome (hg19) using STAR (PMID 23104886) version 2.5.2b retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon (PMID 28263959), and differential expression was detected using DESeq2 (PMID 25516281)
Genome_build: hg19
Supplementary_files_format_and_content: Batch corrected, VST-normalized expression values from DESeq2

source_name: MDA-MB-468 cells

growth_protocol: MDA-MB-468 cells were cultured in 10% FBS, 1% Pen Strep RPMI 1640 (GIBCO 11875093). Mycoplasma detection was routinely performed to ensure cells were not infected with mycoplasma by using MycoAlert Detection kit (Lonza, LT07-218). Cells were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA from triplicates was extracted from MDA-MB-468 cells infected with control or BBOX1 shRNAs by using RNeasy kit with on column DNase digestion (Qiagen).
Library preparation and sequencing were performed by BGI as paired-end 100bp reads.

treatment_protocol: Lentiviral infection was carried out similarly as previously described (55). 293T packaging cell line was used for lentivirus production. Briefly, post transfection with lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions, viruses were collected twice after 48 and 72 hours. After passing through 0.45μm filters, appropriate amount of viruses was used to infect target cells in the presence of 8 μg/ml polybrene (Santa Cruz). After lentivirus infection, cells were maintained in the presence of puromycin (2 μg/ml), hygromycin (200 μg/ml), or blasticidin (10 μg/ml) according to the selection marker of the vector. BBOX1 shRNA sequences were obtained from Broad Institute TRC shRNA library. lenti-shRNA pLKO.1 vectors were obtained from UNC Lenti-shRNA Core Facility and subjected to sequencing for confirmation. Target sequences are BBOX1 sh1 CCTCTACCTTTGTGGACTTTA, BBOX1 sh2 GCTCCCTTTAAAGAGGCTCTT

tag: cell line


title: MDA-MB-468_shBBOX1_ctl_Rep3


title: MDA-MB-468_shBBOX1_sh6_Rep2


title: Basal population from Patient 0233

value: Fresh


title: MDA-MB-468_shBBOX1_ctl_Rep2


title: 38C_DMSO_2

value: DMSO


title: MDA-MB-468_shBBOX1_sh6_Rep3


title: MDA-MB-468_shBBOX1_sh1_Rep3


title: MDA-MB-468_shBBOX1_sh1_Rep2


title: 38C_DMSO_1


title: MDA-MB-468_shBBOX1_sh6_Rep1


title: 34C_DMSO_2


title: 38C_CHX_3


title: Tn-Seq_Caulobacter_crescentus_NA1000(tipFpSA607)

status: Public on Oct 27 2020

data_processing:
Library strategy: Tn-Seq
Base calling: NextSeq Control Software 2.1.0.31, RTA 2.4.11, bcl2fastq2.17 v2.17.1.14
Read sequencing quality control: FastQC v.0.11.5
Alignment: Map with Bowtie for illumina (Galaxy Version 1.1.2), Samtools V0.1.18 (http://samtools.sourceforge.net/)
Tn-Seq raw counts (TnPM normalized) and CDS insertion counts (TnPM normalized): SeqMonk Software v1.40.0 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xlsx file reporting the Tn-Seq analysis (raw counts TnPM normalized and CDS insertion counts TnPM normalized) is organized as follows: Raw_counts_TnPM: column 1: Tn insertion coordinates; column 2: Feature strand; column 3: Feature; column 4: Description; column 5: Tn insertions in ΔtipF pSA607 (TnPM); column 6: Tn insertions in WT (TnPM); CDS_insertions_counts_TnPM: column 1: Start; column 2: End; column 3: Feature window size (kb); column 4: Feature strand; column 5: Feature; column 6: Description; column 7: Tn insertions in ΔtipF pSA607 (TnPM); column 8: Tn insertions in WT (TnPM); column 9:  ΔtipF pSA607/WT ratio.

organism: Caulobacter vibrioides NA1000

growth_protocol: Transposon mutagenesis of NA1000 (WT) and ΔtipF strain carrying the pSA607 plasmid (T5_5’UTR(fljK)::nptII) was done by conjugation with E. coli S17-1 λpir harboring the mini-himar1 Tn encoding gentamycin resistance (pMar2xT7)(Liberati et al., 2006). NA1000 (WT) serves as a control samples and allowed to check that under our experimental conditions (Donor/Recipient cells ratio, cells quantities and incubation time of the matting), Tn transposition is saturated and evenly distributed on the C. crescentus chromosome (no hot spot).

extract_protocol:
For each collection, all resistant clones were pooled and chromosomal DNA was extracted using DNAzol (Lucerna-Chem AG, Switzerland).
Purified genomic DNA was used to generate barcoded Tn-Seq libraries and submitted to Illumina NextSeq High sequencing (Fasteris SA). Tn insertion-specific reads (50 bp long) were sequenced using the himar-Tnseq primer (5’- AGACCGGGGACTTATCAGCCAACCTGTTA-3’) and then mapped (Map_with_Bowtie_for_Illumina_V1.1.2) to the C. crescentus NA1000 genome (NC_011916.1) using the web-based analysis platform Galaxy (https://usegalaxy.org). Using Samtool_V0.1.18, BED file format encompassing the Tn insertion coordinates were generated and then imported into SeqMonk V1.40.0 (www.bioinformatics.babraham.ac.uk/projects/) to assess the total number of Tn insertion per chromosome position (Tn-insertion per millions of reads count) or per coding sequence (CDS truncated from the first 50 and last 50 bp). SeqMonk datasets were exported into Microsoft Excel files for further analyses.

treatment_protocol: An NA1000::Tn(GentR) bank of >100,000 gentamicin- and nalidixic-acid-resistant (20 μg/mL) clones was collected for the control. Following the same experimental conditions, a Tn-library of ΔtipF strain carrying the pSA607 plasmid was generated separately on gentamycin plates containing kanamycin 20 μg/mL and allowed to collect ~5000 colonies.

value: {delta}tipF pSA607


title: 38C_CHX_1


title: 38C_DMSO_3


title: 34C_CHX_3


title: 34C_CHX_1


title: RNA-Seq_Caulobacter_crescentus_NA1000 (flbDTn)_rep1


title: 34C_DMSO_3


title: RNA-Seq_Caulobacter_crescentus_NA1000(flaF)_rep2

data_processing:
Base calling: RTA SCS.2.6, GERALD.1.5.1
Read sequencing quality control: FastQC v.0.11.5
Alignment: BWA aligner v.0.7.15
Raw counts: HTSeq v0.6p1 (htseq-count)
Normalized counts and differential expression analysis: R/Bioconductor package edgeR v.3.18.1
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xlsx file reporting the RNA-Seq analysis (Raw counts, Normalized counts and differential expression analysis) is organized as follows: Raw_counts: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(ΔflaF)_rep1; column 5: NA1000(ΔflaF)_rep2; Normalized_counts_cpm: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(ΔflaF)_rep1; column 5: NA1000(ΔflaF)_rep2; Diff_expression_analysis : column 1: geneID; column 2: log2FC; column 3: log2CPM; column 4: PValue; column 5: FDR;column 6: gene name; column 7: biotype; column 8: description

growth_protocol: Overnight cultures in PYE of C. crescentus NA1000(WT) and ΔflaF cells (two independent biological replicates) were freshly restarted in 10ml of PYE (starting O.D.660nm~0.05) and incubated at 30°C under agitation to reach an O.D.660nm~0,4.

extract_protocol:
Cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer’s instructions and lysates were homogenized through QiaShredder columns (Qiagen). Total RNA was extracted using the RNeasy® extraction kit (Qiagen). Briefly, RNA was then purified on RNeasy kit column. To remove DNA from samples, a first treatment using the On-column DNase I digestion kit (Qiagen) was performed and RNA was extracted according to manufacturer’s instructions. Extracted RNA was subjected to a second DNase treatment using Promega RQ1 at 1 unit/µg RNA and then purified by phenol/chloroform/isoamyl (Sigma) extraction and ethanol precipitation.
Purified total RNA was submitted to the iGE3 Genomics Platform in the CMU (University of Geneva, Faculty of Medicine) for depletion of ribosomal RNA, library preparation, next generation sequencing and differential expression analysis. The total RNA subjected to library preparation using TruSeq ribodepleted Stranded mRNA (SR100-Illumina Hiseq4000) according to manufacturer’s protocols. The sequencing quality control of the reads was done with FastQC v.0.11.5. For the analysis, the reads were mapped with BWA aligner v.0.7.15 to the NCBI C. crescentus NA1000 reference. The table of counts with the number of reads mapping to each gene feature of the NCBI C. crescentus NA1000 was prepared with HTSeq v0.6p1 (htseq-count). For each experimental series, the differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v.3.18.1.

treatment_protocol: 4ml of each cell cultures are collected and resuspended in 200µl of TE buffer.

value: {delta}flaF


title: MDA-MB-468_shBBOX1_sh1_Rep1


title: 34C_DMSO_1


title: RNA-Seq_Caulobacter_crescentus_NA1000(flaF)_rep1


title: Tn-Seq_Caulobacter_crescentus_NA1000(WT)


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)_rep2


title: 293T G4chip rep2

status: Public on Oct 13 2020

city: Beijing

first: Zheng

last: Tan

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description:
293T-G4P-hg19-rep2.narrowPeak
293T-G4P-hg19-ratio-rep2.bigWig

data_processing:
Clean sequence reads in paired-end fastQ were aligned to the hg19, hg38, mm9, or gal5 genome assembly using Bowtie2 version 2.3.4.3 with the parameters: --no-unal --no-discordant --no-mixed --local and the Sensitive preset
bam files of mapped reads were filtered by samtools view version 1.18 using the following parameters: -q 20 -b -F 0x04
peaks were called using MACS2 version 2.1.1 with the following parameters for Homo sapiens: --format BAMPE --gsize 2.7e9 --qvalue 0.001 --keep-dup 1 --nomodel
peaks were called using MACS2 version 2.1.1 with the following parameters for Mus musculus: --format BAMPE --gsize 1.87e9 --qvalue 0.001 --keep-dup 1 --nomodel
peaks were called using MACS2 version 2.1.1 with the following parameters for Mus musculus: --format BAMPE --gsize 1.1e9 --qvalue 0.001 --keep-dup 1 --nomodel
bigwig files were generated using deeptools bamCompare version 3.1.1 with the following parameters:  --minMappingQuality 20,  --binSize 50, --ignoreDuplicates, --operation ratio; Scores represent fold change over input
Genome_build: hg19, hg38, mm9, gal5
Supplementary_files_format_and_content: Bigwig files were obtained using deeptools bamCompare version 3.1.1 with the follwing parameters: --minMappingQuality 20 --ignoreDuplicates  --binSize 50 --normalizeUsing RPKM --scaleFactorsMethod None  --effectiveGenomeSize 2701495761 --centerReads --operation subtract
*subtract-rep*.bigWigs: bigwig files were generated using deeptools bamCompare version 3.1.1 with the following parameters:   --minMappingQuality 20, --binSize 50, --ignoreDuplicates, --operation subtract; Scores represent signal with input signal subtracted.
Supplementary_files_format_and_content: PQS-hg19.BigBed: Chromosome sequence files (hg19) in fasta format were downloaded from the UCSC website (http://genome.ucsc.edu/). PQS motifs (i.e., 4G, 4GL15, Bulge, and GVBQ) were identified and output as bed files using home-made Perl scripts. BigBed files were obtained using the UCSC bedToBigBed tool on the PQS motif bed files.

source_name: Embryonic kidney

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1× penicillin-streptomycin.

extract_protocol:
Nuclei were fragmented using dsDNase (Invitrogen, EN0771) , and the protein-DNA complexes were isolated with anti-FLAG magnetic beads (Sigma, M8823).
Ther library construction was prapared using the NEBNext Ultra II DNA LibraryPrep Kit for Illumina (NEB, E7645) according to the manufacturer's instructions.

value: Embryonic kidney cells

tag: biosample

value: cell line


title: HeLa-S3 G4chip rep1

description:
HeLa-S3-G4P-hg19-rep1.narrowPeak
HeLa-S3-G4P-hg19-ratio-rep1.bigWig

source_name: Cervical carcinoma

value: Cervical carcinoma cells


title: 293T G4chip rep1

description:
293T-G4P-hg19-rep1.narrowPeak
293T-G4P-hg19-ratio-rep1.bigWig


title: DF-1 G4chip rep1

description:
DF-1-G4P-gal5-rep1.narrowPeak
DF-1-G4P-gal5-ratio-rep1.bigWig

organism: Gallus gallus

source_name: Embryonic fibroblast

value: Embryonic fibroblast cells


title: H1975 input rep1

description:
H1975-G4P-hg19-rep1.narrowPeak
H1975-G4P-hg19-ratio-rep1.bigWig

source_name: Lung

value: Lung cells


title: A549 G4chip rep1

description:
A549-G4P-hg19-rep1.narrowPeak
A549-G4P-hg19-ratio-rep1.bigWig

source_name: Epithelial

value: Epithelial cells


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)_rep1


title: Brain_stroke_rep3

status: Public on Jul 29 2020

city: Albuquerque

first: Tamara

last: Roitbak

address: 1 University of New Mexico

institute: University of New Mexico

description: Brain_stroke_rep3  Temporal lobe tissue removed during chemicraniectomy/stroke-ectomy procedure. Patient with malignant hemispheric stroke.

data_processing:
Each sequencing library was analyzed by CLC Genomics Workbench (version20.0.2) using the QIAseq miRNA Quantification workflow and RNA-seq Analysis tool
Briefly, sequence reads were trimmed for adapter sequence, grouped by Unique Molecular Identifiers (UMIs), mapped to miRBase (v22) and miRNA expression calculated by counting the number of distinctive UMI reads corresponding to each miRBase -annotated miRNA
Genome_build: miRBase(v22) - mature.fa
Supplementary_files_format_and_content: tab demlimited text file containing raw counts for all samples
Supplementary_files_format_and_content: GSE155257_Normalized_Counts_All_Samples.xlsx: Excel file includes normalized counts for all samples; whole transcriptome analysis data.
Supplementary_files_format_and_content: GSE155257_Diff_gene_expression.xlsx: Excel file includes differential gene expression in human stroke brain tissue versus control samples.

source_name: temporal lobe

growth_protocol: Tissue specimens were cut longitudinally to obtain two mirror samples from the same tissue block. One portion of the brain tissue was fixed in 10% neutral buffered formalin and subjected to sectioning and histological staining, followed by morphological evaluation. Another “mirror” part of each sample was stored in RNA later and subsequently frozen at -70o C, for further gene and microRNA analysis.

extract_protocol:
Each sample was stored in RNA later and subsequently frozen at -70°C.
miRNA was isolated using the QIAseq miRNA Library kit and sequenced on Illumina NextSeq500

value: brain

tag: disease state

value: stroke


title: Brain_stroke_rep5

description: Brain_stroke_rep5  Temporal lobe tissue removed during chemicraniectomy/stroke-ectomy procedure. Patient with malignant hemispheric stroke.

value: Male


title: DF-1 input rep1


title: 3T3 input rep1

description:
3T3-G4P-mm9-rep1.narrowPeak
3T3-G4P-mm9-ratio-rep1.bigWig


title: HeLa-S3 input rep1


title: H1975 input rep2

description:
H1975-G4P-hg19-rep2.narrowPeak
H1975-G4P-hg19-ratio-rep2.bigWig


title: 293T input rep1


title: 293T input rep2


title: 3T3 G4chip rep1


title: H1975 G4chip rep1


title: A549 input rep1


title: Brain_non-stroke_rep3

description: Brain_non-stroke_rep3. Source: Temporal lobe biopsy samplescollected  from the tissue adjacent to the tumor, or tissue removed when accessing a deep tumor.  Identified by the pathologist as “normal”, based on the absence of gliosis, necrosis, or tumor cells.

value: normal

value: Female


title: Brain_non-stroke_rep2

description: Brain_non-stroke rep2 Source: Temporal lobe biopsy samplescollected  from the tissue adjacent to the tumor, or tissue removed when accessing a deep tumor.  Identified by the pathologist as “normal”, based on the absence of gliosis, necrosis, or tumor cells.


title: A549 input rep2

description:
A549-G4P-hg19-rep2.narrowPeak
A549-G4P-hg19-ratio-rep2.bigWig


title: A549 G4chip rep2


title: Brain_stroke_rep2

description: Brain_stroke_rep2  Temporal lobe tissue removed during chemicraniectomy/stroke-ectomy procedure. Patient with malignant hemispheric stroke.


title: 786-O_USP37_sgscr_Rep3

status: Public on May 27 2020

city: Boston

first: Jeremy

last: Simon

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Reads were filtered for adapter contamination using cutadapt (Martin, 2011) and filtered such that at least 90% of bases of each read had a quality score > 20.
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments (Dobin et al., 2013). Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon (Patro et al., 2017b). Differential expression was detected and Variance-stabilizing transformed (VST) expression values were computed using DESeq2 (Love et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: Batch corrected, VST-normalized expression values from DESeq2

source_name: 786-O cells

growth_protocol: 786-O cells were cultured in DMEM containing 10% fetal bovine serum (FBS) plus 1% penicillin streptomycin. For lentivirus packaging and infection, following lentivirus infection, cells were maintained in the presence of blasticidin (10 μg/ml) or puromycin (2 μg/ml) depending on the vector. All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA from 786-O cells (triplicates) was extracted by using RNeasy kit with on column DNase digestion (Qiagen)
Libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500 with paired-end 150 bp reads

treatment_protocol: SgRNA sequences targeting USP37 and HIF2a were cloned into pLenti CRISPR-V2 puro. 293T packaging cell line was used for lentivirus generation. Lentiviral infection was performed as previously described (25). Briefly, post-transfection with lipofectamine 3000, medium containing viruses was collected twice after 48 and 72 hours. After passing through 0.45 μM filters, an appropriate amount of virus was used to infect target cells in the presence of 8 μg/ml polybrene (sc-134220, Santa Cruz). After incubation for additional one day, target cell lines were selected with appropriate antibiotic.

value: 786-O cells


title: H1975 G4chip rep2