title: BCKDK rep1 H3K27ac h9coD35 SVA-KO


title: GF333_seedling

status: Public on Jan 17 2022

type: SRA

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

country: USA

institute: Kansas State University

description: TPM was estimated using Kallisto

library_source: transcriptomic

data_processing:
All high confidence (HC) and low confidence (LC) gene models from the IWGSC RefSeq v. 1.0, as well as de novo assembled transcripts were combined for estimating the TPM values using Kallisto (v. 0.4.6.0). Gene models with expression standard deviation > 0.5 and expressed (TPM > 0.5) in at least 2 samples have been used in our analyses. This set of genes included 52,511 HC gene model, 29,226 LC gene model and 13,861 de novo assembled transcripts.
Supplementary_files_format_and_content: The TPM values for all expressed HC and LC gene models are provided as an expression data matrix. The file format is gzipped text.

molecule: total RNA

organism: Triticum aestivum

source_name: seedling

extract_protocol: A panel of diverse 400 wheat lines was selected based on the geographic distribution and genetic diversity, and available from the USDA National Small Grains Collection. Total RNA was isolated from 2-week seedlings of 204 lines with each line grown in three biological replicates. Ground tissues from three biological replicates were combined in equal amounts before RNA isolation using RNeasy Plant mini kit. RNA-seq libraries were prepared with TruSeq™ RNA Sample Prep Kit (Illumina) using the Beckman’s Biomek® FXP Laboratory Automation Workstation. Up to eight barcoded RNA-seq libraries were pooled per lane of NextSeq2000 flow cell to generate 2 x 100 bp reads.

tag: age

value: two week seedling

tag: tissue

value: leaf

tag: line


title: GF334_seedling

description: TPM was estimated using Kallisto


title: MBG3

city: New York

first: Joshua

middle: M

last: Weiss

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
md5sum to confirm files copied to server without corruption; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 (Ensemble version 81) and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited text file for every sample with raw counts for every gene
Supplementary_files_format_and_content: table with raw counts for every gene and every sample with genes annotated

organism: Danio rerio

source_name: Zebrafish body skin

extract_protocol:
Cells were FACS sorted into TRIZOL LS and snap-frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng, all having RIN scores > 7.
Reverse transcription and cDNA amplification were performed with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration (Qubit), size distribribution (Agilent Bioanalyzer).

tag: strain

value: Wildtype melanocyte model (Caspers with MiniCoopR-eGFP)

tag: anatomic location

value: Body

tag: gfp+ or gfp-

value: GFP+


title: BCKDK rep3 H3K4me3 h9coD35 SVA-KO

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

library_source: genomic

data_processing:
Trimming of reads: trimmomatic (0.36). ChIP:  leading and trailing bases below quality 3, cutting when average quality per base in a 4-base sliding window is below 15, and dropping reads below a length of 40. RNA: cutting when average quality per base in a 4-base sliding window is below 20, and dropping reads below a length of 30.
Mapping of reads: ChIP: bowtie2 (2.3.3.1) on NCBI hg38 analysis set (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna) with the following settings: --end-to-end --very-sensitive -X 700 -I 50 -q --mm. Duplicates were removed using samtools (1.9) view/sort/rmdup and true multi-mapping reads were filtered out using samtools view -q 2. RNA: HISAT2 (Galaxy Version 2.1.0+galaxy5) on hg38.
Peak calling ChIP: MACS2 (version 2.2.6) callpeak -f BAM -g 2.9e9 --broad --nomodel --nolambda
Assigning reads to features: featureCounts (Galaxy Version 1.6.4+galaxy2)
Coverage tracks: ChIP: bedtools (v2.17.0) genomecov (-bga). RNA: bamCoverage (Galaxy Version 3.3.2.0.0) from the deeptools2 package.
Scaling and merging of replicates: bamCoverage (Galaxy Version 3.3.2.0.0) and wiggletools mean.
Genome_build: hg38 and hg19 (only P300 data)
Supplementary_files_format_and_content: bed.trk = MACS2 output bed file with first line specifying information for uploading to UCSC genome browser.
Supplementary_files_format_and_content: broadPeak = MACS2 output.
Supplementary_files_format_and_content: tabular = featureCounts output for RNA-seq data.

molecule: genomic DNA

organism: Homo sapiens

source_name: cortical organoids day 35

growth_protocol: For cortical organoid formation, hESC colonies were grown on mouse embryonic fibroblasts in daily refreshed hESC medium (DMEM-F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM Non-Essential Amino Acids solution (Gibco), 100 µM 2-mercaptoethanol (Gibco)) and fresh 8 ng/ml bFGF (Sigma)). Colonies of 1-2 mm were transfered to 60 mm ultra low attachment dishes (corning) in 99% hESC medium supplemented with 1 mM sodium pyruvate (Gibco). The next day, media was replaced for differentiation media with fresh 3 µM IWR-1-Endo, 1 µM Dorsomorphin, 10 µM SB-431542 hydrate, and 1 µM Cyclopamine hydrate and changed every other day. On day 3, the dish was placed on a rocker. From day 18 onwards, organoids were cultured in Neurobasal/N2 media (Neurobasal (Gibco) supplemented with 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x N-2 supplement (Gibco)) with 1 µM Cyclopamine hydrate, and from day 24 onwards, no inhibitors were added anymore.

extract_protocol:
Organoids were rinsed in medium, homogonized in a 2ml Kontes Glass Co. dounce and immediately crosslinked after. Cells were lysed, chromatin was sheared to ~400bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform (1:1) and one chloroform extractions followed by DNA precipitation in ethanol and a Zymo DNA Clean & Concentrator clean-up.
TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications: DNA clean & concentrator-5 kit (Zymo research) was used instead of beads for DNA purification. Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified.
ChIP-seq 75bp paired end reads on a NextSeq 550 device.

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the SVA near BCKDK, before cortical organoid formation

tag: cell type

value: h9ESC derived cortical organoids

tag: chip antibody

tag: genotype

value: BCKDK-SVA-KO


title: GF336_seedling

description: TPM was estimated using Kallisto


title: XFG3

source_name: Zebrafish fins

value: Acral melanoma model (Caspers with MiniCoopR-eGFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6-nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA)

value: Fin


title: GF343_seedling

description: TPM was estimated using Kallisto


title: BCKDK rep1 H3K4me3 h9coD35 SVA-KO


title: GF342_seedling

description: TPM was estimated using Kallisto


title: GF345_seedling

description: TPM was estimated using Kallisto


title: BIN1 rep4 H3K4me3 h9coD35 SVA-KO

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the SVA near BIN1, before cortical organoid formation


title: GF344_seedling

description: TPM was estimated using Kallisto


title: XBG3


title: BIN1 rep1 H3K27ac h9coD35 SVA-KO


title: XBN3

value: GFP-


title: F1_rep1

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.0.13 (bowtie2-2.2.3), which can adequately align reads onto the location including splice sites in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.6 software (Agilent Technologies). The read counts allocated for each gene and transcript (UCSC version 2013.3.6) were quantified using a Trimmed Mean of M-value (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for every gene and every sample (all data are summarized in single file)

organism: Mus musculus

source_name: Prefrontal cortex

extract_protocol:
Prefrontal cortex tissues were removed, flash frozen on dry ice, and RNA was extracted using Direct-zol RNA kit. SureSelect Strand-Specific RNA Library Prep for Illumina (Agilent Technology) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols.

value: Prefrontal cortex

value: BALB/c

tag: treatment

value: Sertraline

tag: behavior

value: Responder


title: BIN1 rep2 H3K27ac h9coD35 SVA-KO


title: E1_rep2

value: water

value: Control


title: MFG2


title: BCKDK rep4 H3K4me3 h9coD35 SVA-KO


title: GF347_seedling

description: TPM was estimated using Kallisto


title: MFN2


title: BIN1 rep2 H3K4me3 h9coD35 SVA-KO


title: BIN1 rep1 H3K4me3 h9coD35 SVA-KO


title: MBN2


title: BIN1_rep3_H3K27ac_h9coD35_SVA-KO


title: MBG2


title: GF348_seedling

description: TPM was estimated using Kallisto


title: EV rep3 H3K27ac h9coD35 SVA-KO

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid before cortical organoid formation

value: WT


title: XFN2


title: XFG2


title: XFN3


title: GF341_seedling

description: TPM was estimated using Kallisto

value: two week seedling


title: GF359_seedling

description: TPM was estimated using Kallisto

value: leaf


title: GF36_seedling

description: TPM was estimated using Kallisto


title: XBN2


title: GF360_seedling

description: TPM was estimated using Kallisto


title: MFG1

value: Wildtype melanocyte model (Caspers with MiniCoopR-eGFP)


title: XBG2

value: Body


title: hEBw5 P300 rep2B

extract_protocol:
Organoids were rinsed in medium, homogonized in a 2ml Kontes Glass Co. dounce and immediately crosslinked after. Cells were lysed, chromatin was sheared to ~500bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform:iso-amyl-alcohol(25:24:1) and 2 chloroform:iso-amyl-alcohol(24:1) extractions followed by DNA precipitation in ethanol and Zymo PCR purification columns.
TruSeq DNA Sample Preparation kit (Illumina), following the Low Throughput guidelines with the following additions: Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified. For adapter ligations, 1 ul instead of 2.5 ul of DNA Adapter Index was used.
ChIP-seq 100bp paired end reads on a Illumina HiSeq 2000 device, trimmed to 85bp for mapping


title: GF363_seedling

description: TPM was estimated using Kallisto


title: GF364_seedling

description: TPM was estimated using Kallisto


title: EV rep1 H3K27ac h9coD35 SVA-KO


title: GF362_seedling

description: TPM was estimated using Kallisto


title: GF366_seedling

description: TPM was estimated using Kallisto


title: XFG1

value: GFP+


title: GF361_seedling

description: TPM was estimated using Kallisto


title: XFN1


title: hEBw5 P300 rep1B

value: h9ESC derived cortical organoids


title: GF37_seedling

description: TPM was estimated using Kallisto


title: MBN1


title: EV rep2 H3K27ac h9coD35 SVA-KO


title: EV rep2 H3K4me3 h9coD35 SVA-KO


title: hEBw5 P300 rep1A


title: GF346_seedling

description: TPM was estimated using Kallisto


title: XBN1


title: GF358_seedling

description: TPM was estimated using Kallisto


title: GF370_seedling

description: TPM was estimated using Kallisto


title: MBG1


title: huESC P300 rep2

source_name: hESCs

growth_protocol: hESC colonies were grown on mouse embryonic fibroblasts in daily refreshed hESC medium (DMEM-F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM Non-Essential Amino Acids solution (Gibco), 100 µM 2-mercaptoethanol (Gibco)) and fresh 8 ng/ml bFGF (Sigma)).

extract_protocol:
hESCs were crosslinked, cells were lysed, chromatin was sheared to ~500bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform:iso-amyl-alcohol(25:24:1) and 2 chloroform:iso-amyl-alcohol(24:1) extractions followed by DNA precipitation in ethanol and Zymo PCR purification columns.
TruSeq DNA Sample Preparation kit (Illumina), following the Low Throughput guidelines with the following additions: Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified. For adapter ligations, 1 ul instead of 2.5 ul of DNA Adapter Index was used.
ChIP-seq 100bp paired end reads on a Illumina HiSeq 2000 device, trimmed to 85bp for mapping


title: GF371_seedling

description: TPM was estimated using Kallisto


title: MFN1


title: XBG1


title: huESC P300 rep1


title: EV rep3 H3K4me3 h9coD35 SVA-KO


title: EV rep1 H3K4me3 h9coD35 SVA-KO


title: hEBw5 P300 rep2A


title: rad21, wt, head, e11.5

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, genomic enrichment

source_name: E11.5 head

growth_protocol: Dissected E11.5 heads from WT embryos were pooled and frozen in a dry-ice bath

extract_protocol:
Pellets from 30Million cells were lysed in Farnham lysis buffer (5mM PIPES PH 8.0, 85mM KCl, 0.5% NP-40, supplemented with protease inhibitors). To lyse cells, pellets were reconstituted in 1ml buffer/ 10 million cells and incubated on ice for 10 mins, following which they were dounced and then centrifuged at 2000g, at 40C for 5 mins. The pelleted nuclei were then resuspended in 500µl RIPA (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH8, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS, supplemented with ROCHE Complete protease inhibitor tablets (no EDTA), mixed gently by pipetting, and incubated on ice for 10 mins to achieve complete lysis. Extracted chromatin was then sonicated using Bioruptor (40 cycles of 30’ on and 30’, paused on ice for 5mins, repeated 10 cycles of 30’ on and 30’). Sonicated material was then spun down at 20000g, at 40C for 15 mins. Supernatant was collected in fresh tubes and chromatin was quantified using Qubit high sensitivity DNA kit. 30µg of chromatin was used for the ChIP reactions in a total reaction volume of 1ml, adjusted with RIPA. 30 µl of Protein A/G beads pre-conjugated to 2 µg antibody (by incubation of antibody with washed beads resuspended in 500µl RIPA for 3h) was added to the reaction and chromatin was capture by overnight incubation at 40C, on a rotating platform. The next day, captured chromatin was washed successively as follows: once in low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), twice in lithium chloride wash buffer (250mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice in 1X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Bound chromatin was then eluted in 200 µl freshly prepared direct elution buffer (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA pH8, 0.5% SDS) supplemented with 2 µl RNAse A (10 mg/ml), by incubating on a thermomixer at 650C, at 800 rpm, overnight. The next day, the beads were discarded, and the supernatant was incubated with 3 µl of Proteinase K (20mg/ml) at 550C, 1200rpm, for 2h to reverse crosslinks. DNA was then eluted in 20 µl deionized water using the Zymo DNA Clean and Concentrator kit (Zymo, D4033).
DNA was isolated using the Zymo DNA Clean and Concentrator kit. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0.
PE50

treatment_protocol: Thawed samples were dissociated with mortar and pestle and transferred to 10ml of cold PBS and added 1ml of crosslinking buffer (0.1M NaCL, 1mM EDTA, 0.5mM EGTA, 50mM HEPES pH8.0, 11% formaldehyde). Samples were fixed for 20mins at RT and 1 ml of Glycine 1.4M was added to stop fixation.

value: E11.5 head

value: wt

value: anti-Rad21 antibody (ab154769, Abcam)


title: GF38_seedling

description: TPM was estimated using Kallisto


title: GF374_seedling

description: TPM was estimated using Kallisto


title: TCFL5-eCLIP-rep2

city: Nanjing

first: Weiya

last: Xu

state: Jiangsu

address: No. 818, Tianyuan East Road

department: State Key Laboratory of Reproductive Medicine

country: China

institute: Nanjing Medical University

data_processing:
The clean reads were evaluated using FastQC
Clean reads were aligned to the mouse GRCm38 genome (mm10) by HISAT2
Peaks were called on IP sample using the CLIPper tool
Identified peaks were normalized to the appropriate size-matched input control with ‘Peak_input_normalization_wrapper.pl’ (https://github.com/YeoLab/gscripts) with criteria: p≤10−5 and fold-enrichment ≥8.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig files were created using the program wigToBigWig on the UCSC http server, representing RNA sequencing reads mapped into reference genome.

source_name: testes

extract_protocol:
Lysates were clarified from UV light-treated testicular  seminiferous tubules. protein-RNA complexes were isolated with antibody.
RNA adapter X1A and X1B were ligated to RNA 3’ ends dephosphorylated by FastAP Alkaline Phosphatase (EF0652, Thermo Fisher Scientific). Immunoprecipitation beads were eluted for 10 min at 70°C using washing buffer. Sample were analyzed by NuPAGE (4%–12% gradient precast gels run with MOPS buffer). Cross-linked RNA-protein complexes were transferred onto nitrocellulose membrane (1060008, Amersham Protran Premium GE). Then the membrane was cut from the protein band to 75 kDa above it and RNA was purified using acid phenol/chloroform/isoamyl alcohol (25:24:1) (P1011, Solarbio). RNA adapter RiL19 was ligated to input RNA 3’ ends dephosphorylated by FastAP Alkaline Phosphatase. AR17 primer was used to reverse transcript all RNA and Rand103Tr3 adapter was ligated to cDNA 5’ ends. The ligated cDNA were purified with MyONE Silane beads (37002D, Thermo Fisher Scientific), quantified by qRCR, and amplified with Q5 PCR master mix (M0492L, NEB). The amplified cDNA were run in 3% low melting temp agarose gel (50180, Lonza), cut from 175bp to 350bp, and extracted with QIAGEN gel extraction kit. The cDNA libraries were sequenced on an Illumina NovaSeq.

value: testis

value: post natal day 21

value: TCFL5(Abcam, Ab188075)


title: GF380_seedling

description: TPM was estimated using Kallisto


title: GF381_seedling

description: TPM was estimated using Kallisto


title: TCFL5-eCLIP-rep1


title: GF39_seedling

description: TPM was estimated using Kallisto


title: GF383_seedling

description: TPM was estimated using Kallisto


title: DEREG+ sample 6 - Cell Surface Proteins

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description:
exp07_W3_Treg_processed_data_set_1_pre_filtering.rds
exp07_W3_Treg_processed_data_set_1_pre_filtering.txt
exp07_W3_Treg_processed_data_set_2_filtered.rds
exp07_W3_Treg_processed_data_set_2_filtered.txt

data_processing:
Cellranger 5.0.0 mkfastq was used for base-calling and demultiplexing by unique 8-base indices.
Cellranger 5.0.0 count was used to align reads to reference transcriptome mm10 and quantifying read antibody counts.
The surface protein counts were used to find the origin of each cell (identified by barcode) in pooled experiment. The limit for raw cell surface protein count was determined by in-house script that allowed to identify cells from this experiment and separate them from cells from unrelated, unpublished experiment (cells marked by Mouse Hashtag 1 - 4), empty droplets and cellular doublets.
The reads were demultiplexed into separate samples by barcodes based on raw counts of cell surface proteins of each cell.
Demultiplexed reads were re-aligned to reference transcriptome mm10 with cellranger 5.0.0 count.
Normalization, scaling, identification of variable features, generation of PCA and UMAP projections and clustering were performed using R package Seurat 4.0.3.
Cellular types were annotated using SingleR v1.0.1.
Clusters consisting of dead/contaminating cells were removed.
Steps from log-normalization to clustering were repeated on filtered data set using R package Seurat 4.0.3. The cell cycle scores were using to regress out cell cycle phases during scaling step.
Genome_build: mm10
Supplementary_files_format_and_content: rds files of completed and analyzed data-set in form of SeuratObject containing raw counts, log-normalized counts, detected variable features, UMAP and PCA dimensional reductions, clustering and cell type annotation generated before the removal of dead/contaminating cell types (pre_filtering) and after filtering them (filtered).
Supplementary_files_format_and_content: txt files describing the meta-data content of SeuratObjects within respective rds files.

source_name: DEREG+ RIP-OVA recipient mice

growth_protocol: Female 6 weeks old DEREG- RIP.OVA (n=3) and DEREG+ RIP.OVA (n=3) littermate mice were treated with diphtheria toxin (0.250 µg per mouse in 0.5 ml of PBS, i.p.) on days -2 and -1 prior to the immunization, followed by i.v. injection of 5 × 10^4 OT-I T cells in 200 µl of PBS on day -1. OT-I T cells were obtained from spleens and lymph nodes of Ly5.1 OT-I Rag2-/- mouse. On day 0, mice received Ly5.1 dendritic cells loaded with OVA (10^6 cells per mouse in 200 µl of PBS).

extract_protocol:
The viable CD8a+, CD45.1+, CD45.2- cells were FACS sorted.
The library was built following the  Feature  Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D) using the Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10x Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084).

treatment_protocol: The mice were sacrificed on day 3 after immunization and their spleens were collected. Erythrocytes were lysed with ACK (2 min, on ice), cells were washed and resuspended in PBS/ 2% FBS. Cells were stained with LIVE/DEAD near-IR dye, anti-CD8a BV421, anti-CD45.1 PE, and anti-CD45.2 APC antibodies together with TotalSeq-C anti-mouse hashtag antibodies (Mouse Hashtag 1 - 10, only cells stained with Mouse Hashtag 5 - 10 are related to this experiment).

value: Spleen

tag: sample type

value: HTO

value: CD8+ T cells

value: Ly5.1 OT-I Rag2-/-


title: DEREG+ sample 6 - Gene Expression

value: mRNA


title: DEREG+ sample 4 - Cell Surface Proteins


title: DEREG+ sample 4 - Gene Expression


title: GF41_seedling

description: TPM was estimated using Kallisto

value: two week seedling


title: GF4_seedling

description: TPM was estimated using Kallisto

value: leaf


title: DEREG+ sample 2 - Cell Surface Proteins


title: DEREG- sample 5 - Cell Surface Proteins

source_name: DEREG- RIP-OVA recipient mice


title: DEREG+ sample 2 - Gene Expression


title: GF42_seedling

description: TPM was estimated using Kallisto


title: GF43_seedling

description: TPM was estimated using Kallisto


title: Input


title: DEREG- sample 3 - Cell Surface Proteins


title: GF387_seedling

description: TPM was estimated using Kallisto


title: DEREG- sample 5 - Gene Expression


title: DEREG- sample 3 - Gene Expression


title: GF45_seedling

description: TPM was estimated using Kallisto


title: HEK293_NSP1_noActD_1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
MARS-seq Raw data was processed using UTAP (Kohen et al. 2019) with default parameters.
Corrected counts were normalized by mouse PolyA+ enriched RNA, which was mapped to mouse genome  using STAR (17) not allowing mismatches. Percent of uniquely mapped reads per sample  was used as a normalization factor. Biological replicates were averaged and means were  used for fitting a nonlinear least-squares model assuming first-order decay kinetics:  C=C0*e-kdecayt, while corrected counts at t=0 were used as C0 and inverse of standard  errors of the corrected count means were used as weights for fitting. Half lives of all genes  were then calculated using the following equation: t1/2=ln(2)/kdecay. Genes with mean  corrected read count < 5 at t=0 were removed from subsequent analysis. Negative half  life values and half lives > 24h were set to 24h.
Genome_build: hg19
Supplementary_files_format_and_content: An  spreadsheet including calculated half-life values (using MARS-seq data) and transcript characteristics

molecule: polyA RNA

source_name: HEK293 cell line

growth_protocol: The cells were grown  in DMEM media (Gibco) supplemented with 10% bovine serum and 1%  penicillin/streptomycin (Gibco) in 5%CO2-buffered incubators at 37°C.

extract_protocol:
Total RNA was isolated from HEK293T cells using Bio Tri RNA reagent (Bio-lab) and  mRNA was captured using Oligo d(T)25 magnetic Beads (NEB) according to  manufacturer’s protocol.
Poly(A)-purified RNAs were taken for library preparation using a  derivation of MARS-seq as described (15). Briefly, 10 ng of poly(A)+ RNA was taken for  the first reverse transcription reaction using illumina barcoded RT1 primer. Resultant  barcoded cDNA samples were subsequently pooled according to Ct values of housekeeping gene (GAPDH) (Quality control 1). Pooled cDNA was treated with Exonuclease  I to remove excess primers followed by second strand synthesis using NEB SSS module  enzyme mix. After that, in-vitro transcription was performed using NEB T7 RNA Pol mix  to generate RNA, which was later fragmented and ligated to an adaptor consisting of RD2  using T4 RNA ligase I (NEB) followed by the second reverse transcription reaction. The  library so formed was amplified using Kapa Hifi ready mix (Roche). The amplified RNA  libraries were sequenced using high-throughput 75 bp kit (Illumina FC404-2005) on  NEXTseq 500 sequencer.

treatment_protocol: Actinomycin D (7.5µg/ml) for 0,2,4, and 6 hours

tag: cell line

tag: genotype/variation

value: SARS-CoV-2 NSP1 expression

value: no ActD

tag: library preparation

value: MARS-seq


title: HEK293_NSP1_ActD_6h_3

value: ActD, 6h


title: HEK293_NSP1_noActD_2


title: HEK293_NSP1_noActD_3


title: ANV5_P1

type: RNA

city: Pamplona

first: Fernando

last: Lecanda

address: Avda. Pio XII 55

country: Spain

institute: CIMA

description: Triple Negative Breast cancer

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data was normalized using Bioconductor software and RMA algorithm.

label: Biotin

source_name: Parental cell line

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells lines were cultured in complete RPMI medium.

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells lines were washed twice with PBS at 4ºC prior RNA purification.


title: GF44_seedling

description: TPM was estimated using Kallisto


title: ANV5_P3

description: Triple Negative Breast cancer


title: ANV5_P2

description: Triple Negative Breast cancer


title: ANV5_720_1

description: Triple Negative Breast cancer

source_name: Relapsed cell line


title: ANV5_720_3

description: Triple Negative Breast cancer


title: ANV5_701_3

description: Triple Negative Breast cancer


title: ANV5_720_2

description: Triple Negative Breast cancer


title: HEK293_NSP1_ActD_6h_2


title: ANV5_701_2

description: Triple Negative Breast cancer


title: DEREG- sample 1 - Cell Surface Proteins


title: GF391_seedling

description: TPM was estimated using Kallisto


title: GF46_seedling

description: TPM was estimated using Kallisto


title: HEK293_NSP1_ActD_4h_3

value: ActD, 4h


title: GF47_seedling

description: TPM was estimated using Kallisto


title: DEREG- sample 1 - Gene Expression


title: GF5_seedling

description: TPM was estimated using Kallisto


title: FAP_DABT scRNA-seq

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Libraries were processed through CellRanger v2.1.0 [1], aligned to mouse genome version mm10.
Genome_build: Mus_musculus.GRCm38 - mm10
Supplementary_files_format_and_content: Counts data for single cell RNA-seq

source_name: Fibro-adipogenic progenitors

extract_protocol:
Skeletal muscles were harvested from hind limbs of mice from PBS or Doxo or Doxo+ABT experimental groups. Skeletal muscles from 5 mice were combined for each experimental group. For skeletal muscle dissociation, a kit from Miltenyi Biotech was used (cat#130-098-305). The muscles were chopped into 2-4 mm pieces and enzymatic digestion was performed as described in the product datasheet using as recommended kit enzymes, C Tubes, (Company: Miltenyi, Cat# 130-096-334), and gentleMACS Octo Dissociator with Heaters (cat# 130-096-427). After digestion of the muscle samples, Debris Removal Solution (Company: Miltenyi, cat#130-109-398) was used to achieve cleaner single-cell suspension of muscle tissues. The single cell suspension was stained with CD31, CD45, Sca1, a7, and PDGFRa for FACS (FACS Aria II, BD Bioscieneces). FAPs were identified as Sca1+, PDGFra+, CD31-, CD45- and a7-integrin- and SCs were identified as a7-integrin+, Sca1-, PDGFra-, CD31-, and CD45- {Joe, 2010 #46;Liu, 2015 #47}.
Nuclei were isolated from the biopsies using the Singulator instrument (S2 Genomics).  The instrument was primed with cold nuclei isolation and storage buffers (S2 Genomics) and the biopsy was loaded into the cartridge and covered with the 19.7 mm grinding cap.  The “Nuclei_All_Tissues” protocol was used to isolate nuclei, after which the nuclei were centrifuged for 5 minutes and resuspended in buffer.  The nuclei were counted using a Countess II Automated Cell Counter (Invitrogen), centrifuged again for 5 minutes and resuspended at the proper concentration for use in the Chromium Single Cell 5’ Library and Gel Bead Kit v1 (10X Genomics).
The FAP cells and SCs were isolated using FACS. Cell samples were then prepared for 10X single-cell RNA seq protocol to target 10K cells. The 3’ single-cell RNA seq library preparation was performed by following 10X kit protocol. The QC for cDNA and libraries were performed using Tapestation according to the 10X protocol. Sequencing of the resultant libraries was then performed on Illumina sequencers as per manufacturers protocols.
Samples were processed using the Chromium Single Cell A Chip Kit and Chromium Controller (10X Genomics).  Quality control was performed on the Tapestation 4200 (Agilent Technologies).  Libraries were sequenced in one lane of a NovaSeqS4 by the U.C. Davis Genomics Core.

value: Fibro-adipogenic progenitors


title: FAP_DOXO scRNA-seq

value: DOXO


title: HEK293_NSP1_ActD_4h_2


title: HEK293_NSP1_ActD_4h_1


title: GF51_seedling

description: TPM was estimated using Kallisto


title: FAP_PBS scRNA-seq

value: PBS


title: GF50_seedling

description: TPM was estimated using Kallisto


title: GF52_seedling

description: TPM was estimated using Kallisto


title: ANV5_701_1

description: Triple Negative Breast cancer


title: SAT_DOXO scRNA-seq

source_name: Satellite cells

value: Satellite cells


title: HEK293_NSP1_ActD_2h_2

value: ActD, 2h


title: GF53_seedling

description: TPM was estimated using Kallisto


title: SAT_DABT scRNA-seq


title: GF54_seedling

description: TPM was estimated using Kallisto


title: SAT_PBS scRNA-seq


title: HEK293_GFP_noActD_3

value: GFP expression


title: HEK293_NSP1_ActD_2h_1


title: GF55_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_noActD_2


title: HEK293_GFP_noActD_1


title: HEK293_NSP1_ActD_6h_1


title: GF57_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_ActD_6h_3


title: HEK293_GFP_ActD_6h_2


title: GF59_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_ActD_6h_1


title: HEK293_NSP1_ActD_2h_3


title: HEK293_GFP_ActD_4h_3


title: GF62_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_ActD_2h_3


title: HEK293_GFP_ActD_4h_2


title: GF60_seedling

description: TPM was estimated using Kallisto


title: GF61_seedling

description: TPM was estimated using Kallisto


title: GF63_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_ActD_4h_1


title: HEK293_GFP_ActD_2h_2


title: GF6_seedling

description: TPM was estimated using Kallisto


title: GF56_seedling

description: TPM was estimated using Kallisto


title: GF64_seedling

description: TPM was estimated using Kallisto


title: HEK293_GFP_ActD_2h_1


title: GF58_seedling

description: TPM was estimated using Kallisto


title: GF66_seedling

description: TPM was estimated using Kallisto


title: GF67_seedling

description: TPM was estimated using Kallisto


title: AGS1

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvain algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Genome_build: GRCh38
Supplementary_files_format_and_content: Sparse Cellranger matrix

source_name: iPSC-derived neural mixed population

growth_protocol: Human healthy and patient derived iPSC were firstly differentiated into Neural Stem Cell  (NSC), according to the published Dual Smad inhibition protocol (Chambers et al, 2009). Briefly, iPSCs colonies were detached with accutase (Life Technologies), suspended as single cells and plated on Matrigel (BD Pharmingen)-coated dishes(50,000 cells/cm2) in MEF pre-conditioned iPSC medium (IPSCSM) in the presence of 10 μM of the Rho kinase inhibitor Y-27632 (Sigma). When the cell culture reached ≈90% confluence (usually 2 days after plating), the culture medium was replaced with KSR medium (KSRM) supplemented with 200 ng/ml of rhNOGGIN (R&D) and 10 μM of SB431542 (Sigma). The medium was changed daily for the next 3 days. Thereafter, it was switched every other day in order to gradually expose the cells to increasing (1:3, 1:1, 3:1) ratio of NPC/KSR medium. Two days after the last switch, the cells were detached using accutase and plated on Matrigel-coated dishes in NPCM supplemented with 20 ng/ml bFGF and 20 ng/ml EGF. NSC were then further differentiated into more committed cells reaching a mixed neural population following a protocol adapted from  Meneghini et al, 2017; Santos et al, 2017. NSCs, cultured for a maximum of 6 passages, were detached using accutase and plated on Matrigel-coated dishes (20,000 cells/cm2) in NPCM (day0). During the first 4 days after plating (day4) we gradually replaced NPCM containing bFGF and EGF with an increasing amount of GDM, supplemented with 10 ng/ml PDGF-AA, 10 ng/ml NT3, 10 ng/ml IGF-1, 5 ng/ml HGF, and 60 ng/ml T3. From day4 to day13, medium was changed every other day. From day14 to day34, the medium was switched to the one described in Santos et al, supplemented with 10% FBS and 10ng/ml leukemia inhibitory factor (LIF). The neural mixed-cultured obtained at day34 was used for scRNASeq experiment.

extract_protocol:
Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12-14 cycles, according to the available cDNA quantity).
scRNA-Seq libraries were prepared according to the manufacturer’s instructions

value: AGS1 patient derived iPSCs (TREX1:NM_033629.6:c.[260insAG];[290G > A]:p.[S88 fs*22];[R97H])

tag: iPSc generation

value: Sendai viral vector reprogrammed iPSCs


title: AGS2

value: AGS2 patient derived iPSCs (RNaseH2B:NM_024570.3:c.[529G > A, 529G > A]:p.[A177T]; [A177T])


title: GF68_seedling

description: TPM was estimated using Kallisto


title: GF7_seedling

description: TPM was estimated using Kallisto


title: WT-Cl21

value: healthy donor derived iPSCs


title: CAL-29_WC

city: Lodz

first: Damian

last: Kołat

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

description: CAL-29 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) version 2.
Filtering, barcode trimming and error removal was done using AfterQC tool version 0.9.7.
Reads alignment and mapping to human reference genome (hg38) was performed with the use of Burrows Wheeler Aligner version 0.7.1.7. Unmapped reads were then mapped by HISAT version 2.0.5.
CAGE tags were clustered using the improved Paraclu from RECLU pipeline. Clusters having Counts Per Million (CPM) < 0.1 were discarded.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: Bladder cancer

growth_protocol: Cultured in DMEM medium supplemented with 10% heat-inactivated FBS. Medium was also complemented with 1% L-glutamine and 1% Antibiotic-Antimycotic. Cells were incubated at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA was harvested using Extracol reagent, according to manufacturer protocol (EURX, Gdansk, Poland). Quality of total RNA was assessed by Agilent 2100 Bioanalyzer to confirm that RNA Integrity Number is over 7.0.
RNA libraries were prepared for sequencing using CAGE library preparation Kit (K.K. DNAFORM, Kanagawa, Japan).

treatment_protocol: The cells were transduced in starvation medium with 8 µg/mL polybrene and lentiviral particles at MOI = 3. After 24 h of incubation, the viral medium was changed to full medium. Antibiotic-based clone selection was performed using 1 µg/mL puromycin after 72 h. The cellular variants with WWOX overexpression or without (control) were exposed to a second stable transduction (to perform AP-2α or AP-2γ overexpression). Variants were transduced in starvation medium containing 8 µg/mL polybrene and lentiviral particles at MOI = 3. Changing the starvation medium to the full medium after 24 h was followed by clone selection using 400 μg/mL G418 for 3 weeks.

value: Urinary bladder carcinoma


title: GF69_seedling

description: TPM was estimated using Kallisto

source_name: seedling

value: two week seedling

value: leaf


title: CAL-29_WA

description: CAL-29 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: 256T

type: genomic

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Beadchip were scanned using iscan standard recommended Illumina scanner setting

data_processing: Genome studio v2011.1

label: Cy5 and Cy3

source_name: CRC tissue

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from CRC and normal tissues using Qiagen Dneasy kit according to manufacturer protocol

tag: gender

value: M

tag: disease state

value: Tumor


title: 336N

source_name: Normal tissue

value: F

value: Normal


title: 290T


title: 349T


title: GF70_seedling

description: TPM was estimated using Kallisto

tag: age

tag: tissue


title: 289T


title: CAL-29_WK

description: CAL-29 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and lentiviral blank control (K) during second transduction (no overexpression of AP-2α/γ)


title: CAL-29_KC

description: CAL-29 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)


title: GF73_seedling

description: TPM was estimated using Kallisto

tag: line


title: 342T


title: 343T

value: Tumour


title: CAL-29_KK

description: CAL-29 cells treated with lentrivirus blank controls (KK) during first and second stable transduction


title: 325T


title: 344T


title: HT-1376_WC

description: HT-1376 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)

growth_protocol: Cultured in high-glucose (4.5 g/L) DMEM medium supplemented with 15% heat-inactivated FBS. Medium was also complemented with 1% L-glutamine and 1% Antibiotic-Antimycotic. Cells were incubated at 37°C in a humidified atmosphere of 5% CO2.


title: GF75_seedling

description: TPM was estimated using Kallisto


title: GF76_seedling

description: TPM was estimated using Kallisto


title: CAL-29_KA

description: CAL-29 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: GF71_seedling

description: TPM was estimated using Kallisto


title: GF74_seedling

description: TPM was estimated using Kallisto


title: 345T


title: HT-1376_WA

description: HT-1376 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: 348T


title: GF77_seedling

description: TPM was estimated using Kallisto


title: 344N


title: 332T


title: HT-1376_WK

description: HT-1376 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and lentiviral blank control (K) during second transduction (no overexpression of AP-2α/γ)


title: GF78_seedling

description: TPM was estimated using Kallisto


title: HT-1376_KA

description: HT-1376 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: 290N


title: 342N


title: GF81_seedling

description: TPM was estimated using Kallisto


title: 289N


title: RT-112_WC

description: RT-112 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)

growth_protocol: Cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS. Medium was also complemented with 1% L-glutamine and 1% Antibiotic-Antimycotic. Cells were incubated at 37°C in a humidified atmosphere of 5% CO2.


title: GF82_seedling

description: TPM was estimated using Kallisto


title: 256N


title: GF83_seedling

description: TPM was estimated using Kallisto


title: GF84_seedling

description: TPM was estimated using Kallisto


title: 349N


title: HT-1376_KC

description: HT-1376 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)


title: 345N


title: 336T


title: GF8_seedling

description: TPM was estimated using Kallisto


title: RT-112_WK

description: RT-112 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and lentiviral blank control (K) during second transduction (no overexpression of AP-2α/γ)


title: GF85_seedling

description: TPM was estimated using Kallisto


title: HT-1376_KK

description: HT-1376 cells treated with lentrivirus blank controls (KK) during first and second stable transduction


title: RT-112_KC

description: RT-112 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2γ)


title: RT-112_KA

description: RT-112 cells treated with lentrivirus blank control (K) during first transduction (no WWOX overexpression) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: RT-112_WA

description: RT-112 cells treated with pLenti-GIII-CMV-GFP-2A-Puro system during first transduction (to overexpress WWOX) and pLKO-Neo-CMV system during second transduction (to overexpress AP-2α)


title: 348N


title: 332N


title: GF86_seedling

description: TPM was estimated using Kallisto


title: GF87_seedling

description: TPM was estimated using Kallisto


title: RT-112_KK

description: RT-112 cells treated with lentrivirus blank controls (KK) during first and second stable transduction


title: GF88_seedling

description: TPM was estimated using Kallisto


title: 343N


title: scRNA-Seq Day50_KO1

city: Stanford

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

description:
Day50_KO1
single cell RNA-seq

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to call cluster and generate UMAPs
Monocle was used to perform pseudotime analysis
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

source_name: H9 day50

growth_protocol: hESCs were maintained in Essential 8 plus supplement. Medium was changed to Essential 6 plus RA/BMP4 for 7 days to induce differentiation ("day 7") followed by an additional 43 days in keratinocyte media ("day 50").

extract_protocol:
Single cell suspensions were prepared with Accutase, and any large clumps were removed with 40μM cell strainers. Dead cells were eliminated with a dead cell removal kit (Miltenyi) per manufacturer instructions. 10,000 cells at a concentration of 1,000 cells per μL were resuspended in PBS with 0.04% BSA (Miltenyi).
Library prep was performed with a Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics) per manufacturer instructions.

value: KO


title: GF89_seedling

description: TPM was estimated using Kallisto


title: scRNA-Seq Day50_WT2

description:
Day50_WT2
single cell RNA-seq

value: WT


title: 234T


title: scRNA-Seq Day50_KO2

description:
Day50_KO2
single cell RNA-seq


title: GF92_seedling

description: TPM was estimated using Kallisto


title: GF90_seedling

description: TPM was estimated using Kallisto


title: scRNA-Seq Day50_WT1

description:
Day50_WT1
single cell RNA-seq


title: 325N


title: scRNA-Seq Day7_KO2

description:
Day7_KO2
single cell RNA-seq

source_name: H9 day7


title: scRNA-Seq Day7_WT2

description:
Day7_WT2
single cell RNA-seq


title: scRNA-Seq Day7_KO1

description:
Day7_KO1
single cell RNA-seq


title: 154N


title: GF9_seedling

description: TPM was estimated using Kallisto


title: 154T


title: GF97_seedling

description: TPM was estimated using Kallisto


title: scRNA-Seq Day7_WT1

description:
Day7_WT1
single cell RNA-seq


title: GF93_seedling

description: TPM was estimated using Kallisto


title: GF91_seedling

description: TPM was estimated using Kallisto


title: 14T


title: GF72_seedling

description: TPM was estimated using Kallisto


title: HiChIP WT3

data_processing:
HiC-pro pipeline is used to align and generate contact matrix
FitHiChIP is used to call loops and differential loops
HiC file is generate using HiC-pro
The R package Genova was used to perform aggregate peak analysis and to calculate contact probability, insulation scores, and contact domains.
Genome_build: hg38
Supplementary_files_format_and_content: hic file

growth_protocol: hESCs were maintained in Essential 8 plus supplement. Medium was changed to Essential 6 plus RA/BMP4 for 7 days to induce differentiation.

extract_protocol:
Cells were detached from tissue culture plates with Acctuase. 25x106 cells were crosslinked, lysed, and digested with MboI (NEB) for 2 hours at 37°C.
Each sample was split into two reactions to ensure efficient contact generation. Biotin was incorporated onto DNA ends for 1 hour at 37°C, and then ligated with T4 ligase overnight at room temperature. Nuclei were pelleted, resuspended, and sonicated using a Covaris E220. At this point samples were combined back together. Proximity ligations bound to the cohesion complex were enriched by incubating overnight at 4°C using an SMC1A antibody (Bethyl). Biotinylated DNA was pulled out with Streptavidin C-1 beads (Thermo Fisher), which were then subjected to transposition with 1μL Tn5 (Illumina). DNA was amplified with PCR for 5 cycles and size selected with Ampure XP beads (Beckman Coulter).
Cohesin HiChIP

value: Cohesin


title: 14N


title: sample_98

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
TrimGalore 0.4.2 wrapper tool (https://github.com/FelixKrueger/TrimGalore) was used for removing adaptors and quality trimming, applying the default parameters
Individual libraries were mapped to the salmon genome (RefSeq Assembly ICSASG_v2) using the Hisat2 short read aligner version 2.0.4 (Kim et al., 2015) and the refseq gene anntation.
Transcript levels for the individual libraries was estimated using FeatureCounts (Liao et al., 2014) of the Subread package (http://subread.sourceforge.net/).
Read counts were normalized using Bioconductor R package (version 3.4.4) DESeq2 (version 1.18.1) (Love et al., 2014). Genes of which fewer than five samples had gene counts below or equal to 10 reads were excluded from further analysis prior to normalization.
Differential gene expression was analyzed using Qlucore Omics Explorer 3.5 (Qlucore AB, Lund, Sweden). Prior to statistical analysis, pre-processed RNA sequencing data were log2 transformed.
Genome_build: RefSeq Assembly ICSASG_v2

organism: Salmo salar

source_name: hepatocytes

growth_protocol: Atlantic salmon hepatocytes were isolated using the two-step liver perfusion method described by Søfteland et al. (2009) under semi-sterile (hepatocyte cell isolation) and sterile (cell work) conditions. In brief, during the first step the liver was perfused through the hepatic vein with a perfusion buffer containing 17 mM EDTA (Sigma-Aldrich, Oslo, Norway) to clear the liver of blood, followed by the second perfusion step where the liver was digested by the addition of collagenase VIII (0.1 mg/mL) (Sigma-Aldrich, Oslo, Norway) to the perfusion buffer. The digested liver was transferred to a petri dish with ice cold 1X PBS and gently pulled apart using tweezers, followed by pipetting the tissue suspension up and down using a 5-mL syringe. The homogenate was filtered through a 100 µm nylon mesh. The isolated hepatocytes were washed thrice with cold 1X PBS through centrifugation at 50 G for 5 minutes, and finally resuspended in suppl.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Crawley, UK) was used according to supplier’s protocol to extract and purify total RNA from the cell lysate.
RNA samples (2 µg) were sent to the Norwegian Sequencing Centre (NSC) (www.sequencing.uio.no) in Oslo, Norway, where the sequencing and library preparation were performed. DNA libraries were prepared using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, California, USA) per manufacturer’s protocol. For multiplexing, standard Illumina adaptors were used. The libraries were sequenced using the NextSeq Illumina platform (Illumina, San Diego, California, USA) according to the manufacturer’s instructions, generating single end 75 bp read libraries with an average library size of 10±2 million reads

treatment_protocol: The mycotoxins, beauvericin (BEA, cas 26048-05-5) and enniatin B (ENNB, cas 917-13-5) used in the exposure experiments were purchased from AdipoGen® (AdipoGen® Life Sciences, Nordic BioSite, Oslo, Norway). BEA and ENNB, respectively, were dissolved in dimethyl sulfoxide (DMSO) (Sigma-Aldrich, Oslo, Norway) to constitute a 15 mM stock solution from which dilutions were made. In an initial experiment, the mycotoxins were exposed as single compounds at concentrations of 0.05, 0.5, 1.5, 2.5, and 5 µM, and in a follow-up experiment at 0.05, 2.5, and 5 µM. In both experiments, 0.1% DMSO was used as a control. The mycotoxin stock solutions, as well as the control, were diluted in Leibovitz L-15 medium w/o phenol red (ThermoFisher, Oslo, Norway) supplemented with 9 % FBS (Sigma-Aldrich, Oslo, Norway), 1% salmonid serum (#N82800F, Meridian Life Science, Inc. Memphis, USA), 1% Antibiotic Antimycotic Solution (10000 units penicillin, 10000 µg streptomycin, and 25 µg amphotericin per mL) (Sigma-Aldrich, Oslo, Norway), and from here on denoted as suppl. L-15.

tag: "developmental stage"

value: post smolt


title: 200100T


title: 244T


title: Au_TCPP_3

city: chongqing

first: ke

last: li

address: shazheng street 174

institute: chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM)  was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample ...

source_name: Mouse breast cancer cells

growth_protocol: 10% FBS, 1% penicillin/streptomycin, high glucose DMEM

extract_protocol:
About 10e6 4T1 cells were isolated from different group and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell cultured with medium, Cu-TCPP(Fe)-PEG and Au/Cu-TCPP(Fe)-PEG

value: Mouse breast cancer cells (4T1 cells)

tag: cell states

value: glucose-like oxidase and GSH-consumed

tag: intervention


title: HiChIP WT1

tag: chip antibody


title: Au_TCPP_2


title: sample_99


title: sample_90


title: HiChIP WT2

tag: genotype


title: sample_97

tag: treatment


title: 243T


title: HiChIP AHDC1/GIBBIN KO3

description: AHDC1/GIBBIN KO3


title: Au_TCPP_1


title: Cu_TCPP_3

value: GSH-consumed


title: HiChIP AHDC1/GIBBIN KO2

description: AHDC1/GIBBIN KO2


title: 244N


title: sample_88


title: Cu_TCPP_2


title: sample_89


title: 340T


title: HiChIP AHDC1/GIBBIN KO1

description: AHDC1/GIBBIN KO1


title: 243N


title: Cu_TCPP_1


title: Control_3

value: Normal culture condition

value: Control


title: sample_86


title: Control_2


title: sample_85


title: 335N


title: 335T


title: 259T


title: AHDC1/Gibbin day 7 rep 2

description: AHDC1/Gibbin binding sites at day 7 of differentiation

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
Read coverage depth for each bam file was generated using bedtools genomecov, then deduplicated bam files were filtered to using samtools view for reads with coverage depth of at least 3.
macs2 used for peak calling
Cufffdiff with batch correction for differential peak identification
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, narrowpeak files

extract_protocol:
Briefly, cells were detached with Accutase and crosslinked in solution for 10 minutes in freshly prepared 1% formaldehyde (Thermo Scientific) in PBS. For Gibbin ChIP-seq, freshly collected cells were treated with 5% 1,6-hexanediol in 5mL PBS in suspension for 60 seconds, upon which the solution was immediately diluted with 25mL PBS and 2mL 16% formaldehyde for crosslinking. Cell were quenched in 0.125M glycine, followed by two washes with cold PBS. 25x106 cross-linked cells were used per ChIP replicate. Cells were lysed in lysis buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1X protease inhibitors) for 30 minutes on ice and sonicated twice for 10 minutes on a Diagenode Bioruptor to achieve a chromatin between 200 and 400bp in size. Chromatin was centrifuged, quantified and diluted in dilution buffer up to 2mL (50mM Tris-HCl pH 8.0, 10mM EDTA, 1X protease inhibitors). Sheared chromatin was incubated overnight at 4°C with a each antibody. The next day lysates were incubated with 30μL of Dynabead protein G beads (Invitrogen) for 4 hours at 4°C. Beads were washed twice each with low salt buffer (50mM Tris-HCl pH 8.0, 0.15M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), high salt buffer (50mM Tris-HCl pH 8.0, 0.5M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), and LiCl buffer (50mM Tris-HCl pH 8.0, 0.15M LiCl, 1mM EDTA pH 8.0, 1% Nonidet P-40, 0.1% sodium deoxycholate). DNA was eluted in 100μL of elution buffer (50mM NaHCO3, 1% SDS) and crosslinks were reversed with 4μL of 5M NaCl incubated shaking for 16 hours at 67°C. RNA was removed by adding 1μL of 10mg/mL RNase A for 30 minutes at 37°C. DNA was cleaned using the Qiaquick PCR purification kit (Qiagen) and quantified using Qubit (Invitrogen).
10ng of DNA was used to make libraries with the NEBNext kit (New England Biolabs) and AMPure XP beads (Beckman Coulter) according to the manufacturer instructions.

treatment_protocol: For the AHDC1/Gibbin ChIP-seq, cells were treated with doxycycline for 24 hours to induce an AHDC1/Gibbin expression protein. Biotin was added for

value: Inducible Gibbin-BASU H9 line

value: anti-biotin antibody produced in rabbit, Abcam, CAT#ab53494; RRID:AB_867860

tag: tag

value: HA


title: sample_84


title: Control_1


title: 259N


title: 200100N

value: M


title: 328T

value: Tumor


title: sample_83


title: H3K9me3 day 7 rep 2

description: H3K9me3 marks at day 7 of differentiation

value: Wildtype

value: anti-H3K9me3 antibody prodcued in rabbit, Abcam, CAT# Ab8898; RRID:AB_306848


title: KO3

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the raw reads were trimmed by using Trim Galore (version 0.5.0_dev, Cutadapt version 1.15) with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10), and quantified by using Salmon5. The transcript-level quantification results were converted to the gene-level quantities with tximport R package.
DESeq2 R package was used to normalize the gene-level quantities and followed by differential expression analysis between selected samples with the same package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen_CD8 T cells

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and KO CD8+ T cells were sorted from the spleens of recipient mice 7 days after LM-OVA infection in the co-transfer model.

tag: strain

value: Spleen

value: Med1 KO


title: 337T


title: sample_87


title: 328N

value: Normal


title: 340N


title: AHDC1/Gibbin day 7 rep 1


title: sample_82


title: H3K9me3 day 7 rep 1


title: H3K9me3 day 7 AHDC1/Gibbin KO rep 2

description: H3K9me3 marks at day 7 of differentiation in AHDC1/Gibbin KO cells

value: AHDC1/Gibbin KO


title: 261N

value: F


title: sample_81

value: post smolt


title: KO2


title: GATA3 day 7 AHDC1/Gibbin KO rep 2

description: GATA3 binding sites at day 7 of differentiation in AHDC1/Gibbin KO cells

value: Anti-GATA3 antibody produced in rabbit, Abcam, CAT# ab199428; RRID:AB_2819013


title: sample_80


title: KO1


title: GATA3 day 7 AHDC1/Gibbin KO rep 1


title: 333N


title: WT3

value: WT


title: 337N


title: sample_78

value: ENNB_ DMSO


title: sample_79


title: GATA3 day 7 rep 2

description: GATA3 binding sites at day 7 of differentiation


title: WT2


title: 235T


title: WT1


title: 333T


title: GATA3 day 7 rep 1


title: 308N


title: Neocortex P20 rep3 specimen 758

city: St Lucia

first: Peter

last: Kozulin

state: Queensland

address: Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

data_processing:
cDNA libraries were sequenced on an Illumina HiSeq 2000 with 125 bp paired-end reads using the standard manufacturer’s protocols at the Queensland Brain Institute Centre for Brain Genomics, Queensland, Australia.
Basecalls performed using the standard Illumina Genome Analyzer software and CASAVA version 1.8.2
Reads were trimmed for adaptor sequences and terminal nucleotides with Phred score less than 20 using Cutadapt version 1.18. In addition, reads less than 36 nucleotides were removed.
De novo transcriptome was assembled using Trinity version 2.3.2 with parameters "--seqType fq --SS_lib_type RF"
RSEM version 1.3.1 was used across all samples to estimate transcript abundance against the Trinity-assembled transcriptome
Differential expression analysis across developmental ages was calculated with an exact test pairwise comparison of the counts of mapped reads, normalized against the library size factor of each sample, using edgeR
Genome_build: FTD_Trinity_assembly.fasta (de novo assembly)
Supplementary_files_format_and_content: Trinity-assembled de novo sequences (fasta format) used as a reference for transcript abundance estimation
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text file generated by RSEM that lists ID numbers for all Trinity-assembled transcripts and their corresponding genes

organism: Sminthopsis crassicaudata

source_name: neocortex

extract_protocol:
Dunnart joeys were removed from the pouch and sacrificed by decapitation. Both hemispheres of the neocortex were micro-dissected out, transferred into TRIzol reagent (ThermoFisher), homogenized using 23- and 27-gauge needles and total RNA extracted using the standard TRIzol protocol. The RNA pellet was resuspended in RNase-free water, treated with DNaseI (Qiagen) and column-purified with a RNeasy Minelute kit (#74204, Qiagen). All dunnart RNA samples showed a RNA integrity number (RIN) of 8.6 or higher on a Bioanalyzer 2100 RNA Nano assay (Agilent).
400 ng of total RNA from each dunnart sample was used for cDNA library preparation. RNA samples were depleted of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero (#15065382, Illumina) then fragmented. A Truseq Stranded Total RNA kit v4 (#15031048, Illumina) was then used to perform first- and second-strand cDNA synthesis, followed by adapter ligation and PCR amplification of the cDNA products, as per the standard low sample (LS) protocol.

value: neocortex

tag: developmental stage

value: P20 (stage 23)

value: wild type


title: sample_77


title: CTCF day 7 AHDC1/Gibbin KO rep 2

description: CTCF binding sites at day 7 of differentiation in AHDC1/Gibbin KO cells

value: anti-CTCF antibody produced in rabbit, Active Motif, CAT# 61311; RRID:AB_2614975


title: Neocortex P20 rep2 specimen 746


title: sample_76


title: CTCF day 7 AHDC1/Gibbin KO rep 1


title: Neocortex P20 rep1 specimen 666


title: H3K9me3 day 7 AHDC1/Gibbin KO rep 1


title: sample_75


title: CTCF day 7 rep2

description: CTCF binding sites at day 7 of differentiation


title: sample_74


title: Neocortex P12 rep3 specimen 458

value: P12 (stage 20)


title: CTCF day 7 rep1


title: Neocortex P12 rep2 specimen 451


title: WT iKC rep2

description: wildtype sorted induced keratinocytes

data_processing:
Tophat used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Genome_build: hg38
Supplementary_files_format_and_content: text file, raw counts

source_name: sorted induced keratinocytes

growth_protocol: hESCs were maintained in Essential 8 plus supplement. Medium was changed to Essential 6 plus RA/BMP4 for 7 days to induce differentiation. Medium was then changed to DKSFM plus supplement for a total of 50 days. Keratinocytes were then sorted from this population and maintained in DKSFM on collagen-peptide plates.

extract_protocol:
Cells were removed from the plate with Accutase. For RNA extraction, cells were lysed in Trizol (Invitrogen), the aqueous layer was isolated as indicated by the manufacturer, and RNA was purified with RNeasy columns (Qiagen). DNase (Qiagen) treatment was added to the column prior to elution as per manufacturer instructions.
Libraries for RNA-seq were prepared using the KAPA kit for PolyA enriched mRNA-seq (Illumina) according to the manufacturer’s protocol.


title: sample_73


title: sample_138


title: 288N


title: 308T

value: M

value: Tumor


title: 234N


title: Neocortex P12 rep1 specimen 436


title: WT iKC rep1

description: wildtype sorted induced keratinocytes

value: Wildtype


title: 261T


title: sample_137


title: AHDC1/Gibbin KO iKC rep2

description: AHDC1/Gibbin knockout sorted induced keratinocytes


title: sample_136


title: AHDC1/Gibbin KO iKC rep1


title: no transduction rep2

city: Seattle

first: Jennifer

last: Cherone

state: WA

address: 2211 Elliott Ave Ste 600

institute: Altius Institute for Biomedical Sci

data_processing:
Reads were aligned to the hg38 genome using STAR 2.3.1
Feature Counts was used to generate count files
Genome_build: hg38
Supplementary_files_format_and_content: txt file of counts generated by feature counts

source_name: CD34+ hematopoietic progenitor cell

extract_protocol: Strand-specific, ribosomal RNA (rRNA)-depleted libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian.

value: Bone marrow progenitor cells

value: untreated


title: WT day 7 rep2

description: day 7 differentiation wildtype cells


title: sample_135


title: 288T


title: 309N

value: Normal


title: 330N


title: no transduction rep1


title: 235N


title: WT day 7 rep1

description: day 7 differentiation wildtype cells


title: shuffled shRNA ctrl KD rep2

value: shuffled control shRNA

value: treated with sc shRNA lentivirus


title: 309T

value: F


title: no transduction rep3


title: 138N


title: 330T


title: GATA3 KO day 7 rep2

description: day 7 differentiation AGATA3 knockout cells

value: GATA3 KO


title: shuffled shRNA ctrl KD rep3


title: sample_133

value: post smolt


title: 84N


title: sample_124


title: 245T


title: 138T


title: sample_125


title: 84T


title: 245N


title: b1-integrin KD rep3

value: a4-integrin shRNA

value: treated with a4 shRNA lentivirus


title: a4-integrin KD rep2

value: b1-integrin shRNA

value: treated with b1 shRNA lentivirus


title: 229083T


title: sample_126


title: 151T


title: AHDC1/Gibbin KO day 50 rep2

description: day 50 differentiation AHDC1/Gibbin knockout cells

value: AHDC1/Gibbin KO


title: GATA3 KO day 7 rep1


title: shuffled shRNA ctrl KD rep1


title: sample_121


title: AHDC1/Gibbin KO day 7 rep2

description: day 7 differentiation AHDC1/Gibbin knockout cells


title: a4-integrin KD rep3


title: sample_123


title: sample_134


title: 229083N


title: WT day 50 rep2

description: day 50 differentiation wildtype cells


title: sample_122


title: WT day 50 rep1

description: day 50 differentiation wildtype cells


title: b1-integrin KD rep2


title: a4-integrin KD rep1


title: ATACseq_d7_WT_r2

description: Wild type Non-neural ectoderm cells

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
bedtools2.27.1 multicov to generate normalized counts
DESEQ2 used for differential peak calling
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

growth_protocol: hESCs were maintained in Essential 8 plus supplement. Medium was changed to Essential 6 plus RA/BMP4 for 7 days to induce non-neural ectoderm.

extract_protocol:
Cells were removed from the plate with Accutase. Nuclear DNA was extracted following ATAC-seq the protocol in Buenrostro et al. 2015. Briefly, 7x104 cells were washed with cold PBS and lysed in 0.1% NP40 RSB buffer. Nuclei were Tn5 transposed with Nextera Transposase at 37°C for 30 minutes, then purified with the Qiagen MinElute PCR Purification Kit.
Libraries were amplified for 9-15 total cycles using the Nextera Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified and eluted using the Min-Elute columns (Qiagen). Library concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis (Agilent).

value: WT

tag: cell line


title: sample_118


title: sample_120


title: AHDC1/Gibbin KO day 50 rep1


title: b1-integrin KD rep1


title: Astrocytes_T13_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR v2.7.6a (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include counts of mapped reads for each Sample

source_name: Astrocytes

growth_protocol: Human healthy and patient derived iPSC were firstly differentiated into Neural Stem Cell  (NSC), according to the published Dual Smad inhibition protocol (Chambers et al, 2009). Briefly, iPSCs colonies were detached with accutase (Life Technologies), suspended as single cells and plated on Matrigel (BD Pharmingen)-coated dishes(50,000 cells/cm2) in MEF pre-conditioned iPSC medium (IPSCSM) in the presence of 10 μM of the Rho kinase inhibitor Y-27632 (Sigma). When the cell culture reached ≈90% confluence (usually 2 days after plating), the culture medium was replaced with KSR medium (KSRM) supplemented with 200 ng/ml of rhNOGGIN (R&D) and 10 μM of SB431542 (Sigma). The medium was changed daily for the next 3 days. Thereafter, it was switched every other day in order to gradually expose the cells to increasing (1:3, 1:1, 3:1) ratio of NPC/KSR medium. Two days after the last switch, the cells were detached using accutase and plated on Matrigel-coated dishes in NPCM supplemented with 20 ng/ml bFGF and 20 ng/ml EGF. iPSC-derived NSCs were then expanded and collected for RNA Seq experiment. In parallel, iPSC-derived NSCs were further differentiated into more committed cells reaching a mixed neural population following a protocol adapted from  Meneghini et al, 2017; Santos et al, 2017. NSCs, cultured for a maximum of 6 passages, were detached using accutase and plated on Matrigel-coated dishes (20,000 cells/cm2) in NPCM (day0). During the first 4 days after plating (day4) we gradually replaced NPCM containing bFGF and EGF with an increasing amount of GDM, supplemented with 10 ng/ml PDGF-AA, 10 ng/ml NT3, 10 ng/ml IGF-1, 5 ng/ml HGF, and 60 ng/ml T3. From day4 to day13, medium was changed every other day. From day14 to day34, the medium was switched to the one described in Santos et al, supplemented with 10% FBS and 10ng/ml leukemia inhibitory factor (LIF). The neural mixed-cultured obtained at day34 was detached and replated twice to enrich the glial population. Astrocytes were collected at passage 2 for RNA Seq experiment. iPSC-derived NSCs were also differentiated into Neuronal culture through a commercial protocol with the STEMdiff Neuron Maturation kit following manufacturer’s instructions. Cells were analyzed and used for experiments after 21 days of maturation.

extract_protocol:
Total RNA was extracted from frozen cell pellets using Qiagen RNeasy Mini kit following  manufacturer’s instructions (Qiagen, Hilden, Germany).  RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies,  Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300  Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit  for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly,  mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented  for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently  synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and  universal adapters were ligated to cDNA fragments, followed by index addition and  library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS  Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA),  and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).   The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina  NovaSeq 6000 instrument according to manufacturer’s instructions

tag: cell type

value: iPSC-derived astrocytes

tag: knock-out technology

value: CRISPR-CAS9 engineered knock-out

value: Lentiviral vector reprogrammed iPSCs


title: sample_117


title: Astrocytes_R19_3

tag: iPSc generation


title: ATACseq_d7_GATA3_KO_r2

description: Non-neural ectoderm GATA3 KO cells


title: ATACseq_d7_AHDC1_KO_r2

description: Non-neural ectoderm AHDC1/Gibbin KO cells


title: sample_116


title: ATACseq_d7_GATA3_KO_r1

description: Non-neural ectoderm GATA3 KO cells


title: Astrocytes_R19_1


title: Astrocytes_T13_2


title: sample_113

value: BEA_ DMSO


title: sample_115


title: Astrocytes_WT_3


title: sample_114


title: Astrocytes_WT_2


title: ATACseq_d7_AHDC1_KO_r1


title: Young adult C57 FactorB KO mouse AN-2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Fastq files were imported into the Partek Flow system
Alignment to Mouse mm10 was done with TopHat2
Aligned reads were quantified to annotation model (Partek E/M) using mm10 with settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed by DESeq2 to determine normalized counts and statistical measures between samples types
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Auditory nerve cells

extract_protocol:
Microdissections were performed to isolate the auditory nerves from mouse cochleas. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. The quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Isolated auditory nerves

value: FactorB KO


title: NSC_R19_2

source_name: NSC

value: iPSC-derived NSC


title: NSC_T13_3


title: 145N

tag: gender

tag: disease state

value: Normal


title: 279N

value: M


title: 145T

value: F

value: Tumor


title: 151N


title: 262N


title: sample_110

value: post smolt


title: 279T


title: Young adult C57 FactorB KO mouse AN-3

tag: tissue


title: 262T


title: sample_112


title: NSC_T13_2


title: 144N


title: Young adult C57 mouse AN-3

value: wildtype


title: sample_111


title: 144T


title: AHDC1/Gibbin KO day 7 rep1


title: 179T


title: Young adult C57 mouse AN-2


title: NSC_WT_3


title: NSC_WT_2


title: sample_102


title: sample_101


title: 160T


title: Oocytes_-_Setd1b_KO_Lib_3

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
FastQ sequence files were quality and adaptor trimmed with Trim Galore v0.4.2 using the options --clip_r1 9 and --clip_r2 9.
Mapping and methylation calling of Bisulfite-seq data was performed using Bismark v0.16.3 in PBAT mode against the mouse GRCm38 genome assembly. Trimmed reads were first aligned to the genome in paired-end mode to be able to detect and discard overlapping parts of the reads while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for positions that were covered more than once. Following methylation extraction, CpG context files from PE and SE runs were used to generate a single coverage file (the "Dirty Harry" procedure).
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
Genome_build: GRCm38

source_name: d21 GV oocytes

extract_protocol:
Ovaries were collection from 21-day-old females and digested with 2mg/mL collagenase (Sigma) and 0.02% trypsin solution, agitating at 37°C for 30 min.  GV oocytes were collected in KSOM medium (Sigma) and washed with PBS from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT) and stored at -80C until PBAT protocol was performed. Approximately 100 GV oocytes were collected for three biological replicates of each genotype. Cells were lysed with 0.5% SDS in EB buffer and bisulphite treated with the Imprint DNA Modification kit (Sigma). The resulting DNA was purified using columns and reagents from the EZ DNA Methylation Direct kit (Zymo Research).
First-strand synthesis was performed with Klenow Exo– enzyme (New England Biolabs) using a customized biotin-conjugated adaptor containing standard Illumina adaptor sequences and 9 bp of random sequences (9N), as previously described (Hanna et al., 2018). Following exonuclease I (New England Biolabs) treatment and binding to Dynabeads M-280 Streptavidin beads (Thermo Fisher Scientific), second-strand synthesis was performed with Klenow Exo– enzyme (New England Biolabs) using a customized adaptor containing standard Illumina adaptor sequences and 9 bp of random sequences.  Ten PCR cycles with Phusion High-Fidelity DNA polymerase (New England Biolabs) were used for library amplification with indexed adaptors.  Libraries were multiplexed for 100-bp paired-end sequencing on an Illumina HiSeq 2500.

value: Germinal vesicle oocytes

value: Setd1b floxed/floxed, Gdf9-Cre positive

tag: age


title: sample_119

tag: "developmental stage"


title: NSC_R19_1


title: Neurons_T13_1

source_name: Neurons

value: iPSC-derived neurons


title: 179N


title: Neurons_T13_2


title: Oocytes_-_Setd1b_KO_Lib_2


title: Young adult C57 mouse AN-1


title: sample_109


title: 126T


title: sample_100


title: ATACseq_d7_WT_r1

description: Wild type Non-neural ectoderm cells

value: WT


title: Oocytes_-_Setd1b_KO_Lib_1


title: 126N


title: 720shGFP2

description: Triple Negative Breast cancer

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode vM25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: 720 Control Enpp1 High

extract_protocol:
The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
RNA sequencing was performed by adapting the technology of SCRB-Seq (Bagnoli JW et al., Nat Comm, 2018) to allow for the high cost-efficient multiplexed transcriptome characterization. Briefly, cells were collected in cell lysis buffer and poly-(A)+ RNA were purified using the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific). poly-(A)+ RNA were annealed to a custom primer containing a poly-(T) tract, a Unique Molecule Identifier (UMI), and a sample barcode. Retrotranscription using Template-switching oligonucleotides (TSO) was then used to synthetize and amplify 3’UTR enriched cDNA, resulting in barcoded cDNA fragments. Library preparation was performed using the Nextera XT library preparation protocol which introduces i5-P5 and i7-P7 structure for massive parallel sequencing. Quality control was performed following pre-amplification RT and library preparation to ensure quality and length accuracy, as well as to equilibrate sample pooling. Libraries were then circularized and sequenced using an DNBSeq-G400 sequencer (MGI), using the MGIEasy Circularization Kit (MGI). 5-10 million pair-end reads (100 bp) were sequenced for each sample. Raw sequences were called using Zebra caller (MGI) and demultiplexed using Cutadapt. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

value: FVB/n


title: Neurons_R19_1

value: CRISPR-CAS9 engineered knock-out


title: Young adult C57 FactorB KO mouse AN-1


title: Neurons_WT_2

value: Lentiviral vector reprogrammed iPSCs


title: Oocytes_-_Setd1b_f_f_Lib_3

value: Setd1b floxed/floxed, Gdf9-Cre negative


title: Oocytes_-_Setd1b_f_f_Lib_2


title: 720shGFP1

description: Triple Negative Breast cancer


title: Oocytes_-_Setd1b_f_f_Lib_1


title: 720sh4Enpp12

description: Triple Negative Breast cancer

source_name: Enpp1 depleted cell line


title: 720shGFP3

description: Triple Negative Breast cancer


title: Control patients PBMCs (AB) [20094_0012_B]

city: Munich

first: Markus

last: Joppich

state: Bavaria

address: Amalienstr. 17

department: Department of Informatics

country: Germany

institute: LMU Munich

description:
antibody capture
20094_0012_A_B_raw_feature_bc_matrix.new.h5
20094-0012

data_processing:
Primary data analysis was performed using the bcl2fastq v2.19.1.403 software package.
The Illumina Sequence Analysis Viewer (SAV) 2.4.7 was used for imaging and evaluation of the sequencing run performance.
Sequenced reads were processed using cellranger version 4.0.0 with default settings and refdata-gex-GRCh38-2020-A reference
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger h5 raw feature-barcode matrices

source_name: PBMCs

extract_protocol:
Sample processing described in original article (Pekayvaz et al., Nature Communications 2022)
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for Cell Surface Protein, described in original article (TotalSeq™ anti-human Hashtag Antibodies B0251, A0252, A0253)

value: blood

value: CONTROL

value: PBMCs


title: Pneumonic patients (#7-9) PBMCs sampled at TP3 (AB) [20094_0009_B]

description:
antibody capture
20094_0009_A_B_raw_feature_bc_matrix.new.h5
20094-0009

value: SEVERE


title: Neurons_R19_2


title: 720sh4Enpp11

description: Triple Negative Breast cancer


title: 172N

source_name: Normal tissue

value: M

value: Normal


title: 720sh4Enpp13

description: Triple Negative Breast cancer


title: 146N

value: F


title: Setd1b_WT_GV_Input_1

data_processing:
FastQ sequence files were quality and adaptor trimmed with Trim Galore v0.4.2 using default parameters.
Genome_build: GRCm38
Mapping of ChIP-seq data was performed with Bowtie v2.2.9 against the mouse GRCm38 genome assembly. The resulting hits were filtered to remove mappings with a MAPQ scores < 20.
Supplementary_files_format_and_content: tiled_window_report: SeqMonk annotated probe report over 5kb running windows, quantitated as RPKM values.

extract_protocol:
Ovaries were collection from 21-day-old females and digested with 2mg/mL collagenase (Sigma) and 0.02% trypsin solution, agitating at 37°C for 30 min.  GV oocytes were collected in KSOM medium (Sigma) and washed with PBS from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT) and stored at -80C until ChIP-seq protocol was performed. Approximately 200 GV oocytes were collected for three biological replicates of each genotype for H3K4me3 ULI-nChIP-seq. Samples were thawed on ice and permeabilized using nuclei EZ lysis buffer (Sigma) and 0.1% Triton-X-100 /0.1% deoxycholate. Micrococcal nuclease digestion was completed with 200 U of micrococcal nuclease (New England Biolabs) at 21 °C for 7.5 min. Chromatin samples were precleared in complete immunoprecipitation buffer with Protein A/G beads rotating for 2 hours at 4 °C. For each sample, 125ng of anti-H3K4me3 antibody (Diagenode, C15410003) was bound to Protein A/G beads in complete immunoprecipitation buffer for 3 hours rotating at 4 °C. Chromatin was then added to the antibody-bound beads and samples were rotated overnight at 4 °C. Chromatin-bound beads were washed with two low-salt washes and one high-salt wash and DNA was then eluted from the beads at 65 °C for 1.5 hours. Eluted DNA was purified with solid-phase reversible immobilization (SPRI) purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads (Fisher Scientific) at a 1.8:1 ratio.
Library preparation was completed using the MicroPlex Library Preparation kit v2 (Diagenode) with indexed adaptors, as per the manufacturers guidelines. Libraries were multiplexed for 75 bp Single End sequencing on a NextSeq500.


title: 172T

data_processing: Genome studio v2011.1

source_name: CRC tissue

extract_protocol: Genomic DNA was extracted from CRC and normal tissues using Qiagen Dneasy kit according to manufacturer protocol

value: Tumor


title: Pneumonic patients (#7-9) PBMCs sampled at TP2 (AB) [20094_0008_B]

description:
antibody capture
20094_0008_A_B_raw_feature_bc_matrix.new.h5
20094-0008


title: 160N


title: 141N


title: 141T


title: Neurons_WT_1


title: 720sh3Enpp13

description: Triple Negative Breast cancer


title: Setd1b_WT_GV_H3K4me3_2


title: 720sh3Enpp12

description: Triple Negative Breast cancer


title: Pneumonic patients (#7-9) PBMCs sampled at TP1 (AB) [20094_0007_B]

description:
antibody capture
20094_0007_A_B_raw_feature_bc_matrix.new.h5
20094-0007


title: 720sh3Enpp11

description: Triple Negative Breast cancer


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP3 (AB) [20094_0006_B]

description:
antibody capture
20094_0006_A_B_raw_feature_bc_matrix.new.h5
20094-0006

value: MILD


title: Setd1b_WT_GV_H3K4me3_1

value: Germinal vesicle oocytes


title: 146T


title: 374shGFP3

description: Triple Negative Breast cancer

source_name: 374 Control Enpp1 High

value: Balb/c


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP2 (AB) [20094_0005_B]

description:
antibody capture
20094_0005_A_B_raw_feature_bc_matrix.new.h5
20094-0005


title: 142N


title: Setd1b_WT_GV_Input_4


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP1 (AB) [20094_0004_B]

description:
antibody capture
20094_0004_A_B_raw_feature_bc_matrix.new.h5
20094-0004


title: 161N


title: 374shGFP1

description: Triple Negative Breast cancer


title: Setd1b_KO_GV_H3K4me3_1

value: Setd1b floxed/floxed, Gdf9-Cre positive


title: Setd1b_KO_GV_Input_1


title: 374sh4Enpp13

description: Triple Negative Breast cancer


title: Setd1b_KO_GV_Input_4


title: Pneumonic patients (#1-3) PBMCs sampled at TP2 (AB) [20094_0002_B]

description:
antibody capture
20094_0002_A_B_raw_feature_bc_matrix.new.h5
20094-0002


title: Setd1b_KO_GV_H3K4me3_3


title: Pneumonic patients (#1-3) PBMCs sampled at TP3 (AB) [20094_0003_B]

description:
antibody capture
20094_0003_A_B_raw_feature_bc_matrix.new.h5
20094-0003


title: 161T


title: Pneumonic patients (#1-3) PBMCs sampled at TP1 (AB) [20094_0001_B]

description:
antibody capture
20094_0001_A_B_raw_feature_bc_matrix.new.h5
20094-0001


title: 374sh4Enpp12

description: Triple Negative Breast cancer


title: Setd1b_KO_GV_H3K4me3_4


title: 374shGFP2

description: Triple Negative Breast cancer


title: Control patients PBMCs (GE) [20094_0012_A]

description:
gene expression
20094_0012_A_B_raw_feature_bc_matrix.new.h5
20094-0012


title: 374sh4Enpp11

description: Triple Negative Breast cancer


title: Setd1b_WT_3_RNAseq

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Genome_build: GRCm38
Alignment was done with 0.5.9-1.21009-MPI against a combination of the mm10 reference and a custom exon-exon junction reference was used as support to detect intron spanning reads. The custom reference was created with Ensembl Gene Version 69 mouse annotation
Genecounts were created with featureCounts v.1.4.4 and Ensembl Gene Version 69 mouse annotation was used. The counting was non strand-specific due to the library prep method
Supplementary_files_format_and_content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

extract_protocol:
Ovaries were collection from 21-day-old females and digested with 2mg/mL collagenase (Sigma) and 0.02% trypsin solution, agitating at 37°C for 30 min.  GV oocytes were collected in KSOM medium (Sigma) and washed with PBS from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT). Four GV oocytes for each genotype were collected for single cell RNA-seq (scRNA-seq).
Oocytes deposited in 2.5 µl lysis buffer and cDNA amplified exponentially with SMARTer Ultra Low RNA Kit for 12 cycles. Library construction was performed with NEBNext Ultra DNA Lib Prep Kit.


title: 260T


title: 164N


title: 260N


title: Setd1b_WT_GV_H3K4me3_4


title: 164T


title: 374sh3Enpp13

description: Triple Negative Breast cancer


title: Pneumonic patients (#7-9) PBMCs sampled at TP3 (GE) [20094_0009_A]

description:
gene expression
20094_0009_A_B_raw_feature_bc_matrix.new.h5
20094-0009


title: Pneumonic patients (#7-9) PBMCs sampled at TP2 (GE) [20094_0008_A]

description:
gene expression
20094_0008_A_B_raw_feature_bc_matrix.new.h5
20094-0008


title: 374sh3Enpp11

description: Triple Negative Breast cancer


title: Setd1b_WT_1_RNAseq


title: Pneumonic patients (#7-9) PBMCs sampled at TP1 (GE) [20094_0007_A]

description:
gene expression
20094_0007_A_B_raw_feature_bc_matrix.new.h5
20094-0007


title: Setd1b_KO_4_RNAseq


title: 223T


title: Setd1b_KO_3_RNAseq


title: ANV5Mock3

description: Triple Negative cell line

source_name: ANV5 control cell line

extract_protocol:
The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit
RNA sequencing was performed by adapting the technology of SCRB-Seq (Bagnoli JW et al., Nat Comm, 2018) to allow for the high cost-efficient multiplexed transcriptome characterization. Briefly, cells were collected in cell lysis buffer and poly-(A)+ RNA were purified using the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific). poly-(A)+ RNA were annealed to a custom primer containing a poly-(T) tract, a Unique Molecule Identifier (UMI), and a sample barcode. Retrotranscription using Template-switching oligonucleotides (TSO) was then used to synthetize and amplify 3’UTR enriched cDNA, resulting in barcoded cDNA fragments. Library preparation was performed using the Nextera XT library preparation protocol which introduces i5-P5 and i7-P7 structure for massive parallel sequencing. Quality control was performed following pre-amplification RT and library preparation to ensure quality and length accuracy, as well as to equilibrate sample pooling. Libraries were then circularized and sequenced using an DNBSeq-G400 sequencer (MGI), using the MGIEasy Circularization Kit (MGI). 5-10 million pair-end reads (100 bp) were sequenced for each sample. Raw sequences were called using Zebra caller (MGI) and demultiplexed using Cutadapt. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP3 (GE) [20094_0006_A]

description:
gene expression
20094_0006_A_B_raw_feature_bc_matrix.new.h5
20094-0006


title: ANV5Mock2

description: Triple Negative cell line


title: 374sh3Enpp12

description: Triple Negative Breast cancer


title: 58T


title: 58N


title: Setd1b_KO_2_RNAseq


title: 223N


title: ANV5Mock1

description: Triple Negative cell line


title: ANV5Enpp13

description: Triple Negative cell line

source_name: Enpp1 overexpresant cell line


title: Setd1b_KO_1_RNAseq


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP1 (GE) [20094_0004_A]

description:
gene expression
20094_0004_A_B_raw_feature_bc_matrix.new.h5
20094-0004


title: Pneumonic patients (#1-3) PBMCs sampled at TP3 (GE) [20094_0003_A]

description:
gene expression
20094_0003_A_B_raw_feature_bc_matrix.new.h5
20094-0003


title: Pneumonic patients (#1-3) PBMCs sampled at TP2 (GE) [20094_0002_A]

description:
gene expression
20094_0002_A_B_raw_feature_bc_matrix.new.h5
20094-0002


title: 136T