title: Alim Development ATACseq Rep2

description:
Alim_consensusPeaks_rpkm.txt
Alim_Dev_1

data_processing:
Fastq filles underwent read trimming using Trimgalore (v0.4.1)
Fastq files were mapped using --very-sensitve parameter on Bowtie2 (v2.2.5)
Duplicate reads were flagged and removes with Picard tools (v2.22.1) and SAMtools (v1.5)
Tn5 base shifting corrected by alignmentSieve in deepTools (version 3.2.1)
Peaks called using MACS2 (version 2.1.1.20160309)
Genome_build: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783 ; South American Killifish: GCA_001266775.1
Supplementary_files_format_and_content: Concensus Peak files across replicates and timepoints. Columns 1-11 are Bed format entries and all following are RPKM-normalized readcounts within each sample.


title: Astr Development ATACseq Rep1

status: Public on Jun 17 2024

type: SRA

city: Stanford

first: Anne

last: Brunet

state: California

address: 290 Jane Stanford Way

department: Genetics

country: USA

institute: Stanford University

description:
Astr_consensusPeaks_rpkm.txt
Astr_Dev_1

library_source: genomic

molecule: genomic DNA

organism: Iconisemion striatum

source_name: Dissected Embryo (Whole Body)

growth_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described. Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development. We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species. we next monitored the onset of heartbeat, and stage diapause embryos at 6 days (Dia 6d) and 1 month of diapause (Dia 1m) as exhibiting a continuously decreasing heartbeat rate since diapause onset (<45 beat-per-minute (BPM)) as described in Hu et al. For embryos in 1 month diapause (Dia 1m), we additionally made sure that there was no heartbeat by monitoring them for 5 minutes under a stereoscope to verify that they were not prematurely exiting the diapause state. For embryos in development, embryos that had an increase in heartbeat rate 1 day after heartbeat onset (>45 BPM), but before the visual pigmentation in eyes was developed (i.e. before pharyngula stage) were designated as developing embryos (Dev). All the diapause and development stages stage are identical to our previous study, except Pre-Dia stage which is a day before the onset of heartbeat.

extract_protocol:
To generate nuclei-suspension for ATAC-seq libraries, snap frozen embryo samples (~10 embryos per sample) were thawed for 1 minute and resuspended at 4oC in 200ml EZ-lysis buffer (Sigma Aldritch No. 3408). Samples were then transferred to 250 ml mini-douncers (DWK (Kimble) 885300-0000) and dounced 25 times with pestle A and B respectively. After a 2 minute incubation following douncing, samples were spun at 500g for 5 minutes to precipitate nuclei, and the EZ-lysis supernatant was removed. Nuclei were then resuspended in 250ml PBS (ThermoFisher No. AM9624) and an aliquot of 5µl of nuclei was incubated with 5ml of 0.4% trypan blue stain (ThermoFisher No. 15250061) for counting the total intact nuclei counts.
Samples of ~25,000 nuclei were then suspended in a Tn5 transposition mix (65ml of tagmentation DNA buffer (Illumina No. 20034197), 63ml of nuclease-free water, and 2.5ml of tagmentation DNA enzyme I (e.g Tn5 transposase) (Illumina No. 20034197) for 20 minutes at 37oC. Following incubation, the mix was purified using the Qiagen mini-elute kit (Qiagen No. 28206) to isolate tagmented DNA. PCR amplification and subsequent qPCR monitoring was performed as described in the original ATAC-seq protocol (~14-18 cycles of PCR). Amplified DNA from the PCR reaction was purified using the Qiagen mini-elute kit (Qiagen No. 28206), as recommended by the manufacturer. Samples were subsequently pooled and sequenced using next-generation short-read sequencing on an Illumina NEXTseq 550.

treatment_protocol: All collected embryos were wildtype and untrated for the duration of their development.

tag: tissue

value: Dissected Embryo (Whole body)

tag: Stage

value: Development

tag: time point

value: Development (>60BPM)


title: ko_d9_1

type: RNA

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

description: day 9 post-tamoxifen

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: To determine differentially expressed genes between genotypes over multiple timepoints, gene expression was fit to linear models using the Limma package with R (v3.5)37. For gene signature scoring, z-scores were calculated for each gene per sample and gene signature scores were calculated using the averaged z-scores for genes in each signature.

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: jejunum

label_protocol: RNA quality control, amplification and hybridization to Affymetrix Mouse Gene 1.0 ST array was conducted by the Genome Technology Access Center  (GTAC) in the Department of Genetics at Washington University in St Louis.

growth_protocol: For inducible gene ablation, tamoxifen (MilliporeSigma) was dissolved in the corn oil (MilliporeSigma) at final concentration of 20 mg/mL and i.p. injected to mice at the dose of 75 mg/kg body weight for five consecutive days. Mice were sacrificed and intestinal tissues were isolated at days 6, 9, and 12.

extract_protocol: RNA was extracted from the whole tissue small intestinal samples with an RNeasy Micro Kit (Qiagen).

tag: genotype

value: Fgfr1op KO

value: day 9 post-tamoxifen


title: Astr Pre-Diapause ATACseq Rep2

description:
Astr_consensusPeaks_rpkm.txt
Astr_preDia_2

value: Pre-Diapause (K-vesicle)


title: Alim Development ATACseq Rep1.5

description:
Alim_consensusPeaks_rpkm.txt
Alim_Dev_1.5

data_processing:
Fastq filles underwent read trimming using Trimgalore (v0.4.1)
Fastq files were mapped using --very-sensitve parameter on Bowtie2 (v2.2.5)
Duplicate reads were flagged and removes with Picard tools (v2.22.1) and SAMtools (v1.5)
Tn5 base shifting corrected by alignmentSieve in deepTools (version 3.2.1)
Peaks called using MACS2 (version 2.1.1.20160309)
Assembly: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783 ; South American Killifish: GCA_001266775.1
Supplementary files format and content: Concensus Peak files across replicates and timepoints. Columns 1-11 are Bed format entries and all following are RPKM-normalized readcounts within each sample.

organism: Austrofundulus limnaeus

tag: timing


title: Alim Pre-Diapause ATACseq Rep1

description:
Alim_consensusPeaks_rpkm.txt
Alim_preDia_1


title: wt_d12_1

description: day 12 post-tamoxifen

value: wt

value: day 12 post-tamoxifen


title: Alim Pre-Diapause ATACseq Rep1.5

description:
Alim_consensusPeaks_rpkm.txt
Alim_preDia_1.5


title: Superior cervical ganglion, SHR, rep4

city: Chongqing

first: Chaohong

last: Li

address: Yuzhong Road

country: China

institute: Chongqing Medical University

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseqor PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001)
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Superior cervical ganglion

extract_protocol:
RNA was extracted using Trizol reagent (Thermo Fisher Scientific). 200 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols on the BGISEQ-500 sequencing platform

value: Superior cervical ganglion


title: Astr Pre-Diapause ATACseq Rep1

description:
Astr_consensusPeaks_rpkm.txt
Astr_preDia_1


title: Superior cervical ganglion, WKY, rep4


title: Superior cervical ganglion, WKY, rep3


title: Superior cervical ganglion, WKY, rep2


title: Adrenal gland, SHR, rep3

source_name: Adrenal gland

value: Adrenal gland


title: Superior cervical ganglion, SHR, rep2


title: Superior cervical ganglion, SHR, rep1


title: Adrenal gland, WKY, rep3


title: DNA methylation data of EGFR-altered tumor case 2

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina Infinium MethylationEPIC v1 or Illumina Infinium MethylationEPIC v2 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

organism: Homo sapiens

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 2

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE samples using MagPurix FFPE DNA Extraction Kit according to manufacturer's instructions.

tag: methylation class

value: Sarcoma MPNST-like (score 0.7)


title: Adrenal gland, WKY, rep2


title: Alim Development ATACseq Rep1

description:
Alim_consensusPeaks_rpkm.txt
Alim_Dev_1


title: Alim Diapause 1 Month ATACseq Rep1

description:
Alim_consensusPeaks_rpkm.txt
Alim_1M_1

value: Diapause

value: Diapause 1 Month


title: Superior cervical ganglion, WKY, rep1


title: DNA methylation data of EGFR-altered tumor case 9

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 9

value: DFSP (score 0.87)


title: Adrenal gland, SHR, rep2


title: Adrenal gland, WKY, rep1


title: Adrenal gland, SHR, rep4


title: Left ventricle, SHR, rep4

source_name: Left ventricle

value: Left ventricle


title: DNA methylation data of EGFR-altered tumor case 8

source_name: EGFR-altered tumor with morphology of predominantly myxoid Spindle cell Tumor, case 8

value: Chondrosarcoma family (score 0.31)


title: Left ventricle, SHR, rep3


title: Adrenal gland, SHR, rep1


title: DNA methylation data of EGFR-altered tumor case 5

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 5

value: Sarcoma MPNST-like (score 0.5)


title: Left ventricle, WKY, rep4


title: DNA methylation data of EGFR-altered tumor case 3

source_name: EGFR-altered tumor with infantile Fibrosarcoma-like morphology, case 3

value: Lipoma (score 0.4)


title: DNA methylation data of EGFR-altered tumor case 14

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 14

value: DFSP (score 0.74)


title: Adrenal gland, WKY, rep4


title: Left ventricle, WKY, rep3


title: Left ventricle, WKY, rep2


title: DNA methylation data of EGFR-altered tumor case 7

source_name: EGFR-altered tumor with lipofibromatosis-like morphology, case 7

value: MPNST-like sarcoma (score 0.51)


title: Human and mouse rep 1

city: New York

first: Sumin

last: Jang

state: NY

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode analysis and gene expression quantification was done using CellRanger v3.1.0
Assembly: mm10 and hg38
Supplementary files format and content: tab-delimited gene expression matrix (UMI)

organism:
Homo sapiens
Mus musculus

extract_protocol:
Embryoid bodies were dissociated with papain and DNase I, followed by FACS to select GFP+ cells.
Library was prepared according to manufacturer's protocol (10X Genomics: single cell 3')

treatment_protocol: Prior to differentiation, human and mouse pluripotent stem cells were transduced with a lentivirus harboring unique 6bp barcode sequences downstream of CAGGS-driven GFP.

tag: cell line

tag: mouse strain

tag: cell type

value: Human iPS + mouse ES

tag: treatment

value: in vitro motor neuron differentiation


title: Left ventricle, SHR, rep2


title: Left ventricle, SHR, rep1


title: DNA methylation data of EGFR-altered tumor case 13

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 13

value: MPNST-like sarcoma (score 0.50)


title: DNA methylation data of EGFR-altered tumor case 4

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 4

value: Well- / dedifferentiated liposarcoma (score 0.43), Sarcoma MPNST-like (score 0.33)


title: DNA methylation data of EGFR-altered tumor case 1

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 1

value: Well- / dedifferentiated liposarcoma (score 0.6)


title: at-endosperm-H3_replicate2_col_Cm_x_ler

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-endosperm of TEmob Columbia-0 INT (female) crossed with Landsberg-erecta (male)

data_processing:
cutNtag: PE reads were trimmed using the trim_galore tool and mapped to the Arabidopsis (TAIR10) genome using Bowtie2 (Langmead & Salzberg, 2012) (parameters --no-unal --no-mixed --no-discordant --phred33 --local --very-sensitive-local). Mapped reads were sorted and indexed using SAMtools (Danecek et al., 2021). Read coverage was estimated and normalized to 1x sequencing depth (reads per genome coverage, RPGC) using the bamCoverage from deepTools (Ramírez et al., 2014) (parameters -bs50 --effectiveGenomeSize 119481543 --normalizeUsing RPGC --skipNAs). Signal-to-noise ratio was normalized with H3 data by calculating the log2 ratio in 50 bins across the genome using bigwigCompare from deepTools. Parent-of-origin methylation was performed as previously described (Moreno-Romero et al., 2016).
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: cutNtag:bigWig parental-specific (for parents LER and COL) coverage files normalised as reads per genomic content (RPGC)

organism: Arabidopsis thaliana

source_name: endosperm

growth_protocol: Seeds were surface sterilized with 70% ethanol and washed three times with sterile water. Sterilized seeds were sown on 1⁄2MS plates containing 0.5% sucrose and 0.8% agar, stratified for 2 days at 4°C and germinated under long-day conditions (16h light/8h darkness) at 21°C. Seedlings were transferred to soil after 10–12 days and grown in phytotrons under long day conditions (day 21°C, night 20°C 70% humidity, 150μE light intensity).

extract_protocol:
We coupled the previously published INTACT protocol for endosperm-nuclei purification (Moreno-Romero et al., 2017) with Cleavage Under Targets & Tagmentation (CUT&Tag) (Kaya-Okur et al., 2019). Tissue homogenization and nuclei purification were performed as previously described (Del Toro-De León & Köhler, 2019) except that MgCl2 was replaced by spermidine 0.5 mM in the Honda buffer to prevent pAG-Tn5 activation by residual MgCl2. All steps were performed with streptavidin-bound nuclei. INTACT-purified endosperm nuclei from 250 mg of siliques at 4DAP were resuspended in Antibody150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete™ Mini EDTA-free Protease Inhibitor, 0.01% Digitonin, 2 mM EDTA pH 7.5). Primary antibody incubation was performed overnight at 4°C with gentle shaking using anti-H3K9me2 (Diagenode Cat. No. C15410060), Anti-Histone H3 (Sigma-Aldrich Cat. No. H9289) or anti-H3K27me3 (Cell Signaling Technology Cat. No. 9733T) antibodies. Secondary antibody incubation was performed with Guinea Pig anti-Rabbit IgG, (Antibodies-Online Cat. No. ABIN101961) for 30 min at RT with Digitonin150 Buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete™ Mini EDTA-free Protease Inhibitor, 0.01% Digitonin). Beads were washed twice with Digitonin150 Buffer and incubated with pAG-Tn5 (EpiCypher Cat No. 15-1017) for 1hr in Digitonin300 Buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete™ Mini EDTA-free Protease Inhibitor, 0.01% Digitonin). Beads were washed twice with Digitonin300 Buffer and tagmentation was performed at 37ºC for 1hr with Tagmentation Buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete™ Mini EDTA-free Protease Inhibitor, 0.01% Digitonin, 10 mM MgCl2). Beads were washed with TAPS Buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA) and the tagmentation reaction was quenched with SDS Release Buffer (10 mM TAPS, pH 8.5, 0.1% SDS). Tagmented chromatin fragments were released by incubation for 1hr at 58ºC. SDS Quench Buffer (0.67% Triton-X 100) was added to the samples and library amplification was performed. We prepared unique index Nextera-compatible libraries with custom-designed index primers. PCR was performed with Non-hot Start Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific™ Cat No. F530S) for 14 cycles. Final DNA library fragment purification was performed with SPRI beads (ratio of 1.3 μl of SPRI beads to 1 μl of PCR product) and washed twice with 80% ethanol. The final library was resuspended in 0.1x TE buffer.
CUT&Tag customized Nextera library

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of INT line (Col) and the INT line pollinated with Ler

value: endosperm

value: AT F1-Endosperm Columbia TEmob x Landsberg

value: TEmob Col (maternal) x Ler (paternal)


title: at-endosperm-H3K27m3_replicate1_ler_x_col_Cm

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with TEmob Columbia-0 INT (male)

value: AT F1-Endosperm Landsberg x Columbia TEmob

value: Ler (maternal) x TEmob Col (paternal)


title: Left ventricle, WKY, rep1


title: at-endosperm-H3K9m2_replicate1_ler_x_col_Cm


title: Nfur Pre-Diapause RNAseq Rep2

data_processing:
read trimming with Trim Galore (version 0.4.5)
Genome Alignment using STAR (version 2.7.1a) No reference genome is available for the red-striped killifish, so the reads from red-striped killifish RNA-seq libraries were aligned to the genome of its close relative, lyretail killifish.
Keep only uniquely mapped reads using samtools (version 1.5) samtools view -q255
Readcounts obtained using feature counts function from Subread package (version 2.0.1)
Normalized expression using DESeq2 (version1.30.1)
Genome_build: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783
Supplementary_files_format_and_content: Read counts files for each speacies from featurecount of Subread package

organism: Nothobranchius furzeri

growth_protocol: Animals were housed in automated circulating water system with pH maintained at 6-7.5 and conductivity maintained between 3500 and 4500μS/cm with a 10% system water exchange every day by reverse osmosis treated water. Adult fish were manually fed Otohime fish diet (Reed Mariculture, Otohime C1 [Ep1 for the South American killifish]) twice a day during weekdays and once a day during weekends.

extract_protocol:
For each stage in each species, roughly 8-30 embryos were carefully dissected in ice-cold PBS using biological-grade tweezers (Electron Microscopy Sciences, 72700-D) to carefully remove the chorion, the enveloping layer, and the yolk without damaging the embryo body. Freshly dissected embryos were then quickly rinsed with ice-cold PBS, and all the PBS was carefully removed. Embryo bodies were then snap-frozen in liquid nitrogen and stored at -80°C. We used 8-10 snap-frozen embryos for RNA-seq. Snap frozen embryos at -80°C were thawed on ice for 1 minute and washed with 200µl ice-cold PBS. The embryos were then dissociated and homogenized with ~25 Zirconia/Silicon 0.5mm glass beads (RPI, Research Products International Corp, 9834) using FastPrep® -24 homogenizer (MB Biomedicals, 116004500) for 20 seconds, followed by centrifugation (17000g for 3 minutes). After centrifugation, 10.5µl of the supernatant was used as input to the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara, 634890) for the cDNA synthesis followed by amplification with 12 cDNA amplification cycles. Amplified cDNA was validated with Agilent 2100 Bioanalyzer using Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).
The DNA libraries were then generated using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). Library quality and concentration were assessed by the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent Technologies, Cat. No. 5067-4626), followed by high throughput sequencing on Illumina HiSeq platform with 2 x 150bp paired end reads.

treatment_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described (12). Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development (12, 17). We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species

value: Dissected Embryo (Whole body)

value: Pre-Diapause (K-vesicle)


title: at-endosperm-H3K9m2_replicate1_col_Cm_x_ler


title: at-endosperm-H3_replicate2_ler_x_col_Cm


title: at-endosperm-H3K9m2_replicate2_ler_x_col_Cm


title: Nfur Pre-Diapause RNAseq Rep3


title: at-endosperm-H3K27m3_replicate2_ler_x_col_Cm


title: DNA methylation data of EGFR-altered tumor case 10

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 10

value: MPNST-like sarcoma (score 0.52)


title: Nfur Pre-Diapause RNAseq Rep1

source_name: Dissected Embryo (Whole Body)


title: DNA methylation data of EGFR-altered tumor case 11

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 11

value: MPNST-like sarcoma (score 0.49)


title: at-endosperm-H3K27m3_replicate2_col_Cm_x_ler


title: at-endosperm-H3K9m2_replicate2_col_Cm_x_ler


title: DNA methylation data of EGFR-altered tumor case 12

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 12

value: DFSP (score 0.91)


title: Astr Pre-Diapause RNAseq Rep5


title: Nfur Pre-Diapause RNAseq Rep4


title: DNA methylation data of EGFR-altered tumor case 6

source_name: EGFR-altered tumor with morphology of fibrous hamartoma of infancy, case 6

value: DFSP (score 0.35)


title: at-endosperm-H3_replicate1_col_Cm_x_ler


title: at-endosperm-H3_replicate1_ler_x_col_Cm


title: at-endosperm-H3K27m3_replicate2_ler_x_col_C

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0 INT (male)

value: AT F1-Endosperm Landsberg x Columbia WT

value: Ler (maternal) x Col (paternal)


title: at-endosperm-H3K27m3_replicate2_col_C_x_ler

description: Arabidopsis thaliana F1-endosperm of Columbia-0 INT (female) crossed with Landsberg-erecta (male)

value: AT F1-Endosperm Columbia WT x Landsberg

value: Col (maternal) x Ler (paternal)


title: Astr Pre-Diapause RNAseq Rep2


title: at-endosperm-H3_replicate2_col_C_x_ler


title: at-endosperm-H3_replicate2_ler_x_col_C


title: Astr Pre-Diapause RNAseq Rep1


title: Astr Pre-Diapause RNAseq Rep4


title: at-endosperm-H3K9m2_replicate2_ler_x_col_C


title: Hydractinia symbiolongicarpus, whole-body, scRNA-seq, batch 1, library 20

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

description: SPLiT-seq

data_processing:
Barcode processing and adapter trimming were made using SPLiT-seq toolbox (https://github.com/RebekkaWegmann/splitseq_toolbox), CutAdapt  v2.8 (https://github.com/marcelm/cutadapt), pairfq makepairs (https://github.com/sestaton/Pairfq) and Picard v2.21.1-SNAPSHOT (https://github.com/broadinstitute/picard)
Transcriptome mapping was made with STAR-2.7.3a (https://github.com/alexdobin/STAR/releases/tag/2.7.3a)
Assembly: HSymV2.1 assembly available in NCBI
Supplementary files format and content: Tab-separated values files and matrix files

organism: Hydractinia symbiolongicarpus

source_name: Mixed whole-body gastrozooid, gonozooid and stolon

extract_protocol:
We used ACME dissociation to dissociate whole animals into fixed and permeable cell suspensions. Dissociated cells were proccessed using a SPLiT-seq protocol (we sorted singlets by FACS during SPLiT-seq, right before the cell lysis step).
We followed the SPLiT-seq library construction pipeline (Dynabeads cDNA purification, template switching, PCR amplification, size selection, tagmentation, indexed-PCR amplification and second size selection). Size selection was performed using Roche KAPA Pure Beads at 0.6X-0.8X ratios. Tagmentation was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer´s instructions.

value: WT


title: Astr Pre-Diapause RNAseq Rep3


title: Hydractinia symbiolongicarpus, whole-body, scRNA-seq, batch 1, library 29

description: SPLiT-seq

source_name: Whole-body gonozooid

value: Whole-body gonozooid


title: at-endosperm-H3K9m2_replicate2_col_C_x_ler

value: endosperm


title: Hydractinia symbiolongicarpus, whole-body, scRNA-seq, batch 1, library 27

description: SPLiT-seq

source_name: Whole-body gastrozooid

value: Whole-body gastrozooid


title: at-endosperm-H3_replicate1_ler_x_col_C


title: Aaus Pre-Diapause RNAseq Rep4

organism: Aphyosemion australe


title: Hydractinia symbiolongicarpus, whole-body, scRNA-seq, batch 1, library 9

description: SPLiT-seq

source_name: Mixed whole-body gastrozooid and gonozooid


title: at-endosperm-H3K27m3_replicate1_ler_x_col_C


title: Aaus Pre-Diapause RNAseq Rep5


title: Brain_Immature-2_Genotype-EE_Rep4

city: Helsinki

first: Ehsan

middle: Pashay

last: Ahi

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

description: Nanostring data analysis on mRNA isolated from the brain of Atlantic salmon (S-salar) in different maturation status with different vgll3 genotypes (EE or LL)

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter a Custom made Panel containing 342 unique pairs of 100bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occurred for 20 hours at 65°C, then reactions were held at 4°C until they were placed on the nCounter Prep Station. Wash protocol: Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and flurophore degradation was prevented with the addition of SlowFade.

scan_protocol: After hybridization, the sample strip was transferred to the nCounter Prep Station for purification and immobilization in a sample cartridge. After immobilization, the cartridge was analyzed with the nCounter Digital Analyzer by taking images of the immobilized fluorescent reporters. The number of images taken corresponded to the number of reporters counted. The raw count data was exported as a csv file.

data_processing: RCC files containing raw counts for 342 genes provided from nanostring were loaded into nSolver Analysis Software 4.0 and normalized for housekeeping genes and positive controls.

label: No label

organism: Salmo salar

source_name: Atlantic salmon brain

label_protocol: Not applicable

growth_protocol: Described in Debes, P. V., N. Piavchenko, J. Erkinaro, and C. R. Primmer, 2020 Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon. Proc. R. Soc. B Biol. Sci. 287: 20200867.

extract_protocol: RNA was extracted from wholee brain using a NucleoSpin RNA kit (Macherey-Nagel GmbH & Co. KG). The collected samples were transferred to tubes containing 1.4 mm ceramic beads from Omni International, along with Buffer RA1 and DDT (350 µl of RA1 and 3.5 µl of 1M DDT). Homogenization was performed using the Bead Ruptor Elite (Omni International) at a frequency of 30 Hz for a total of 2 min (in 6 cycles of 20 s each). The subsequent RNA extraction procedures adhered to the guidelines provided by the manufacturer, with the kit also including an integrated DNase stage to eliminate any remaining genomic DNA (gDNA). At the conclusion of this process, the RNA extracted from each individual sample was eluted using 50 µl of nuclease-free water. To assess RNA quantity, measurements were taken using the NanoDrop ND-1000 instrument (Thermo Scientific, Wilmington, DE, USA), while the quality of the RNA was evaluated through the employment of the 2100 BioAnalyzer system (Agilent Technologies, Santa Clara, CA, USA). The RNA integrity number (RIN) exceeded 7 for all samples.

treatment_protocol: Not applicable

value: Whole brain

tag: Sex

value: Male

tag: maturity

value: EE


title: Brain_Immature-2_Genotype-LL_Rep4

value: LL


title: Superior cervical ganglion, SHR, rep3

source_name: Superior cervical ganglion

value: Superior cervical ganglion


title: Brain_Mature_Genotype-LL_Rep4

value: Mature


title: Brain_Immature-1_Genotype-LL_Rep4


title: Brain_Immature-2_Genotype-EE_Rep3


title: Brain_Immature-1_Genotype-LL_Rep3


title: at-endosperm-H3K9m2_replicate1_ler_x_col_C


title: at-endosperm-H3K27m3_replicate1_col_C_x_ler


title: at-endosperm-H3_replicate1_col_C_x_ler


title: Aaus Pre-Diapause RNAseq Rep1

value: Dissected Embryo (Whole body)

value: Pre-Diapause (K-vesicle)


title: Brain_Mature_Genotype-LL_Rep3


title: Aaus Pre-Diapause RNAseq Rep2


title: Brain_Mature_Genotype-EE_Rep4


title: Aaus Pre-Diapause RNAseq Rep6


title: at-endosperm-H3K9m2_replicate1_col_C_x_ler


title: 6419C5 MRTX1133 resistant, replicate 2

city: Boston

first: Julien

last: Dilly

state: MA

address: 450 Brookline avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
FASTQ files for paired parental and resistant cell lines were aligned using STAR aligner (version 2.6.1c) with GRCh38 reference for human lines and GRCm38.p6 for mouse lines or to obtain raw read counts.
Assembly: GRCh38 (human cell lines) and GRCm38.p6 (murine cell lines)
Supplementary files format and content: comma-separated values files containing the counts values for each replicates and cell lines

growth_protocol: Cell lines were cultured at 37°C in 5% CO2 in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% FBS and 1% penicillin/streptomycin (6694C2, 6499C4, 6419C5, PANC-1) or Roswell Park Memorial Institute (RPMI) medium supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin (Panc 02.03)

extract_protocol:
Parental and MRTX1133 resistant cell lines were trypsinized and washed with PBS twice, cell pellets were collected, and total RNA was extracted using the RNeasy Plus Kits for RNA Isolation according to the manufacturer’s protocol (Qiagen; Cat. #73404). Total RNA was sent to Novogene (Sacramento, CA) for mRNA sequencing library preparation and next generation sequencing using Illumina NovoSeq. All the conditions and cell lines were prepared in triplicate.
Library preparation conducted by Novogene Corporation: mRNA enrichment by (poly)A capture, and then fragmented mRNA into 100-200nt using enzyme digestion, and final step with cDNA reverse transcription and PCR to add sequencing adaptor to the library.

treatment_protocol: MRTX1133-resistant human and murine cell lines were generated from parental cell lines by continuous dose escalation from as low as 1nM to 10μM. Once resistance to MRTX1133 was confirmed, resistant cell lines were routinely maintained in the corresponding medium with 1uM (10% of the maximum dose reached during the evolution of resistance) of MRTX1133.

value: Pancreatic ductal adenocarcinoma


title: 6419C5 MRTX1133 resistant, replicate 3


title: Aaus Pre-Diapause RNAseq Rep3


title: Dvir imago 5d 2

city: Moscow

first: Aleksandra

middle: M

last: Ozerova

address: Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1

department: Life sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

description: adults 5d 2

data_processing:
Low-quality nucleotides and reads were systematically eliminated using the fastp tool with the default parameters. Subsequently, the filtered reads were aligned to the respective reference genomes with the kallisto pseudomapping procedure and the BDGP6.46 and DvirRS2 assemblies as references for D. melanogaster and D. virilis, respectively.
Assembly: BDGP6.46 for D. melanogaster and DvirRS2 for D. virilis
Supplementary files format and content: {species}_vst_matrix.csv files contain comma-separated table witth normalized expression values for each sample and each replicate.

organism: Drosophila virilis

source_name: whole body

growth_protocol: The flies, spanning all developmental stages, were reared on the standard Drosophila wheat meal-yeast-sugar-agar medium and maintained at a constant temperature of 25°C.

extract_protocol:
The samples underwent a thorough rinsing process to remove any residual food and yeast, using the PBS buffer. Following this step, total RNA was extracted from the samples using RNAzol RT reagent (MRC, Cincinnati, OH, USA), following the manufacturer’s recommended protocols. RNA quality assessments were performed through gel electrophoresis, and the RNA samples were carefully stored in ethanol at -70°C, in preparation for subsequent experimental procedures.
Ribosomal RNA depletion was conducted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Subsequently, RNA library preparation was carried out with the NEBNext® Ultra™ II Directional RNA Library Prep Kit, and the prepared libraries were sequenced on the Illumina HiSeq4000 platform.

value: whole body

tag: replicate

value: biol rep 2

tag: gender

value: male

tag: developmental stage

value: imago


title: Dvir imago 5d 1

description: adults 5d 1

value: biol rep 1


title: 6419C5 parental replicate 3

value: WT


title: 6419C5 MRTX1133 resistant, replicate 1


title: Brain_Immature-2_Genotype-LL_Rep3


title: Brain_Immature-2_Genotype-LL_Rep2


title: Brain_Mature_Genotype-LL_Rep2


title: Brain_Immature-1_Genotype-LL_Rep2


title: Brain_Mature_Genotype-LL_Rep1


title: Brain_Immature-1_Genotype-EE_Rep4


title: Dvir pupae 72h 3

description: pupae 72h 3

value: biol rep 3

value: unknown

value: pupae


title: Brain_Immature-1_Genotype-EE_Rep3

value: Whole brain

value: Male


title: 6419C5 parental replicate 2


title: Dvir imago 5d 3

description: adults 5d 3


title: Dvir pupae 72h 2

description: pupae 72h 2


title: Brain_Immature-1_Genotype-EE_Rep2

value: EE


title: 6419C5 parental replicate 1


title: Brain_Immature-1_Genotype-LL_Rep1

value: LL


title: Brain_Immature-2_Genotype-LL_Rep1


title: Dvir pupae 72h 1

description: pupae 72h 1


title: Brain_Immature-2_Genotype-EE_Rep2


title: Brain_Mature_Genotype-EE_Rep3

value: Mature


title: Brain_Immature-1_Genotype-EE_Rep1


title: Brain_Immature-2_Genotype-EE_Rep1


title: Dvir pupae 36h 3

description: pupae 36h 3


title: A2780R biol rep 3

city: Florence

first: Matteo

last: Lulli

address: viale Morgagni 50

institute: University of Florence

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Assembly: hg38
Supplementary files format and content: A2780S A2780R ver2.xlsx

extract_protocol:
Total RNA was isolated from A2780S and A2780R cells by means of NucleoSpin Total RNA kit according to the manufacturer’s protocol (Macherey-Nagel, PA, USA)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: ovarian cancer


title: Brain_Mature_Genotype-EE_Rep2


title: A2780R biol rep 2


title: Brain_Mature_Genotype-EE_Rep1


title: A2780R biol rep 1


title: Dvir pupae 36h 2

description: pupae 36h 2


title: A2780S biol rep 2


title: Dvir pupae 36h 1

description: pupae 36h 1


title: A2780S biol rep 3


title: A2780S biol rep 1


title: 6499C4 MRTX1133 resistant, replicate 1


title: Dvir pupae P5 3

description: pupae P5 3


title: 6499C4 parental replicate 2


title: Dvir pupae P5 2

description: pupae P5 2


title: 6499C4 parental replicate 1


title: Dvir pupae P5 1

description: pupae P5 1


title: 6499C4 MRTX1133 resistant, replicate 3


title: Dvir pupae P4 3

description: pupae P4 3


title: Respiratory mucosa, IAV X31 rechallenge, 5dprc, hashtag oligo

first: Jose

last: Ordovas-Montanes

address: 300 Longwood Ave

department: Gastroenterology, Hepatology and Nutrition Research

institute: Boston Children's Hospital

description: HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads

library_source: other

data_processing:
FASTQs, cell count matrices, and hashtag oligo counts were generated using cellranger v6.0.1 through cumulus tools (https://cumulus.readthedocs.io/en/stable/)
Cellbender was then applied to the raw h5 output files to correct for transcript spill-over with the following parameters: expected_cells=30000, fpr=0.01, total_droplets_included=50000
Cellbender corrected cells were then filtered based on Unique Molecular Identifiers (UMI) count (>750 & <10000), number of detected genes (>500), and percentage of mitochondrial genes (<15%). Finally, cells labeled as doublets by demultiplexing were removed
Downstream clustering analysis was performed using Seurat (v.4.2.1) using scTransform normalization and corrected counts.
Remaining doublets were removed by inspection upon subclustering routines by identifying clusters expressing mutually exclusive cell type lineage markers
Assembly: GRCm39 + custom IAV PR8 genome (NCBI Taxonomy ID #211044; segment sequences: NC_002023.1, NC_002022.1, NC_002021.1, NC_002020.1, NC_00219.1, NC_2018.1, NC_002017.1, and NC_002016.1)
Supplementary files format and content: Cellranger output files: XXX.h5 contains the raw unfiltered cell count matrix
Supplementary files format and content: Cellranger output files: XXX.csv contains the hashtag oligo counts; feature_barcodes.csv contains the TotalSeqB Hashtag antibody oligo sequences used for every sample

molecule: protein

source_name: Nasal mucosa, respiratory mucosa

extract_protocol:
Tissue was harvested by microdissection and digested in RPMI (w/ FBS, HEPES, and P/S) for 20 min (LNG) or 30 min (RM/OM). Following enzyme inactivation with EDTA and filtration through a 70 µm membrane, ACK lysis was performed on ice for 1min. Epithelial cells were partially depleted using Biotin Binder Dynabeads pre-loaded with anti-biotin anti-EpCAM antibody during a 20min incubation on ice. Following bead removal, cells were stained with TotalSeqB Hashtag antibodies for 20 minutes before washing, counting, and combining. Finally, cells were captured and processed on either a 10x Chromium or X controller using the 3' transcriptome v3.1 kit and feature barcoding kits.
Libraries were constructed as outlined in the 10x Genomics guide for Dual-indexed 3' transcriptomics v3.1 with Feature Barcoding.

treatment_protocol: Mice were infected intranasally with a low volume of IAV PR8 (5 µl/nostril) while awake to restrict infection to the nasal mucosa.

value: Nasal mucosa, respiratory mucosa

value: IAV PR8, IAV X31

tag: timepoint

value: female

tag: disease state

value: heterologous rechallenge

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 23


title: 6694C2 MRTX1133 resistant, replicate 3

value: Pancreatic ductal adenocarcinoma


title: Respiratory mucosa, IAV X31 rechallenge, 5dprc, gene expression

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript

tag: tissue

value: mRNA


title: 6694C2 MRTX1133 resistant, replicate 2

tag: genotype

value: WT


title: 6499C4 MRTX1133 resistant, replicate 2


title: Respiratory mucosa, IAV X31 rechallenge, 2dprc, hashtag oligo

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 22


title: Dvir pupae P4 2

description: pupae P4 2

value: whole body

value: biol rep 2

value: unknown

value: pupae

tag: timing


title: 6499C4 parental replicate 3


title: Respiratory mucosa, IAV X31 rechallenge, 2dprc, gene expression


title: Dvir pupae P4 1

description: pupae P4 1

value: biol rep 1


title: 6694C2 parental replicate 3


title: Respiratory mucosa, IAV PR8 rechallenge, 5dprc, hashtag oligo

value: IAV PR8, IAV PR8

value: homologous rechallenge

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 20


title: Respiratory mucosa, IAV, 60dpi, bio rep2, gene expression

value: Nasal mucosa, respiratory mucosa

value: IAV PR8

value: primary infection


title: Respiratory mucosa, IAV, 60dpi, bio rep2, hashtag oligo

value: female

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 21


title: Respiratory mucosa, IAV PR8 rechallenge, 5dprc, gene expression

value: mRNA


title: Dvir pupae P3 3

description: pupae P3 3

value: biol rep 3


title: Respiratory mucosa, IAV PR8 rechallenge, 2dprc, hashtag oligo

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 19


title: 6694C2 parental replicate 2

value: Pancreatic ductal adenocarcinoma

value: WT


title: Dvir pupae P3 2

description: pupae P3 2

value: whole body

value: biol rep 2

value: unknown


title: HMGB2_Input

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
Paired-end reads were processed for adapter removal and mapped to the hg38 reference genome using Bowtie2.
RPKM normalized bigwigs were generated using deeptools.
Peaks were called using macs2. For HMGB2 the significant cut-off was q-value 0.03. For the SON default parameters were applied
Peak consistency between replicates was evaluated using IDR and p-value ranking
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Lung Tissue

extract_protocol:
For SON ChIPmentation, cells were extracted and fixed at room temperature with 1% formaldehyde for 10 minutes. For HMGB2 ChIPmentation, cells were initially fixed with 1.5 mM EGS at room temperature for 20 minutes 1% formaldehyde for 10 minutes followed by incubation with
Antibody incubation, washes, Tagmentation and DNA extraction were performed as described in the methods section

value: Lung Tissue

value: Human Embryonic Fibroblast

value: input


title: SON_D3

value: ICM 3 days


title: SON_Control

value: untreated (control)


title: SON_D6

value: ICM 6 days


title: HMGB2

value: untreated


title: 6694C2 parental replicate 1


title: Respiratory mucosa, IAV PR8 rechallenge, 2dprc, gene expression

value: Nasal mucosa, respiratory mucosa

value: IAV PR8, IAV PR8

value: female

value: homologous rechallenge


title: Dvir pupae P3 1

description: pupae P3 1

value: biol rep 1

value: pupae


title: Respiratory mucosa, IAV, 60dpi, bio rep1, hashtag oligo

value: IAV PR8

value: primary infection

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 18


title: Lung IM, R213G, 14d hypoxia, rep3

city: Aurora

first: Caitlin

middle: Vanessa

last: Lewis

state: Colorado

address: University of Colorado Denver AMC, 12700 East 19th Avenue, Mail Stop B131

department: Pediatrics

institute: University of Colorado

data_processing:
FastQC v0.11.9 for quality control and UMI-tools v1.1.1 for UMI extraction
Trim Galore! V0.6.6 to trim adapter and low-quality sequences
Alignment to mm10 genome and BAM file filtering using STAR v2.6.1d, SAMtools v1.9 and UMI-tools
Genes assigned using featureCounts v2.0.1
Differential gene expression analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: excel spreadsheet of normalized read count matrix

source_name: lung

extract_protocol:
RNA was harvested from FACS isolated IMs using the Qiagen RNeasy Micro Kit. 20 ng total RNA was used for library preparation
RNA libraries prepared using Illumina Novaseq protocol

treatment_protocol: Mice exposed to 4 or 14 days of hypobaric hypoxia (FiO2 10%) vs normoxia

value: lung

value: intersitial macrophage

value: R213G SOD3

value: 14 day hypoxia


title: Lateral nasal gland, IAV, 14dpi, hashtag oligo

source_name: Nasal mucosa, lateral nasal gland

value: Nasal mucosa, lateral nasal gland

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 17


title: Dvir pupae P2 3

description: pupae P2 3

value: whole body

value: biol rep 3

value: unknown


title: Lateral nasal gland, IAV, 14dpi, gene expression

value: female

value: mRNA


title: 6694C2 MRTX1133 resistant, replicate 1

value: Pancreatic ductal adenocarcinoma

value: WT


title: Lung IM, R213G, 14d hypoxia, rep2


title: Dvir pupae P2 2

description: pupae P2 2

value: biol rep 2

value: pupae


title: Olfactory mucosa, IAV, 14dpi, hashtag oligo

source_name: Nasal mucosa, olfactory mucosa

value: Nasal mucosa, olfactory mucosa

value: IAV PR8

value: primary infection

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 16


title: Lung IM, R213G, 14d hypoxia, rep1

value: lung

value: intersitial macrophage

value: R213G SOD3

value: 14 day hypoxia


title: Dvir pupae P2 1

description: pupae P2 1

value: whole body

value: biol rep 1


title: Respiratory mucosa, IAV, 14dpi, hashtag oligo

value: Nasal mucosa, respiratory mucosa

value: female

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 15


title: Lung IM, R213G, 4d hypoxia, rep3

value: 4 day hypoxia


title: Olfactory mucosa, IAV, 14dpi, gene expression

value: mRNA


title: Dvir pupae P1 3

description: pupae P1 3

value: biol rep 3

value: unknown

value: pupae


title: Lateral nasal gland, naive, hashtag oligo

value: Nasal mucosa, lateral nasal gland

value: naive

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 5


title: Lung IM, R213G, 4d hypoxia, rep2

value: lung


title: Lung IM, R213G, 4d hypoxia, rep1

value: intersitial macrophage


title: Olfactory mucosa, naive, gene expression

value: Nasal mucosa, olfactory mucosa


title: Lung IM, R213G, normoxia, rep3

value: R213G SOD3

value: untreated/normoxia


title: Respiratory mucosa, naive, gene expression


title: Dvir pupae P1 1

description: pupae P1 1

value: whole body

value: biol rep 1


title: Respiratory mucosa, naive, hashtag oligo

value: Nasal mucosa, respiratory mucosa

value: female

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 3


title: Lateral nasal gland, naive, gene expression

value: mRNA


title: Dvir larvae 2instar 3

description: larvae 2nd instar 3

value: biol rep 3

value: unknown

value: larvae


title: Dvir pupae P1 2

description: pupae P1 2

value: biol rep 2

value: pupae


title: YY1aid_async_auxin_TT-seq_rep3

city: Philadelphia

first: Jessica

last: Lam

state: PA

address: 3615 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

description:
Nascent RNA
YY1aid_ttseq_spikein_counts_htseq.txt
YY1aid_ttseq_sample_counts_htseq.txt

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
The paired-end TT-seq reads were trimmed using Trim Galore v0.6.10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were aligned to the mouse mm9 and Drosophila dm6 assemblies and sorted using STAR v2.7.10b4.
Index and skip alignments with MAPQ smaller than 7 in the resulting genome alignment BAM files using SAMtools v1.145.
The TT-seq signal and bigwig files normalized by spike-in reads was generated by deepTools v3.5.26.
Assembly: mm9
Supplementary files format and content: bw: strand-specific bigwig tracks of TT-seq signals. Txt: gene-level counts
Library strategy: TT-seq

extract_protocol:
Exponentially growing cells in T-150 flasks were labeled with 500 μM 4-thiouridine (4SU) (MedChemExpress), for 5 minutes. The cells were processed with 2 mL TRIzol Reagent (Invitrogen) for every 10 million G1E-ER4 cells and total RNAs was extracted following the user manual. 500 ng of 4SU-labeled Drosophila Schneider 2 (S2) cells total RNA as spike in was mixed with 100 μg of collected 4SU-labeled G1E-ER4 total RNA. Mixed RNA was fragmentated using a final concentration of 0.2 M NaOH for 18 minutes and neutralized with a final concentration of 0.5 M Tris-HCl (pH 6.8). RNA was purified by isopropanol precipitation. Labelled RNA was biotinylated in 300 μL of biotinylation mix (fragmented total RNA, 10 mM HEPES pH 7.5, 1 mM EDTA, 0.167 mg/mL MTSEA-biotin (Biotium)) for 1 hour at room temperature and purified with phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)) extraction. Denature the biotinylated RNA from at 65 °C for 10 minutes, followed by rapid cooling on ice for 5 minutes. The denatured biotinylated RNA was bound with Dynabeads MyOne Streptavidin C1 (Invitrogen) at room temperature for 30 minutes, eluted with 100 mM DTT and subsequently purified by isopropanol precipitation. Quality of total RNA extraction, RNA fragmentation (we aimed for an RNA size distribution between 25 and 500 nt), and purified 4SU-labeled RNA were determined using Agilent TapeStation RNA ScreenTape (Agilent).
Strand-specific sequencing libraries were generated with the Illumina Stranded Total RNA Prep (Illumina) and IDT for Illumina RNA UD Indexes Set A, Ligation (Illumina). Library size was determined using Agilent TapeStation High Sensitivity DNA ScreenTape (Agilent).

value: Erythroblast

value: YY1-AID subline


title: Respiratory mucosa, IAV, 60dpi, bio rep1, gene expression

value: IAV PR8

value: primary infection


title: YY1aid_async_auxin_TT-seq_rep2


title: at-endosperm-H3K27m3_replicate1_col_Cm_x_ler

source_name: endosperm

value: endosperm

value: AT F1-Endosperm Columbia TEmob x Landsberg

value: TEmob Col (maternal) x Ler (paternal)


title: Olfactory mucosa, naive, hashtag oligo

value: Nasal mucosa, olfactory mucosa

value: naive

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 4


title: YY1aid_async_auxin_TT-seq_rep1


title: Dvir larvae 2instar 2

description: larvae 2nd instar 2

value: whole body


title: Lung IM, R213G, normoxia, rep1

value: lung

value: intersitial macrophage

value: R213G SOD3

value: untreated/normoxia


title: Respiratory mucosa, IAV, 14dpi, gene expression

value: Nasal mucosa, respiratory mucosa

value: female

value: mRNA


title: Lung IM, R213G, normoxia, rep2


title: YY1aid_async_untreated_TT-seq_rep3

value: Erythroblast

value: YY1-AID subline

value: untreated


title: Dvir larvae 2instar 1

description: larvae 2nd instar 1

value: biol rep 1

value: unknown

value: larvae


title: YY1aid_async_untreated_TT-seq_rep2


title: YY1aid_async_untreated_TT-seq_rep1


title: Lung IM, WT, 14d hypoxia, rep3

value: C57BL/6J (WT)

value: 14 day hypoxia


title: Dvir embryo 15h 3

description: embryo 15h 3

value: biol rep 3

value: embryo


title: RNAseq_YY1aid_async_auxin24h_rep3

data_processing:
For the YY1-AID RNA-seq reads were downsampled to 30 million reads per sample. Reads were aligned with salmon (v0.13.1) using default settings. Gene level counts were generated with tximport (v1.20.0). Differential expression analysis was performed with DESeq2. We employed a significance threshold of Benjamini-Hochberg corrected padj < 0.05. The apelgm method was used to shrink log-fold change values
Assembly: mm9
Supplementary files format and content: raw counts calculated by DESeq2

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen, #74104), according to the manufacturer’s instructions. Genomic DNA was then eliminated with QIAshredder (Qiagen, #79656) followed by on-column DNAse digestion.
500ng of total RNA was used as input for library prep. RNA-seq libraries were prepared using the TruSeq Stranded mRNA kit (Illumina, #20020594).

value: ES-derived erythroid progenitor cells

tag: cell cycle_stage

value: asynchronous


title: RNAseq_YY1aid_async_auxin48h_rep3


title: Lung IM, WT, 14d hypoxia, rep2

value: lung

value: intersitial macrophage


title: RNAseq_YY1aid_async_auxin0h_rep3


title: Lung IM, WT, 14d hypoxia, rep1


title: RNAseq_YY1aid_async_auxin24h_rep2


title: RNAseq_YY1aid_async_auxin48h_rep2


title: Lung IM, WT, 4d hypoxia, rep3

value: 4 day hypoxia


title: Dvir embryo 15h 1

description: embryo 15h 1

value: whole body


title: RNAseq_YY1aid_async_auxin4h_rep2


title: RNAseq_YY1aid_async_auxin0h_rep2


title: Lung IM, WT, 4d hypoxia, rep2


title: RNAseq_YY1aid_async_auxin48h_rep1


title: PANC-1 MRTX1133 resistant, replicate 3

tag: cell line

value: Pancreatic ductal adenocarcinoma

value: WT


title: RNAseq_YY1aid_async_auxin24h_rep1

value: YY1-AID subline


title: PANC-1 MRTX1133 resistant, replicate 2


title: Lung IM, WT, 4d hypoxia, rep1


title: RNAseq_YY1aid_async_auxin4h_rep1


title: Lung IM, WT, normoxia, rep4

value: untreated/normoxia


title: PANC-1 MRTX1133 resistant, replicate 1


title: RNAseq_YY1aiduntreated_rep2


title: PANC-1 parental replicate 3


title: Lung IM, WT, normoxia, rep3


title: RNAseq_YY1aid_async_auxin0h_rep1


title: RNAseq_clone3_untreated_rep2

value: YY1-AID subline3


title: RNAseq_YY1aid_async_auxin4h_rep3


title: Dvir embryo 15h 2

description: embryo 15h 2

value: biol rep 2

value: unknown


title: PANC-1 parental replicate 2


title: Lung IM, WT, normoxia, rep2

value: C57BL/6J (WT)


title: RNAseq_clone3_untreated_rep1


title: RNAseq_YY1aiduntreated_rep1


title: Lung IM, WT, normoxia, rep1


title: YY1aid_async_Auxin_H3K27ac_ChIPseq_rep2

description:
YY1aid_async_Auxin_H3K27ac_chip.bw
YY1aid_async_auxin_H3K27ac_peaks.bed

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
For ChIP-seq, alignment was performed with bowtie2 default settings, de-duplicated, and filtered for MAPQ>20
To generate bigwig files, we used deeptools (v3.5.1) bamCoverage (binSize=20, smoothLength=60, normalizeUsing=BPM)
To generate peak calls, we used macs2 (v2.2.7) with matched input and q=0.05
Assembly: mm9
Supplementary files format and content: bw: tracks of processed ChIP-seq  signals. bed: list of ChIP-seq peak coordinates.

extract_protocol:
For ChIP-seq, DNA from lysed cells was sonicated, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106).
We used the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) with unique dual-indexed primers (NEB E6440).

tag: antibody

value: anti-H3K27ac Active Motif 39133


title: YY1aid_async_Auxin_H3K27ac_ChIPseq_rep1

tag: cell type


title: CTCFaid_async_auxin_YY1_ChIPseq_rep1

description:
CTCFaid_async_auxin_YY1_chip.bw
CTCFaid_async_auxin_YY1_peaks.bed

tag: treatment

value: anti-YY1 Active Motif 61980


title: Panc 02.03 MRTX1133 resistant, replicate 2


title: CTCFaid_async_untreated_YY1_ChIPseq_rep1

description:
CTCFaid_async_untreated_YY1_chip.bw
CTCFaid_async_untreated_YY1_peaks.bed

value: untreated


title: adipose-derived stem cells, KO, 3-4 weeks

city: Shanghai

first: Yan

state: Shanghai

address: 800 Dong Chuan Road

institute: Shanghai Jiao Tong University

description: KO

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains the FPKM value of gene in every sample

source_name: Adipose

extract_protocol:
Abdominal fat pad were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Adipose

value: Trappc9 knock out


title: RNAseq_parental_rep2

value: ES-derived erythroid progenitor cells

value: parental

value: asynchronous


title: CTCFaid_async_auxin_YY1_ChIPseq_rep2


title: Panc 02.03 MRTX1133 resistant, replicate 1


title: adipose-derived stem cells, WT, 3-4 weeks

description: WT


title: YY1aid_async_auxin_LDB1_ChIPseq_rep2

description:
YY1aid_async_auxin_LDB1_chip.bw
YY1aid_async_auxin_LDB1_peaks.bed

value: anti-CLIM2 Santa Cruz sc-365074


title: Panc 02.03 parental replicate 3

value: Pancreatic ductal adenocarcinoma


title: YY1aid_async_untreated_LDB1_ChIPseq_rep2

description:
YY1aid_async_untreated_LDB1_chip.bw
YY1aid_async_untreated_LDB1_peaks.bed


title: YY1aid_async_auxin_LDB1_ChIPseq_rep1


title: YY1aid_async_untreated_LDB1_ChIPseq_rep1


title: Panc 02.03 parental replicate 2

value: WT


title: PANC-1 parental replicate 1


title: DRD2 neurons, Trappc9 KO1, 3-4 weeks

source_name: Brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain


title: YY1aid_untreated_midg1_rep4_MicroC

description:
YY1aid_mg1_untreated.mcool
YY1aid_mg1_compartmentEV1_untreated.bw
YY1aid_mg1_untreated_log2insulationscore.bw
YY1aid_mg1_merged_boundaries.bed
YY1aid_mg1_merged_domains.bedpe
YY1aid_midg1_merged_loops.bedpe

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
For Micro-C, we generated .mcool files with the distiller pipeline (v3.3)
Micro-C analysis was performed with cooltools (v0.5.0) and rGMAP
For ChIP-seq, alignment was performed with bowtie2 default settings, de-duplicated, and filtered for MAPQ>20
To generate bigwig files, we used deeptools (v3.5.1) bamCoverage (binSize=20, smoothLength=60, normalizeUsing=BPM)
To generate peak calls, we used macs2 (v2.2.7) with matched input and q=0.05
Assembly: mm9
Supplementary files format and content: mcool: Micro-C contact map. bw: tracks of processed ChIP-seq or Micro-C signals. bedpe: list of Micro-C loop coordinates. bed: list of ChIP-seq peak coordinates.
Library strategy: Micro-C

extract_protocol:
For ChIP-seq, DNA from lysed cells was sonicated, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106). For Micro-C, DNA was digested with MNase, proximity-ligated, and extracted using phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Gel extraction was used to select for fragments between 250-400bp. DNA was purified with Zymoclean Gel DNA Recovery kit (D4007).
We used the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) with unique dual-indexed primers (NEB E6440).

value: YY1-AID subline


title: DRD2 neurons, WT3, 3-4 weeks


title: Panc 02.03 parental replicate 1


title: YY1aid_untreated_midg1_rep3_MicroC


title: YY1aid_untreated_midg1_rep2_MicroC


title: RNAseq_parental_rep1


title: IMR90, siBANF1, RNA-seq, replicate 2

data_processing:
Paired-end RNA-seq reads were mapped to human reference genome build hg38 using STAR ver. 2.7.3a with default parameters, uniquely mapped gene counts quantified using HTSeq ver. 0.12.4, and normalizes using the RUVs module of the RUVseq package ver. 1.30.0.
Differentially expressed genes were defined via the DEseq2 ver. 1.36.0 package using its default Wald test and deemed as DEGs when they had a Padj <0.05 and absolute log2FC >0.6.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including the raw counts

growth_protocol: Proliferating primary lung fibroblasts (IMR90) isolates (I79 and I83, passage 5; Coriell) were grown in MEM (M4655, Sigma-Aldrich) supplemented with 1x non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
IMR90 were washed with 1x PBS and harvested directly in Trizol (Invitrogen, 15596018). RNA was isolated from this lysate by using the Direct-zol RNA MiniPrep Kit (Zymo Research, R2052:1074069) including an on-column DNase I treatment step according to the manufacturer’s instructions.
The library was constructed with the TruSeq kit (Illumina) before paired-end sequencing on a NovaSeq6000 platform (Illumina)

treatment_protocol: Senescence was induced after treating the cells for up to 6 days with 10μM inflachromene (ICM; Cayman Chemicals)

value: primary lung fibroblasts

value: BANF1 knockdown

value: ICM inducing senescence


title: IMR90, siBANF1, RNA-seq, replicate 1


title: Panc 02 03 MRTX1133 resistant, replicate 3


title: DRD2 neurons, WT1, 3-4 weeks


title: YY1aid_untreated_asyn_rep5_MicroC

description:
YY1aid_async_untreated.mcool
YY1aid_async_untreated_compartmentEV1.bw
YY1aid_async_untreated_log2insulationscore.bw
YY1aid_async_merged_boundaries.bed
YY1aid_async_merged_domains.bedpe
YY1aid_async_merged_loops.bedpe

value: asyn


title: YY1aid_untreated_asyn_rep4_MicroC


title: DRD2 neurons, Trappc9 KO2, 3-4 weeks


title: IMR90, siSRRM2, RNA-seq, replicate 2

value: SRRM2 knockdown


title: YY1aid_untreated_asyn_rep3_MicroC


title: CTCFaid_async_untreated_YY1_ChIPseq_rep2

value: anti-YY1 Active Motif 61980


title: YY1aid_untreated_asyn_rep2_MicroC

value: untreated


title: DRD2 neurons, WT2, 3-4 weeks


title: YY1aid_untreated_asyn_rep1_MicroC


title: YY1aid_midG1_untreated_Pol2_ChIPseq_rep3

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
For Micro-C, we generated .mcool files with the distiller pipeline (v3.3)
Micro-C analysis was performed with cooltools (v0.5.0) and rGMAP
For ChIP-seq, alignment was performed with bowtie2 default settings, de-duplicated, and filtered for MAPQ>20
To generate bigwig files, we used deeptools (v3.5.1) bamCoverage (binSize=20, smoothLength=60, normalizeUsing=BPM)
To generate peak calls, we used macs2 (v2.2.7) with matched input and q=0.05
Assembly: mm9
Supplementary files format and content: mcool: Micro-C contact map. bw: tracks of processed ChIP-seq or Micro-C signals. bedpe: list of Micro-C loop coordinates. bed: list of ChIP-seq peak coordinates.

tag: chipantibody

value: anti-RPB1 Cell Signaling 14958


title: YY1aid_midG1_untreated_Pol2_ChIPseq_rep1


title: IMR90, ICM, RNA-seq, replicate 2


title: YY1aid_midG1_untreated_Pol2_ChIPseq_rep2


title: IMR90, ICM, RNA-seq, replicate 1


title: YY1aid_untreated_midg1_rep1_MicroC


title: YY1aid_midG1_auxin_Pol2_ChIPseq_rep3


title: 19336X13 spore forming 1

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

description: LCM SID

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 104
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.6a in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.32.0
Assembly: GRCm39
Supplementary files format and content: featureCount output files combined into a tab-delimited raw count matrix

source_name: small intestine duodeum

growth_protocol: Mice were housed in sterile conditions and fed a normal chow diet sterilized by autoclaving. Eight week old B6 male mice were used. Spore Forming colonized animals were colonized born to parents colonized with Spore Forming bacteria.

extract_protocol:
RNA extraction: After tissue was collected 350uL of Qiagen buffer RLT+ beta mercaptone ethonal was added and incubated at room temperature for 30 min for lysis before being stored in the -80C. RNA was extracted with the RNeasy micro kit from Qiagen with on column DNase I digest and eluted in 14uL RNAse free H2O. Samples have been stored at -80C.
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

value: small intestine duodeum


title: 19336X4 germ free 4

description: LCM SID


title: 19336X16 spore forming 4

description: LCM SID


title: 19336X15 spore forming 3

description: LCM SID


title: 19336X14 spore forming 2

description: LCM SID


title: YY1aid_midG1_auxin_Pol2_ChIPseq_rep1

value: ES-derived erythroid progenitor cells


title: 19336X3 germ free 3

description: LCM SID


title: IMR90, siHMGB2, RNA-seq, replicate 1

value: HMGB2 knockdown


title: 19336X2 germ free 2

description: LCM SID


title: YY1aid_lateG1_untreated_Pol2_ChIPseq_rep3


title: IMR90, wild type, RNA-seq, replicate 2


title: YY1aid_lateG1_untreated_input

value: input


title: YY1aid_midG1_auxin_Pol2_ChIPseq_rep2


title: IMR90, siSRRM2, RNA-seq, replicate 1


title: IMR90, siHMGB2, RNA-seq, replicate 2


title: YY1aid_lateG1_untreated_Pol2_ChIPseq_rep1


title: YY1aid_lateG1_auxin_Pol2_ChIPseq_rep2


title: YY1aid_lateG1_auxin_input


title: IMR90, wild type, RNA-seq, replicate 1


title: YY1aid_midG1_auxin_input


title: YY1aid_lateG1_auxin_Pol2_ChIPseq_rep1


title: YY1aid_earlyG1_untreated_Pol2_ChIPseq_rep3


title: YY1aid_lateG1_auxin_Pol2_ChIPseq_rep3


title: YY1aid_midG1_untreated_input


title: PC, GRWT, rep3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm39 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples

source_name: intestinal epithelial cells

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate a sequencing library using the truseq stranded library prep kit accorting to the manufacturers instructions

treatment_protocol: The small intestine of WT and GRvillinKO mice was isolated, crypts were taken from the tissue and a single cell suspension was made for FACS sorting. Cells were sorted as PCs or non-PCs and collected for RNA isolation

value: PC

tag: strain


title: PC, GRWT, rep2


title: nonPC, GRWT, rep3

value: nonPC

value: GRKO


title: PC, GRWT, rep1

value: WT


title: Ag11

city: New Haven

first: Daniel

last: Jane-Wit

state: CT

address: 10 Amistad St

institute: Yale University

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0)
Gene expression levels were quantified using StringTie (v1.3.3b) with gene models (v27) from the GENCODE project
Differentially expressed genes were identified using DESeq2 (v 1.22.1)
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

growth_protocol: HEK cell lines were incubated at 37°C with 5% CO2, 10%FBS DMEM medium.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (74104, Qiagen), and sent for bulk RNA-seq with polyA selection.
RNA libraries were prepared for sequencing using standard Illumina protocols with polyA selection

treatment_protocol: HEK cell lines were transduced with vector or A197-270 tandem plasmids in Day1, then treated with or without IFN-gamma in Day2, and harvested in Day4.

value: HEK was transduced withA197-270 plasmid in Day 1, then treated with IFN-gamma in Day 2, and in Day 4 cells were harvested.


title: Ag12


title: YY1aid_earlyG1_untreated_Pol2_ChIPseq_rep1

value: YY1-AID subline


title: YY1aid_earlyG1_untreated_Pol2_ChIPseq_rep2


title: YY1aid_lateG1_untreated_Pol2_ChIPseq_rep2


title: YY1aid_earlyG1_auxin_Pol2_ChIPseq_rep3


title: YY1aid_earlyG1_untreated_input


title: 19336X1 germ free 1

description: LCM SID


title: nonPC, GRWT, rep2


title: YY1aid_earlyG1_auxin_Pol2_ChIPseq_rep2


title: Vg8

value: HEK was transduced with Flag vector in Day 1, then treated with IFN-gamma in Day 2, and in Day 4 cells were harvested.


title: YY1aid_earlyG1_auxin_Pol2_ChIPseq_rep1


title: PC, GRKO, rep3


title: YY1aid_earlyG1_auxin_input


title: Vg7


title: YY1aid_auxin_midg1_rep3_MicroC

description:
YY1aid_mg1_auxin.mcool
YY1aid_mg1_compartmentEV1_auxin.bw
YY1aid_mg1_auxin_log2insulationscore.bw
YY1aid_mg1_merged_boundaries.bed
YY1aid_mg1_merged_domains.bedpe
YY1aid_midg1_merged_loops.bedpe

value: auxin


title: nonPC, GRWT, rep1


title: PC, GRKO, rep2


title: YY1aid_auxin_midg1_rep2_MicroC


title: Ag10


title: Vg9


title: A6

value: HEK was transduced with A197-270 plasmid in Day 1, then in Day 4 cells were harvested.


title: YY1aid_auxin_midg1_rep4_MicroC


title: PC, GRKO, rep1


title: YY1aid_auxin_asyn_rep4_MicroC

description:
YY1aid_async_auxin.mcool
YY1aid_async_auxin_compartmentEV1.bw
YY1aid_async_auxin_log2insulationscore.bw
YY1aid_async_merged_boundaries.bed
YY1aid_async_merged_domains.bedpe
YY1aid_async_merged_loops.bedpe

value: asyn


title: YY1aid_auxin_asyn_rep5_MicroC


title: A5


title: A4


title: nonPC, GRKO, rep3


title: YY1aid_auxin_midg1_rep1_MicroC


title: YY1aid_auxin_asyn_rep3_MicroC


title: YY1aid_auxin_asyn_rep2_MicroC


title: YY1aid_async_untreated_YY1b_ChIPseq_rep2

description:
YY1aid_async_untreated_YY1b.bw
YY1aid_async_untreated_YY1b_peaks.bed

value: anti-YY1 Bethyl A301-778A

value: asynchronous


title: YY1aid_auxin_asyn_rep1_MicroC


title: V3

value: HEK was transduced with Flag vector in Day 1, then in Day 4 cells were harvested.


title: V2


title: nonPC, GRKO, rep2


title: nonPC, GRKO, rep1


title: YY1aid_async_untreated_YY1b_ChIPseq_rep1

value: untreated


title: YY1aid_async_untreated_YY1_ChIPseq_Rep3

description:
YY1aid_async_untreated_YY1_chip.bw
YY1aid_async_untreated_YY1_peaks.bed

value: ES-derived erythroid progenitor cells

value: anti-YY1 Active Motif 61980


title: YY1aid_async_untreated_YY1_ChIPseq_Rep2


title: YY1aid_async_untreated_YY1_ChIPseq_Rep1


title: H3K14la

city: Tianjin

first: 爱源

last: 王

state: —Please choose an option—

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin

department: Department of Biochemistry and Molecular Biology

institute: TianjinMedical University

data_processing:
FastQC tool was used to examine metrics, such as sequencing error rate, sequencing depth, and fragment length distribution
Aligned the preprocessed reads to a reference genome using alignment tool (Bowtie2)
Peak calling was performed using the model-based analysis of ChIP–seq (MACS2)
BigWig files were generated through Deeptools
Assembly: hg38
Supplementary files format and content: bigWig narrowPeak
Library strategy: CUT&Tag

source_name: Hela cells

extract_protocol:
Hela cells  were collected and counted for incubation with pre-treated ConA beads. Subsequently, cells are resuspended in an Antibody Buffer and incubated overnight at 4 °C with the corresponding primary antibody . The secondary antibodies were diluted in appropriate proportions and incubate them with the cells at room temperature. Subsequently, pA/G-Tnp transposons were rotated and incubated with the samples for 1 h to activate the translocase fragment DNA and extract DNA.
DNA library was constructed with TruePreP Index Kit V2 for Illumina (TD202, Vazyme Biotech). The library was purified by VAHTS DNA Clean Beads (N411, Vazyme Biotech)

value: Hela cells

value: no overexpression

tag: chip antibody


title: YY1aid_async_untreated_Pol2_ChIPseq_rep3

value: anti-RPB1 Cell Signaling 14958


title: YY1aid_async_untreated_RAD21_ChIPseq_Rep2

description:
YY1aid_async_untreated_RAD21_chip.bw
YY1aid_async_untreated_RAD21_peaks.bed

value: anti-RAD21 abcam ab992


title: KPC_3947, Early Vehicle, snRNAseq

description: 10X Genomics

data_processing:
BCL files were converted to FASTQ using Illumina’s BCL Convert Tool. CellRanger (version 7.0.1) was used to demultiplex the FASTQ reads, and align them to the mm10 mouse transcriptome (mm10_premrna-1.2.0). We then used CellBender remove background (version 0.2.0) Terra workflow (snapshot 11) to remove ambient RNA and other technical artifacts from the count matrices. We used a false positive rate of 0.01 along with a number of epochs ranging between 150 and 200 and a learning rate comprised between 5e-5 and 1e-4. We set the parameters “expected cells” based on the estimated number of cells from the CellRanger output. For downstream analyses, we used CellBender’s output file (out_filtered.h5). Next, we filtered the combined gene expression matrix to only include high-quality nuclei using the following criteria: total genes in ]400-6,000[, total counts in ]1,000-35,000[, percent mitochondrial counts < 5%, percent ribosomal counts < 5%, cellular complexity (log10 Genes per UMI) > 0.8. We identified doublets at a per-sample basis using the quality control filtering steps previously mentioned in combination with DoubletFinder (version 2.0.3) and removed them from each gene*nuclei expression matrices. We additionally removed genes that were not detected in at least 100 nuclei across the entire dataset.
Assembly: mm10
Supplementary files format and content: R Data Serialization (rds)

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Samples were prepared as previously described (Hwang et al. Nature genetics 2022, PMID: 35902743). Briefly, ST stock solution was prepared in nuclease-free water with a final concentration of 146 mM NaCl (Thermo Fisher Scientific, Cat. #AM9759), 20 mM Tricine (VWR, Cat #. E170-100G), 1mM CaCl2 (VWR, Cat. # 97062-820) and 21 mM MgCl2 (Sigma-Aldrich, Cat. # M1028). 2mL of NST nuclei isolation solution was prepared for each sample by adding 0.2% Nonidet P40 Substitute (Thermo Fisher Scientific, Cat. #AAJ19628AP), 0.01% bovine serum albumin (New England Biolabs, Cat. # B9000S), 0.15 mM of spermine (Sigma-Aldrich, Cat. # S3256-1G), 0.5 mM spermidine (Sigma-Aldrich, Cat. # S2626-1G), and 1:40 Protector RNase Inhibitor (Roche, Cat. # 3335399001) to ST stock. For each specimen, 3 ml working ST buffer was made by adding 1:100 Protector RNase Inhibitor to ST stock. Nuclei resuspension solution (NRS) was prepared by adding 1% BSA (Miltenyi, Cat. # 130- 091-376) and 1:40 Protector RNase inhibitor to PBS (Gibco, Cat. # 10010023). Snap-frozen tumor chunks were placed in microcentrifuge tubes with 1mL NST and manually minced with fine straight tungsten carbide scissors (Fine Science Tools; Cat. # 15514-12) for 8 min. Nuclei suspension was then passed over a 30-micron cell strainer (Miltenyi Biotec; Cat. # 130-098-458) into a 15 mL conical tube (ThermoFisher Scientific; Cat. # 339651). Microcentrifuge tubes and strainers were washed with an additional 1mL NST, then nuclei suspensions were diluted with 3mL ST buffer. Following this, suspensions were centrifuged for 5 min at 500g, 4 °C with slow brake. Following inspection of the pellet, the supernatant was removed, and the pellet was resuspended in 150-200 μL of NRS and then passed through a FACS tube filter (Falcon; Cat. #352235). Nuclei were then quantified using a disposable hemocytometer (inCYTO; Cat. # 82030-472) in brightfield and then diluted or concentrated in NRS, as described in section 1.1 of the 10x 3’ v3.1 Single Cell Gene Expression protocol (https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry).
Single-cell gene expression libraries were generated using the above-mentioned 10x protocol (https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry), up to 12 samples were pooled per flow-cell and then sequenced on a NovaSeq S2 (Illumina) with the following paired-end read configuration: read 1: 28 nt; read 2: 90 nt; i7 index read: 10 nt; i5 index read: 10 nt

value: Pancreatic ductal adenocarcinoma

tag: Sex

value: Male

tag: time point_(days)

value: Vehicle


title: V1


title: YY1aid_async_untreated_RAD21_ChIPseq_Rep1

value: YY1-AID subline


title: KPC_3920, Early Vehicle, snRNAseq

description: 10X Genomics


title: H3K14ac


title: KPC_3975, Early Vehicle, snRNAseq

description: 10X Genomics


title: YY1aid_async_untreated_Pol2_ChIPseq_rep2


title: YY1aid_async_untreated_input

value: input


title: YY1aid_async_untreated_Pol2_ChIPseq_rep1


title: DPF2_D274A

value: expressing FLAG-tagged DPF2_D274A

value: anti-FLAG


title: YY1aid_async_untreated_H3K27ac_ChIPseq_rep2

description:
YY1aid_async_untreated_H3K27ac_chip.bw
YY1aid_async_untreated_H3K27ac_peaks.bed

value: anti-H3K27ac Active Motif 39133


title: KPC_3917, Early MRTX1133, snRNAseq

description: 10X Genomics


title: DPF2_D274A-R300A

value: expressing FLAG-tagged DPF2_D274A-R300A


title: KPC_3767, Early MRTX1133, snRNAseq

description: 10X Genomics

value: Female


title: YY1aid_async_untreated_CTCF_ChIPseq_Rep2

description:
YY1aid_async_untreated_CTCF_chip.bw
YY1aid_async_untreated_CTCF_peaks.bed

value: untreated

value: anti-CTCF Millipore 07-729

value: asynchronous


title: YY1aid_async_untreated_CTCF_ChIPseq_Rep1

value: ES-derived erythroid progenitor cells


title: YY1aid_async_untreated_H3K27ac_ChIPseq_rep1


title: KPC_3777, Early MRTX1133, snRNAseq

description: 10X Genomics


title: YY1aid_async_auxin_YY1b_ChIPseq_rep2

description:
YY1aid_async_auxin_YY1b.bw
YY1aid_async_auxin_YY1b_peaks.bed

value: auxin

value: anti-YY1 Bethyl A301-778A


title: CD20 nanoCAR T cell, 70 KO, rep3

city: Ghent

first: Stijn

last: De Munter

address: Corneel Heymanslaan 10

institute: Ghent University

data_processing:
The sequencing adapters were trimmed from the reads using fastp and -a was set to CTGTCTCTTATA. Afterwards the RNA-seq data was aligned to the human reference genome (GRCh38/hg38) and quantified using the Gencode version 41 gene annotation with STAR (version 2.7.6a). For the alignment the following parameters were set: --twopassMode Basic, --chimSegmentMin 20, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 10.
Differential Expression Analysis: The raw counts were subsequently loaded into R (version 4.3.2) for further processing with DeSeq2 (version 1.42.0). For the differential expression analysis with the DeSeq function, we used the following design formula: ~Donor + Condition, to take into account the batch effect stemming from the different donors. CD70 CAR T cells with wildtype CD70 were used as a reference during this analysis. Significantly differentially expressed genes were defined as having a p-adjusted value of < 0.05.
For the heatmap visualizations the raw counts were normalized with the vst function and subsequently batch corrected for the donor effect through the limma package (version 3.58.1) with the removeBatchEffect function. The batch corrected counts were finally scaled row wise through the scale function and visualized with the pheatmap package (version 1.0.12).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Healthy T cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Lymphoprep density gradient centrifugation from healthy buffy coats. The percentage of CD3+ cells was determined by flow cytometry and T-cells were stimulated with Immunocult Human CD3/CD28/CD2 T-cell activator per fabricator instructions in IMDM supplemented with 10% FCS, 2 mM l-glutamine, 100 IU/mL penicillin and 100 IU/mL streptomycin (complete IMDM, cIMDM), in the presence of 10 ng/mL IL-15 and IL-7. After 48 hours, cells were harvested and nucleofected using the Lonza Amaxa 4D-nucleofector X unit (program EH-110) in the presence (CD70 KO) or absence (CD70 WT) of CRISPR/Cas9 protein complexed with CD70-specific gRNA. Cells were resuspended at a concentration of 1x10e6 cells/20µl P3 Primary Cell Nucleofector Solution supplemented with Supplement 1 (Lonza) and 20 µM RNP. Following nucleofection, cells were harvested, placed in fresh cIMDM + 10 ng/ml IL-7 + 10 ng/ml IL15 and allowed to rest for 24 hours at 37°C, 7% CO2. After resting, the cells were harvested and and resuspended in retroviral supernatant and centrifuged for 90 minutes at 1000g at 32°C on retronectin coated plates. Cells were harvested two days after transduction and cultured at a density of 1 to 2 x 10e6 cells per ml. Every two days, cells were counted and fresh medium supplemented with cytokines was added. nanoCAR+ cells were sorted on day 12 after stimulation on a BD FACS Aria II. Cells were washed two times with PBS + 0.2% BSA and lysed in RLT lysis buffer (QIAgen).

extract_protocol:
mRNA was isolated using RNeasy Mini kit (Qiagen) per manufacturer’s instructions.
Library preparation was performed with the Illumina Stranded mRNA prep Ligation kit (20040534, Illumina) according to the manufacturer’s instructions except for the following steps: i) six minute fragmentation, ii) 50 minute first strand cDNA synthesis and iii) additional Ampure bead clean-up at the end. The libraries were subsequently sequenced on a NovaSeq6000 (Illumina) paired-end (2x150bp) with an average of 40M reads per sample.

treatment_protocol: Polyclonal T cell activation, nucleofection, transduction

value: Healthy T cells

value: CD70 KO


title: YY1aid_async_auxin_YY1_ChIPseq_Rep3

description:
YY1aid_async_auxin_YY1_chip.bw
YY1aid_async_auxin_YY1_peaks.bed

value: anti-YY1 Active Motif 61980


title: YY1aid_async_auxin_YY1b_ChIPseq_rep1


title: CD20 nanoCAR T cell, 70 WT, rep3

value: CD70 WT

value: Polyclonal T cell activation, nucleofection, transduction


title: KPC_3716, Vehicle, snRNAseq

description: 10X Genomics

value: Pancreatic ductal adenocarcinoma

value: Vehicle


title: DPF2_wt

value: Hela cells

value: expressing FLAG-tagged DPF2_wt

value: anti-FLAG


title: KPC_3600, MRTX1133 resistant, snRNAseq

description: 10X Genomics

value: Female


title: YY1aid_async_auxin_YY1_ChIPseq_Rep2

value: YY1-AID subline


title: CD70 nanoCAR T cell, 70 KO, rep3


title: YY1aid_async_auxin_YY1_ChIPseq_Rep1


title: YY1aid_async_auxin_RAD21_ChIPseq_Rep2

description:
YY1aid_async_auxin_RAD21_chip.bw
YY1aid_async_auxin_RAD21_peaks.bed

value: anti-RAD21 abcam ab992


title: KPC_3587, Vehicle, snRNAseq

description: 10X Genomics


title: CD70 nanoCAR T cell, 70 WT, rep3


title: KPC_3518, Vehicle, snRNAseq

description: 10X Genomics


title: YY1aid_async_auxin_Pol2_ChIPseq_rep2

value: anti-RPB1 Cell Signaling 14958

value: asynchronous


title: KPC_3441, MRTX1133 resistant, snRNAseq

description: 10X Genomics


title: CD20 nanoCAR T cell, 70 KO, rep2


title: YY1aid_async_auxin_Pol2_ChIPseq_rep1

value: ES-derived erythroid progenitor cells


title: YY1aid_async_auxin_Pol2_ChIPseq_rep3


title: YY1aid_async_auxin_input

value: auxin

value: input


title: CD20 nanoCAR T cell, 70 WT, rep2

value: Healthy T cells


title: YY1aid_async_auxin_CTCF_ChIPseq_Rep2

description:
YY1aid_async_auxin_CTCF_chip.bw
YY1aid_async_auxin_CTCF_peaks.bed

value: anti-CTCF Millipore 07-729


title: KPC_3422, Vehicle, snRNAseq

description: 10X Genomics


title: KPC_3421S, MRTX1133 resistant, snRNAseq

description: 10X Genomics


title: CD70 nanoCAR T cell, 70 WT, rep2

value: CD70 WT


title: OB, snRNA-Seq, replicate 2

city: Cologne

first: Sophie

last: Steculorum

address: Gleueler Straße 50

department: Metabolism Research

institute: Max Planck Institute

description: 10x Genomics

data_processing:
Raw reads were processed with cell ranger (v.6.1.2).
Assembly: aligned to Ensembl genome GRCm39 release 105_cr6.1.2
Supplementary files format and content: Matrix files

source_name: Olfactory Bulb

extract_protocol:
Tissue homogenization was carried out in a 7 ml Dounce tissue grinder. Frozen olfactory bulbs were transferred into 1 ml of ice-cold homogenization buffer (NIM 2), IGEPAL 0.4% (v/v), RNasIn 0.4 µl-1, SuperAsin 0.2 µl-1, 0.15 mM spermine, 0.5 mM spermidine). Homogenization was carried out by 10 strokes of loose pestle ‘A’ followed by 20 strokes of tight pestle ‘B’ after a 5 min incubation on ice. Homogenates were filtered through 20 µm cell strainers and centrifuged at 1000 g for 10 min at 4°C. Supernatant was removed by decanting and the nuclei pellets were resuspended in 1 ml FACS buffer (0.15 mM spermine, 0.5 mM spermidine, 0.2 U µl-1 protector RNase inhibitor, IGEPAL 0,4% (v/v), BSA 1% (wt/vol) and DAPI 1µM in RNAase-free PBS). 300 µl of suspension from each of three individual nuclear isolations were combined for one replicate and subjected to FACS. Cell-sorting was performed with FACSAria III system (BD Biosciences) using a 70 µm nozzle. Gating for forward and side scatter was used for doublet discrimination and sorting was performed selecting singlets in the DAPI+ population. 100.000 events were directly sorted into 10 µl of diluted nuclei buffer reaching a final concentration of ~1% BSA (wt/vol) and 0.2 U µl-1 protector RNase inhibitor.
Libraries were prepared using the Chromium Next GEM Automated Single Cell 3’ Reagent Kit v3.1 (10x Genomics, #1000268) following the manufacturer’s instructions. Libraries were sequenced on a HiSeq4000 (Illumina) with 150-bp paired-end sequencing of read 2

value: Olfactory Bulb

value: male


title: KPC_3421L, MRTX1133 resistant, snRNAseq

description: 10X Genomics

value: Pancreatic ductal adenocarcinoma


title: OB, snRNA-Seq, replicate 1

description: 10x Genomics


title: CD70 nanoCAR T cell, 70 KO, rep2

value: CD70 KO

value: Polyclonal T cell activation, nucleofection, transduction


title: CD20 nanoCAR T cell, 70 KO, rep1


title: G1E-ER4_prometa_YY1_ChIPseq_rep2

description:
YY1_prometa_chip.bw
YY1_prometa-emergent_peaks.bed

value: G1E-ER4 MD-mCherry subline

value: anti-YY1 Active Motif 61980

value: prometa


title: melanocyte, sphere assay, siSASH1, rep3

first: Aik Choon

last: Tan

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

data_processing:
Raw FASTQ files were trimmed by using cutadapt (version 3.5), aligned against the human reference genome GRCh38 (release 106) using STAR aligner (v2.7.8a) and quantified using RSEM pipeline.  Differentially expressed gene analysis was performed by using edgeR package.
Assembly: human reference genome GRCh38 (release 106)
Supplementary files format and content: TPM

source_name: HEMn-MP

growth_protocol: Monolayer cells grown in Gibco 254 media with HMGS-2 supplement.

extract_protocol:
Qiagen RNeasy Mini Plus with Qiashredder
Total RNA-seq

treatment_protocol: Cells were detached and transfected with 100pmol siRNAs with Lonza Nucleofector 4D, Solution P2, program DS-137. Five hours after transfections, cells detached and seeded in sphere forming assay. Cells harvested for RNA extraction 24hrs post nucleofection.

value: HEMn-MP

value: primary melanocyte

value: SASH1 knockdown

value: stem-like cell enrichment with sphere assay


title: CD20 nanoCAR T cell, 70 WT, rep1


title: KPC_3395, Vehicle, snRNAseq

description: 10X Genomics

value: Female

value: Vehicle


title: KPC_3379, MRTX1133 resistant, snRNAseq

description: 10X Genomics


title: melanocyte, sphere assay, siSASH1, rep2


title: G1E-ER4_prometa_YY1_ChIPseq_rep3

value: ES-derived erythroid progenitor cells


title: YY1aid_async_auxin_RAD21_ChIPseq_Rep1

value: YY1-AID subline

value: anti-RAD21 abcam ab992

value: asynchronous


title: G1E-ER4_prometa_YY1_ChIPseq_rep1


title: G1E-ER4_midg1_YY1_ChIPseq_rep3

description:
YY1_midG1_chip.bw
YY1_midg1-emergent_peaks.bed


title: KPC_3323, MRTX1133 resistant, snRNAseq

description: 10X Genomics

value: Male


title: melanocyte, sphere assay, siSASH1, rep1


title: G1E-ER4_midG1_YY1_ChIPseq_rep1


title: melanocyte, sphere assay, siSCRAMBLE, rep3

value: WT


title: CD70 nanoCAR T cell, 70 WT, rep1

value: Healthy T cells

value: CD70 WT


title: Lateral nasal gland, IAV, 8dpi, hashtag oligo

description: HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads

data_processing:
FASTQs, cell count matrices, and hashtag oligo counts were generated using cellranger v6.0.1 through cumulus tools (https://cumulus.readthedocs.io/en/stable/)
Cellbender was then applied to the raw h5 output files to correct for transcript spill-over with the following parameters: expected_cells=30000, fpr=0.01, total_droplets_included=50000
Cellbender corrected cells were then filtered based on Unique Molecular Identifiers (UMI) count (>750 & <10000), number of detected genes (>500), and percentage of mitochondrial genes (<15%). Finally, cells labeled as doublets by demultiplexing were removed
Downstream clustering analysis was performed using Seurat (v.4.2.1) using scTransform normalization and corrected counts.
Remaining doublets were removed by inspection upon subclustering routines by identifying clusters expressing mutually exclusive cell type lineage markers
Assembly: GRCm39 + custom IAV PR8 genome (NCBI Taxonomy ID #211044; segment sequences: NC_002023.1, NC_002022.1, NC_002021.1, NC_002020.1, NC_00219.1, NC_2018.1, NC_002017.1, and NC_002016.1)
Supplementary files format and content: Cellranger output files: XXX.h5 contains the raw unfiltered cell count matrix
Supplementary files format and content: Cellranger output files: XXX.csv contains the hashtag oligo counts; feature_barcodes.csv contains the TotalSeqB Hashtag antibody oligo sequences used for every sample

extract_protocol:
Tissue was harvested by microdissection and digested in RPMI (w/ FBS, HEPES, and P/S) for 20 min (LNG) or 30 min (RM/OM). Following enzyme inactivation with EDTA and filtration through a 70 µm membrane, ACK lysis was performed on ice for 1min. Epithelial cells were partially depleted using Biotin Binder Dynabeads pre-loaded with anti-biotin anti-EpCAM antibody during a 20min incubation on ice. Following bead removal, cells were stained with TotalSeqB Hashtag antibodies for 20 minutes before washing, counting, and combining. Finally, cells were captured and processed on either a 10x Chromium or X controller using the 3' transcriptome v3.1 kit and feature barcoding kits.
Libraries were constructed as outlined in the 10x Genomics guide for Dual-indexed 3' transcriptomics v3.1 with Feature Barcoding.

value: Nasal mucosa, lateral nasal gland

value: IAV PR8

tag: timepoint

value: female

value: primary infection

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 14


title: Lateral nasal gland, IAV, 8dpi, gene expression

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript

tag: disease state

value: mRNA


title: G1E-ER4_midG1_YY1_ChIPseq_rep2

value: G1E-ER4 MD-mCherry subline

value: anti-YY1 Active Motif 61980


title: CD70 nanoCAR T cell, 70 KO, rep1

value: CD70 KO

value: Polyclonal T cell activation, nucleofection, transduction


title: YY1aid_async_auxin_CTCF_ChIPseq_Rep1

value: ES-derived erythroid progenitor cells

value: YY1-AID subline

value: anti-CTCF Millipore 07-729


title: melanocyte, sphere assay, siSCRAMBLE, rep2

value: HEMn-MP

value: primary melanocyte

value: WT

value: stem-like cell enrichment with sphere assay


title: melanocyte, sphere assay, siSCRAMBLE, rep1


title: Olfactory mucosa, IAV, 8dpi, hashtag oligo

value: Nasal mucosa, olfactory mucosa

value: IAV PR8

tag: library type

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 13


title: G1E-ER4_lateg1_YY1_ChIPseq_rep3

description:
YY1_lateG1_chip.bw
YY1_lateg1-emergent_peaks.bed