title: Nr4a1 neutrophil, stimulated, rep1

city: Pittsburgh

first: Brian

last: Campfield

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: University of Pittsburgh School of Medicine

description: Library name: SN1

data_processing:
Sequencing was performed on an Illumina NextSeq 2000, using a P2 flow cell.  The pooled library was loaded at 750 pM and sequencing was carried out with read lengths of 58 bp, with a target of 30 million reads per sample.  Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12)
Raw reads underwent pre-alignment quality control (QC) and trimming.  Reads were then aligned using STAR (2.7.8a) via Partek Flow Bioinformatics software.  Transcript normalization and gene expression analysis were performed using DESeq2 with FDR step-up used for multiple test correction.  Hierarchical clustering was performed in both supervised and unsupervised manners by genotype/treatment.  Gene set enrichment analysis using gene ontogeny terms were generated by significant hits (FDR<0.001).
Assembly: mm39 whole genome
Supplementary files format and content: xlsx files including FPKM values for each sample

source_name: primary neutrophils

growth_protocol: Primary neutrophils were isolated via negative magnetic selection from WT and Nr4a1-/- BM using EasySepTM Mouse Neutrophil Enrichment Kit

extract_protocol:
RNA isolation using RNeasy Micro Kit
Illumina Stranded mRNA Library Prep kit (Illumina: 20040534)
50 ng of input RNA was used for each sample.  Following adapter ligation, 15 cycles of indexing PCR were completed, Illumina RNA UD Indexes.  Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300. Libraries were normalized and pooled to 2 nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/ml) of the libraries

treatment_protocol: Cells were incubated with or without K. pneumoniae at a MOI of 0.4 in killing assay media for 30 minutes at 37 

value: primary neutrophils

value: neutrophils

value: Klebsiella pneumoniae


title: Human RPE/choroid scRNA rep11

status: Public on Mar 25 2025

type: SRA

city: Stanford

first: Sean

middle: K

last: Wang

state: CA

address: 269 Campus Drive

department: Genetics

country: USA

institute: Stanford University

description: scRNA-seq

library_source: transcriptomic

data_processing:
Demultiplexed scRNA- and scATAC-seq fastq files were inputted into the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics to generate barcoded count matrices of gene expression and ATAC data. For each sample, count matrices were loaded in ArchR and selected for barcodes that appeared in both the scRNA-seq and scATAC-seq datasets. Samples in ArchR were quality control filtered for nuclei with 200-10,000 RNA transcripts, <1% mitochondrial reads, <5% ribosomal reads, TSS enrichment >4, and >1,000 ATAC fragments. Quality control filtered nuclei subsequently underwent automated removal of doublets using the filterDoublets function in ArchR, which identifies and removes the nearest neighbors of simulated doublets.
scRNA-seq data from nuclei remaining after quality control filtering and automated removal of doublets were analyzed using Seurat (version 3.1.5). After merging all preprocessed samples into a single Seurat object, gene expression counts were normalized using the NormalizeData function, scaled using the ScaleData function, and batch corrected using Harmony. Graph-based clustering was then performed on the Harmony-corrected data using the top 30 principal components at a resolution of 0.3. Cluster identities were manually annotated based on the expression of canonical marker genes. Clusters expressing marker genes from different cell types were designated as putative doublets and excluded, after which re-clustering was performed using the same parameters. Clusters with no detected marker genes were also excluded, after which the dataset was also re-clustered.
scATAC-seq data were analyzed using ArchR (version 1.0.1) based on barcoded cell type identities from scRNA-seq. For each cell type, pseudo-bulk ATAC replicates were created using the addGroupCoverages function with default parameters. Chromatin accessibility peaks on chromosomes 1-22 and X and outside of blacklist regions were then called using the addReproduciblePeakSet function and MACS2.
HiChIP sequencing files were initially processed using the HiC-Pro pipeline (version 2.11.0) to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Filtered read pairs from HiC-Pro were subsequently converted into .hic files and inputted into HiCCUPS from the Juicer pipeline to call loops.
Assembly: hg38
Supplementary files format and content: tsv and mtx files represent raw gene counts for each barcode in the file scRNA-seq dataset. fragments files represent aggregated scATAC-seq fragments organized by cell type.
Supplementary files format and content: hic files represent all valid interaction pairs detected by HiC-Pro following H3K27ac HiChIP of human RPE/choroid tissue. bedpe files represent H3K27ac HiChIP loops detected by HiCCUPS.

molecule: nuclear RNA

organism: Homo sapiens

source_name: RPE/choroid

extract_protocol:
Nuclei were isolated from frozen RPE/choroid using a modified Omni-ATAC protocol (doi.org/10.17504/protocols.io.6t8herw)
Joint scRNA- and scATAC-seq libraries were prepared using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions. HiChIP libraries were prepared according to Mumbach et al., 2016.
scRNA-seq, scATAC-seq, and H3K27ac HiChIP

tag: tissue

value: RPE/choroid


title: WTliver2

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description:
WTliver2
KOlivervsWTliver_diffexpr-results.csv

data_processing:
*library strategy: tRNAseq
Reads  were processed using the minm-tRNAseq pipeline.
Assembly: hg38
Supplementary files format and content: Differential expression of tRNA isodecoders

molecule: total RNA

organism: Mus musculus

source_name: mouse

extract_protocol:
total RNA were extracted and subjected to small RNA enrichment.
tNRAs were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

tag: cell line

value: mouse

tag: cell type

value: liver

tag: genotype

value: WT


title: Human RPE/choroid scRNA rep12

description: scRNA-seq


title: Nr4a1 neutrophil, stimulated, rep3

description: Library name: SN3

molecule: polyA RNA

tag: treatment


title: Human RPE/choroid scRNA rep14

description: scRNA-seq


title: Nr4a1 neutrophil, stimulated, rep2

description: Library name: SN2


title: Nr4a1 neutrophil, unstimulated, rep3

description: Library name: N3

value: unstimulated


title: Human RPE/choroid scRNA rep10

description: scRNA-seq


title: Nr4a1 neutrophil, unstimulated, rep2

description: Library name: N2


title: Human RPE/choroid scRNA rep13

description: scRNA-seq


title: Human RPE/choroid scRNA rep8

description: scRNA-seq


title: Human RPE/choroid scRNA rep7

description: scRNA-seq


title: WT neutrophil, stimulated, rep3

description: Library name: SW3


title: Human RPE/choroid scRNA rep6

description: scRNA-seq


title: WT neutrophil, stimulated, rep1

description: Library name: SW1


title: Human RPE/choroid scRNA rep9

description: scRNA-seq


title: Nr4a1 neutrophil, unstimulated, rep1

description: Library name: N1


title: WT neutrophil, unstimulated, rep3

description: Library name: W3


title: Human RPE/choroid scRNA rep3

description: scRNA-seq


title: WT neutrophil, unstimulated, rep2

description: Library name: W2


title: Human RPE/choroid scATAC rep16

description: scATAC-seq

library_source: genomic

molecule: genomic DNA


title: Human RPE/choroid scATAC rep14

description: scATAC-seq


title: WT neutrophil, stimulated, rep2

description: Library name: SW2


title: Human RPE/choroid scATAC rep15

description: scATAC-seq


title: Human RPE/choroid scATAC rep12

description: scATAC-seq


title: Human RPE/choroid scATAC rep11

description: scATAC-seq


title: H3K4me1_mESCs_KO_rep2

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
For H3K4me3, H3K27me3, H3K27ac, H3K4me1 and IκBα ChIP, trimmed reads were aligned to reference genome (GRCm38 Ensembl release 102) with Bowtie2 (v2.4.4) which was executed with default parameters (Langmead & Salzberg, 2012). Multimapped reads and those exhibiting MAPQ < 20 were removed.
For H3K9me3 data, trimmed reads were aligned with ShortStack (v3.8.5) (Axtell, 2013). Randomly placed multimappers were removed from the mapped reads.
For all histone marks and IκBα ChIP, duplicated reads were marked with SAMtools (v1.15) (Danecek et al., 2021). ENCODE blacklisted regions (mm10 v2) were removed prior to peak calling except for H3K9me3 (Amemiya et al., 2019).
BigWig files were individually generated using deepTools (v3.5.1) bamCoverage with -ignoreDuplicates -binSize 10 -smoothLength 30 -effectiveGenomeSize 2308125349 -normalizeUsing RPGC and -extendReads Fragment_Length options (Ramírez et al., 2016) where Fragment_Length was retrieved from PhantomPeakQualTools results except for H3K9me3 where 150bp was considered. For IκBα ChIP, duplicates were kept.
For H3K9me3, H3K27me3, H3K27ac and H3K4me1 data, peak calling was conducted by means of epic2 (v0.0.52) with -effective-genome-fraction 0.8452 -fragment-size Fragment_Length options and chromosome sizes only referring to canonical chromosomes (Stovner & Sætrom, 2019). For H3K4me3 and IκBα ChIP, MACS2 (v2.2.7.1) was used to identify peaks with -nomodel -extsize Fragment_Length -g 2308125349 options (Zhang et al., 2008). In case of IκBα ChIP, one duplicate per location was considered (--keep-dup 1). In all cases, corresponding input samples as control sample were used for peak calling.
Assembly: mm10
Supplementary files format and content: bigWig, H3K4me3 narrowPeak files and H3K27me3/H3K9me3 epic2 txt called peaks (except for Input sample)

growth_protocol: mESCs were cultured on plastic dishes precoated with 0.1% (w/v) Gelatin (Sigma; G2500-100G) with DMEM-ES medium. DMEM-ES is composed by DMEM basal medium (Sigma-Aldrich; Cat #D5796) supplemented with 15% FBS (ESC-qualified; Gibco Cat #26140079), 1X Glutamax (Gibco; Cat #35050061), 1X NEAA (Gibco; Cat#11140050), 1mM Sodium Pyruvate (Gibco; Cat#11360070), 103U/mL Leukemia Inhibitory Factor (LIF) (Millipore, Cat #ESG1107) and 0.125mM 2-mercaptoethanol (Gibco; Cat#31350010).

extract_protocol:
mESCs were cross-linked by incubating them initially in Gold (Diagenode), and then they were further crosslinked in DPBS (Gibco, Cat #14190094) supplemented with 1% formaldehyde (Sigma-Aldrich; Cat #252549) for 10 min rocking at room temperature. Cross-linking was stopped using 125 mM Glycine (Sigma-Aldrich, Cat #G8790) rocking for 5 minutes at room temperature. Cell nuclei were isolated by incubating cell pellets in a buffer containing 5mM Pipes pH 8, 85mM KCl and 0.5% NP40, and later incubated on ice for 10 minutes followed by centrifuge at 4000 rpm for 5 minutes at 4ºC. Nucleus were lysed in a buffer containing 1% SDS, 10mM EDTA and 50 mM Tris-HCl pH 8.1 and incubated on ice for 10 min. Samples were sonicated 25 cycles (30´´on/30´´off) and SDS was removed by incubating the sonicated sample on ice for 1 hour and later centrifuged for 15 at 4ºC and 16000g. 60μg of chromatin was incubated with 10 μg of ANTI-FLAG® M2 (Sigma-Aldrich, Cat #F1804). Samples were pulled down by a 50/50 mix of Dynabeads A (Invitrogen, Cat #10002D) and G (Invitrogen, Cat #10003D). Samples were washed 4 times in 0.1% SDS, 1% Triton-X, 2mM EDTA, 20mM Tris-HCl pH 8 and 150mM NaCl; followed by 1 wash in TE pH 8. For H3K4me1 and H3K27Ac ChIP-seqs, cells were crosslinked only with PBS and 1% formaldehyde as described, and cross-linking solution was reverted by Glycine as previously described. Cells were lysed by resuspending cell pellet in ice-cold ChIP buffer (1 volume of SDS buffer [100mM NaCl, 50mM Tris-HCl pH 8.1, 5mM EDTA pH 8, 0.5% SDS] and 0.5 volume of triton dilution buffer [100mM Tris-HCl pH 8.6, 100mM NaCl, 5mM EDTA pH 8, 5% Triton X-100]) supplemented with protease/phosphatase inhibitor cocktail (1X cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche, Cat #11873580001), 1 mM PMSF, 1mM Sodium Ortovanadate and 20 mM β-Glycerol phosphate), and samples were sonicated using sonication beads (Diagenode; Cat #C01020031) and the Bioruptor Pico Sonicator (Diagenode; Cat #B01060010) for 20 cycles (each cycle 30 seconds on/30 seconds off) or till DNA fragments have 100-300bp size. Chromatin was quantified, and 30 μg of chromatin was incubated with every 5μg of antibody rotating for 16 hours (or overnight) at 4ºC. Samples were pulled down by incubation with Protein A-Sepharose™ CL-4B (previously hydrated and blocked with 0.05% BSA) for 3h at 4ºC in rotation. Sample was washed with a low salt washing buffer (50mM HEPES pH 7.5, 140mM NaCl and 1% Triton) three times, one wash with a high salt wash buffer (50mM HEPES pH 7.5, 500mM NaCl and 1% Triton) and one wash with TE pH 8 (10mM Tris-HCl pH8, 1mM EDTA). Samples were then eluted in 1% SDS and 100mM NaHCO3. Samples were descrosslinked by incubating for 16 hours (or overnight) at 65ºC shaking at 450 rpm, and were treated with Proteinase K for 1h at 45ºC. DNA was purified using QIAquick PCR Purification Kit (Qiagen, Cat #28106), following the manufacturer’s instructions.
Libraries prepared according to manufacturer's instructions (SE 50bp reads)

value: mouse embryonic stem cells

tag: chip antibody

value: H3K4me1 (ab8895, Abcam)

value: IkappaBalpha-/-

value: knock-out

tag: time

value: Timepoint 0h


title: H3K4me1_H3K27ac_mESCs_KO_input


title: Human RPE/choroid scATAC rep10

description: scATAC-seq


title: H3K4me1_H3K27ac_mESCs_WT_input

value: IkappaBalpha+/+

value: wildtype


title: Human RPE/choroid scATAC rep13

description: scATAC-seq


title: Human RPE/choroid scATAC rep8

description: scATAC-seq


title: H3K4me1_mESCs_KO_rep1


title: Human RPE/choroid scATAC rep9

description: scATAC-seq


title: H3K4me1_mESCs_KO_rep3


title: H3K4me1_mESCs_WT_rep3


title: H3K4me1_mESCs_WT_rep2


title: WT neutrophil, unstimulated, rep1

description: Library name: W1


title: Human RPE/choroid scATAC rep5

description: scATAC-seq


title: Human RPE/choroid scATAC rep6

description: scATAC-seq


title: Human RPE/choroid scATAC rep7

description: scATAC-seq


title: H3K27ac_mESCs_KO_rep2

value: H3K27ac (ab8895, Abcam)


title: H3K27ac_mESCs_KO_rep1


title: Human RPE/choroid scATAC rep3

description: scATAC-seq


title: H3K4me1_mESCs_WT_rep1


title: H3K27ac_mESCs_WT_rep3


title: Human RPE/choroid scATAC rep2

description: scATAC-seq


title: Human RPE/choroid scATAC rep1

description: scATAC-seq


title: scATAC-Seq of human kidney, library5

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

description:
Barcode to donor allocations can be found in the seurat object
Library5_feature_bc_matrix.h5
Library5_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
BCL files from Illumina sequencing runs were demultiplexed for GEX and ATAC samples using cellranger-arc mkfastq (v2.0.2, 10x Genomics). The base mask Y28n*,I10n*,I10n*,Y151 and --filter-dual-index or Y100n*,I8n*,Y24,Y100n* and --filter-single-index to generate GEX or ATAC FASTQ files respectively. Reads were aligned to the precomputed GRCh38 (hg38) reference genome provided by 10x Genomics, and quantification as well as joint cell calling was performed using cellranger-arc count (v2.0.2).
Due to donor pooling each library included cell barcodes from multiple different samples. To allocate barcodes to their original donor cellsnp-lite (v1.2.2) and vireo (v0.2.3) were used. Barcodes passing cellranger-arc filters were genotyped (independently for GEX and ATAC libraries) by searching for SNPs present in sequencing reads using cellsnp-lite with the options --minMAF 0.1 (and --UMItag None for ATAC files) using a SNP reference of 7.4 million SNPs from the 1000 Genomes Project with an allele frequency >5% (provided by cellsnp-lite). To infer the donors of each nuclei barcode using genetic variants that segregate between samples, a Bayesian model implemented by vireo was used (with option –N equal to the number of donors in the library) As donors were predicted independently for GEX and ATAC libraries, conflicts in donor assignments arising in small number of nuclei barcodes were resolved using the following logic: i) barcodes assigned as doublet in either modality or unassigned in both modalities were removed; ii) barcodes which were unassigned in one modality but not the other were assigned to the donor predicted by the successful modality iii) barcodes with conflicting donor assignments were removed.
Assembly: hg38
Supplementary files format and content: feature_bc_matrix.h5 is the cellranger-arc output file containing GEX and ATAC count matrices in h5 format
Supplementary files format and content: atac_fragments.tsv.gz contains ATAC fragment information needed for ATAC analysis
Supplementary files format and content: seurat_object_multiome.rds contains processed and annotated data as Seurat R object
Supplementary files format and content: cell_meta_data.tsv contains cell metadata for all retained cells post filtering

source_name: Human kidney cortex

extract_protocol:
Nuclei were isolated from snap-frozen nephrectomy samples using an adapted 10x Genomics Demonstrated protocol (CG000375, Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing)
Nuclei were stained with 10ml of 7-AAD viability staining solution and sorted on a BD FACSAria™ Fusion cell sorter fitted with a 100ml nozzle into a tube prepared with 200ml of 10% BSA in PBS supplemented with 50ul RNase inhibitor for a final volume of 2ml. Between 3 and 5 samples from individual donors were pooled at pre-defined proportions based on counts of 7-AAD+ nuclei  and a total of 500,000 nuclei were sorted per pool.
Sorted nuclei were centrifuged (500g, 5min, 4°C) and resuspended in 100ml lysis buffer with 0.01% NP40 Substitute, 0.01% Tween-20, 0.001% Digitonin and 2% BSA. After 2 minutes wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 2% BSA, 1mM DTT, 1U/ml RNase inhibitor, 0.1% Tween-20) was added and nuclei were centrifuged (500g, 5min, 4°C) and resuspended in 20ml diluted nuclei buffer (20X Nuclei Buffer, 1mM DTT, 1U/ml RNase inhibitor in nuclease-free water).
Nuclei suspensions were counted using a LUNA-FX7 cell counter and processed immediately using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (v1.0, 10x Genomics) according to manufacturer protocol (CG000338, User Guide Chromium Next GEM Single Cell Multiome ATAC + Gene Expression). Briefly, per library between 20,000 to 40,000 nuclei were input into the transposition reaction before portioning into gel beads. After reverse transcription and pre-amplification aliquots of the pooled transposed DNA and cDNA were used to generate separate ATAC and GEX libraries.
After quantification GEX and ATAC libraries were pooled at molarity ratio of 40:60 respectively and sequenced using an Illumina NovaSeq6000 flow cell (with the read lengths R1:151bp I1:10bp I2:24bp R2:151bp) for a target yield of approximately 50,000 reads/cell and 75,000 reads/cell for gene expression and ATAC libraries respectively. In total 6 libraries consisting of 7 individual control and 5 UUO individual samples were prepared and analysed.

tag: group

value: Library5, pool of 4 donors

value: Human kidney cortex

tag: condition

value: healthy and injured kidney nephrectomy tissue


title: H3K27ac_mESCs_WT_rep1


title: H3K27ac_mESCs_WT_rep2


title: Human RPE/choroid scATAC rep4

description: scATAC-seq


title: H3K4me3_mESCs_KO_rep2

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
For H3K4me3 and H3K27me3 data, trimmed reads were aligned to reference genome (GRCm38 Ensembl release 102) with Bowtie2 (v2.4.4) which was executed with default parameters (Langmead & Salzberg, 2012). Multimapped reads and those exhibiting MAPQ < 20 were removed.
For H3K9me3 data, trimmed reads were aligned with ShortStack (v3.8.5) (Axtell, 2013). Randomly placed multimappers were removed from the mapped reads.
For all three histone marks, duplicated reads were marked with SAMtools (v1.15) (Danecek et al., 2021). ENCODE blacklisted regions (mm10 v2) were removed prior to peak calling except for H3K9me3 (Amemiya et al., 2019).
BigWig files were individually generated using deepTools (v3.5.1) bamCoverage with -ignoreDuplicates -binSize 10 -smoothLength 30 -effectiveGenomeSize  2308125349  -normalizeUsing RPGC  and -extendReads  Fragment_Length options (Ramírez et al., 2016) where Fragment_Length was retrieved from PhantomPeakQualTools results except for H3K9me3 where 150bp was considered.
For H3K9me3 and H3K27me3 data, peak calling was conducted by means of epic2 (v0.0.52)  with -effective-genome-fraction 0.8452 -fragment-size Fragment_Length options and chromosome sizes only referring to canonical chromosomes (Stovner & Sætrom, 2019). For H3K4me3 narrow profile, MACS2 (v2.2.7.1) was used to identify peaks with -nomodel -extsize Fragment_Length -g 2308125349 options (Zhang et al., 2008).
Assembly: mm10
Supplementary files format and content: bigWig, H3K4me3 narrowPeak files and H3K27me3/H3K9me3 epic2 txt called peaks (except for Input sample)

extract_protocol:
mESCs were cross-linked by incubating them in a cross-link solution (50 mM HEPES pH 8.0, 10 mM NaCl, 1 mM EDTA, 0.5 mM EGTA (Egtazic acid)) supplemented with 0.5% formaldehyde (Sigma-Aldrich; Cat #252549). Samples were Incubated for 10 min rocking at RT. Cross-linking was stopped by adding 1.25 M Glycine, 10 mM Tris-HCl pH 8.0 into the sample and incubating for 5 min rocking at RT. Cells were then lysed with 1 mL of lysis buffer (10 mM Tris-HCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Na-butyrate, 20 mM β-glycerol-phosphate, 0.1 mM Naorthovanadate and cOmplete™ Protease Inhibitor Cocktail) for 30 min at 4ºC. Samples were then resuspended in sonication buffer (10 mM Tris-HCl pH 8.0, 0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Na-butyrate, 20 mM β-glycerol-phosphate, 0.1 mM Na Orthovanadate and 1% SDS), and they were sonicated using sonication beads (Diagenode; Cat #C01020031) and the Bioruptor Pico Sonicator (Diagenode; Cat #B01060010) for 7 min, to fragment DNA into 500 bp peaces. Fragmented DNA was concentrated using Vivaspin 20 columns (Sartorius; Cat #VS2032), and unspecific binding was blocked by incubating the sample with 1% BSA, 1μg salmon sperm DNA, unspecific pre-immune IgG for 2h rocking. To immunoprecipitate, samples were incubated with 5 μg of antibody (see table MM3) at 4ºC overnight. Chromatin-IgG complexes were pull down using protein A/G sepharose beads (GE Healthcare; Cat #17-0618-01 and #17-0780-01) for 2h rocking at 4ºC. Cross-linked DNA-protein was reverted by incubating samples at 65 ºC overnight. DNA was purified using GFX Kit (GE Healthcare Life Sciences; Cat #28-9034-71), following the manufacturer’s instructions
Libraries prepared according to manufacturer's instructions (SE 50bp reads)

value: IkappBalpha-/-


title: scATAC-Seq of human kidney, library4

description:
Barcode to donor allocations can be found in the seurat object
Library4_feature_bc_matrix.h5
Library4_atac_fragments.tsv.gz

value: Library4, pool of 5 donors


title: H3K4me3_mESCs_KO_input


title: scATAC-Seq of human kidney, library3

description:
Barcode to donor allocations can be found in the seurat object
Library3_feature_bc_matrix.h5
Library3_atac_fragments.tsv.gz

value: Library3, pool of 4 donors


title: scATAC-Seq of human kidney, library2

description:
Barcode to donor allocations can be found in the seurat object
Library2_feature_bc_matrix.h5
Library2_atac_fragments.tsv.gz

value: Library2, pool of 5 donors


title: H3K4me3_mESCs_KO_rep3


title: H3K27ac_mESCs_KO_rep3


title: H3K4me3_mESCs_KO_rep1


title: scATAC-Seq of human kidney, library1

description:
Barcode to donor allocations can be found in the seurat object
Library1_feature_bc_matrix.h5
Library1_atac_fragments.tsv.gz

value: Library1, pool of 3 donors


title: snRNA-Seq of human kidney, library6

description:
Barcode to donor allocations can be found in the seurat object
Library6_feature_bc_matrix.h5

library_source: transcriptomic single cell

value: Library6, pool of 5 donors


title: H3K4me3_mESCs_WT_rep1

value: mouse embryonic stem cells

value: IkappBalpha+/+


title: snRNA-Seq of human kidney, library3

description:
Barcode to donor allocations can be found in the seurat object
Library3_feature_bc_matrix.h5


title: snRNA-Seq of human kidney, library5

description:
Barcode to donor allocations can be found in the seurat object
Library5_feature_bc_matrix.h5


title: H3K27me3_mESCs_KO_input


title: snRNA-Seq of human kidney, library4

description:
Barcode to donor allocations can be found in the seurat object
Library4_feature_bc_matrix.h5


title: H3K4me3_mESCs_WT_input


title: scATAC-Seq of human kidney, library6

description:
Barcode to donor allocations can be found in the seurat object
Library6_feature_bc_matrix.h5
Library6_atac_fragments.tsv.gz


title: H3K27me3_mESCs_WT_input


title: H3K27me3_mESCs_KO_rep3


title: snRNA-Seq of human kidney, library2

description:
Barcode to donor allocations can be found in the seurat object
Library2_feature_bc_matrix.h5


title: H3K27me3_mESCs_WT_rep3


title: Irradiated R5

data_processing:
Adapter sequences were removed using Trimmgalore. Reads were aligned (hg38) and quantified using STAR. Differential expression was assessed using DeSeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw gene counts for each sample

source_name: Kidney

extract_protocol:
poly-A enrichment
TruSeq RNA Library Prep Kit v2

value: Kidney

value: Primary renal epithelial cells

value: Irradiated


title: H3K27me3_mESCs_KO_rep1

value: knock-out

value: Timepoint 0h


title: Control R5

value: Control


title: H3K27me3_mESCs_KO_rep2


title: snRNA-Seq of human kidney, library1

description:
Barcode to donor allocations can be found in the seurat object
Library1_feature_bc_matrix.h5


title: H3K4me3_mESCs_WT_rep2

value: wildtype


title: H3K27me3_mESCs_WT_rep1


title: H3K9me3_mESCs_KO_input


title: H3K27me3_mESCs_WT_rep2


title: Irradiated R3


title: Irradiated R4


title: H3K9me3_mESCs_WT_input


title: Caco-2_Pellet_P100_rep1

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Library name: 5

data_processing:
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the genome and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: small RNA seq.: microRNA count files

source_name: Colorectal

growth_protocol: Caco-2 cells were cultured with DMEM supplemented with 20% FBS and 1% Pen/Strep and incubated at 37°C and 5% CO2.

extract_protocol:
For extracellular RNA isolation, media was collected and centrifuged to remove cell debris. Total exRNA was isolated from a portion of the supernatant by nucleic acid precipitation, followed by Trizol. The other portion of supernatant was centrifuged at 40,000xg. P40 exRNA was isolated from the resulting pellet using Trizol. The supernatant was collected and centrifuged at 100,000xg. S100 RNA was isolated from the supernatant by nucleic acid percipitation and subsequent Trizol isolation. P100 exRNA was isolated from the pellet using Trizol. Intracellular RNA was isolated from the Caco-2 cells using Trizol.
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. We sent all sRNA libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads.

treatment_protocol: Once cells reached 80% confluence, the growth media was changed to FBS and antibiotic free media and cells were allowed to incubate for 24 hours prior to isolation.

value: Colorectal

value: Epithelial

value: WT

tag: fraction

tag: batch


title: KOcereb2_S2_R1_001

description:
KOcereb2
KOcelebvsWTceleb_diffexpr-results.csv

value: mouse

value: cerebellum

value: KO


title: Control R3


title: Irradiated R2


title: Control R2


title: H3K9me3_mESCs_KO_rep3

value: IkappBalpha-/-


title: H3K9me3_mESCs_KO_rep2


title: H3K9me3_mESCs_WT_rep3


title: H3K9me3_mESCs_KO_rep1


title: Control R1


title: Control R4


title: H3K9me3_mESCs_WT_rep2


title: H3K9me3_mESCs_WT_rep1


title: Human RPE/choroid scRNA rep2

description: scRNA-seq

value: RPE/choroid


title: H3K4me3_mESCs_WT_rep3

value: mouse embryonic stem cells


title: Human RPE/choroid scRNA rep5

description: scRNA-seq


title: Irradiated R1


title: Human RPE/choroid scRNA rep4

description: scRNA-seq


title: Human RPE/choroid scRNA rep1

description: scRNA-seq


title: Pig ESCs cultured without feeder cells (LDN-treated; Rep.3)

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Following cluster amplification of denatured templates, paired-end sequencing (2 × 100 bp) was performed using an Illumina NovaSeq6000 (Illumina). The base call quality for each sequenced read was assessed using the FastQC program (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads were filtered according to the following criteria: > 10% skipped bases (marked as ‘N’s), > 40% of bases with a quality score < 20, and reads with an average quality score of < 20. The filtering was performed using Cutadapt v. 1.6 (24). Filtered reads were mapped to the reference genome (pig, Sscrofa10.2. Ensembl release 77) using TopHat v. 2.0.12.1 (25). Gene expression levels were measured with Cufflinks v. 2.2.1 (26) using the gene annotation database. Noncoding gene regions were excluded from gene expression measurement using the –mask option. To improve the accuracy of the measurement, multiread correction and frag bias correction options were applied.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Pig embryonic stem cells

growth_protocol: The pig ESCs were cultured in ESC medium [DMEM/F12 containing 15% (v/v) KnockOut™ Serum Replacement (KSR), 0.1% (v/v) chemically defined lipid concentrate (LC), 1× GlutaMAXTM supplement, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic (all from Gibco, Gaithersburg, MD, USA) supplemented with 20 ng/mL FGF2 (R&D Systems, Minneapolis, MN, USA), 5 ng/mL ActA (R&D Systems), 1.5 µM CH (Cayman Chemical, Ann Arbor, MI, USA), and 2.5 µM IWR-1 (Sigma–Aldrich, St. Louis, MO, USA)]. Pig ESCs were subcultured every 5–7 days. Twenty-four hours before subculturing, pig ESCs were cultured with ESC culture medium containing 10 µM Y-27632 (Santa Cruz Biotechnology, Dallas, TX, USA). Expanded colonies were dissociated into small clumps using TrypLE™ Express (Gibco). These clumps were transferred onto new feeder cells and cultured with ESC medium containing 10 µM Y-27632 (Santa Cruz Biotechnology) for 24 h. Next, attached clumps were cultured with ESC medium lacking Y-27632 for 4–6 days. The medium was changed every 24 h, and pig ESCs were cultured under humidified conditions in an atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Before RNA and DNA extraction from pig ESCs cultured with feeder cells, SSEA4-positive undifferentiated pig ESCs were sorted using a MACS Cell Separation System (Miltenyi Biotec, Germany) to remove differentiated cells and feeder cells. The dissociated pig ESCs were reacted with an anti-SSEA4 antibody (1:200; MAB4304, Millipore) and anti-mouse IgG microbeads (1:5; Miltenyi Biotec). SSEA4-positive cells were sorted on an LS column (capacity, 1 × 108 magnetically labeled cells; Miltenyi Biotec) according to the manufacturer’s instructions. Total RNA was extracted from pig fetal fibroblasts, and SSEA4-positive ESCs were sorted using TRIzol reagent (Invitrogen).
The quality of RNA samples was examined using an Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA, USA). The extracted RNA samples were used for the construction of cDNA libraries. cDNA library preparation and RNA-Seq analysis were performed by Theragen Etex (www.theragenetex.com, Korea). The libraries were prepared for 100-bp paired-end sequencing using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNAs were purified and fragmented from 2 μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were transformed to single-stranded cDNAs using random hexamer primers. The products were used as templates for the preparation of double-stranded cDNA. After sequential end repair, A-tailing, and adapter ligation, the cDNA libraries were amplified by PCR. The quality of the cDNA libraries was evaluated using the Agilent 2100 BioAnalyzer (Agilent). The cDNA libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: For adaptation to feeder-free culture, pig ESCs cultured with feeder cells were transferred to MatrixTM-coated plates (SPL Life Sciences, Pocheon, Korea) at a 1:5 to 1:10 split ratio with feeder-free (FF-) ESC medium. The cells were cultured in FF-ESC medium [DMEM/F12 containing 15% (v/v) KSR, 0.1% (v/v) LC, 1× glutamax, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic (all from Gibco) supplemented with 20 ng/mL FGF2 (R&D Systems), 5 ng/mL ActA (R&D Systems), 1.5 µM CH (Cayman Chemical), 2.5 µM IWR-1 (Sigma–Aldrich), and 250 nM LDN-193189 (Cayman Chemical)]. Pig ESCs were subcultured every 5–7 days. Twenty-four hours before subculturing, pig ESCs were cultured with FF-ESC culture medium containing 10 µM Y-27632 (Santa Cruz Biotechnology, Dallas, TX, USA). Next, expanded colonies were dissociated into small clumps using TrypLE™ Express (Gibco). These clumps were transferred onto new MatrixTM-coated plates and cultured with FF-ESC medium containing 10 µM Y-27632 (Santa Cruz Biotechnology) for 24 h. Next, attached clumps were cultured with FF-ESC medium lacking Y-27632 for 4–6 days. The medium was changed every 24 h, and pig ESCs were cultured under humidified conditions in an atmosphere containing 5% CO2 at 37 °C. Pig ESCs cultured over 3 passages in the absence of feeder cells were used for further analysis, including immunostaining, teratoma assay, PCR analysis, and RNA sequencing.

value: without feeder cells, LDN-treated


title: Pig ESCs cultured without feeder cells (LDN-treated; Rep.2)


title: Human RPE and choroid H3K27ac HiChIP

description: H3K27ac HiChIP


title: MB272_relapse_A2-1

type: RNA

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center

description: Raw data files include tab-separated values files containing x-y-z location for each transcript (txt format) and staining images (tiff format).Processed data include output gene expression matrix (csv format)

hyb_protocol: The sections were thoroughly washed and primed before the specific probes against our genes of interest were hybridized at 37°C overnight

scan_protocol: Molecular Cartography observation chamber was transferred to the machine for eight automated iterations of coloring and imaging to decipher the transcript localization of the 100 different genes of interest in the tissue

data_processing:
The detection of cell boundaries was performed with QuPath v0.3.2. Gene expression counts were computed per cell and extracted using Resolve Bioscience plugin in the ImageJ2 toolkit.
Matrix contains the gene selected for spatial selection.

source_name: Tumor

extract_protocol: OCT-embedded samples were cryo-sectioned into 10 µm sections onto protocol slides.

value: Tumor

tag: tumor type

value: Medulloblastoma

tag: tumor class

tag: somatic aberration

value: MYC


title: MB294_C2-2

value: MYCN


title: MB294_C2-1


title: Pig ESCs cultured with feeder cells (Rep.3)

value: with feeder cells


title: Bd21,drought,rep49

city: Cambridge

first: Jie

last: Yun

state: MA

address: 77 MASS

department: CEE

institute: MIT

data_processing:
Raw sequence reads were trimmed by Trimmomatic (trimmomatic-0.39) with 2:30:10:1:true and Cutadapt (v2.10)to remove adapters and poly(A) tails with -a A{20} and -m 25
Reads were aligned to reference transcriptome using Bowtie2 (v2.4.0) with seedlength -L 25 and mismatch allowance -n 2 and other default parameters suggested by next step RSEM
Reads with the same unique molecular identifier (UMI) and aligned to the same genes were removed to eliminate PCR bias during library generation using a custom script
RNA-Seq by Expectation-Maximization (RSEM, 1.3.3) was used to estimate counts to account for non-specifically aligned reads with --estimate-rspd
Assembly: Bdistachyon_556_v3.2.transcript_primaryTranscriptOnly and LT558597 Bd21 plastome
Supplementary files format and content: csv file includes raw counts for each samples

organism: Brachypodium distachyon

source_name: leaf

growth_protocol: Plants were grown in growth chambers with 50% humidity, 500 mmol photons m-2 s-1 light intensity and a controlled temperature of 25oC day/20oC night (12h/12h). Plants were bottom watered with tap water (pH=5-6) every other day throughout the experiment, supplemented with DYNA-GRO GROW Liquid Plant Food 7-9-5 (Dyna-Gro, Richmond, CA, USA) over the first 32 days.

extract_protocol:
Approximately 100mg of tissue was used for RNA extraction using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer instructions, followed by DNase treatment (On-Column DNase I Digestion Set, Sigma-Aldrich, USA). 25ng of RNA for 214 samples were aliquoted at a normalized concentration of 5 ng/μL for sequencing
MIT BioMicro Center performed RNA-seq library construction and sequencing following the approach of High-Throughput 3' Digital Gene Expression with 26 + 80 bases pair-end run with 6 nucleotide index

treatment_protocol: Starting the 33rd day after sowing, control plants were watered to 85% FC every night while dry-down plants were allowed to decrease their soil water content to 55% FC over 6 days (5% decrease each day) by daily bringing soil water content to the specified water contents.

value: leaf

value: bulk

value: drought


title: Pig ESCs cultured without feeder cells (Rep.2)

value: without feeder cells


title: N4059_22_A1-2


title: Pig ESCs cultured without feeder cells (LDN-treated; Rep.1)


title: Pig ESCs cultured with feeder cells (Rep.2)


title: Pig ESCs cultured without feeder cells (Rep.1)


title: MB110_D1-1


title: Bd3-1,control,rep58

value: control


title: Bd21,drought,rep48


title: Bd21,drought,rep47


title: Bd3-1,drought,rep58


title: Bd3-1,drought,rep59


title: MB110_D2-2


title: Bd3-1,control,rep57


title: methylation_TUMOR_9

type: genomic

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre, University of Copenhagen

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

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

data_processing: RnBeads v2.6.0

label: cy3 and cy5

source_name: Ampullary carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified with AllPrep (Qiagen) according to manufacturer’s instructions

value: Ampullary carcinoma


title: N4059_22_A1-1


title: Pig ESCs cultured without feeder cells (Rep.3)


title: methylation_TUMOR_15


title: Pig ESCs cultured with feeder cells (Rep.1)


title: Bd3-1,control,rep56


title: adult heads, FBXO11 RNA2 2, neuronal knockdown

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description: Library name: HU-230984

data_processing:
Reads were converted to .fastq format and demultiplexed using bcl2fastq v2.17.
Adapter trimming and quality filtering was performed using cutadapt v1.18. Quality control after trimming was done using fastqc v0.11.8.
processed reads were mapped to the Drosophila reference genome BDGP6.11, Ensembl Annotation v98 using STAR aligner v.2.6.1.
Mapped reads were counted for all non-overlapping exons. The sum of all exons determines the number of reads per gene and was obtained using samtools v1.8 and subreadv1.6.1.
Differential gene expression (DGE) analysis was performed using DESeq2 v1.24.0 and for noise removal, the apeglm package was used.
Assembly: Drosophila reference genome BDGP6.11, Ensembl Annotation v98
Supplementary files format and content: tab delimited text includes raw counts for each sample

organism: Drosophila melanogaster

source_name: head

extract_protocol:
RNA extraction using Rneasy lipid tissue mini kit and Trizol
the TrueSeq Stranded mRNA kit (Illumina)

value: head

value: FBXO11 KD3


title: methylation_TUMOR_12


title: methylation_TUMOR_10


title: methylation_TUMOR_8


title: MB292_B2-3


title: adult heads, FBXO11 RNA1 3, neuronal knockdown

description: Library name: HU-230979

value: FBXO11 KD1


title: Bd21,control,rep48


title: Bd3-1,control,rep55


title: MB110_D2-1


title: Bd3-1,drought,rep57


title: adult heads, FBXO11 RNA2 1, neuronal knockdown

description: Library name: HU-230982

value: FBXO11 KD2


title: adult heads, FBXO11 RNA1 2, neuronal knockdown

description: Library name: HU-230977


title: Bd3-1,drought,rep55


title: methylation_TUMOR_7


title: adult heads, FBXO11 RNA1 1, neuronal knockdown

description: Library name: HU-230976


title: methylation_TUMOR_3


title: methylation_TUMOR_14


title: MB292_B2-2


title: methylation_TUMOR_16


title: MB292_B2-1


title: Bd3-1,control,rep53


title: MB91_C2-1


title: methylation_TUMOR_6


title: methylation_TUMOR_11


title: adult heads, FBXO11 Control 1/2 3, neuronal knockdown

description: Library name: HU-230974

value: FBXO11 WT


title: Bd21,control,rep47


title: methylation_TUMOR_13


title: Bd3-1,drought,rep54


title: Bd3-1,drought,rep52


title: MB272_A2-2


title: methylation_TUMOR_4


title: MB272_A2-1


title: adult heads, FBXO11 Control 1/2 2, neuronal knockdown

description: Library name: HU-230968


title: Bd3-1,control,rep51


title: Bd3-1,drought,rep53


title: adult heads, FBXO11 Control 1/2 1, neuronal knockdown

description: Library name: HU-230964


title: Bd3-1,control,rep50


title: methylation_TUMOR_1


title: Bd3-1,drought,rep56


title: methylation_TUMOR_2


title: MB129_A1-2


title: Bd3-1,drought,rep51


title: Bd3-1,control,rep47


title: MB294_C1-1


title: Bd3-1,control,rep49


title: Bd3-1,drought,rep50


title: neuron FBXO11 WT 3

description: Library name: HU-238286

data_processing:
Reads were converted to .fastq format and demultiplexed using bcl2fastq v2.17.
Adapter trimming and quality filtering was performed using cutadapt v1.18. Quality control after trimming was done using fastqc v0.11.8.
Processed reads of RNA-Seq on human samples were mapped to the human reference genome hg19 with the Ensembl gene annotation GRCh37.87 using STAR aligner v2.7.5a.
Read counts were obtained using the subread featureCounts program v.2.01.
Differential gene expression (DGE) analysis was performed using DESeq2 v1.24.0 and for noise removal, the apeglm package was used.
Assembly: human reference genome hg19 with the Ensembl gene annotation GRCh37.87
Supplementary files format and content: tab delimited text includes raw counts for each sample

source_name: hIPSC-derived neurons

extract_protocol:
Rneasy Mini Kit
the TrueSeq Stranded mRNA kit (Illumina)

value: hIPSC-derived neurons


title: Bd3-1,control,rep48


title: Bd21,control,rep46


title: MB129_A1-1

value: Tumor


title: MB177_W6A2

value: Medulloblastoma


title: methylation_TUMOR_5


title: neuron FBXO11 WT 1

description: Library name: HU-238284


title: neuron FBXO11 KO 3

description: Library name: HU-238283

value: FBXO11 KO


title: Bd3-1,control,rep52


title: neuron FBXO11 WT 2

description: Library name: HU-238285


title: Bd3-1,drought,rep48


title: Bd3-1,drought,rep49


title: neuron FBXO11 KO 2

description: Library name: HU-238282


title: Bd3-1,control,rep46


title: Bd21,drought,rep46


title: Bd21,drought,rep45


title: Bd3-1,drought,rep47


title: MB249_W2A1


title: Bd3-1,control,rep44


title: MB183_W0A1

value: MYCN


title: MB177_W6A1


title: Bd3-1,control,rep45


title: MB249_W2A2


title: Bd3-1,drought,rep46


title: MB165_W3A1


title: HCT116, ORC5KO, replicate 1, SNS-seq

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

description: SNS-seq

data_processing:
Raw reads were adapter- and quality-trimmed using trim_galore v0.6.4 (https://github.com/FelixKrueger/TrimGalore) discarding reads shorter than 18 bp. Trimmed reads were aligned to the reference genome (human genome build GRCh38) with bowtie v1.2.377 (-v 2 –best –strata –tryhard -m 1 –chunkmbs 256). Peaks were called from the resulting alignments using MACS v2.2.646 (--nomodel –extsize 275 -q 0.01) without input and consensus peaks for each condition were computed from replicates using BedTools intersect v2.27.178. Consensus peaks were then clustered using ClusterScan v0.2.179 setting -n 2 and -d to the median interpeak distance of the respective consensus peak set and subsequently filtered with BedTools intersect v2.27.178 to only retain peaks within a cluster. Resulting peak sets for each condition pair compared were then merged using BedTools merge v2.27.1.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw counts of WT and ORC1KO
Supplementary files format and content: tab delimited text file includes raw counts of WT and ORC2KO
Supplementary files format and content: tab delimited text file includes raw counts of WT and ORC5KO
Library strategy: SNS-Seq

source_name: Colon cancer cell

growth_protocol: HCT116 and ORCKO cells cultured in McCoy's 5a Medium with 10% fetal bovine serum and 50 U/mL penicillin-streptomycin.

extract_protocol:
Genomic DNA was extracted and short nascent DNA was enriched via size selection and lamda exonuclease digestion.
Libraries were prepared following standard Illumina protocols.

value: Colon cancer cell

value: epithelial

value: ORC5 knockout


title: neuron FBXO11 KO 1

description: Library name: HU-238281


title: HCT116, ORC5KO, replicate 2, SNS-seq

description: SNS-seq


title: Bd21,drought,rep44

value: leaf

value: bulk

value: drought


title: Bd21,control,rep45

value: control


title: HCT116, ORC2KO, replicate 2, SNS-seq

description: SNS-seq

value: ORC2 knockout


title: Bd21,control,rep44


title: HCT116, ORC2KO, replicate 1, SNS-seq

description: SNS-seq


title: Bd3-1,drought,rep45


title: KPC2 cells, Resistant

first: Song

last: Li

state: Pennsylvania

address: 335 Sutherland Dr, Pittsburgh, PA 15213, Salk Pavilion room 223

institute: University of Pittsburgh

description: Library name: KPC2, Gemcitabine resistant

data_processing:
Data was analyzed by following HISAT2-Stringtie-Ballgown workflow published on Nature Protocol.(Pertea, M., Kim, D., Pertea, G. et al, Nat Protoc 11, 1650–1667 (2016).)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreas

growth_protocol: Both KPC2 wild-type and gemcitabine-resistant cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1× GlutaMAX, and antibiotics in a humidified atmosphere with 5% CO₂ at 37 °C. Gemcitabine-resistant cells were additionally maintained with 260 ng/mL gemcitabine.

extract_protocol:
RNA prepared by University of Pittsburgh Sequencing Core
Library was prepared by University of Pittsburgh Sequencing Core

treatment_protocol: Wild-type cells received no treatment, while resistant cells were subjected to long-term treatment with 260 ng/mL gemcitabine.

value: Pancreas

value: Caner cell

value: Gemcitabine resistant


title: Bd21,drought,rep43


title: HCT116, ORC1KO, replicate 1, SNS-seq

description: SNS-seq

value: ORC1 knockout


title: KPC2 cells, Wild type

description: Library name: KPC2, Wild type

value: Wild type


title: Bd3-1,drought,rep44


title: Bd21,drought,rep42


title: HCT116, ORC1KO, replicate 2, SNS-seq

description: SNS-seq


title: HCT116, WT, replicate 2, SNS-seq

description: SNS-seq

value: WT


title: Bd21,control,rep43


title: Bd3-1,control,rep43


title: Bd3-1,control,rep42


title: Bd3-1,drought,rep43


title: SK-MEL-28 siDANCR cells (2)

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

institute: University of Bath

description: Library name: Dan_s_2

data_processing:
Quality controls were applied for cleaning data for adapters and trimming of low quality sequence ends using trim_galore version 0.4.4
Cleaned data was aligned using FLASH v1.2.11 and mapped to the hg19 genome using bowtie version 1.1.2
Statistical analysis was performed with the Bioconductor package DESeq2
Assembly: Gencode v19, genome assembly hg19
Supplementary files format and content: Excel file includes transcript id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj

growth_protocol: SK-MEL-28 human melanoma cells were cultured in 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was purified using the GeneJET RNA purification Kit (ThermoFisher Scientific). Residual genomic DNA was then removed using DNA-free™ DNA Removal Kit (ThermoFisher Scientific).
polyA 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 dUTP for strand specific library.

treatment_protocol: siRNA transfection using lipofectamine

value: Melanoma cells


title: SK-MEL-28 siDANCR cells (3)

description: Library name: Dan_s_3


title: Bd3-1,control,rep41


title: Intervertebral disc, Streptozocin-High-Fat-Diet, replicate 3

city: St Louis

first: Christian

middle: E

last: Gonzalez

state: MO

address: 450 S Euclid Ave

department: Orthopaedic Surgery

institute: Washington University in St Louis

description: Library name: SH20610

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: GRCm38.101
Supplementary files format and content: .tsv containing all gene counts and transcript counts for all samples

source_name: Intervertebral disc

extract_protocol:
Flash-frozen IVDs were pulverized and reconstitued in TRIzol. Samples were quadruple filtered via column extraction and centrifugation and remained in DNA/RNA-free water until analysis.
Library preparation was performed with 1-50ng of total RNA.  ds-cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique index tags.

treatment_protocol: Streptozocin-High-Fat-Diet Mice were given a lead-in phase of high fat (80% kcal fat) diet for 4-6 weeks. Following the lead-in STZHFD mice were injected with 100 mg/kg Streptozocin, and maintained on a high fat diet for another 12 weeks. At this point, mice were sacrificed and had IVDs harvested for RNAseq

value: Intervertebral disc

value: Streptozocin-High-Fat-Diet


title: Intervertebral disc, Streptozocin-High-Fat-Diet, replicate 4

description: Library name: SH20RIP


title: Intervertebral disc, Streptozocin-High-Fat-Diet, replicate 1

description: Library name: SH20NT


title: Intervertebral disc, Streptozocin-High-Fat-Diet, replicate 2

description: Library name: SH20612


title: GG

city: Chengdu

first: shi

middle: yu

last: jun

address: No. 37, Guoxue Lane

country: China

institute: West China hospital

description: 10X Genomics

data_processing:
The demultiplexing,  barcodes processing, gene counting and aggregation were made using Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latestwhat-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
The whole colon (approximately 9-10 cm and weighted at circa 0.5 g) was freshly collected, dissected, washed, and cut open longitudinally, then placed it in cold DPBS (Gibco) with ice, rinsed for 5 times. Tissues were cut into 2-3 mm size with ophthalmic scissors, washed 15 times with DPBS. Biopsies were incubated in chelation medium (DPBS with 2 mM EDTA) at 37°C for 80 min with agitation. The supernatant was removed and replaced every 20 min, and the epithelial crypts contained supernatant was then digested into a single-cell suspension by dissociation with TrypLE Express (Gibco) containing 50 μg/ml DNase I (STEMCELL) for 1 h at 37°C. The epithelial single-cell suspension was washed and filtered with 40 μm cell strainers.  For further processing, cell counts and viability were confirmed with a Countess II automated cell counter (ThermoFisher Scientific) with confirmation by manual hemocytometer. In all single-cell and exploratory experiments, samples were processed immediately.
Library was performed according to the manufacter's instructions (single ce 3' v2 protocol,10x Genomics). Firstly, single cell suspension should be obtained, and the single cell suspension should be tested for activity, and the cell activity is >90% before subsequent experiments can be carried out. To ensure the capture efficiency of the subsequent cells, the cell concentration is required to be controlled in the range of 700-1200cell/ul. During library preparation, Gel Bead and cells containing primer sequences linked to cell barcode and UMI (unique molecular identifier) are wrapped in "oil droplets" to form GEM (Gel Bead in Emulsion). Cells are lysed in this system and reverse transcribed to form full-length cDNA sequences. After the oil droplets are broken and purified, the cDNA library is amplified by PCR and sequencing primers are attached.

value: Colon

value: epithelial cells

value: c-Kit+ cells derived cells

value: One intraperitoneal injection of Tamoxifen(1mg/20g)


title: Bd21,control,rep42

value: leaf

value: bulk


title: SK-MEL-28 siDANCR cells (1)

description: Library name: Dan_s_1


title: Intervertebral disc, Wild-type, replicate 4

description: Library name: SH17617

value: Wild-type


title: Bd3-1,drought,rep42

value: drought


title: NG

description: 10X Genomics

value: the whloe colonic epithelial cells


title: WT, M19, quadriceps, 3 weeks old

first: Yonne

last: Menezes

description: Library name: WT_TD139_M19_quad_S19

data_processing:
Sequence reads were trimmed for adaptor sequence during demultiplexing
Sequence reads quality was checked using CLC Genomics Workbench 25
Read count extraction and normalization were performed using CLC Genimics Workbench 24.0.1
Principal component analysis of samples was performed for each condition (WT and dyW), (dyW TD139 and dyW PBS)
Assembly: mm10
Supplementary files format and content: csv files include RPKM values for each sample
Supplementary files format and content: csv files include RPKM values for each sample

source_name: Quadriceps muscles

growth_protocol: Colony of healthy (C57BL/6J) and hemizygotes mutant (B6.129S1(Cg)-Lama2tm1Eeng/J; strain #013786, knock-out of the laminin alpha 2 gene) mice were maintained at the animal facility, Rangos Research Building, University of Pittsburgh.

extract_protocol:
Total RNA was isolated from mice quadriceps using TRIzol reagent (ThermoFisher, cat#15596026).  1 ug of total RNA was used for the contruction of sequencing libraries.
RNA libraries were prepared using Illumina Stranded mRNA library kit (Illumina). Sequencing was performed using NextSeq 2000 platform with pair-end 58 bp reads

treatment_protocol: At age 5 weeks old, mice were sacrificed and quadriceps isolated. The quadriceps was preserved in liquid nitrogen-chilled isopentane, and immediately submerged in liquid nitrogen and subsequently stored in -80 °C until further use.

value: Quadriceps muscles

tag: Sex

value: Male

tag: disease state

value: Healthy control mouse

tag: age

value: 3 weeks

tag: strain


title: SK-MEL-28 control cells (3)

description: Library name: Neg_s_3

tag: cell line


title: Bd3-1,control,rep54

tag: tissue

tag: cell type

value: control


title: Bd21,control,rep41

tag: genotype

tag: treatment


title: Intervertebral disc, Wild-type, replicate 3

description: Library name: SH17620


title: SK-MEL-28 control cells (1)

description: Library name: Neg_s_1

value: Melanoma cells


title: Bd3-1,control,rep40


title: WT, M12, quadriceps, 3 weeks old

description: Library name: WT_TD139_M12_quad_S12

value: Female

value: WT


title: Bd21,drought,rep41


title: SK-MEL-28 control cells (2)

description: Library name: Neg_s_2


title: WT, M21, quadriceps, 3 weeks old

description: Library name: WT_PBS_M21_quad_S21


title: CS8

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

description: Library name: IGS_MLI_074rCap

data_processing:
Reads were mapped to the human genome Hg38 using HISAT2(v2.0.4),
Counts were obtained using the Python library HTseq82.
Assembly: Hg38
Supplementary files format and content: tsv of counts of each sample

source_name: whole blood

extract_protocol:
A total of 2.5 mL of venous blood was collected from each study participant during acute illness and before initiation of antimalarial treatment. Blood was collected into PreAnalytiX PAXgene Blood RNA collection tubes (Qiagen). RNA extractions were performed with the PreAnalytiX PAXgene Blood RNA extraction kit in accordance with the manufacturer’s instructions.
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used for cDNA synthesis and library preparation

value: whole blood

tag: match group

value: CM + SMA

value: 3 years

tag: ethnicity

value: Dogon

tag: blantyre coma_scale

tag: hemoglobin g_dl

tag: parasitemia

tag: age years

tag: blood type

value: O

tag: rh factor

tag: type cat

value: case

tag: blantyre coma_scale_2

tag: cm sma

value: both


title: HCT116, WT, replicate 1, SNS-seq

description: SNS-seq

value: Colon cancer cell

value: epithelial


title: Bd21,drought,rep40

value: leaf

value: bulk

value: drought


title: WT, M14, quadriceps, 3 weeks old

description: Library name: WT_PBS_M14_quad_S14

value: Quadriceps muscles

tag: Sex

value: Male

tag: disease state

value: Healthy control mouse

tag: age

value: 3 weeks

tag: strain


title: Intervertebral disc, Wild-type, replicate 1

description: Library name: SH17618

tag: tissue

value: Intervertebral disc

tag: genotype

value: Wild-type

tag: batch


title: Intervertebral disc, Wild-type, replicate 2

description: Library name: SH17RIP

tag: treatment


title: Intervertebral disc, Lepr heterozygous, replicate 3

description: Library name: dbhet3

value: db/+ heterozygous


title: Bd3-1,drought,rep41

tag: cell type


title: HCEC, CREBBP-KO, replicate 3

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

description:
HCEC_C2_R3
WIL855A30

data_processing:
Adapter trimming was performed with cutadapt (v.1.9.1) with parameters “--minimum-length = 25 --quality-cutoff = 20 -a AGATCGGAAGAGC”.
The RSEM package (v.1.3.0) in conjunction with the STAR alignment algorithm (v.2.5.2a) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser79. The parameters used were “--star-output-genome-bam --forward-prob 0".
Assembly: hg19
Supplementary files format and content: RSEM estimated gene counts

growth_protocol: HCEC-1CT cells were acquired from Evercyte (CHT-039-0229) and cultured in a mix of  4 parts DMEM (Gibco) to 1 part Medium 199 (Sigma-Aldrich M4530) containing 2 % Cosmic Calf Serum (GE HyClone SH30087.02), 4 mM GlutaMAX (Gibco 35050038), 20 nM hEGF (Sigma-Aldrich E9644), 100 μM Insulin (Sigma-Aldrich I9278), 2 mg/mL Apo-transferrin (Sigma-Aldrich T2036), 5 nM sodium selenite (Sigma-Aldrich S5261), and 1 μg/mL Hydrocortisone (Sigma-Aldrich H0396). hTERT-HME1 [ME16C] cells were acquired from ATCC (CRL-4010) and cultured in complete HuMEC medium (Gibco 12752010) with 2 % FBS (Gibco 16000-044). All media contained 100 U/ml penicillin and 100 μg/mL streptomycin (Sigma P4333), and cells were cultured in normoxia at 37°C in 5% CO2.

extract_protocol:
RNA was extracted using Total RNA was isolated using an RNeasy Plus Mini kit (Qiagen 74136).
Sequencing libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche KK8581) according to manufacturer’s instructions. Adapter ligation was carried out using the KAPA Unique Dual-Indexed Adapters Kit (15μM) (Roche- KK8727) according to manufacturer’s instructions. To remove short fragments such as adapter dimers, two SPRISelect bead clean-ups were done (0.63x SPRI and 0.7x SPRI). The library was amplified with Kapa HiFi HotStart PCR master mix plus Library Amplification Primer mix in 13 PCR cycles as recommended by the manufacturer. Amplified libraries were purified via a SPRISelect 1x bead cleanup. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies). Libraries were pooled and sequenced on the HiSeq4000 (Illumina) in SR100 configuration to an average read depth of 25M.

tag: cell line

value: colonic epithelial cells

value: CREBBP-KO


title: DYW, M17, quadriceps, 3 weeks old

city: Pittsburgh

address: 4401 Penn Ave

description: Library name: DYW_TD139_M17_quad_S17

value: Female

value: DYW

value: LAMA-2 CMD diseased mouse


title: DYW, M18, quadriceps, 3 weeks old

description: Library name: DYW_TD139_M18_quad_S18


title: Bd21,drought,rep39


title: Intervertebral disc, Lepr heterozygous, replicate 2

description: Library name: dbhet2


title: HCEC, CREBBP-KO, replicate 2

description:
HCEC_C2_R2
WIL855A29


title: Intervertebral disc, Lepr heterozygous, replicate 1

description: Library name: dbhet1


title: DYW, M16, quadriceps, 3 weeks old

description: Library name: DYW_TD139_M16_quad_S16


title: Bd21,control,rep40

value: control


title: DYW, M24, quadiceps, 3 weeks old

description: Library name: DYW_PBS_M24_quad_S22


title: HCEC, CREBBP-KO, replicate 1

description:
HCEC_C2_R1
WIL855A28


title: Intervertebral disc, Lepr deficient, replicate 3

description: Library name: dbdb3

value: db/db


title: Intervertebral disc, Lepr deficient, replicate 2

description: Library name: dbdb2


title: HCEC, ARID1A-KO, replicate 3

description:
HCEC_A3_R3
WIL855A24


title: Bd3-1,control,rep39

value: leaf


title: Bd21,drought,rep38

value: bulk


title: Intervertebral disc, Lepr deficient, replicate 1

description: Library name: dbdb1


title: HCEC, ARID1A-KO, replicate 2

description:
HCEC_A3_R2
WIL855A23


title: Mediastinal lymph node B cells, feature barcode (hashing) library

city: Maywood

first: Yee Ling

last: Wu

state: IL

address: 2160 S. 1st Ave

department: Microbiology and Immunology

institute: Loyola University Chicago

description:
Library name: YW-8
10X Genomics

data_processing:
Demultiplexing, barcoding processing, gene counting and sequence alignment were performed using Cell Ranger (v8) multi to generate processed data files for each library separated by each biological replicate using feature barcode (hashing) libraries.
Assembly: GRCm38 - mm10
Supplementary files format and content: Tab-separated values, comma-separated values, and matrix files

source_name: mediastinal lymph node

extract_protocol:
Mice were injected with fluorophore-conjugated anti-CD45 3 minutes before sacrifice to label circulating cells. Cells were isolated from the lungs by mincing tissue and digesting in 2 mL solution of 750 U/mL collagenase I and 200 U/mL DNase I in RPMI for 45 minutes at 37 C. Digested lungs were passed through 70 micron cell strainers, diluted with 10 mL of 30% Percoll in RPMI and centrifuged for 930 g for 10 minutes with no brake. Red blood cells were lysed for 5 mins at RT in ACK lysis buffer and cells were washed and resuspended in PBS + 2% FBS. Cells were isolated from mediastinal lymph nodes by mushing through 70 micron cell strainers followed by washing and resuspending in PBS + 2% PBS. Isolated cells from each of 3 mice were pre-enriched with EasySep Mouse Pan-B Cell Isolation Kit (STEMCELL), then stained with anti-CD19 and anti-IgD antibodies and cell hashing antibodies (BioLegend TotalSeq-C0301 Hashtag 1, C0302 Hashtag 2, and C0303 Hashtag 3), then equal numbers of cells from each mouse were pooled for sorting in PBS + 2% FBS + DAPI (1:2000). Pooled cells were sorted as live (DAPI negative), non-circulating (i.v. anti-CD45 negative), CD19+/low to include plasma cells and IgD low to exclude naive cells. Sorted cells were washed and resuspended in PBS without calcium or magnesium + 0.05% BSA.
Libraries were prepared using 10X Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for cell hashing. 20,000 cells per tissue were loaded into individual wells of Chromium Next GEM Chip K and partiioned into Gel Bead-In-Emulsions (GEM) and barcoding by 10X Genomics Chromium Controller. Reverse transcription, cDNA amplification, and library contstruction for 5' gene expression, BCR V(D)J, and feature barcode (hashing) libraries were performed according to manufacturer's instructions. During library construction Illumina i5 and i7 index sequences were added.

treatment_protocol: Intranasal administration of ragweed pollen and ovalbumin

value: mediastinal lymph node

value: B cells

value: BALB/cJ


title: HCEC, ARID1A-KO, replicate 1

description:
HCEC_A3_R1
WIL855A22


title: Bd21,control,rep39


title: DYW, M23, quadriceps, 3 weeks old

description: Library name: DYW_PBS_M23_quad__S23

value: Quadriceps muscles


title: Bd3-1,control,rep38


title: HCEC, WT, replicate 2

description:
HCEC_WT_R2
WIL855A17

value: WT


title: Bd3-1,drought,rep40

value: drought


title: HCEC, WT, replicate 3

description:
HCEC_WT_R3
WIL855A18


title: Mediastinal lymph node B cells, BCR VDJ library

description:
Library name: YW-5
10X Genomics


title: DYW, M15, quadriceps, 3 weeks old

description: Library name: DYW_PBS_M15_quad_S15

value: Male

value: 3 weeks


title: DYW, 2557, quadriceps, 5 weeks old

description: Library name: DYW_2557_quad_S8

value: 5 weeks


title: WT, M20, quadriceps, 3 weeks old

description: Library name: WT_PBS_M20_quad_S20

value: Healthy control mouse


title: DYW, 2555, quadriceps, 5 weeks old

description: Library name: DYW_2555_quad_S9


title: Lung B cells, BCR VDJ library

description:
Library name: YW-4
10X Genomics

source_name: Lung

value: Lung


title: DYW, 2501, quadriceps, 5 weeks old

description: Library name: DYW_2501_quad_S7

value: DYW


title: Bd21,drought,rep37


title: HCEC, WT, replicate 1

description:
HCEC_WT_R1
WIL855A16

value: colonic epithelial cells


title: DYW, 2561, quadriceps, 5 weeks old

description: Library name: DYW_2561_quad_S6

value: LAMA-2 CMD diseased mouse


title: Bd3-1,drought,rep39


title: Lung B cells, feature barcode (hashing) library

description:
Library name: YW-7
10X Genomics


title: WT, 2499, quadriceps, 5 weeks old

description: Library name: WT_2499_quad_S3


title: HSW-15-110_3

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

description: Library name: MBFgIsolatesRNA-60

data_processing:
Illumina Casava1.7 software used for basecalling
reads trimmed using trimmomatic v0.36 for adapter sequences and low-quality reads
trimmed reads mapped to F. graminearum using hisat2
count data generated using featureCounts
Differential expression analysis performed using DESeq2
Assembly: F. graminearum PH-1 (ASM24013v3)
Supplementary files format and content: tab delimited count data sheets

organism: Fusarium graminearum

source_name: Mycelia

growth_protocol: Isolates were cultured in 60mm petri plates (Catalog No:  FB0875713A, Fisherbrand)in Potato Dextrose Agar (PDA - Catalog No:  0013-17-6, Difco) with Streptomycin sulfate (Catalog No: S6501-010, SIGMA-Aldrich). Plates were incubated at 20C for 7days

extract_protocol:
Mycelia was ground and RNA extraction was performed using the Trizol Reagent (Ambion), according to the manufacturer’s instructions. RNA was quantified using Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit
RNA libraries were prepared for sequencing using standard illumina protocols

value: Mycelia

value: PDA + Streptomycin sulfate


title: Lung B cells, gene expression library

description:
Library name: YW-1
10X Genomics


title: HME, CREBBP-KO, replicate 1

description:
HME_C2_R1
WIL855A13

value: mammary epithelial cells

value: CREBBP-KO


title: Bd21,control,rep37

value: leaf

value: bulk

value: control


title: Mediastinal lymph node B cells, gene expression library

description:
Library name: YW-2
10X Genomics

value: mediastinal lymph node

value: B cells

value: BALB/cJ


title: Bd3-1,drought,rep38

value: drought


title: WT, 2556, quadriceps, 5 weeks old

description: Library name: WT_2556_quad_S2

value: Quadriceps muscles

value: Male

value: WT

value: 5 weeks


title: Bd21,control,rep38


title: WT, 2494, quadriceps, 5 weeks old

description: Library name: WT_2494_quad_S1

value: Female

value: Healthy control mouse


title: HSW-15-110_2

description: Library name: MBFgIsolatesRNA-59

value: Mycelia


title: HME, ARID1A-KO, replicate 2

description:
HME_A3_R2
WIL855A8


title: Bd3-1,control,rep37


title: HME, ARID1A-KO, replicate 3

description:
HME_A3_R3
WIL855A9


title: Bd21,drought,rep36


title: HME, ARID1A-KO, replicate 1

description:
HME_A3_R1
WIL855A7


title: HSW-15-110_1

description: Library name: MBFgIsolatesRNA-58

value: PDA + Streptomycin sulfate


title: Bd3-1,control,rep36


title: HME, CREBBP-KO, replicate 3

description:
HME_C2_R3
WIL855A15

value: mammary epithelial cells


title: Small intestine, day 14, rep1

city: Montreal

first: Irah

last: King

state: QC

address: 1001 Decarie Blvd

institute: McGill University Healthy Centre

description: Library name: Sample 11

data_processing:
Raw reads are clipped for adapter sequence, trimmed for minimum quality (Q30) in 3’ and filtered for minimum length of 32 bp using Trimmomatic.
Surviving read pairs were aligned to Mus_musculus assembly GRCm38 by the ultrafast universal RNAseq aligner STAR45 using the recommended two passes approach.
Aligned RNA Seq reads were assembled into transcripts and their relative abundance was estimated using Cufflinks and Cuffdiff.
Assembly: GRCm38
Supplementary files format and content: CSV (raw counts)

source_name: small intestine

extract_protocol:
Whole duodenal tissue was harvested and flash frozen and stored at −80 °C. Total RNA was extracted by crushing the tissue using a pestle and mortar on dry ice and extracted by using the QIAGEN RNeasy Mini Kit as per the manufacturer’s instructions. In all, 1 μg of RNA was reverse-transcribed by QuantiTect Reverse Transcription Kit (Thermofisher).
Extracted RNA was controlled for integrity using the Agilent Bioanalyzer (RNA Analysis), Stranded libraries were prepared using the NEB mRNA stranded library prep Kit (New England Biolabs).

value: small intestine

value: Hpb infected


title: Small intestine, day 14, rep2

description: Library name: Sample 12


title: Small intestine, day 6, rep2

description: Library name: Sample 10


title: HSW-15-103_2

description: Library name: MBFgIsolatesRNA-56


title: HME, WT, replicate 3

description:
HME_WT_R3
WIL855A3


title: Bd3-1,drought,rep37

value: leaf

value: bulk


title: HME, WT, replicate 2

description:
HME_WT_R2
WIL855A2


title: Small intestine, day 6, rep1

description: Library name: Sample 9


title: HME, WT, replicate 1

description:
HME_WT_R1
WIL855A1


title: Bd21,control,rep36

value: control


title: HSW-15-30 _3

description: Library name: MBFgIsolatesRNA-54


title: Small intestine, day 4, rep2

description: Library name: Sample 8


title: Bd21,drought,rep35


title: WES_NORMAL_16

data_processing:
Library strategy: DNA-seq
Fastq reads were trimed with Trimmomatic v. 0.36
Reads were mapped to hg19 genome with bowtie2, default parameters
Duplicates were removed with picard-tools v. 2.1.1
Realighnment  near indels were performed with GenomeAnalysisTK
Base quality were recalibrated with GenomeAnalysisTK
Variants were called with VarScan v2.3.9 and SomaticSniper
Filtering to reduce the rate of false positive calls was performed with Varscan2 fpfilter.pl (--max-mapqual-diff 30 --max-mmqs-diff 50 --max-var-mmqs 100 --min-var-count 3 --min-strandedness 0.01).
Common somatic variants and germline variants were filtered out with use of dbSNP147 database and high confidence germline calls from Varscan2 across the dataset.
Genome_build: hg19
Supplementary_files_format_and_content: Maf file with table of somatic mutations in AMPAC tumors called by Varscan and SomaticSniper, caller is specified in the  'caller' column

extract_protocol:
Isolation of matched DNA was performed with AllPrep (Qiagen) according to manufacturer’s instructions
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient diagnosis

value: Ampullary carcinoma

value: normal tissue

tag: gender

tag: Stage

value: III


title: HSW-15-30 _2

description: Library name: MBFgIsolatesRNA-53


title: Small intestine, day 4, rep1

description: Library name: Sample 7


title: HSW-15-103_3

description: Library name: MBFgIsolatesRNA-57


title: Bd21,control,rep35


title: WES_NORMAL_15


title: HSW-15-30 _1

description: Library name: MBFgIsolatesRNA-52


title: Small intestine, day 2, rep1

description: Library name: Sample 5


title: WES_NORMAL_14

value: IV


title: HSW-15-114_3

description: Library name: MBFgIsolatesRNA-51


title: Small intestine, day 2, rep2

description: Library name: Sample 6


title: HSW-15-114_1

description: Library name: MBFgIsolatesRNA-49


title: HSW-15-114_2

description: Library name: MBFgIsolatesRNA-50


title: Small intestine, day 1, rep1

description: Library name: Sample 3


title: WES_NORMAL_12

value: Male

value: II


title: Small intestine, day 1, rep2

description: Library name: Sample 4


title: Bd3-1,control,rep35


title: HSW-15-103_1

description: Library name: MBFgIsolatesRNA-55


title: Bd21,control,rep34


title: WES_NORMAL_11


title: Bd3-1,drought,rep36

value: drought


title: WES_NORMAL_13


title: Bd21,drought,rep34


title: Bd3-1,control,rep34


title: HSW-15-95 _2

description: Library name: MBFgIsolatesRNA-47


title: Small intestine, uninfected, rep2

description: Library name: Sample 2

value: Uninfected


title: Small intestine, uninfected, rep1

description: Library name: Sample 1


title: HSW-15-95 _1

description: Library name: MBFgIsolatesRNA-46


title: Setd8KD_3

city: Ikoma

first: Taito

last: Matsuda

country: Japan

institute: Nara Institute of Science and Technology

data_processing:
RNA-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence. Processed reads were mapped to the mouse genome mm10 genome using STAR. DESeq2 package was used for differential gene expression analysis.
Sequence reads for ChIP-seq were trimmed based on read length and read quality using the Trimmomatic tool kit and aligned to the mouse genome (mm10) using Bowtie2 (v2.2.4). All redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools (v0.1.19)95.
Sequencing reads for ATAC-seq were mapped to the mouse reference genome (mm10) from the University of California, Santa Cruz (UCSC) Genome Browser using Bowtie2 (v2.2.4). Open chromatin regions were analyzed using MACS2 software (v2.1.0.20141030) against BAM data compiled by BEDTools.
Assembly: mm10
Supplementary files format and content: TPM (RNA-seq), biigWig (ChIP-seq)

source_name: Hippocampus

extract_protocol:
mRNAs were collected using a Dynabeads mRNA DIRECT Micro Kit (Invitrogen), and the purified mRNAs were subjected to cDNA library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols. ATAC-seq was performed as previously described by Buenrostro, et al. (PMID:2559105). After transpisition reaction with transposase enzyme in Illumina Nextra DNA Preparetion Kit (#FC-121-1030). For H4K20me1 analysis, CUT&RUN (PMID: 28079019) was employed. Sequencing libraries for CUT&RUN were made using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs)
Llibraries were prepared for sequencing following standard Illumina protocols
RNA-seq, ATAC-seq, CUT&RUN

treatment_protocol: Lentiviruses were produced by transfecting HEK293T cells with the lentivirus constructs pCMV-VSV-G-RSV-Rev and pCAG-HIVgp using polyethylenimine. Samples were collected 3 days after viral infection with puromycin selection.

value: Hippocampus

value: Neural stem/progenitor cells


title: Bd21,control,rep33

data_processing:
Raw sequence reads were trimmed by Trimmomatic (trimmomatic-0.39) with 2:30:10:1:true and Cutadapt (v2.10)to remove adapters and poly(A) tails with -a A{20} and -m 25
Reads were aligned to reference transcriptome using Bowtie2 (v2.4.0) with seedlength -L 25 and mismatch allowance -n 2 and other default parameters suggested by next step RSEM
Reads with the same unique molecular identifier (UMI) and aligned to the same genes were removed to eliminate PCR bias during library generation using a custom script
RNA-Seq by Expectation-Maximization (RSEM, 1.3.3) was used to estimate counts to account for non-specifically aligned reads with --estimate-rspd
Assembly: Bdistachyon_556_v3.2.transcript_primaryTranscriptOnly and LT558597 Bd21 plastome
Supplementary files format and content: csv file includes raw counts for each samples

extract_protocol:
Approximately 100mg of tissue was used for RNA extraction using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer instructions, followed by DNase treatment (On-Column DNase I Digestion Set, Sigma-Aldrich, USA). 25ng of RNA for 214 samples were aliquoted at a normalized concentration of 5 ng/μL for sequencing
MIT BioMicro Center performed RNA-seq library construction and sequencing following the approach of High-Throughput 3' Digital Gene Expression with 26 + 80 bases pair-end run with 6 nucleotide index


title: WES_NORMAL_9

value: I


title: WES_NORMAL_10

value: Female


title: Setd8KD_2


title: HSW-15-23 _3

description: Library name: MBFgIsolatesRNA-45

value: Mycelia

value: PDA + Streptomycin sulfate


title: HSW-15-95 _3

description: Library name: MBFgIsolatesRNA-48


title: HSW-15-23 _2

description: Library name: MBFgIsolatesRNA-44


title: Bd21,drought,rep33

value: leaf


title: HME, CREBBP-KO, replicate 2

description:
HME_C2_R2
WIL855A14

value: mammary epithelial cells

value: CREBBP-KO


title: Setd8KD_1


title: Bd3-1,control,rep33

value: bulk

value: control


title: HSW-15-23 _1

description: Library name: MBFgIsolatesRNA-43


title: Bd21,control,rep32


title: HSW-15-73 _3

description: Library name: MBFgIsolatesRNA-42


title: Ctrl_2


title: Ctrl_3


title: WES_NORMAL_5

value: Ampullary carcinoma

value: normal tissue


title: WES_NORMAL_4

value: Male

value: IV


title: Bd21,drought,rep32

value: drought


title: WES_NORMAL_6

value: II


title: HSW-15-73 _2

description: Library name: MBFgIsolatesRNA-41


title: WES_NORMAL_3

value: Unclear


title: HSW-15-73 _1

description: Library name: MBFgIsolatesRNA-40


title: Ctrl_1

value: Hippocampus

value: Neural stem/progenitor cells


title: WES_NORMAL_8

value: I


title: EBs_96h_KO_rep3

city: Barcelona

first: Anna

last: Bigas

address: Dr. Aiguader 88

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
Trimmed reads were aligned to reference genome (GRCm38 release 102 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1
Uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with exon as feature.
Raw counts matrix was imported into R Statistical software (v4.2.1). Prior to statistical analysis, those genes with less than 10 raw counts across the 6 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.38.3)
Assembly: mm10
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Raw_counts.txt: RNAseq Raw expression levels for each gene (55,487 rows) in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Norm_counts.txt. Normalized expression levels including the expression of 25,319 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.38.3)

extract_protocol:
Total RNA was extracted from cells using Qiagen RNeasy Mini Kit (#74106) following manufacturer's instructions. RNA quality was measured by Nanodrop and Agarose gel
Library was prepared according to manufacturer's instructions (PE 125bp paired-end reads)

value: mouse embryoid bodies

value: IkappBalpha-/-

value: knock-out

tag: time

value: Timepoint 96h


title: WES_NORMAL_2


title: Bd3-1,drought,rep35

value: leaf


title: HSW-15-11 _3

description: Library name: MBFgIsolatesRNA-39

value: Mycelia

value: PDA + Streptomycin sulfate


title: EBs_96h_KO_rep2


title: WES_NORMAL_7

value: Ampullary carcinoma

value: Female


title: Bd21,drought,rep31

value: bulk


title: Bd21,control,rep31

value: control


title: WES_TUMOR_16

value: Ampulla of Vater  tumor tissue

value: undefined

value: Male

value: III


title: EBs_96h_WT_rep3

value: IkappBalpha+/+

value: wildtype


title: EBs_96h_KO_rep1

value: mouse embryoid bodies


title: WES_NORMAL_1

value: normal tissue


title: Bd3-1,control,rep32


title: Bd3-1,drought,rep33

value: drought


title: HSW-15-11 _2

description: Library name: MBFgIsolatesRNA-38


title: WES_TUMOR_15

value: intestinal


title: HSW-15-85 _3

description: Library name: MBFgIsolatesRNA-36


title: EBs_96h_WT_rep2

value: Timepoint 96h


title: HSW-15-11 _1

description: Library name: MBFgIsolatesRNA-37

value: Mycelia


title: WES_TUMOR_14

value: pancreatobiliary

value: IV


title: Bd21,control,rep30

value: leaf


title: Bd21,drought,rep30

value: bulk


title: Bd3-1,drought,rep34


title: WES_TUMOR_13

value: Ampullary carcinoma


title: EBs_96h_WT_rep1


title: HSW-15-85 _2

description: Library name: MBFgIsolatesRNA-35

value: PDA + Streptomycin sulfate


title: Bd3-1,control,rep31

value: control


title: HSW-15-85 _1

description: Library name: MBFgIsolatesRNA-34


title: WES_TUMOR_12

value: Ampulla of Vater  tumor tissue

value: Male

value: II


title: HSW-15-40 _3

description: Library name: MBFgIsolatesRNA-33


title: EBs_48h_KO_rep2

value: IkappBalpha-/-

value: knock-out

value: Timepoint 48h


title: Bd3-1,drought,rep32

value: drought


title: HSW-15-40 _2

description: Library name: MBFgIsolatesRNA-32


title: EBs_48h_KO_rep1

value: mouse embryoid bodies


title: WES_TUMOR_11

value: Female


title: Bd3-1,drought,rep31


title: WES_TUMOR_10

value: I


title: HSW-15-40 _1

description: Library name: MBFgIsolatesRNA-31

value: Mycelia


title: EBs_48h_WT_rep3

value: IkappBalpha+/+

value: wildtype


title: HSW-15-87 _3

description: Library name: MBFgIsolatesRNA-30


title: EBs_48h_WT_rep2


title: WES_TUMOR_9

value: intestinal


title: Bd3-1,control,rep30

value: leaf

value: bulk


title: Bd21,control,rep29

value: control


title: HSW-15-87 _2

description: Library name: MBFgIsolatesRNA-29

value: PDA + Streptomycin sulfate


title: WES_TUMOR_8

value: Ampullary carcinoma

value: Ampulla of Vater  tumor tissue

value: Male


title: EBs_48h_KO_rep3

value: IkappBalpha-/-

value: knock-out


title: EBs_48h_WT_rep1

value: Timepoint 48h


title: WES_TUMOR_7

value: undefined

value: IV


title: HSW-15-87 _1

description: Library name: MBFgIsolatesRNA-28


title: Bd21,control,rep28


title: mESCs_KO_rep3

value: mouse embryonic stem cells

value: Timepoint 0h


title: WES_TUMOR_6

value: II


title: WES_TUMOR_5


title: HSW-15-39 _3

description: Library name: MBFgIsolatesRNA-27

value: Mycelia


title: mESCs_KO_rep2


title: Bd3-1,drought,rep30

value: drought


title: mESCs_KO_rep1


title: Bd21,drought,rep28

value: leaf


title: HSW-15-39 _2

description: Library name: MBFgIsolatesRNA-26


title: Bd3-1,control,rep29

value: bulk


title: WES_TUMOR_3

value: intestinal

value: Female

value: Unclear


title: HSW-15-57 _3

description: Library name: MBFgIsolatesRNA-24

value: PDA + Streptomycin sulfate


title: HSW-15-39 _1

description: Library name: MBFgIsolatesRNA-25


title: WES_TUMOR_4

value: Ampullary carcinoma

value: Ampulla of Vater  tumor tissue

value: Male


title: Bd21,drought,rep29


title: mESCs_WT_rep3

value: IkappBalpha+/+

value: wildtype


title: mESCs_WT_rep2


title: Bd3-1,drought,rep29


title: WES_TUMOR_2

value: IV


title: mESCs_WT_rep1

value: mouse embryonic stem cells


title: HSW-15-57 _2

description: Library name: MBFgIsolatesRNA-23


title: Bd3-1,control,rep28

value: control


title: PC9 EF1a-NKX2-1 100nM osimertinib 33day RNA-seq Rep2

city: Boston

first: Matthew

last: Meyerson

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
NKX2-1_RNAseq_TPM.csv
JLP-R114

data_processing:
Paired-end RNA-seq reads were trimmed using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. RNA-seq reads were mapped to the human reference genome (hg38) using STAR (Dobin et al., 2013) version 2.3.1 with default parameters.
Raw read counts were generated with Rsubread featureCounts against the hg38 refFlat annotation from UCSC—reads were allowed to map to multiple annotations (allowMultiOverlap=T) but we only counted the primary alignment of each read (primaryOnly=T). Significance was assessed using the R package DESeq2. Significantly changing genes were assessed with a Bonferri-corrected p value≤1e-3 and a fold change≥1.5 to determine set of significantly changing genes. Transcripts per million (TPM) were determined from featureCounts raw counts normalized per million total reads.
Assembly: GRCh38
Supplementary files format and content: Transcripts per million normalized reads for the hg38 refFlat annotation.

growth_protocol: Cell lines were cultured in RPMI + 10% Fetal Bovine Serum + 1X PenStrep

extract_protocol:
RNA was extracted from cell pellets stored at -80°C using an RNeasy Mini Kit (Qiagen) with on-column DNase digestion using RNase-Free DNase Set (Qiagen). RNA was eluted in RNase-free ddH2O, and quantified by nanodrop. RNA integrity was determined using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Electrophoresis Bioanalyzer, all RNA samples used for RNA-seq had a RNA integrity number (RIN) > 9.0.
1000-2000µg of RNA was polyA-selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB). Final libraries were quantified using Qubit, pooled, and sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were spinfected with knockdown constructs at day 0, changed over to hard selection (1µg/mL puromycin) on day 1, then reduced to low selection (0.5µg/mL puromycin) on day 4. On day 7 post-infection, cells were harvested for RNA extraction.

value: lung adenocarcinoma


title: Bd21,drought,rep27

first: Jie

last: Yun


title: HSW-15-57 _1

description: Library name: MBFgIsolatesRNA-22

value: Mycelia


title: Bd3-1,control,rep27


title: HSW-15-31 _3

description: Library name: MBFgIsolatesRNA-21


title: PC9 EF1a-NKX2-1 100nM osimertinib 33day RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R113


title: HSW-15-31 _2

description: Library name: MBFgIsolatesRNA-20


title: RNA_TUMOR_15

first: Jesper

last: Andersen

data_processing:
RNAseq reads were trimmed with Trimmomatic 0.36
Reads were alighed to human hg19 genome with STAR v2.3
Reads duplicates arisen from sequencing process were removed with Picard 2.1.1
Read were mapped to gencode.v28lift37 genes annotaion extended with noncoding transcripts annotaion from NONCODEv5 and Mitranscriptome
Htseq 0.6.0 was used to obtain raw read counts
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample with gene biotype description column

extract_protocol:
Isolation of RNA was performed with AllPrep (Qiagen) according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: III


title: PC9 EF1a-GFP 100nM osimertinib 33day RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R112


title: RNA_TUMOR_14

value: pancreatobiliary


title: RNA_TUMOR_13


title: PC9 EF1a-GFP 100nM osimertinib 33day RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R111


title: PC9 EF1a-NKX2-1 100nM osimertinib 10day RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R110


title: Bd3-1,drought,rep27

value: leaf

value: bulk

value: drought


title: Bd3-1,drought,rep28


title: PC9 EF1a-NKX2-1 100nM osimertinib 10day RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R109


title: RNA_TUMOR_12

value: intestinal

value: II


title: WES_TUMOR_1

value: Ampullary carcinoma

value: Female


title: HSW-15-21 _1

description: Library name: MBFgIsolatesRNA-16

value: PDA + Streptomycin sulfate


title: Bd21,drought,rep26


title: RNA_TUMOR_11

value: Ampulla of Vater  tumor tissue


title: HSW-15-21 _2

description: Library name: MBFgIsolatesRNA-17


title: RNA_TUMOR_16

value: undefined

value: Male


title: PC9 EF1a-GFP 100nM osimertinib 10day RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R108


title: HSW-15-31 _1

description: Library name: MBFgIsolatesRNA-19


title: Bd3-1,drought,rep26


title: HSW-15-19 _3

description: Library name: MBFgIsolatesRNA-15


title: HSW-15-19 _2

description: Library name: MBFgIsolatesRNA-14


title: Bd21,control,rep26


title: PC9 EF1a-NKX2-1 100nM osimertinib 24h RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R076


title: HSW-15-21 _3

description: Library name: MBFgIsolatesRNA-18


title: HSW-15-19 _1

description: Library name: MBFgIsolatesRNA-13


title: Bd21,control,rep25


title: RNA_TUMOR_8

value: I


title: RNA_TUMOR_7

value: IV


title: PC9 EF1a-GFP 100nM osimertinib 24h RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R074

value: lung adenocarcinoma


title: Bd21,drought,rep25


title: Bd3-1,control,rep26

value: control


title: RNA_TUMOR_6


title: PC9 EF1a-GFP 100nM osimertinib 24h RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R073


title: Bd21,drought,rep24


title: RNA_TUMOR_5


title: HSW-15-63 _2

description: Library name: MBFgIsolatesRNA-11

value: Mycelia


title: HSW-15-63 _1

description: Library name: MBFgIsolatesRNA-10


title: RNA_TUMOR_10

value: pancreatobiliary


title: HSW-15-27 _3

description: Library name: MBFgIsolatesRNA-09


title: RNA_TUMOR_9


title: PC9 EF1a-NKX2-1 DMSO RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R072


title: Bd3-1,control,rep25

value: leaf


title: RNA_TUMOR_4


title: PC9 EF1a-GFP 100nM osimertinib 10day RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R107


title: PC9 EF1a-NKX2-1 DMSO RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R071


title: Bd3-1,control,rep24

value: bulk


title: RNA_TUMOR_3

value: Unclear


title: HSW-15-27 _2

description: Library name: MBFgIsolatesRNA-08


title: Bd3-1,drought,rep25

value: drought


title: RNA_TUMOR_2

value: intestinal


title: HSW-15-63 _3

description: Library name: MBFgIsolatesRNA-12


title: PC9 EF1a-NKX2-1 100nM osimertinib 24h RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R075


title: PC9 EF1a-GFP DMSO RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R070


title: Bd21,drought,rep23


title: PC9 EF1a-GFP DMSO RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R069


title: HSW-15-3_3

description: Library name: MBFgIsolatesRNA-06


title: HCC78 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R092

value: dCas9-KRAB-MeCP2 sgE764