title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mid_stg12_equiv_stamens, 11w (rep. 1)


title: ATACseq_grh1::degron_Auxin_24h_Rep2

status: Public on Sep 17 2025

type: SRA

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: 3616F16

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were trimmed with Cutadapt v 1.18 using the parameters “-a NCTGTCTCTTATA -A NCTGTCTCTTATA --minimum-length=10 --overlap=1”. The N in the adapter was used to remove one additional nucleotide in every read in order to ensure correct downstream alignment of adapter reads with Bowtie. Trimmed reads were mapped to the C. elegans genome (ce11) using the qAlign function from the R package QuasR (v 1.42.1) with standard parameters which deploys the aligner Bowtie. The fragment size distributions of the individual libraries showed multiple peaks, the short fraction corresponding to transcription factor footprints (<120bp) and long fraction to nucleosomes (>120bp). We thus considered fragments with a read length of less than 120 bp for further analysis. We quantified the number of reads in all the ATAC-seq peaks (obtained from the N2 timecourse, see other series in the same super series) using the function qCount() in the package QuasR. We further performed quantile normalization to correct for non-linear trends in the data, followed by log2 transformation with a pseudocount of 32 (log2(x+32)). In the first replicate of the GRH-1 degron time course we noticed two outlier samples, EtOH_24h and Auxin_25h showing lower correlation to all other samples but high correlation to the each other. These two samples were simultaneously processed together, suggesting a technical batch effect. We corrected for this batch effect, by first calculating the average ATAC-seq intensity profile of those two samples and then subtracting the average profile of the neighboring 4 samples in the time course. This resulted in a batch correction vector, which we then subtracted from the 2 outlier samples to obtain corrected intensities for those 2 samples.
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw ATAC-seq read counts for all ATAC-seq peaks (obtained from the N2 timecourse)
Supplementary files format and content: tab-delimited text file with normalized log2 ATAC-seq read counts for all ATAC-seq peaks  (obtained from the N2 timecourse)

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Synchronized L1 animals were grownat at 20oC and at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Following the addition of treatments, animals were collected every hour (over 12-13 hours), and washed 3 times with M9 befor flash freezing the pellet in liquid N2. Samples were stored at -80 until further processing. Note that in replicate Rep1 ethanol and auxin were added at 21h of development while in Rep2 this was done at 20h.

extract_protocol:
Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Briefly, 7 rounds of douncing (3 times / round) were performed in Omni-ATAC buffer, and nuclei were seperated from worm debry by slow centrifugation. Isolated nuclei were then tagmented according to the Omni-ATAC protocol (Corces et al., 2017, Nat Methods), and DNA isolated using the MinElute PCR purification kit (28004, Qiagen).
Isolated DNA was amplified using NEB Next High-Fidelity PCR Master Mix (M0541S, NEB), and barcoded illumina sequencing primers before Ampure XP bead purification.

tag: strain

tag: genotype

tag: tissue

value: Whole animal

tag: treatment

value: Auxin

tag: time of_treatment

tag: time of_larval_development


title: ATACseq_grh1::degron_Auxin_22h_Rep2

description: Library name: 3616F14


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 21d (rep. 1)

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: root

growth_protocol: All plants were grown on soil, except those used for the collection of early-stage root samples, which were grown on 0.8% plant agar plates, pH 5.8, containing ½ MS and vitamins (Duchefa M0222).

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

tag: cultivar

value: Arabidopsis thaliana (Col-0)

value: root


title: ATACseq_grh1::degron_Auxin_21h_Rep2

description: Library name: 3616F13


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_stg12_equiv_carpels, 11w (rep. 2)

organism: Tarenaya hassleriana

source_name: carpels

value: Tarenaya hassleriana (ES1100)

value: carpels


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 14d (rep. 3)


title: ATACseq_grh1::degron_EtOH_31h_Rep2

description: Library name: 3616F11

value: EtOH


title: 21DIV_KCl_3h_1

city: CABA

first: Damian

last: Refojo

state: CABA

address: Godoy Cruz 2390

country: Argentina

institute: Biomedicine Research Institute of Buenos Aires (IBioBA)

data_processing:
Raw reads were aligned to the Mus musculus genome (version mm10) using STAR(76)
Reads were quantified using End Sequence Analysis Toolkit(77) for 3' RNA libraries.
Differential gene expression analysis was done with edgeR
Libraries were sequenced 2 times to increase coverage. Fastq files were merged and processed together afterwards (we are providing both sequenced runs separately in the each Exp folders)
Assembly: mm10
Supplementary files format and content: ExpA_ESAT_merged.gene.txt and ExpD_ESAT_merged.gene.txt

molecule: polyA RNA

organism: Mus musculus

source_name: forebrain primary neuronal cultures

growth_protocol: Neurons were dissected from embryonic day 16 to 17.5 (E16 - E17.5) CD1 embryos of mixed sex. Culture preparation was performed as previously described (Dotti, Sulluvan, and Banker 1988). Briefly, forebrain (cortex and hippocampal) from CD1 mouse embryos were dissected and a neuronal suspension was prepared through Trypsin digestion and mechanical disruption of the tissue. Neurons were plated in 24 multi-well plates at a density of 80cells/mm2 (150.000 cells per well) and maintained in Neurobasal-A media (ThermoFisher) with 2% B27 and 0.5 mMGlutaMAX-I (ThermoFisher) at 37 °C and 5% CO2. CD1 mice were provided by our Specific Pathogen Free Animal Facility. All procedures were approved by National Department of Animal Care and Health (SENASA, Argentina) and were following the general guidelines of the National Institute of Health (NIH, USA).

extract_protocol:
RNA was extracted using the RNeasy mini kit with in-column DNase treatment
30ng of RNA was used as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol

treatment_protocol: Neurons were used between 19–23 DIV or at DIV7 when indicated. Stimulations were performed in neuronal growing media adding drugs at indicated final concentration.  No previous silencing was performed in any of the stimulation protocols. Massive membrane depolarization was achieved by applying 55 mM extracellular potassium chloride (KCl). To induce synaptic stimulation, we triggered neuronal activity by treating neurons with 50uM Bicuculline (Sigma). As indicated in the DIV7 - 21 DIV comparison, we also added 2.5mM M 4-Aminopyridine (Sigma) to the 50uM Bicuculline treatment. Synaptic rebound was induced performing TTX withdrawal was performed (Rutherford et al., 1997; Saha et al., 2011). Cultures were treated with 1 uM TTX (Tocris) for 48hs, and the TTX was then washed out through seven exchanges of 1 ml of medium with fresh control medium. Control neurons were washed identically and processed in parallel. Results are shown in comparison to TTX control situation (silenced neurons TTX, 48hs). Each stimulation was sustained until indicated time.

value: forebrain primary neuronal cultures

value: CD1 mice

value: KCl 180min


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 14d (rep. 2)


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_stg12_equiv_carpels, 11w (rep. 1)


title: ATACseq_grh1::degron_EtOH_30h_Rep2

description: Library name: 3616F10


title: 21DIV_Bicuculline_3h_3

value: BIC 180min


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 14d (rep. 1)


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mature_pollen, 11w (rep. 3)

source_name: pollen

value: pollen


title: 21DIV_TTXwithdrawal_3h_1

value: TTXw 180min


title: ATACseq_grh1::degron_EtOH_29h_Rep2

description: Library name: 3616F9


title: 21DIV_Bicuculline_3h_2


title: ATACseq_grh1::degron_Auxin_23h_Rep2

description: Library name: 3616F15


title: ATACseq_grh1::degron_EtOH_28h_Rep2

description: Library name: 3616F8


title: 21DIV_KCl_3h_2


title: 21DIV_TTXwithdrawal_45min_1

value: TTXw 45min


title: 21DIV_TTXwithdrawal_45min_3


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mature_pollen, 11w (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 7d (rep. 3)


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_stg12_equiv_carpels, 11w (rep. 3)


title: 21DIV_BasalTTX_0min_4

value: TTX 48h


title: ATACseq_grh1::degron_EtOH_27h_Rep2

description: Library name: 3616F7


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 7d (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 5d (rep. 3)


title: RNA-Seq of Tarenaya hassleriana (ES1100): flower_stg12, 11w (rep. 2)

source_name: flowers

value: flowers


title: 21DIV_Basal_0min_1


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 5d (rep. 2)


title: ATACseq_grh1::degron_EtOH_25h_Rep2

description: Library name: 3616F5


title: RNA-Seq of Tarenaya hassleriana (ES1100): flower_stg12, 11w (rep. 1)


title: 21DIV_BasalTTX_0min_3


title: ATACseq_grh1::degron_EtOH_24h_Rep2

description: Library name: 3616F4


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 5d (rep. 1)


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mature_pollen, 11w (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 7d (rep. 2)


title: 21DIV_BasalTTX_0min_2


title: ATACseq_grh1::degron_EtOH_23h_Rep2

description: Library name: 3616F3


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_maturation_zone, 5d (rep. 3)


title: 21DIV_Basal_0min_2


title: 21DIV_BasalTTX_0min_1


title: RNA-Seq of Tarenaya hassleriana (ES1100): flower_stg12, 11w (rep. 3)


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_inflorescence, 11w (rep. 2)

source_name: inflorescence apex

value: inflorescence apex


title: 23DIV_4APBic_3h_3


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_maturation_zone, 5d (rep. 1)


title: ATACseq_grh1::degron_EtOH_21h_Rep2

description: Library name: 3616F1

value: Whole animal


title: ATACseq_grh1::degron_EtOH_26h_Rep2

description: Library name: 3616F6


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_vegetative, 11d (rep. 2)

source_name: vegetative apex

value: vegetative apex


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_maturation_zone, 5d (rep. 2)

value: Arabidopsis thaliana (Col-0)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_root_tip, 5d (rep. 2)

value: root


title: 23DIV_4APBic_15min_2

value: BIC 15min


title: ATACseq_grh1::degron_EtOH_22h_Rep2

description: Library name: 3616F2


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_inflorescence, 11w (rep. 1)

value: Tarenaya hassleriana (ES1100)


title: ATACseq_grh1::degron_Auxin_30h_Rep1

description: Library name: 3536F10

value: Auxin


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_vegetative, 11d (rep. 1)


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_inflorescence, 11w (rep. 3)


title: RNA-Seq of Tarenaya hassleriana (ES1100): leaf_1+2, 11d (rep. 3)

source_name: leaf

value: leaf


title: 23DIV_KCl_3h_3

value: forebrain primary neuronal cultures

value: CD1 mice


title: ATACseq_grh1::degron_Auxin_28h_Rep1

description: Library name: 3536F8


title: RNA-Seq of Tarenaya hassleriana (ES1100): leaf_1+2, 11d (rep. 2)


title: 23DIV_4APBic_15min_1


title: RNA-Seq of Tarenaya hassleriana (ES1100): apex_vegetative, 11d (rep. 3)


title: 23DIV_KCl_3h_1

value: KCl 180min


title: RNA-Seq of Tarenaya hassleriana (ES1100): leaf_1+2, 11d (rep. 1)


title: ATACseq_grh1::degron_Auxin_31h_Rep1

description: Library name: 3536F11


title: ATACseq_grh1::degron_Auxin_26h_Rep1

description: Library name: 3536F6


title: 23DIV_KCl_3h_2


title: ATACseq_grh1::degron_Auxin_29h_Rep1

description: Library name: 3536F9


title: 23DIV_4APBic_3h_2

value: BIC 180min


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_root_tip, 5d (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_root_tip, 5d (rep. 3)


title: RNA-Seq of Tarenaya hassleriana (ES1100): hypocotyl, 11d (rep. 3)

source_name: hypocotyl

value: hypocotyl


title: ATACseq_grh1::degron_Auxin_25h_Rep1

description: Library name: 3536F5


title: 23DIV_KCl_15min_3

value: KCl 15min


title: RNA-Seq of Tarenaya hassleriana (ES1100): hypocotyl, 11d (rep. 1)


title: 23DIV_KCl_15min_1


title: RNA-Seq of Tarenaya hassleriana (ES1100): hypocotyl, 11d (rep. 2)


title: 23DIV_KCl_15min_2


title: ATACseq_grh1::degron_Auxin_24h_Rep1

description: Library name: 3536F4


title: ATACseq_grh1::degron_Auxin_27h_Rep1

description: Library name: 3536F7


title: Piezo1 silenced 2

type: RNA

city: Firenze

first: Giulia

last: Carangelo

address: Viale Pieraccini 6

country: Italy

institute: University of Florence

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix; Thermo Fisher Scientific, Inc.).

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters.

data_processing: Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.

label: biotin

organism: Homo sapiens

source_name: cell culture patient2

label_protocol: With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled.

growth_protocol: 3 primary cell culture were transfected with LNA scramble or LNA Piezo1 Gapmer antisense oligonucluotide.

extract_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip WT Plus Kit (Affymetrix; Thermo Fisher Scientific, Inc.).

value: Piezo1 silenced 2


title: RNA-Seq of Tarenaya hassleriana (ES1100): root_whole_root, 5d (rep. 3)


title: scramble 3

source_name: cell culture patient3

treatment_protocol: Biotin-labeled cDNA targets were synthesized

value: scramble 3


title: ATACseq_grh1::degron_Auxin_23h_Rep1

description: Library name: 3536F3


title: 23DIV_Basal_0min_3


title: Piezo1 silenced 3

value: Piezo1 silenced 3


title: sip53-2

city: Guangzhou

first: Haoyu

last: Liang

address: Sun yat-sen Cancer center

country: China

institute: Sun yat-sen Cancer center

data_processing:
Data processing for RNA-seq involves several critical steps to convert raw sequencing reads into meaningful transcriptomic insights. First, raw sequencing data (usually in FASTQ format) are quality-controlled using tools like FastQC to assess read quality, identify potential biases, and remove low-quality reads. After that, reads are trimmed for adapter sequences and low-quality bases using tools like Trimmomatic or Cutadapt. Next, the clean reads are aligned to a reference genome or transcriptome using aligners like STAR, HISAT2, or TopHat. Alternatively, for de novo RNA-seq, reads can be assembled without a reference genome using tools like Trinity. Once the reads are aligned or assembled, quantification of gene expression is performed, typically using tools such as HTSeq, featureCounts, or Salmon, which count the number of reads mapped to each gene or transcript. Differential expression analysis is then conducted using software like DESeq2 or EdgeR to identify genes or transcripts with significant expression changes between conditions. Finally, the processed data is visualized through tools like volcano plots, heatmaps, or principal component analysis (PCA) to interpret and present the biological findings.
Assembly: mm10
Supplementary files format and content: gene_expression.xls

source_name: Ovarian clear cell carcinoma

extract_protocol:
RNA is extracted from the sample using a reagent like TRIzol. The quality and quantity of RNA are assessed using a spectrophotometer or a bioanalyzer. Next, the RNA is typically treated with DNase to remove any contaminating genomic DNA. Poly(A) RNA is then enriched, often using oligo(dT) beads, to isolate mRNA from the total RNA pool, although ribosomal RNA (rRNA) depletion methods can also be used. The mRNA is then reverse transcribed into cDNA using a reverse transcriptase enzyme. The cDNA is fragmented to a suitable size, and adapters are ligated to the fragments to facilitate amplification and sequencing. The library is amplified by PCR, and the resulting products are sequenced using high-throughput sequencing platforms (e.g., Illumina, PacBio, or Oxford Nanopore). The data are then analyzed to quantify gene expression, detect novel transcripts, and explore alternative splicing events.
After amplification, the library is typically size-selected to ensure a uniform fragment size distribution, and the quality and quantity of the library are assessed using techniques such as gel electrophoresis or a Bioanalyzer. The final library is ready for sequencing on a high-throughput platform.

value: Ovarian clear cell carcinoma

tag: cell line

tag: cell type

value: Ovarian clear cell carcinoma cancer cell

value: p53 knock down


title: 23DIV_Basal_0min_2


title: RNA-Seq of Tarenaya hassleriana (ES1100): root_whole_root, 5d (rep. 2)

value: root


title: sip53-1


title: RNA-Seq of Tarenaya hassleriana (ES1100): root_whole_root, 5d (rep. 1)


title: ATACseq_grh1::degron_EtOH_31h_Rep1

description: Library name: 3536F24

value: Whole animal

value: EtOH


title: 23DIV_Basal_0min_1


title: ATACseq_grh1::degron_EtOH_30h_Rep1

description: Library name: 3536F23


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_mid_stg12_stamens, 6w/7w/20d (rep. 3)

organism: Capsella rubella

source_name: stamens

value: Capsella rubella (Monte Gargano)

value: stamens


title: scramble 2

value: scramble 2


title: siGYS1-2

value: GYS1 knock down


title: Scramble 1

source_name: cell culture patient1

value: Scramble 1


title: siGYS1-1


title: 7DIV_4APBic_3h_3

value: forebrain primary neuronal cultures

value: CD1 mice

value: BIC 180min


title: Piezo1 silenced 1

value: Piezo1 silenced 1


title: ATACseq_grh1::degron_EtOH_29h_Rep1

description: Library name: 3536F22


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_mid_stg12_stamens, 6w/7w/20d (rep. 2)


title: 7DIV_4APBic_3h_2


title: ATACseq_grh1::degron_EtOH_28h_Rep1

description: Library name: 3536F21


title: NC-2

value: WT


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_mid_stg12_stamens, 6w/7w/20d (rep. 1)


title: ATACseq_grh1::degron_Auxin_22h_Rep1

description: Library name: 3536F2

value: Auxin


title: ATACseq_grh1::degron_EtOH_27h_Rep1

description: Library name: 3536F20


title: 7DIV_4APBic_3h_1


title: NC-1

value: Ovarian clear cell carcinoma


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_early_stg12_carpels, 6w/7w/21d (rep. 3)

value: carpels


title: 7DIV_4APBic_15min_3

value: BIC 15min


title: ATACseq_grh1::degron_EtOH_26h_Rep1

description: Library name: 3536F19


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_early_stg12_carpels, 6w/7w/21d (rep. 2)


title: 7DIV_4APBic_15min_2


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organ_early_stg12_carpels, 6w/7w/21d (rep. 1)


title: WT7_S16

city: Minneapolis

first: Preethy

last: Parthiban

email: parth034@umn.edu, xrevelo@umn.edu

state: MN

address: 2231 6th St SE

department: Integrative Biology and Physiology

country: USA

institute: University of Minnesota

description: Library name: WT7_S16

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed were determined using CLCGWB (edgeR)  software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: mouse (GRCm38)
Supplementary files format and content: Revelo033_raw_counts.txt contain raw counts

source_name: Heart

extract_protocol:
Total RNA was extracted from cardiac tissue using the RNeasy Plus Mini kit (Qiagen 74104)
Libraries were constructed by UMN Genomic Center

value: Heart

value: Wildtype

value: TAC

tag: time

value: 1 week


title: WT6_S15

description: Library name: WT6_S15


title: 7DIV_4APBic_15min_1


title: ATACseq_grh1::degron_EtOH_25h_Rep1

description: Library name: 3536F18

value: Whole animal

value: EtOH


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organs_mature_pollen, 6w/7w/22d (rep. 3)

value: Capsella rubella (Monte Gargano)

value: pollen


title: ATACseq_grh1::degron_EtOH_24h_Rep1

description: Library name: 3535F17


title: ATACseq_grh1::degron_EtOH_23h_Rep1

description: Library name: 3535F16


title: WT4_S14

description: Library name: WT4_S14


title: 7DIV_KCl_3h_2

value: forebrain primary neuronal cultures

value: KCl 180min


title: WT3_S13

description: Library name: WT3_S13


title: ATACseq_grh1::degron_EtOH_22h_Rep1

description: Library name: 3536F15


title: WT2_S12

description: Library name: WT2_S12


title: 7DIV_KCl_3h_1

value: CD1 mice


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organs_mature_pollen, 6w/7w/22d (rep. 1)


title: WT1_S11

description: Library name: WT1_S11


title: ATACseq_grh1::degron_Untreated_21h_Rep1

description: Library name: 3536F1

value: Untreated


title: 7DIV_KCl_15min_3

value: KCl 15min


title: RNA-Seq of Capsella rubella (Monte Gargano): flower_stg12, 6w/7w/20d (rep. 3)

value: flowers


title: WS2_S10

description: Library name: WS2_S10

value: Sham


title: Red_3

city: Los Angeles

first: Sean

middle: Patrick

last: Curran

state: CA

address: 3715 McClintock Ave #350

department: Geronotology

institute: University of Southern California

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining ploy-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using DESeq2 R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package
Assembly: ce11
Supplementary files format and content: csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package

source_name: AWB & AWC Neurons

growth_protocol: OP50-raised and Methylobacterium-raised  WT and odr-1lf worms were egg prepped and allowed to synchronize overnight into L1 population. Worms were dropped on OP50 or Methylobacterium and raised until Day 1 adult (72 hours later, neuronal RNAseq).

extract_protocol:
Zymo Direct-zol RNA Miniprep kit (Cat. #R2052) was used. In brief, worms were homogenized in TRI reagent and then run through the kit. Sample concentration was tested via qubit and 1 ug/sample was sent for sequencing.
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: At Day 1 Adult, worms were washed off plates, sorted for RFP-positive cells and collected for RNA processing.

value: AWB & AWC Neurons

value: Methylobacterium/Red


title: RNA-Seq of Capsella rubella (Monte Gargano): flower_stg12, 6w/7w/20d (rep. 2)


title: 7DIV_KCl_15min_2


title: Red_2


title: WS1_S9

description: Library name: WS1_S9

value: Heart


title: RNA-Seq of Capsella rubella (Monte Gargano): flower_stg12, 6w/7w/20d (rep. 1)


title: Red_1


title: 7DIV_KCl_15min_1


title: OP50_3

value: E. coli/OP50


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_inflorescence, 6w/7w/17d (rep. 3)

value: inflorescence apex


title: KT5_S6

description: Library name: KT5_S6

value: CCL24 KO

value: TAC

value: 1 week


title: 7DIV_Basal_0min_4


title: 7DIV_KCl_3h_3


title: RNA-Seq of Capsella rubella (Monte Gargano): floral_organs_mature_pollen, 6w/7w/22d (rep. 2)

value: Capsella rubella (Monte Gargano)


title: 7DIV_Basal_0min_3


title: KT4_S5

description: Library name: KT4_S5


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_inflorescence, 6w/7w/17d (rep. 2)


title: OP50_2


title: OP50_1


title: ATACseq_grh1::degron_Auxin_28h_Rep2

description: Library name: 3616F20

source_name: Whole animal

value: Whole animal

value: Auxin


title: KT2_S4

description: Library name: KT2_S4


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_inflorescence, 6w/7w/17d (rep. 1)


title: 7DIV_Basal_0min_2

value: forebrain primary neuronal cultures


title: KT1_S3

description: Library name: KT1_S3


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_vegetative, 7d (rep. 3)

value: vegetative apex


title: Male mouse, scRNAseq

description: C57Bl/6, 10x Genomics

library_source: transcriptomic single cell

data_processing:
Basecall performed with cellranger mkfastq v6.1.2
Single cell feature counts performed with cellranger count v6.1.2
Reference genome alignment performed with STAR v2.7.5a_2020-06-29
Assembly: mm10
Supplementary files format and content: All tab-separated values files

source_name: kidney

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions
Libraries were sequenced on an Illumina NextSeq500 (Illumina Inc., San Diego, CA).

treatment_protocol: Mice received doxycycline induction at 19 days of age and sacrified at 30 days of age

value: kidney

value: Total cells from glomerulus kidney

value: healthy


title: odr-1lf_Red_4

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining ploy-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using DESeq2 R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package
Assembly: ce11
Supplementary files format and content: csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package
Supplementary files format and content: MD5_L4.txt is MD5 checksums for whole animal RNAseq.

source_name: Whole Animal

growth_protocol: OP50-raised and Methylobacterium-raised  WT and odr-1lf worms were egg prepped and allowed to synchronize overnight into L1 population. Worms were dropped on OP50 or Methylobacterium and raised until L4 (48 hours later, whole animal RNAseq).

treatment_protocol: At L4, worms were washed off plates and collected for RNA processing.

value: Whole Animal


title: KS2_S2

description: Library name: KS2_S2

value: Sham


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_vegetative, 7d (rep. 2)


title: KS1_S1

description: Library name: KS1_S1


title: Female mouse, scRNAseq

description: C57Bl/6, 10x Genomics


title: RNA-Seq of Capsella rubella (Monte Gargano): apex_vegetative, 7d (rep. 1)


title: odr-1lf_Red_2

value: Methylobacterium/Red


title: FRC_FRC_CCM_96h_treated_2

first: Angela

last: Riedel

state: Bavaria

address: Josef-Schneider-Straße 2

department: Mildred-Scheel-Nachwuchszentrum (MSNZ) für Krebsforschung

institute: University Hospital Würzburg

description:
FRC_treated_with_CCM_2
FRC_control_library

data_processing:
Raw BCL files were de-multiplexed and corresponding FASTQ files for gene expresion libraries were aligned  with the Subread package in R to generate the expression matrix. For Alignment mouse genome mm10  was used (mm10).
The differential analysis was performed using DEseq2 R package (1.32.0).To exclude low quality genes, genes that were detected in less than 2 samples and those that had less than 10 reads were removed
Assembly: mm10
Supplementary files format and content: comma-separated files of raw counts for each sample
Supplementary files format and content: comma-separated files of filtered counts  for each sample

source_name: FRCs

growth_protocol: Cells were grown  in RPMI-1640 supplemented with 10 % fetal bovine serum  (FBS,Sigma-Aldrich, #F7524), 100 U/ml penicillin-streptomycin (Gibco, #15140-122), 10 mM HEPES buffer (#) and 15 µM ß-mercaptoethanol. Condition media was done with 70% cells for 24h in plain RPMI.

extract_protocol:
Total RNA was isolated for each sample using Rneasy micro kit (QIAGEN) according to the manufacturer instructions
Libraries were processed using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB #E7490)  as recommended by the manufacturer ,Poly A mRNA was isolated from 500 ng of total RNA by means of NEBNext Poly(A) mRNA Magnetic Isolation Module. Subsequently, the isolated poly mRNA was fragmented with the help of temperature and the preparation continued following the recommendation of the manufacturer. The quantity and the quality of the libraries were assessed using Bioanalyzer High Sensitivity DNA Analysis. Finally, The libraries were sequenced using Illumina NextSeq500

treatment_protocol: Fibroblastic reticular cells (cell line) were treated for 96h (refreshing media every 48h) with supplemented (1% P/S and 2% FBS) conditioned media (CM) from either control cells (CCM, FRC cell line) or tumor cells (TCM, 4T1 and 67NR cell lines)

value: FRCs

value: CCM (FRC)


title: RNA-Seq of Capsella rubella (Monte Gargano): leaf_1+2, 7d (rep. 3)

value: leaf


title: FRC_67NR_TCM_96h_treated_2

description:
FRC_treated_with_67NR_TCM_2
FRC_67NR_CM_library

value: TCM (67NR)


title: Region_2_0038556_Uninvolved

type: other

city: Stanford

first: Benjamin

last: Pham

address: 257 Campus Drive

institute: Stanford University

data_processing: Custom gene probes were added to tissue samples to hybridize with target RNA and then stained to perform cell segmentation. Samples are then run on a Xenium Analyzer with performs fluorescent probe hybridization and imaging to identify the RNA within each cell of a tissue.

molecule: other

source_name: Normal Bowel

extract_protocol: We harvested 1cm-thick wedge from 5 intestinal strictures and 3 normal bowel samples.   The sample was placed in a 1.5cm x 1.5cm block (TissueTek) with pre-chilled OCT and processed according to the Xenium In Situ Tissue Preparation Guide by 10X Genomics. Briefly, we flash froze tissue samples in OCT using a Thermo Scientific Thermo-Flask benchtop container filled with liquid nitrogen and a small, round, metal bowel with 1-inch height worth of 2-methylbutane. A pair of needle-drivers was used to maneuver the 2-methylbutane bowl in and out of the Thermo-Flask. The OCT block was placed in the 2-methylbutane bowl and lowered into the liquid nitrogen until the tissue was completely frozen. The tissue was then placed on dry ice and transferred to a -80 freezer. Tissues were cyrosectioned at -20C onto Xenium slide with an area of 12mm x 24mm.

value: Small Intestine


title: odr-1lf_Red_1


title: RNA-Seq of Capsella rubella (Monte Gargano): leaf_1+2, 7d (rep. 2)


title: FRC_4T1_TCM_96h_treated_2

description:
FRC_treated_with_4T1_TCM_2
FRC_4T1_CM_library

value: TCM (4T1)


title: Region_1_0038556_Stricture

source_name: Intestinal Stricture


title: odr-1lf_OP50_4

value: E. coli/OP50


title: odr-1lf_OP50_3


title: FRC_FRC_CCM_96h_treated_1

description:
FRC_treated_with_CCM_1
FRC_control_library


title: RNA-Seq of Capsella rubella (Monte Gargano): leaf_1+2, 7d (rep. 1)

value: Capsella rubella (Monte Gargano)


title: Region_2_0038555_Stricture


title: Region_1_0038438_Stricture


title: Region_2_0038438_Uninvolved


title: Region_1_0038555_Stricture


title: RNA-Seq of Capsella rubella (Monte Gargano): hypocotyl, 9d (rep. 1)

value: hypocotyl


title: EpiChromo_Screen_maintenance_unsorted_rep2

city: Boston

first: Harleen

last: Saini

state: MA

address: 240 Longwood Avenue

institute: Harvard Medical School

description:
EpiChromo_Screen_maintenance_Gene_Summary.txt
EpiChromo_Screen_maintenance_counts.txt

data_processing:
Guide sequences were extracted from the raw sequencing reads with a modified version of the Python script “count_spacers.py” (Joung et al., 2017) using a ‘‘CGAAACACC’’ search prefix, and a counts matrix was generated in each sample. Next, counts files of eGFP-positive sorted cells and of unsorted population of cells subject to comparison were input into MAGeCK algorithm (version 0.5.9.4) (Li et al., 2014) and log2 fold changes (LFCs) and P-values (negative binomial distribution) were calculated for each sgRNA using the ‘mageck test –k’ command with default settings. MAGeCK uses a modified robust ranking aggregation (α-RRA) algorithm to calculate gene level P-values and the Benjamini-Hochberg procedure to calculate gene level false discovery rate FDR values (Li et al., 2014; Wang et al., 2019).
Assembly: GRCm38/mm10
Supplementary files format and content: Two sets of tab delimited tables for the CRISPR-Cas9 Screen are provided. Filenames with the tag "Gene_Summary" include MaGECK output files of gene-level analysis and filenames with the tag "counts" contain non-normalized read counts for each sgRNA used as input for MaGECK analysis.
Library strategy: CRISPR Screen

growth_protocol: E14TG2a mES cells (ATCC, #CRL-1821) were cultured on 0.1% gelatin-coated (Sigma, #G1890) plates in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS) (Gibco, #10437), 1% MEM non-essential amino acid (Gibco, #11140), 2 mM Glutamine (Gibco, #25030081), 100 μM β-mercaptoethanol (Sigma, #63689), 10 U/ml penicillin/streptomycin (Gibco, #15140), 1,000 U/ml LIF (Stemcell, #78056) at 37 °C with 5% CO2

extract_protocol: Cell pellets from eGFP sorted and unsorted cells were treated with proteinase K and DNAse-free RNase A in lysis buffer (50 mM KCl, 10 mM Tris-HCl (pH8.3), 2.5 mM MgCl2-6 H2O, 0.45% NP-40, 0.45% Tween-20) and genomic DNA (gDNA) was initially purified using phenol/chloroform/isoamyl alcohol and then ethanol precipitated. PCR of gDNA was performed to attach sequencing adaptors and barcode samples. gDNA of each sample was divided into multiple 50 μl reactions containing a maximum of 2.5 μg gDNA per reaction. For each PCR reaction we used: 0.75 μl of ExTaq DNA polymerase (Clontech), 5 μl of (10x) ExTaq buffer, 4 μl of dNTPs provided with the enzyme, 2.5 μl of P5 stagger primer mix (stock at 10 μM) and 2.5 μl of P7 uniquely barcoded primer (stock at 10 μM). PCR cycling conditions were an initial 3 min at 95 °C; followed by 30 s at 95 °C, 30 s at 53 °C, 30 s at 72 °C, for 23 cycles; and a final 10 min extension at 72 °C. PCR products for each sample were pooled, electrophoresed in an agarose gel, purified (NucleoSpin® Extract II) and sequenced on an Illumina NextSeq 500

value: Embryonic stem cells


title: RNA-Seq of Capsella rubella (Monte Gargano): root_whole_root, 4d (rep. 3)

source_name: root

value: root


title: odr-1lf_OP50_2


title: FRC_67NR_TCM_96h_treated_1

description:
FRC_treated_with_67NR_TCM_1
FRC_67NR_CM_library


title: RNA-Seq of Capsella rubella (Monte Gargano): hypocotyl, 9d (rep. 2)


title: FRC_4T1_TCM_96h_treated_1

description:
FRC_treated_with_4T1_TCM_1
FRC_4T1_CM_library


title: Region_1_0038414_Stricture


title: WT_Red_2

value: WT


title: odr-1lf_OP50_1


title: WT_Red_1


title: EpiChromo_Screen_maintenance_eGFP+_rep1


title: WT_Red_4


title: Cfra_H3K4me3_rep2

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
All ChIP-seq data was analysed using fastp to trim the reads, and these were mapped to the genomes using bowtie2, allowing a maximum insert size of 2000 base pairs (-I 2000). Duplicate reads were removed using Sambamba. DeepTools2 was used to generate bigwig files and to visualise epigenomic data, as well as Integrative Genome Viewer.
Assembly: Creolimax fragrantissima assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Spizellomyces punctatus: GCF_000182565.1, Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: GCF_000004985.1
Supplementary files format and content: ChIP-seq bigwig files were generated with DeepTools2 using the bamCoverage tool (bamCoverage -bs 10 --normalizeUsing CPM -p $cores -b "$prefix".dedup.bam -o "$prefix".bigwig)

organism: Creolimax fragrantissima

source_name: microorganism

growth_protocol:
Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C.
Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C. Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034. Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).

extract_protocol:
Fixed cell pellets are treated with 2 ul of 3%SDS, to achieve a final concentration of 0.5% SDS. Cells are thoroughly re-suspended and lysed on ice for 10 min. Lysates are transferred into 0.1 ml Bioruptor Microtubes (Diagenode C30010015, Liège, Belgium) and the chromatin was sheared using an NGS Bioruptor Sonicator (Diagenode) at High Intensity and cycles of 30'' ON/30'' OFF.
100 ng chromatin per species was pooled per ChIP. Pooled chromatin was incubated at 4°C for 12−14 h with rotation with 2.5 µg anti-H3K27ac (Abcam, ab4729) or  2.5 µg anti-H3K4me3 (Millipore, 07-473). Immunoprecipitated complexes were captured using a mix of Protein A (16-661, Sigma-Aldrich) and Protein G magnetic beads (16-662, Sigma-Aldrich), washed, and reverse crosslinked for 30 min at 55°C followed by an hour at 68°C. Immunoprecipitated DNA was purified using SPRI beads (A63881, Beckman Coulter). The NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) was used to produce the resulting ChIP libraries according to the manufacturer's protocol.

treatment_protocol: No treatments were performed.

value: Axenic culture

tag: library type

value: ChIP-seq with anti-H3K4me3 (Millipore, 07-473)

value: 14 days culture

value: microorganism


title: odr-1lf_Red_3

value: Whole Animal

value: Methylobacterium/Red


title: Region_2_0038414_Uninvolved


title: RNA-Seq of Capsella rubella (Monte Gargano): hypocotyl, 9d (rep. 3)


title: EpiChromo_Screen_maintenance_unsorted_rep1


title: RNA-Seq of Capsella rubella (Monte Gargano): root_whole_root, 4d (rep. 2)


title: EpiChromo_Screen_maintenance_eGFP+_rep2


title: ∆scpB IP

city: Ecublens VD

first: Hon-Wing

last: Liu

address: Le Biophore, CH-1015 Lausanne

institute: Université de Lausanne

description:
Library name: 60B1_Del_IP
60B_APR_IP.txt

data_processing:
Sequencing data from ChIP and input samples were mapped and sorted (by coordinate) to the Bsu reference genome NC_000964 (centered on its first coordinate) using Bowtie2 (sensitive settings) and samtools sort respectively on the Galaxy project website (https://usegalaxy.org/). Reads were filtered for mapping quality (MAPQ) greater than 10, reduced to bins of 250 bp, and normalized for total read count in SeqMonk. The data were exported and visualized in Graphpad Prism 10.
Assembly: NC_000964 (1A700)
Supplementary files format and content: Read Count Quantitation and generation of Annotated Probe Report (APR) in .txt format with SeqMonk (used All Reads, Correct for total read count, Correcct for Milion Reads)

organism: Bacillus subtilis

growth_protocol: Bacillus subtilis cells were grown in 1x SMM minimal media at 37C until exponential phase.

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using a Bandelin Sonopuls HD2070. DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp.
DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. 20-30 million sequence reads were obtained on a NovaSeq 6000 system with 150-bp read length

value: 1A700, specR::scpA del(scpB), trpC2


title: EpiChromo_Screen_establishment_eGFP+_rep2

description:
EpiChromo_Screen_establishment_Gene_Summary.txt
EpiChromo_Screen_establishment_counts.txt


title: Smc(R583A, R643A, R645A) Input

description:
Library name: 60B1_3A_INP
60B_APR_Input.txt

value: 1A700, smc(R583A, R643A, R645A) ftsY::ermB, trpC2


title: WT Input

description:
Library name: 60B1_WT_INP
60B_APR_Input.txt

value: 1A700, smc ftsY::ermB, trpC2


title: Smc(R583A, R643A, R645A) IP

description:
Library name: 60B1_3A_IP
60B_APR_IP.txt


title: EpiChromo_Screen_establishment_unsorted_rep2


title: WT IP

description:
Library name: 60B1_WT_IP
60B_APR_IP.txt


title: ΔwbbM in meropenem sample1

status: Public on Sep 16 2025

city: Beijing

first: Jiangqing

last: Huang

address: No 3, 1st Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

description:
Library name: ΔwbbM-MEM-1
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM in meropenem

data_processing:
Initial quantification was performed using Qubit2.0 Fluorometer, diluting the library to 1.5ng/ul, followed by an Agilent 2100 bioanalyzer for the insert size of the library.
After qualified library check, different libraries are pooled according to the requirements of effective concentration and target data volume for Illumina sequencing. The basic principle of Sequencing is Sequencing by Synthesis.
Fastq software was used for quality control analysis of the sequenced data.
Bowtie2 software was used to conduct genomic localization analysis of the filtered sequencing columns.
Subread software was used to count the number of reads covered by each gene (including new predicted genes) from inception to termination.
Assembly: Reference genome of Klebsiella NK01067 strain (accession number: GCA_023573585.1).
Supplementary files format and content: gene_fpkm.txt

organism: Klebsiella pneumoniae

source_name: bacterial cell

growth_protocol: Strains (including NK01067 and its ΔwbbM mutant) were cultured at 37°C condition and routinely cultured in lysogeny broth (LB), or on LB with 8 μg/L meropenem was used for exposure.

extract_protocol:
The RNA of strains was extracted using the High Purity RNA Extraction Kit (Qiagen, China) according to manufactured protocol. Then agarose gel electrophoresis and Nanodrop were performed to verify the RNA content and concentration, respectively.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit follow ing manufacturer's protocols.

treatment_protocol: No application.

value: {delta}wbbM

value: bacterial cell

value: meropenem


title: ΔwbbM in meropenem sample3

description:
Library name: ΔwbbM-MEM-3
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM in meropenem


title: Cfra_H3K4me3_rep1


title: ΔwbbM sample3

description:
Library name: ΔwbbM-3
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM

value: control


title: NK01067 in meropenem sample2

description:
Library name: NK01067-MEM-2
RNA-seq of Klebsiella pneumoniae NK01067 in meropenem


title: ∆scpB Input

description:
Library name: 60B1_Del_INP
60B_APR_Input.txt


title: WT_Red_3


title: EpiChromo_Screen_establishment_unsorted_rep1


title: Cfra_H3K27ac_rep1

value: ChIP-seq with anti-H3K27ac (Abcam, ab4729)


title: WT_OP50_3

value: E. coli/OP50


title: NK01067 sample3

description:
Library name: NK01067-3
RNA-seq of Klebsiella pneumoniae NK01067


title: WT_OP50_2


title: Cfra_H3K27ac_rep2


title: NK01067 sample1

description:
Library name: NK01067-1
RNA-seq of Klebsiella pneumoniae NK01067


title: RNA-Seq of Capsella rubella (Monte Gargano): root_whole_root, 4d (rep. 1)

value: Capsella rubella (Monte Gargano)

value: root


title: EpiChromo_Screen_establishment_eGFP+_rep1

value: Embryonic stem cells


title: WT_OP50_1

value: WT


title: PT8, ADT

city: Taoyuan

first: Wei-Ting

last: Ku

address: No. 259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

description:
Library name: PT8_ADT
10x Genomics

data_processing:
FASTQ files were processed with Cell Ranger (10X Genomics, v7.0.1) using GRCh38 as the reference genome to generate gene-barcode matrices.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Output file. matrix.mtx.gz: sparse matrix of gene expression values; barcodes.tsv.gz: list of cell barcodes; features.tsv.gz: gene annotations corresponding to rows of the matrix
Supplementary files format and content: Cell Ranger Output file. clonotypes.csv; filtered_contig_annotations.csv
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Single-cell suspensions were obtained from tumor, non-tumor, and blood samples. Tumor tissues were digested enzymatically and filtered; PBMCs were isolated by Ficoll density gradient centrifugation. Cells were washed, counted, and viability was confirmed prior to library preparation.
Single-cell 5' RNA-seq libraries were prepared using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics) following the manufacturer's protocol, and sequenced on an Illumina NovaSeq 6000.

value: PBMC

value: Lymphocytes

value: ADT


title: PT8, GEM

description:
Library name: PT8_GEM
10x Genomics

value: GEM


title: PT7, TCR

description:
Library name: PT7_TCR
10x Genomics

value: TCR


title: PT7, GEM

description:
Library name: PT7_GEM
10x Genomics


title: PT7, ADT

description:
Library name: PT7_ADT
10x Genomics


title: ΔwbbM sample2

description:
Library name: ΔwbbM-2
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM


title: ΔwbbM in meropenem sample2

description:
Library name: ΔwbbM-MEM-2
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM in meropenem


title: ΔwbbM sample1

description:
Library name: ΔwbbM-1
RNA-seq of Klebsiella pneumoniae NK01067 ΔwbbM


title: PT6, ADT

description:
Library name: PT6_ADT
10x Genomics

value: Leukocytes


title: NK01067 in meropenem sample3

description:
Library name: NK01067-MEM-3
RNA-seq of Klebsiella pneumoniae NK01067 in meropenem


title: WT_OP50_4

value: Whole Animal


title: NK01067 in meropenem sample1

description:
Library name: NK01067-MEM-1
RNA-seq of Klebsiella pneumoniae NK01067 in meropenem


title: NK01067 sample2

description:
Library name: NK01067-2
RNA-seq of Klebsiella pneumoniae NK01067


title: PT8, TCR

description:
Library name: PT8_TCR
10x Genomics


title: PT5, ADT

description:
Library name: PT5_ADT
10x Genomics


title: PT4, GEM

description:
Library name: PT4_GEM
10x Genomics


title: PT3, GEM

description:
Library name: PT3_GEM
10x Genomics

value: T cells


title: PT2, NT, TCR

description:
Library name: PT2_NT_TCR
10x Genomics

source_name: Adjacent normal tissue

value: Adjacent normal tissue


title: PT5, TCR

description:
Library name: PT5_TCR
10x Genomics


title: PT6, TCR

description:
Library name: PT6_TCR
10x Genomics


title: PT5, GEM

description:
Library name: PT5_GEM
10x Genomics


title: PT3, ADT

description:
Library name: PT3_ADT
10x Genomics


title: PT4, TCR

description:
Library name: PT4_TCR
10x Genomics


title: PT6, GEM

description:
Library name: PT6_GEM
10x Genomics


title: PT4, ADT

description:
Library name: PT4_ADT
10x Genomics


title: PT2, NT, GEM

description:
Library name: PT2_NT_GEM
10x Genomics


title: PT3, TCR

description:
Library name: PT3_TCR
10x Genomics


title: PT2, PB, ADT

description:
Library name: PT2_PB_ADT
10x Genomics


title: PT2, T, ADT

description:
Library name: PT2_T_ADT
10x Genomics

source_name: Tumor

value: Tumor


title: PT2, T, TCR

description:
Library name: PT2_T_TCR
10x Genomics


title: PT2, PB, GEM

description:
Library name: PT2_PB_GEM
10x Genomics


title: PT2, T, GEM

description:
Library name: PT2_T_GEM
10x Genomics


title: PT1, Tissue, TCR

description:
Library name: PT1_Tissue_TCR
10x Genomics

source_name: Tumor, Adjacent normal tissue

value: Tumor, Adjacent normal tissue


title: PT1, Tissue, GEM

description:
Library name: PT1_Tissue_GEM
10x Genomics


title: PT2, PB, TCR

description:
Library name: PT2_PB_TCR
10x Genomics


title: PT1, Tissue, ADT

description:
Library name: PT1_Tissue_ADT
10x Genomics


title: PT1, PB, GEM

description:
Library name: PT1_PB_GEM
10x Genomics


title: Siglec-10 antibody treated B3

city: Chicago

first: Pratima

address: 300 E. Superior Street

institute: Northwestern University

description: Library name: B3-Ab2-3_S6_L001

data_processing:
RNA-seq data were aligned to the hg19 human genome using STAR-aligner (v 2.7.10a), and salmon (v 1.10.1) was used to estimate read counts and RPKM values. Raw counts were analyzed for differential expression using DESeq2
Assembly: Human genome GRCh38.p14
Supplementary files format and content: xlsx file with normailzed counts

source_name: Human TAMs

extract_protocol:
Single Cell RNA Purification Kit (Norgen)
Low Input RNA Library Prep Kit (Takara Biosciences)

value: Human TAMs


title: PT1, PB, TCR

description:
Library name: PT1_PB_TCR
10x Genomics


title: Siglec-10 antibody treated B2

description: Library name: B2-Ab2-2_S5_L001


title: Isotype treated A3

description: Library name: A3-Isotype-3_S3_L001


title: Siglec-10 antibody treated B1

description: Library name: B1-Ab2-1_S4_L001


title: Isotype treated A2

description: Library name: A2-Isotype-2_S2_L001


title: PT2, NT, ADT

description:
Library name: PT2_NT_ADT
10x Genomics


title: Isotype treated A1

description: Library name: A1-Isotype-1_S1_L001


title: scRNA-seq of Homo sapiens: 382-71 d57 lymph node, bio rep 1

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description:
Library name: ELAB-WU382-71-WU382-71_d57_GEX_1
10x Genomics

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v6.0.1
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.
Supplementary files format and content: aggregation.csv.gz contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: lymph node

extract_protocol:
Fine-needle aspiration was performed on draining ipsilateral axillary lymph nodes.
Libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' gene expression workflow.

value: lymph node

tag: isolate

tag: timepoint

value: post-boost d57


title: scRNA-seq of Homo sapiens: 382-71 d57 lymph node, bio rep 2

description:
Library name: ELAB-WU382-71-WU382-71_d57_GEX_2
10x Genomics


title: scRNA-seq of Homo sapiens: 382-70 d57 lymph node, bio rep 2

description:
Library name: ELAB-WU382-70-WU382-70_d57_GEX_2
10x Genomics


title: scRNA-seq of Homo sapiens: 382-70 d57 lymph node, bio rep 1

description:
Library name: ELAB-WU382-70-WU382-70_d57_GEX_1
10x Genomics


title: scRNA-seq of Homo sapiens: 382-69 d57 lymph node, bio rep 1

description:
Library name: ELAB-WU382-69-WU382-69_d57_GEX_1
10x Genomics


title: scRNA-seq of Homo sapiens: 382-69 d57 lymph node, bio rep 2

description:
Library name: ELAB-WU382-69-WU382-69_d57_GEX_2
10x Genomics


title: scRNA-seq of Homo sapiens: 382-67 d57 lymph node, bio rep 2

description:
Library name: ELAB-WU382-67-WU382-67_d57_GEX_2
10x Genomics


title: scRNA-seq of Homo sapiens: 382-67 d57 lymph node, bio rep 1

description:
Library name: ELAB-WU382-67-WU382-67_d57_GEX_1
10x Genomics


title: scRNA-seq of Homo sapiens: 382-65 d57 lymph node, bio rep 2

description:
Library name: ELAB-WU382-65-WU382-65_d57_GEX_2
10x Genomics


title: scRNA-seq of Homo sapiens: 382-65 d57 lymph node, bio rep 1

description:
Library name: ELAB-WU382-65-WU382-65_d57_GEX_1
10x Genomics


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HEPG2 cells, UNT, Replicate 1

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

description: Library name: SRSF7_HEPG2_UNT_Rep1

data_processing:
(1) The sequencing reads (R1) from FASTQ files were analyzed with a custom bioinformatics pipeline, which involves STAR aligner tool for mapping to annotate CRISPR guides. Cell Barcode (CBC) and Unique Molecular Identifier (UMI) sequences were retrieved based on the adjacent plasmid vector regions and used to exclude PCR duplicates from the samples. Splicing outcomes were assessed from the R2 reads to link the phenotype to gene knockout perturbation to understand regulatory influence.
(2) PSI (Percent Spliced In) was calculated and analyzed across a particular CRASP-Seq library to identify gene hits in a specific sample with a 10% FDR intergenic control threshold. We also considered guide proportion of more than or equal to 0.5 for a gene to be a hit. Additionally, every sample was technically segregrated into two replicates based on single cell lineage (SCL) groups. Any hit consistently appearing in both the technical replicates were considered as valid regulators ensruring a stringent selection.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with separate sheets containing (1) Whole library guide dPSI values across all the splicing reporter screens, (2) All identified hits across all the reporters and their respective gene dPSI values, (3)-(7) Individual splicing reporter hits and their respective gene dPSI values.
Library strategy: CRISPR Screen

growth_protocol: HAP1, and RPE1 cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. HepG2 cells were cultured in Eagle's Minimum Essential Medium with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads
cDNA synthesis was performed using primers with Unique Molecular Identifier (UMI) sequences.  cDNAs were PCR amplified using illumina sequencing indexes such as i7,P7,i5, and P5 for paired-end sequencing. Next-generation sequencing was performed on an Illumina NovaSeq 6000 platform (200 cycles kit) except for LMNA Base Editor screens which were performed on an Illumina NovaSeq X Plus platform.

treatment_protocol: For the SRSF7 CRASP-Seq screens, cells were treated with 100 µg/mL cycloheximide four hours before cell harvesting and RNA extraction.

value: Human liver cancer cell line

value: UNT


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HAP1 cells, UNT, Replicate 1

description: Library name: SRSF7_HAP1_UNT_Rep1

value: Near-haploid cell line derived from KBM-7 human CML cell line


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HAP1 cells, UNT, Replicate 2

description: Library name: SRSF7_HAP1_UNT_Rep2


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in RPE1 cells, UNT, Replicate 2

description: Library name: SRSF7_RPE1_UNT_Rep2

value: Human retinal pigment epithelial-1 cell line


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HEPG2 cells, UNT, Replicate 2

description: Library name: SRSF7_HEPG2_UNT_Rep2


title: PT1, PB, ADT

description:
Library name: PT1_PB_ADT
10x Genomics

value: PBMC


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in RPE1 cells, CHX, Replicate 1

description: Library name: SRSF7_RPE1_CHX_Rep1

value: CHX


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HEPG2 cells, CHX, Replicate 2

description: Library name: SRSF7_HEPG2_CHX_Rep2


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in RPE1 cells, UNT, Replicate 1

description: Library name: SRSF7_RPE1_UNT_Rep1


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in RPE1 cells, CHX, Replicate 2

description: Library name: SRSF7_RPE1_CHX_Rep2


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HAP1 cells, CHX, Replicate 2

description: Library name: SRSF7_HAP1_CHX_Rep2


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HEPG2 cells, CHX, Replicate 1

description: Library name: SRSF7_HEPG2_CHX_Rep1


title: mRNA-Seq for PKM splicing reporter CRASP-Seq assay in RPE1 cells

description: Library name: PKM_RPE1


title: mRNA-Seq for PKM splicing reporter CRASP-Seq assay in HEPG2 cells

description: Library name: PKM_HEPG2


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in RPE1 cells, WT

description: Library name: LMNA_RPE1_WT


title: mRNA-Seq for SRSF7 splicing reporter CRASP-Seq assay in HAP1 cells, CHX, Replicate 1

description: Library name: SRSF7_HAP1_CHX_Rep1


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in HEPG2 cells, WT

description: Library name: LMNA_HEPG2_WT


title: mRNA-Seq for PKM splicing reporter CRASP-Seq assay in HAP1 cells

description: Library name: PKM_HAP1


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in HAP1 cells, WT

description: Library name: LMNA_HAP1_WT


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in RPE1 cells, MUT

description: Library name: LMNA_RPE1_MUT


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in HAP1 cells, MUT

description: Library name: LMNA_HAP1_MUT


title: mRNA-Seq for LMNA splicing reporter CRASP-Seq assay in HEPG2 cells, MUT

description: Library name: LMNA_HEPG2_MUT


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in RPE1 cells, U6 wt T1

description: Library name: FAS_RPE1_T1


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in RPE1 cells

description: Library name: FAS_17D_RPE1


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in HAP1 cells, U6 wt T1

description: Library name: FAS_HAP1_T1


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in HEPG2 cells

description: Library name: FAS_17D_HEPG2


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in HAP1 cells, U6 wt T4

description: Library name: FAS_HAP1_T5


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in RPE1 cells, U6 wt T4

description: Library name: FAS_RPE1_T5


title: mRNA-Seq for FAS splicing reporter CRASP-Seq assay in HAP1 cells

description: Library name: FAS_17D_HAP1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in RPE1 cells, U6 wt T4

description: Library name: EZH2_HAP1_T5


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in RPE1 cells, U6 wt T1, Replicate 1

description: Library name: EZH2_RPE1_T1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in RPE1 cells, U6 wt T1, Replicate 2

description: Library name: EZH2_v3_RPE1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in HAP1 cells, U6 wt T4

description: Library name: EZH2_RPE1_T5


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in HAP1 cells, U6 wt T1, Replicate 1

description: Library name: EZH2_HAP1_T1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in RPE1 cells

description: Library name: EZH2_17D_RPE1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in HAP1 cells, U6 wt T1, Replicate 2

description: Library name: EZH2_v3_HAP1


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in HAP1 cells

description: Library name: EZH2_17D_HAP1


title: 6a_11a

city: Zurich

first: Magdalini

last: Kanari

address: Lengstrasse 30

department: Oncology

institute: University Children's Hospital Zurich

description: Library name: hsid03049

data_processing:
Cell Ranger used to demultiplex, align the raw data and to generate the count matrix
Assembly: hg19
Supplementary files format and content: Tab separated values files and matrix files

source_name: Acute lymphoblastic leukemia

extract_protocol: Samples were multiplexed and pooled to a total of 10000 cells per run. Then, they were loaded and sequenced with the use of an Illumina platform. The standard library protocol for 10x genomics single cell RNA sequencing for live cells was followed based on the manufacturer’s instructions

treatment_protocol: Mice were euthanised and their femurs were extracted. The bone marrow was flushed in order to isolate the leukemic cells. Finally, leukemic samples were isolated via fluorescence activated cell sorting.

value: Acute lymphoblastic leukemia


title: LK47_U48_A61

description: Library name: nvid00937


title: LK61

description: Library name: nvid00938


title: Fetal_lung_human_gdTCR

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

description:
FLUgd_filtered_contig_annotations.csv
FLUgd_filtered_contig.fasta

data_processing:
CellRanger (v7.1.0) software from 10x Genomics was used to demultiplex and map sequencing reads against GRCm39 and GRCh38 genomes. Count matrices were loaded into R using ´read10x’ function form Seurat R package. All downstream analyses were conducted using Seurat v5.0.0 in R v4.3.2. Low-quality and doublet cells were filtered out using the minimum cutoffs nFeature_RNA > = 200, % mitochondrial gene >5%. ‘Cellcyclescoring´ function from Seurat package was used to determine cell cycle phase of cells in the datasets (G1, G2 or S).  ScaleData function was used to normalize and stabilize variance in the datasets regressing out percent mitochondria genes, percent ribosomal genes, cell cycle scores, nFeatureRNA and TRDV TRGV genes. Principal component analysis (PCA) was subsequently performed using the RunPCA function with 30 principal components. To account for batch effects in integration of datasets, the Harmony algorithm was applied using the RunHarmony function. The Harmony embeddings were extracted using the Embeddings function. Dimensionality reduction was then carried out using the RunUMAP function, based on the top 10-20 Harmony components to generate a two-dimensional UMAP projection for visualization. The nearest-neighbor graph was constructed with the FindNeighbors function, and clustering was performed using the Louvain algorithm via the FindClusters function at a resolution of 0.5.
Assembly: GRCh38 & GRCm39
Supplementary files format and content: GEX: matrix.mtx features.tsv barcodes.tsv. matrix files include transcript count from each single-cell GEX library. barcodes tsv files includes the barcodes present in that single-cell GEX library and features tsv file includes the ID of the genes detected in that single-cell GEX library. TCR: filtered_contig_files include CDR3 junctions in csv and fasta format

source_name: fetal lung

extract_protocol:
Mouse lung cells from individual subjects (8 fetal (Day 0) and 8 adults (10weeks old)) were stained with barcoded hashing antibodies TotalSeq-C 5′ chemistry, following the recommendations of the manufacturer (Biolegend), prior to staining for FACS sorting. Human lung cells from 6 fetal lungs samples (18-23 weeks old) were individually hashed with MULTI-Seq lipid barcodes as previously described (McGinnis Nat Methods 2019) followed by staining for FACS sorting. For all samples, CD3+ γδTCR+ cells were sorted on FACS Aria III cell sorter (BD Biosciences).
Libraries for sc RNA and TCR sequencing were generated from 1.5-2*104 FACS-pool sorted γδ T cells using the Chromium Single Cell 5’ Library Gel Bead and Construction kit as well as Chromium Single Cell V(D)J Enrichment Kit (10x Genomics, CA, USA) according to the user guidelines (v2 Chemistry, Single Cell V(D)J protocol number CG000330). Single-cell TCR & gene expression libraries were generated according to Chromium Single Cell V(D)J protocol (10x Genomics). 2μL of cDNA amplified and purified from GEMs (“Gel bead in Emulsion” droplets) were used to amplify γδTCR CDR3 sequences. Custom primers specific for TRDC and TRGC constant gene segments were designed for this purpose. In brief, for the first step in the enrichment of CDR3 sequences the custom outer primer sets followed by second target enrichment (inner) primer sets. The remaining volume of cDNA was used for construction of gene expression library according to 10X Genomics protocol instructions. Agilent Bioanalyzer High Sensitivity DNA chips were used to check quality control read-outs of sc RNA-seq and sc TCR-seq libraries using a Bioanalyzer 2100 machine (Agilent Technologies). Indexed libraries were pooled and sequenced on Illumina NovaSeq 6000 from BRIGHTcore (Brussels Interuniversity Genomics High Throughput core) platform.

value: fetal lung

value: Gamma delta T cell

tag: age

value: 18-13 wk gestation time


title: Donor 3 CMA Rep3

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ generated with bcl2fastq (version 2.20.0.422) files were processed using the nf-core/rnaseq pipeline (version 3.12, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the human transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCh38
Supplementary files format and content: *_quant.sf.gz: Salmon transcript quantification file (tab-sparated text, https://salmon.readthedocs.io/en/latest/file_formats.html); to be used together with salmon_tx2gene.tsv by software accepting Salmon data

source_name: C type Adipocytes

growth_protocol: Primary mesenchymal and myeloid-derived adipocyte precursors were grown in 15 cm tissue culture plates in Growth Media (GM): Alpha-MEM (Corning #10-022-CV) supplemented with 10% FBS (Gemini #100-106) and 0.1% penicillin/streptomycin (Sigma #P4333). Upon confluence, cells were differentiated for seven days in Complete Differentiation Media (CDM): DMEM/F12 (Corning #10-092-CV) supplemented with 33 μM D-biotin (Sigma #B4639), 17 μM pantothenate (Sigma #P5155), 1 μM rosiglitazone (Fisher #NC9331406), 0.5 mM 3-isobutyl-1-methylxanthine (IBMX; Sigma #I5879), 2 nM 3,3’,5-triiodo-L-thyronine (T3; Sigma #T6397), 10 μg/mL transferrin (Sigma #T8158), and 100 nM insulin (Sigma #I9278). Cultures were then maintained for seven days in adipocyte maintenance media (AMM): DMEM/F12 supplemented with 33 μM D-biotin, 17 μM pantothenate, and 10 nM insulin (same suppliers as CDM). At the end of the seven-day AMM period, cells pellets were collected and used for RNA isolation.

extract_protocol:
RNA was isolated from cell pellets using the Qiagen RNeasy Plus kit (Qiagen #74136) according to the manufacturers protocol
Libraries were constructed by the CU Genomics Shared Facility.

value: C type Adipocytes


title: Fetal_lung_human_lipid

description:
FLUgd_matrix.mtx.gz
FLUgd_features.tsv.gz


title: Donor 3 HSCDA Rep1

source_name: B type Adipocytes

value: B type Adipocytes


title: Donor 3 HSCDA Rep2


title: Donor 3 CMA Rep1


title: Donor 2 CMA Rep3


title: Donor 2 HSCDA Rep2


title: Donor 2 CMA Rep1


title: Donor 1 CMA Rep1


title: Donor 1 CMA Rep3


title: mRNA-Seq for EZH2 splicing reporter CRASP-Seq assay in HEPG2 cells

description: Library name: EZH2_17D_HEPG2


title: Donor 1 HSCDA Rep1


title: NCI-H1975cells,chloroform parts of Flos Magnoliae_3

city: xi'an

first: wu

last: qing

state: shanxi

address: zhangjiacun

institute: Xi'an Jiaotong University

data_processing:
Based on Illumina sequencing platform
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

extract_protocol:
RNA is extracted from cells and the RNA sample is then subjected to rigorous quality control, primarily through Agilent 2100 bioanalyzer
Build the NEB database according to the common or chain-specific method (Parkhomchuk et al., 2009)

value: epithelium

value: lung cancer cells

value: WT


title: NCI-H1975cells,chloroform parts of Flos Magnoliae_2


title: NCI-H1975cells,magnolin_4


title: NCI-H1975cells,chloroform parts of Flos Magnoliae_1


title: 6a_11a(2)

description: Library name: hsid03050


title: NCI-H1975cells,magnolin_3


title: NCI-H1975cells,magnolin_1


title: NCI-H1975cells, control_4


title: Fetal_lung_human_GEX

description:
FLUgd_matrix.mtx.gz
FLUgd_features.tsv.gz
FLUgd_barcodes.tsv.gz


title: NCI-H1975cells, control_2


title: NCI-H1975cells, control_1


title: HCC827AR cells_2

value: afatinib resistance


title: HCC827AR cells_1


title: HCC827 cells_2


title: HCC827, input

city: Shenyang

first: sihong

last: chen

address: Wenhua Road

institute: Shenyang Pharmaceutical University

data_processing:
Basecalling was performed using CASAVA version 1.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Reads were aligned to the hg19 genome assembly using Hisat version 2.2.1
Peaks were called uing MACS v2.2.7 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
The HCC827 and HCC827_Er cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA.
The ChIP DNA was purified by QIAquick PCR Purification Kit (Cat. 28104; QIAGEN) following the manufacturer’s protocol.  The ChIP DNA library preparation was performed by using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (Cat. E7645S; NEB).  Paired-end sequencing was performed with Illumina NovaSeq platform.

value: Human non-small cell lung cancer cells

tag: chip antibody


title: HCC827 cells_1


title: HCC827_Er, ChIP

value: H3K56cr (Thermo Scientific; PA5-112529)


title: HCC827_Er, input


title: Donor 2 HSCDA Rep1


title: HCC827, ChIP


title: NCI-H1975cells,chloroform parts of Flos Magnoliae_4


title: Donor 1 HSCDA Rep3


title: Donor 5; TZM

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Quality control and trimming of fastq files was done using Fastp (version 0.22.0) using the default settings except for the minimum read length requirement setting, which was adjusted to 50bp.
The trimmed sequence reads were then aligned to STAR (version 2.7.10), and count matrices were generated using htseq-count (version 0.13.5)
Samples were excluded from analysis if the percentage of uniquely mapped reads was <75% and/or >20% of reads mapped to multiple loci, eliminating the sample represented by library R2022-407 from further analysis.
Differential expression analysis was performed DESeq2 (version 1.38.3).
Assembly: GRCh38
Supplementary files format and content: Group log2 fold-change, p-value and q-value are represented for each transcript and isoform in the group comparison processed data files.

source_name: Microvascular/Adipose

growth_protocol: Microvascular endothelial cells were isolated from adipose tissue from five donors without known cardiovascular disease using magnetic beads containing CD31 antibodies.  Endothelial cell identity was verified via FACs analysis with VE-cadherin to confirm that >85% of cells were endothelial cells. Cell lines were subcultured into five individual plates and grown on gelatin in endothelial cell growth media (Lonza, CC-3202).

extract_protocol:
RNA from cultured endothelial cells was prepared by phase separation using a TRIzol-chloroform method.
Libraries were constructed using Illumina’s TruSeq stranded mRNA library kit with unique dual indexing protocol and amplified for sequencing by qPCR (Kapa Library Quantification Kit, Kapa Biosystems).
Sequencing produced 150-bp paired end reads across up to two lanes. Reads from samples run in multiple lanes were merged prior to quality control and trimming.

treatment_protocol: Cells in a monolayer were treated with doxorubicin (Dox,0.1µM), trastuzumab (TZM, 10 µg/ml), paclitaxel (PTX, 1 µM), or their respective controls (endothelial cell growth media only for Dox and TZM; DMSO for PTX) for 24 hours with a total of five conditions per donor-derived endothelial cell line.

value: Microvascular/Adipose

tag: disease state

value: breast cancer

value: Primary Endothelial

value: TZM


title: Donor 5; PTX

value: PAX


title: NCI-H1975cells, control_3


title: Donor 3; PTX


title: Donor 5; Untreated

value: Untreated


title: Donor 4; Untreated


title: Donor 5; DOX

value: DOX


title: Donor 3; TZM


title: NCI-H1975cells,magnolin_2


title: Donor 3; DOX


title: Donor 4; TZM


title: Donor 4; DOX


title: Donor 3; Untreated


title: Donor 2; TZM


title: Donor 2; PTX


title: Donor 2; Untreated


title: Donor 1; TZM


title: Donor 1; PTX


title: Donor 1; DMSO

value: DMSO


title: Donor 4; PTX


title: S12, WT, D28-Neuron

city: Irvine

first: Vivek

last: Swarup

state: California

address: Biological Sciences III, 3224

institute: UCI

data_processing:
data demultiplexing, barcoded processing, and open chromatin accessibility processing were made using 10x cellranger for snATAC ; gene expression counting  for snRNA was made using ParseBiocience split-pipe v1.0.3. Bulk RNA was prcessed using STAR
Assembly: hg38
Supplementary files format and content: .rda file,

source_name: iPSC

extract_protocol:
Frozen brain tissue pieces were placed in 500 μL chilled 0.1× Lysis Buffer (1X lysis buffer diluted with lysis dilution buffer) and immediately homogenized 15 times using a pellet pestle (Fisherbrand™ Pellet Pestle™ Cordless Motor with RNase-Free Disposable Pellet Pestles, Catalog No.12-141-364). The homogenized tissues were then incubated for 15 mins followed by addition of 500 μL of chilled Wash Buffer and filtration through a 70 μm Cell Strainer (Miltenyi Biotech). In the next step, a sucrose gradient (Nuclei PURE Prep Nuclei Isolation Kit, Cat\#NUC201-1KT, Sigma) was prepared and nuclei were spun at 13,000 g for 45 minutes at 4°C. After centrifugation, the debris and myelin from the top of the sucrose gradient were removed. Nuclei were resuspended, washed, filtered (through a 40 μm cell strainer), counted (using a cell counter), and then incubated in a Transposition Mix.
Transposed nuclei were loaded on 10X Genomics Next GEM Chip H (10x Genomics) to generate single-cell GEMS. GEMs were then transferred, incubated, and cleaned for further processing.  Single nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC v2 (10x Genomics) reagents kit as per the manufacturer’s instructions. Library size distribution and average fragment length, of each library, were assessed with Agilent TapeStation High Sensitivity D5000 ScreenTapes and the concentrations were quantitated using Qubit Fluorometer.  Libraries were sequenced on a NovaSeq 6000 (Illumina) in paired-end mode (read1N: 50 cycles, index i7: 8, index i5:16 cycles, read 2N:50 cycles) to generate approximately 500 M reads per sample.
snATAC-seq, snRNA-seq, RNA-seq

value: iPSC


title: Donor 5; DMSO


title: Donor 1; DOX


title: S3, UBE3A, D0-iPSC


title: Donor 2; DMSO


title: 16, Control, snATAC

source_name: Brain

value: Brain


title: Donor 1; Untreated


title: 14, Control, snATAC


title: S11, UBE3A, D28-Neuron


title: Donor 4; DMSO


title: S9, UBE3A, D28-Neuron


title: S10, WT, D28-Neuron


title: Pick's disease and Control snRNA

description: Split-pool tech barcoded samples, please see the sample loading list in GSE259298_snRNA_sample-list.txt. After processed by split-pipe v1.0.3, ambinet RNA was removed by cellbender, which changed the unique barcode to its index. So, we kindly suggest you process this split-pool snRNA data yourself if you want to use the processed data we provided. Sample metadata can been found in the supplymental tables. Samples include: 7, Pick's disease 8, Pick's disease 9, Control 11, Pick's disease 13, Pick's disease 14, Control 16, Control 17, Pick's disease


title: Donor 3; DMSO


title: S8, WT, D28-Neuron


title: S7, UBE3A, D28-Neuron


title: 6, Control, snATAC


title: 5, Control, snATAC


title: S4, WT, D0-iPSC


title: 4, Control, snATAC


title: S5, UBE3A, D0-iPSC


title: 24, Pick's disease, snATAC


title: S2, WT, D0-iPSC


title: 1, Pick's disease, snATAC


title: 17, Pick's disease, snATAC


title: 2, Control, snATAC


title: 15, Control, snATAC


title: Donor 2; DOX


title: S1, UBE3A, D0-iPSC


title: 3, Pick's disease ,snATAC


title: 13, Pick's disease, snATAC


title: 11, Pick's disease, snATAC


title: 9, Control, snATAC


title: 8, Pick's disease, snATAC


title: 10, Control, snATAC


title: HASMC, RNA, VEC_rep 2

city: Guangzhou

first: yulong

last: zhong

state: Guangdong Province

address: 1838 Guangzhou Avenue North

department: physiology

institute: Southern Medical University

data_processing:
Sequencing reads were trimmed by cutadapt (v 4.3) to get high quality reads. High quality reads were aligned to the human reference genome hg19 using hisat2 (v 2.2.1) with default parameters. The mapped reads were sorted using Samtools (v 1.13), retaining any reads with a MAPQ less than 30. Reads count was conducted by htseq-count (2.0.2) with a customized GTF file.
Assembly: hg19
Supplementary files format and content: count, fpkm

source_name: HASMC

growth_protocol: HASMCs were cultured in primary smooth muscle cell low serum culture system (PriMed-iCell-004, Bioscience Inc) according to the vender's protocol and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
The total RNA was extracted from the platelets using Trizol reagent (Invitrogen, 15596026). 5-10 μg of total RNA was utilized for constructing sequencing libraries.
The library construction follows the protocol of Illumina’s reagent kit (Illumina® Stranded mRNA Prep, Ligation #20040534).

treatment_protocol: The HASMCs were infected with VEC or Ad-TAX1BP3 adenovirus for 48 hours, and then RNA was harvested.

value: HASMC

value: Human primary aortic smooth muscle cell


title: HASMC, ATAC, Ad.TAX1BP3_rep 1

data_processing:
Sequencing reads were trimmed by cutadapt (v 4.3) to get high quality reads. High quality reads were aligned to the human reference genome hg19 using Bowtie2 (v 2.2.5) with the parameter of "-X 2000". The mapped reads were sorted using Samtools (v 1.13), retaining any reads with a MAPQ less than 30. Duplicated reads were removed by Picard (v 2.7). Peaks were called by MACS2 (v 2.2.7.1).  Bigwig files were generated from bam files using deeptools (v 3.5.1) bamCoverage. All samples were normalized to 1 million reads with binsize as 50-bp by "--scaleFactor --binSize 50" parameters.
Assembly: hg19
Supplementary files format and content: bigwig files and bed files.

extract_protocol:
We conducted ATAC-seq based on Omni-ATAC with some modifications. Briefly, 50000 fresh HASMCs were collected and rinsed twice with cold PBS. Cells were spun down at 500 g for 5 min at 4 °C. Cells were resuspended with 50 μL ATAC-seq Lysis Buffer, and incubated on ice for a duration of 3 min. Then we added 1 mL of ATAC-seq Wash Buffer to dilute the lysis reagents. After wash with ATAC-seq Wash Buffer, cells were resuspended with 50 μL Reaction mix (16.5 μL PBS, 0.5 μL 100x cocktail, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 0.2 μL 20 μM PAT-MEA/B, 10 μL 5x TMgCl-DMF, 21.7 μL ddH2O). Tagmentation was conducted at 37 °C for 30 min at 1000 rpm. To quench Tagmentation, we added 250 μL of DNA Binding Buffer from the DNA Clean and Concentrator-5 Kit and mixed well. Preliminary libraries were purified with the DNA Clean and Concentrator-5 Kit.
Follwing Omni-ATAC protocol. After PCR enrichment using 2X KAPA master mix,fragments were purified using the Zymo DNA Clean and Concentrator-5 Kit.

treatment_protocol: The HASMCs were infected with VEC or Ad-TAX1BP3 adenovirus for 48 hours, and then ATAC-seq was performed.

value: overexpression TAX1BP3


title: HASMC, RNA, VEC_rep 3


title: HASMC, RNA, Ad.TAX1BP3_rep 1


title: HASMC, RNA, Ad.TAX1BP3_rep 2


title: HASMC, ATAC, VEC_rep 4


title: HASMC, ATAC, Ad.TAX1BP3_rep 4


title: HASMC, ATAC, Ad.TAX1BP3_rep 3


title: HASMC, ATAC, Ad.TAX1BP3_rep 2


title: HASMC, ATAC, VEC_rep 2


title: jc8265_HPAFII_HNF4G_knockout_FOXA1

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

description:
AN21CUK023263
HNF4G KO + FOXA9

data_processing:
STAR, version 2.6.1a, was used to align reads against human hg38 or mouse mm10 reference genome.
The read counting was performed using featureCounts v2.0.4.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Assembly: GRCh38,GRCm38
Supplementary files format and content: text

source_name: HNF4G knockout + FOXA1

growth_protocol: Mouse cells were grown in DMEM 10% FBS, Sodium pyruvate. HPAF-II cells were grown in MEM media.  The cells were injected into NSG mice and tumours were monitored using ultra sound. The mice were killed at an humane endpoint and tumours were extracted and processed for RNA seq

extract_protocol:
Maxwell® RSC simplyRNA Cells Kit
RNAseq libraries were prepared using Illumina’s TruSeq mRNA Stranded Sample prep kit.

treatment_protocol: No treatment was performed on these cells. Lentiviral over expression and CRISPR KO's  were generated and this has been indicated in the descriptions.

value: pancreatic adenocarcinoma

value: orthotopic xenograft HPAF-II

value: Tumour 5

value: CRISPR

value: CRISPR HNF4G KO+FOXA1


title: jc8261_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023260
HNF4G KO + FOXA5

value: Tumour 3


title: jc8260_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023260
HNF4G KO + FOXA4

value: Tumour 2


title: jc8258_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023259
HNF4G KO + FOXA2

value: Spleen met


title: Sublibrary 8, PlexinB1 Parse-seq

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: SCI-PB1CTRL-KOSublib8

data_processing:
The single-nucleus RNA-seq dataset was demultiplexed using the Trailmaker platform. Unfiltered count matrices were uploaded, and background noise was removed by setting a minimum transcript threshold per cell on a per-sample basis (≥ 500 transcripts). Barcodes associated with high mitochondrial gene content (> 0.5%) were excluded to filter out dying or stressed cells. Outliers in gene-to-transcript ratio distributions were removed using spline regression filtering (P values < 0.001). Doublets were identified and removed using the scDblFinder method.
Assembly: mm39
Supplementary files format and content: Processed data is provided in the form of 10x files (barcodes, features, and matrix files), for both the pre- and post-filtering datasets. Additional informative  metadata is provided for the filtered dataset. For the unfiltered dataset, a Seurat object is provided in the form of a RData file (RDS).

source_name: Spinal cord

extract_protocol:
To isolate nuclei from spinal cord tissue, approximately 10 mm of spinal cord encompassing the injury site was dissected and finely minced. Nuclei were extracted using a nuclei extraction buffer (Miltenyi Biotec, #130-128-024). The resulting suspension was enriched for nuclei using anti-Nucleus MicroBeads (Miltenyi Biotec, #130-132-997). Nuclei were subsequently fixed using the Evercode Nuclei Fixation Kit v3 (Parse Biosciences, ECFN3300).
Split-seq cDNA libraries 49 were generated by iterative barcoding of nuclei via multiwell plating using the Evercode Whole Transcriptome (WT) v3 kit (ECWT3300; Parse Biosciences).

treatment_protocol: Spinal cord injury

value: Spinal cord

value: neural cells

value: WT and PB1KO

value: uninjured or 7 dpi


title: jc8256_HPAFII_Cas_9_FOXA1

description:
AN21CUK023258
Cas-9 + FOXA1

source_name: Cas-9 + FOXA1

value: CRISPR Cas-9-FOXA1


title: Sublibrary 5, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib5


title: Sublibrary 7, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib7


title: Sublibrary 4, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib4


title: HASMC, ATAC, VEC_rep 3


title: Sublibrary 1, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib1


title: HASMC, ATAC, VEC_rep 1


title: jc8264_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023262
HNF4G KO + FOXA8

value: Peritoniuem met


title: jc8263_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023262
HNF4G KO + FOXA7

value: Tumour 4


title: jc8248_HPAFII_HNF4G_knockout_EV

description:
AN21CUK023249
HNF4G KO-EV

source_name: HNF4G knockout-EV

value: Tumour 1

value: CRISPR HNF4G KO-EV


title: RNAseq_WT_Rep3

city: Dublin 2

first: Adrian

middle: P.

last: Bracken

state: Co. Dublin

address: Smurfit institute of Genetics, Lincoln Place, Trinity College Dublin

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-Seq and Cut&Run reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. ChIP-Rx reads were aligned to a metagenome mm10_hg38 by bowtie2. PCR duplicate reads were removed by Picard. RNA-Seq fastqs of WT ESCs were aligned to mm10 using STAR and bigwigs were generated using deepTools bamCoverage for visualisation in UCSC Genome Browser.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a), for ChIP-Rx samples. Generally, normalization factor (a) was calculated by 1 divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, ChIP-Seq and Cut&Run bigwigs were generated by BamCoverage at 10 bp resolution and using RPKM normalization. ChIP-Rx bigwig files were generated with Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: E14 WT mESCs, Rep3

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were split and media was changed every 2 days. For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium was changed daily.

extract_protocol:
For RNA-Seq: Cell pellets from WT ESCs were collected at different days (representing Replicates 1,2 and 3) and total mRNA extracted using the Qiagen RNeasy Mini Kit.
ChIP-Seq/Rx library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. The CUT&RUN experiments were performed following the Epicypher CUT&RUN Protocol v1.5.1. The Monarch PCR & DNA Cleanup Kit (New England Biolabs) protocol was used to purify the DNA. RNASeq Libraries were prepared by Novogene and sequenced using NovaSeq X Plus PE150.
Illumina NextSeq 500, 75-bp single end (rescues samples); NextSeq2000, 75-bp single end (AEBP2 KO ChIPs); NextSeq2000, 50-bp paired-end

treatment_protocol: No treatment applicable.

value: E14 WT mESCs, Rep3

value: mouse embryonic stem cell


title: jc8247_HPAFII_Cas_9_EV

description:
AN21CUK023248
Cas-9-EV

value: pancreatic adenocarcinoma

value: orthotopic xenograft HPAF-II

value: CRISPR Cas-9-EV


title: jc8262_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023261
HNF4G KO + FOXA6

value: peri mets in fat

value: CRISPR

value: CRISPR HNF4G KO+FOXA1


title: RNAseq_WT_Rep1

source_name: E14 WT mESCs, Rep1

value: E14 WT mESCs, Rep1


title: HASMC, RNA, Ad.TAX1BP3_rep 3

value: HASMC

value: Human primary aortic smooth muscle cell

value: overexpression TAX1BP3


title: jc8259_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023259
HNF4G KO + FOXA3


title: RNAseq_WT_Rep2

source_name: E14 WT mESCs, Rep2

value: E14 WT mESCs, Rep2


title: Sublibrary 6, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib6

value: Spinal cord

value: neural cells

value: WT and PB1KO

value: uninjured or 7 dpi


title: jc8253_HPAFII_HNF4G_knockout_EV

description:
AN21CUK023252
HNF4G KO-EV

value: Peritoniuem met

value: CRISPR HNF4G KO-EV


title: jc8244_HPAFII_Cas_9_EV

description:
AN21CUK023244 *
Cas-9-EV

value: pancreatic adenocarcinoma

value: Tumour 1


title: jc6731_AsPC_1_HNF4A

description:
HNF4A ASPC-1-Rep 1
ASPC-1 HNF4A
untreated

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences. Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

source_name: Pancreatic adenocarcinoma

growth_protocol: HPAF-II & ASPC-1 cells were grown in MEM & RPMI High 10% FBS, Sodium pyruvate. KPC mouse cells were grown in DMEM 10% FBS

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012. Antibodies used are specified above FOXA1-ab5089, HNF4G-atlas HPA005438, PRMT1-atlas HPA069769,H3K27Ac-ab4729,flag-sigma-F1804,GATA6-RD-AF1700
DNA was prepared for Illumina sequencing on the Nova Seq 6000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: untreated or CRISPR pertubation

value: Pancreatic adenocarcinoma

value: WT

value: untreated


title: jc8255_HPAFII_Cas_9_FOXA1

description:
AN21CUK023255
Cas-9 + FOXA1

value: orthotopic xenograft HPAF-II

value: Tumour 2

value: CRISPR

value: CRISPR Cas-9-FOXA1


title: LIVERcre10

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

description: Library name: LIVERcre10

data_processing:
Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed one alignment with up to two mismatches per read. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline. A gene was included in the analysis if it met all the following criteria: the maximum RPKM reached four at any time point, the gene length was >200 bp
Differential expression analysis. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis of differentially expressed genes. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway.
Assembly: mm10 (GRCm38)
Supplementary files format and content: DEGs upregulates and downregulated (Normalized abundance-HEATMAPs)

source_name: LIVER

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen). The aqueous phase containing the RNA was loaded onto a gDNA Eliminator Spin Column (Qiagen, USA) for elimination of genomic DNA, and RNA was isolated using the RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. Total RNA (500 to 1000 ug) was reverse transcribed into cDNA using the M-MLV reverse transcriptase (Invitrogen),
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: LIVER

value: Acypap1r1 floxed/floxed

value: AAV-Cre


title: jc8252_HPAFII_HNF4G_knockout_EV

description:
AN21CUK023252
HNF4G KO-EV

value: Tumour 4


title: jc8254_HPAFII_Cas_9_FOXA1

description:
AN21CUK023254
Cas-9 + FOXA1


title: Sublibrary 3, PlexinB1 Parse-seq

description: Library name: SCI-PB1CTRL-KOSublib3

value: Spinal cord

value: neural cells

value: WT and PB1KO


title: jc6733_AsPC_1_HNF4A

description:
HNF4A ASPC-1-Rep 2
ASPC-1 HNF4A
untreated


title: jc8257_HPAFII_HNF4G_knockout_FOXA1

description:
AN21CUK023259
HNF4G KO + FOXA1

value: CRISPR HNF4G KO+FOXA1


title: jc6725_AsPC_1_HNF4G

description:
HNF4G ASPC-1-Rep 1
ASPC-1 HNF4G
untreated


title: HASMC, RNA, VEC_rep 1

value: HASMC

value: Human primary aortic smooth muscle cell