title: RPB1degron_125nM_dTAGv1_3

description: Library name: 125nM_3

data_processing:
Adapters were trimmed from single-end reads with fastp using options --disable_trim_poly_g, --disable_quality_filtering, --length_required 16, --length_limit 125, -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC. UMI sequences were then extracted from the fastq files using umi_tools extract. The resulting reads were aligned against a combined human/drosophila genome (GRCh38/dm6) using hisat2 (default settings) and PCR duplicates were subsequently removed using the umi-tools dedup function with default settings.  BAM files were then converted to strand-specific bigwig files containing only the first nucleotide of the 5’ end of aligned reads, which corresponds to the 3’ end of RNA transcripts, using deeptools bamcoverage with options --normalizeUsing CPM -p 16 --binSize 1 --filterRNAstrand=forward/reverse --Offset 1.
Assembly: GRCh38
Supplementary files format and content: bigwig - spike-in normalised coverage of 3' end of nascent RNA
Library strategy: PRO-Seq

molecule: nuclear RNA

source_name: HEK293 Flp-In TREX

extract_protocol:
PRO-seq was performed as described previously. Briefly, DMSO or dTAGV-1-treated cells or Drosophila S2 cells were permeabilized and counted. 1 million permeabilized cells (nuclei) per sample were mixed with 5% spike-in Drosophila S2 permeabilized cells (nuclei) in 50 μl, then mixed with 50 μl 2X Run-On Master Mix containing biotin-tagged CTP and UTPs (PerkinElmer, NEL542001EA-NEL545001EA) to perform the run-on reaction at 37°C for 5 min. The reaction was terminated by adding TRIzol LS followed by total RNA extraction. Total RNA was denatured by adding NaOH to 200 mM and then purified on a Bio-Rad RNase free P-30 column following the manufacturer’s instructions. Then the 3’ RNA adaptor ligation was performed, and the biotin labeled RNA was enriched on Streptavidin beads. Next 5’ hydroxyl repair and de-capping reactions were performed on-bead followed by 5’ RNA adaptor ligation. After these enzymatic reactions, the Streptavidin beads with bound biotin labeled RNA were washed. Biotin labeled RNA was released from the Streptavidin beads using TRIzol/ chloroform extraction followed by precipitation.
Reverse transcription was performed off-bead to get cDNA. 1.54 μl out of the 20 μl reverse transcription reaction was used to do a test amplification (qRT-PCR) to determine the amplification cycle number, then full-scale amplification was performed with 15 cycles. PCR products were cleaned up and selected on SPRI beads for sequencing. The libraries were then sequenced on an Illumina NextSeq 2000 (Genomics Platform at University of Copenhagen), yielding 100bp single-end reads.

treatment_protocol: RPB1 degron cells were seeded at a density of 4 million cells in a 10cm plate and were either treated with DMSO or different concentrations of dTAGv-1 for 16 hours before harvest.

value: HEK293 Flp-In TREX

value: 125nM dTAGv1


title: Control-D3 ctr2

status: Public on Nov 19 2025

type: SRA

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

country: USA

institute: UNIVERSITY OF FLORIDA

library_source: transcriptomic

data_processing:
Illumina NovaSeq 6000-S4 was used to sequence the libraries for 2 x 150 cycles
The genome of Mus musculus (version GRC38, mm10) from the Ensembl database was used as the reference sequences for RNA-seq analysis
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis
The cleaned reads of each sample were mapped to the reference sequences using the read mapper of the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a). The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2)70 samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis
PCA analysis (for detecting outlier samples) and volcano plot analysis based on all identified genes in each analysis were performed with the R-package (v4.1.3). The gene expressions were analyzed by a DESeq2-based R pipeline. Genes were considered differentially expressed if the log2 fold change was > |1| and if the adjusted P-value was < 0.01. Bowtie2 (version 2.5.4) was used for searching gene and exon for each sample
Assembly: Mus musculus (version GRC38, mm10)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: Mice were housed under a 12hrs/12hrs day/night cycle and had ad libitum access to food and water

extract_protocol:
total RNA was isolated using Trizol Reagent (15596026, Thermo Fisher) according to the manufacturer’s protocol. RNA from primary FAPs was extracted with Qiagen RNeasy Micro Kit (74004, Qiagen) following manufacturer’s protocol.
RNA-seq libraries were constructed at the ICBR Gene Expression and Genotyping Core Lab using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, United States) following the manufacturer’s recommendations. A total of 1000 ng samples of RNA with RNA integrity numbers (RIN) greater than 5.6 were used

treatment_protocol: Tamoxifen (TAM) dissolved in corn oil was delivered via intraperitoneal (IP) injection to mice at 12-13 weeks of age for 5 consecutive days (100ug/g body weight). five times the amount of body weight (g) in microliters of tamoxifen (TAM) mixed in corn oil (20mg/mL). At least 1 week between the final TAM injection and subsequent experiments was done to allow washout of TAM. Both male and female mice were used as indicated in each experiment.

tag: tissue

value: skeletal muscle

tag: treatment

value: muscles were embedded in OCT and then frozen in melting 2-methylbutane cooled by liquid nitrogen


title: AB18215.txt

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 145

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cell_metadata.csv

molecule: polyA RNA

growth_protocol: hTREM2 mice were s.c. injected with 1M MC38 tumor cells (day 0). Mice were intravenously treated with 200 µg per dose of anti-RSV, anti-TREM2, anti-PD-1, anti-TREM2 + anti-PD1, anti-CTLA-4, anti-TREM2 + anti-CTLA-4, MiTE-144, MiTE-144 + anti-PD1, or MiTE-144 + anti-CTLA-4 on days 8 and 10 (n = 5). Immune cells were isolated on day 11, FACS sorted (total CD45+ and T/NK cell enrichment) and underwent scRNAseq employing SPID-seq resulting in a total of 45,505 high-quality cells from 45 mice.

extract_protocol:
Tumors were minced into small pieces on ice and digested using RPMI supplemented with 1mg/ml Collagenase IV (LS004188, Enco) and 0.05mg/ml DnaseI (DnaseI, Sigma Aldrich) at 37 degrees for three times 8 min. In between the incubation steps, the tissue was further dissociated using a gentleMACS dissociator (130-093-235, Miltenyi Biotec). After digestion, the cells were filtered trough a 100um cell strainer and washed with ice cold PBS.  Cells were stained with FACS antibodies and viability dye for 30min on ice. After washing them again with ice cold PBS, cells were sorted and acquired on a BD FACS Symphony 6 flow cytometer. After excluding doublets and dead cells, two 384-well plates of CD45+ cells and CD90.2+ and/or NK1.1+ (=T/NKT/NK/ILCs) were sorted per sample The 384-well plates contained a lysis solution, mineral oil and barcoded poly(T) reverse transciption primers enabeling scRNA sequencing.
SPID-seq92, an adapted version of the MARS-seq pipeline93, was used to generate scRNA-seq libraries. In short, polyadenylated mRNA from individual cells that had been sorted into 384-well plates was captured, followed by a barcoding step of the mRNA during reverse transcription into cDNA. cDNA of each plate was pooled into a single tube, and was fragmented and amplified to generate sequencing-ready libraries for NovaSeq X plus (Illumina) sequencing. Quality control was performed on each library created from a plate.

tag: cell line

tag: cell type

tag: genotype

tag: mouse id

tag: batch


title: K562_1k_1D_B_rep2

city: Beijing

first: Zejia

last: Cui

address: Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

data_processing:
*library strategy: SCOPTE-C
The preprocessing of SCOPE-C reads was similar to the Hi-C data. Firstly, the raw reads of the SCOPE-C two libraries, 150-200 bp short fragments (marked as B) and 200-700 bp long fragments (marked as A), were filtered by Cutadapt v2.6 and pre-processed using HiC-Pro v2.11.4. In brief, clean reads were mapped to the reference genomes (hg19 for human, rheMac10 for macaque, and mm10 for mouse) with bowtie2 v2.3.5. If a read pair locates in the same restriction fragment (DpnII), it was classified as dangling ends (inward), dumped pairs (same strand), or self-cycled (outward). We only retained dangling ends of two libraries combined which were less than 100 bp, they represented the openness of chromatin. Then, the uniquely aligned dangling ends were used to call peak by MACS2 v2.2.5 with “macs2 callpeak --keep-dup all -q 0.01 --extsize 200 --shift 100 --nomodel” options. If read pairs that mapped to two different restriction fragments, they were considered valid pairs and generated interaction heatmaps. Similarly, we merged the valid pairs of two libraries to generate 500 kb, 50 kb, and 25 kb bin size interaction matrixes. The 500 kb matrix was used to define AB compartments by R package HiTC (https://code.bioconductor.org/browse/HiTC/). The 50 kb matrix was used to identify TAD boundaries by matrix2insulation.pl (https://github.com/blajoie/crane-nature-2015). Finally, we used the model in Fit-Hi-C to calculate the statistical significance interactions with the 25 kb matrix. Significant loops were then selected by Fit-Hi-C reported Q value (Q < 0.00001).
Assembly: hg19,mm10,rheMac10
Supplementary files format and content: bigwig,narrowPeak
Supplementary files format and content: bedpe,hic

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: Human B lymphoid cells (GM12878), human chronic myeloid leukemia cells (K562) and human Burkitt’s lymphoma cells (NAMALWA) were cultured in the medium (RPMI 1640; Thermo Fisher, 11875093) containing 10% fetal bovine serum, 100 units/mL penicillium and 100 μg/mL streptomycin.Human HeLa-S3 cell line (HeLa) were cultured in the medium (DMEM; Thermo, C11995500BT) containing 10% fetal bovine serum (FBS; Gibco, 10099141), 100 units/mL penicillium and 100 μg/mL streptomycin (Thermo Fisher, 15140122).Mouse ES cells (mESCs) were cultured on 0.1% gelatin (BD, 214340) pre-coated dishes in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, 11995065) containing 15% fetal bovine serum, 100 units/mL penicillium and 100 μg/mL streptomycin, leukemia-inhibiting factor (LIF) (Millipore, ESG1107), GlutaMAX (Thermo Fisher, 35050061), nucleoside mix (Adenosine, Sigma, A4036; Guanosine, Sigma, G6264;Uridine, Sigma, U3003; Cytidine, Sigma, C4654; Thymidine, Sigma, T1895), β-mercaptoethanol (β-ME; Sigma, M6250), and non-essential amino acids (NEAA; 100X, Gibco, 11140050).Mouse Neural Stem Cells (mNSCs) was performed as previously described (Dongchang Xiao et al., 2018). mNSCs were cultured in the NSC medium containing the N3 medium supplemented with 10 ng/ml recombinant mouse EGF (R&D systems) and 10 ng/ml recombinant human bFGF (R&D Systems), with or without 2 ng/ml Dox (Sigma). The N3 medium contains DMEM/F12 (Life Technologies) with 1x Pen/Strep, 25 μg/ml insulin (Sigma), 50 μg/ml Apo-transferrin (Sigma), 1.28 ng/ml progesterone (Sigma), 16 ng/ml putrescine (Sigma), and 0.52 μg/ml sodium selenite (Sigma). The SCR029 cells were cultured in the Neural Stem Cell Expansion Medium (Chemicon, SCM003) supplemented with 20 ng/ml mouse EGF, 20 ng/ml human bFGF, and 2 μg/ml heparin (Sigma).

extract_protocol:
DNA purification by Phenol-chloroform extraction assay, and biotin Pull-down by Dynabeads Streptavidin T1 beads (Life technologies, 65602) with 100 μL of 1X Tween Washing Buffer twice (1X TWB: 5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). Separate on a magnet and discard the solution. Resuspend the beads in 25 μL of 2X Binding Buffer (2X BB: 10 mM Tris-HCl (pH 7.5); 1 mM EDTA; 2 M NaCl) and add to the DNA elution. Incubate at room temperature for 15 min. Separate on a magnet and discard the solution. Wash the beads by adding 100 μL of 1X TWB and transferring the mixture to a new tube. Heat the tubes on a Thermomixer at 55℃for 2 min with mixing. Reclaim the beads using a magnet. Discard supernatants.
Construction of the SCOPE-C library for sequencing includes crosslinking and lysis, restriction and digestion, biotin–dATP labeling, proximity ligation, open chromatin fragmentation, DNA purification and biotin pull-down, library construction. Subsequent Biotin Pull-down by Dynabeads Streptavidin T1 beads, SCOPE-C DNA was resuspended in 19 μL of ddH2O. Add 33 μL PCR mix, 25 μL 2X NEB Q5 HiFi Hot Start PCR Master Mix, 2.5 μL universal primer, 2.5 μL indexed primer. PCR-amplifies the libraries for 16 cycles. Run the PCR product directly on a 1.5% long gel. Cut the band from the gel, isolating the size of 150-200 bp and 200-500 bp and extract DNA with MinElute Gel Extraction Kit (Qiagen, 28604), respectively. Quantify the concentration with qubit 4.0.

value: bone marrow

value: lymphoblast cell line

value: wild type


title: AB18214.txt

description: Library name: Sample 144

treatment_protocol: hTREM2 mice were s.c. injected with 1M MC38 tumor cells (day 0). Mice were intravenously treated with 200 µg per dose of anti-RSV, anti-TREM2, anti-PD-1, anti-TREM2 + anti-PD1, anti-CTLA-4, anti-TREM2 + anti-CTLA-4, MiTE-144, MiTE-144 + anti-PD1, or MiTE-144 + anti-CTLA-4 on days 8 and 10 (n = 5). Immune cells were isolated on day 11, FACS sorted (total CD45+ and T/NK cell enrichment) and underwent scRNAseq employing SPID-seq resulting in a total of 45,505 high-quality cells from 45 mice.


title: K562_1k_3D_A_rep2

description: allK562_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: RPB1degron_125nM_dTAGv1_2

city: Copenhagen

first: Jesper

middle: Q

last: Svejstrup

address: Blegdamsvej 3B

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: 125nM_2

growth_protocol: RPB1 degron cells were cultured in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 100U/mL penicillin, and 100µg/mL streptomycin in humidified atmosphere with 5% CO2 at 37°C.

value: RPB1 degron D4


title: AB18220.txt

description: Library name: Sample 150


title: Control-D3 ctr1


title: RPB1degron_DMSO_15min_DRB_release_3

description: Library name: DMSO_15min_DRB_release_3

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.20.0.422) and resultant FASTQ files were quality checked using MultiQC (v1.11). Reads were aligned to the GRCh38 genome using hisat2 (v2.2.1) with default options, followed by identification of PCR duplicates using picard Markduplicates (v2.27.3). Further analysis was conducted as in Gregersen et al. (2020). Briefly, bp-resolution read-depth coverage was calculated over intervals representing non-overlapping, protein-coding genes at least 60kb in width, extended -2kb:+120kb around the TSS region. Counts were normalized for sequencing depth (RPM) and meta-profiles were created by taking a trimmed mean across genes at each bp location. A smoothing spline was fitted to each meta-profile using R’s smooth.spline function (spar=0.3). Wave peaks were subsequently calculated as the maximum point on the spline for each sample, ensuring that wave peaks advanced with time. Elongation rates in kb/min were estimated by fitting a linear model to the wave peak positions of all samples (i.e. 15, 30, and 45 minutes post release) as a function of time.
Assembly: GRCh38
Supplementary files format and content: bigwig, CPM normalized

extract_protocol:
Following a 10 minute pulse with 1mM 4sU, media was aspirated and cells were harvested by the addition of 1mL Trizol to stop the reaction. To isolate total RNA, one-fifth of chloroform was added to lysates and shaken well, followed by centrifugation (12000g, 5 minutes at 4C). The upper aqueous phase was transferred to MaXtract high-density phase-lock tubes, that were previously prepared according to manufacturer’s instructions, and an equal volume of chloroform/isoamyl alcohol (24:1) was added. Lysates were then centrifuged again (12000g, 5 minutes at 4C) and the upper aqueous phase was transferred to a new tube. The RNA was then precipitated through the addition of 1.1X volumes of 100% isopropanol, incubation at room temperature for 20 minutes and centrifugation (12000g, 20 minutes at 4C). RNA pellets were washed once with 85% (v/v) ethanol, and air dried at room temperature before resuspension in Ultrapure DNase/RNase-free distilled water. As an external reference control, 500ng S.cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) nascent RNA was spiked-in to 100µg of H.sapiens total RNA. The RNA was then fragmented by the addition of 20µL 1M NaOH and incubation on ice for 20 minutes. Fragmentation was stopped by the addition of 80µL 1M Tris HCl pH 6.8 and material was purified twice using the Micro Bio-Spin P-30 Gel Columns according to manufacturer’s instructions. Thiol-specific biotinylation of RNA was performed using 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 mg MTSEA biotin-XX linker in a final volume of 250µL and incubation at room temperature for 30 minutes in the dark. Biotinylated RNA was then purified by addition of 250μL of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol)), followed by shaking and addition to MaXtract high-density phase-lock tubes that were previously prepared according to manufacturers instructions. Following centrifugation (12000g, 5minutes at 4C), the upper aqueous phase was transferred to a new tube and biotinylated RNA was precipitated using one-tenth the volume 5M NaCl and 1.1X volume 100% isopropanol, followed by incubation at room temperature for 10 minutes and centrifugation (20000g, 20 minutes at 4C). RNA pellets were washed once in 85% (v/v) ethanol, air dried at room temperature, and resuspended in 50µL Ultrapure DNase/RNase-free distilled water. The RNA was then denatured by incubating for 10 minutes at 65°C in the dark. Biotinylated RNA was separated from the total RNA pool by addition of 100 μL μMACS Streptavidin MicroBeads and incubation for 15 minutes at room temperature with constant rotation. Beads were then applied to a μColumn pre-equilibrated with 100 µL nucleic acid equilibration buffer and immobilised on a magnetic stand, washed twice with pre-warmed (55°C) wash buffer (100 mM Tris HCl pH 7.4 10mM EDTA, 1M NaCl and 0.1% (v/v) Tween 20) and biotinylated RNA was eluted by two additions of 100μL 100 mM DTT, 5 minutes apart. Purification of biotinylated RNA was performed using the RNeasy MinElute kit according to manufacturer’s instructions, where 1050 μL 100% ethanol and 750 μL RLT buffer was added per 200μL reaction to precipitate RNA < 200 nt.
Sequencing libraries were prepared from biotinylated RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (without additional fragmentation) and NEBNextMultiplex Oligos for Illumina (Unique Dual Index UMI adapters RNA Set 1) and were sequenced on the NextSeq 2000 (P3 50 kit).

treatment_protocol: RPB1 degron cells were seeded at a density of 4 million cells in a 10cm plate and were either treated with DMSO or different concentrations of dTAGv-1 for 16 hours before harvest. After 12.5 hours, transcription was synchronized by the addition of 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hours, followed by a release from DRB inhibition for 15, 30, or 45 minutes prior to harvest. During the final 10 minutes prior to harvest, cells were pulsed for 1mM 4-thiouridine, to metabolically label nascently transcribed RNA.

value: DMSO; 100uM DRB for 3.5hr


title: RPB1degron_125nM_dTAGv1_1

description: Library name: 125nM_1


title: FID-D3 trt2


title: NAMALWA_1k_3D_A_rep1

description: allNAM_intraOnly.spline_pass1.res25000.significances.loop.bedpe

source_name: lymphoma

value: lymphoma

value: NAMALWA

value: human Burkitt lymphoma cell line


title: RPB1degron_62nM_dTAGv1_3

description: Library name: 62nM_3

value: 62nM dTAGv1


title: K562_1k_1D_B_rep1


title: mouse_IN_1k_3D_A_rep6

description: mouse.iN_intraOnly.spline_pass1.res25000.significances.loop.bedpe

source_name: Mouse cerebral cortex

value: Mouse cerebral cortex

value: Neuron

value: interneurons


title: mouse_IN_1k_1D_B_rep6

description: mouseBrain_1k_iN.allMerged.macs2.peaks.narrowPeak


title: K562_1k_3D_A_rep1


title: AB18213.txt

description: Library name: Sample 143


title: AB18212.txt

description: Library name: Sample 142


title: RPB1degron_62nM_dTAGv1_2

description: Library name: 62nM_2


title: RPB1degron_DMSO_15min_DRB_release_2

description: Library name: DMSO_15min_DRB_release_2


title: AB18211.txt

description: Library name: Sample 141


title: RPB1degron_62nM_dTAGv1_1

description: Library name: 62nM_1


title: AB18210.txt

description: Library name: Sample 140


title: HeLa_bulk_3D_A_rep3

description: hela_all_intraOnly.spline_pass1.res10000.significances.loop.bedpe

source_name: cervix adenocarcinoma

value: cervix adenocarcinoma

value: HeLa

value: Human cervical cancer cell line


title: RPB1degron_32nM_dTAGv1_3

description: Library name: 32nM_3

value: HEK293 Flp-In TREX

value: 32nM dTAGv1


title: mouse_IN_1k_1D_B_rep4


title: AB18209.txt

description: Library name: Sample 139


title: RPB1degron_32nM_dTAGv1_2

description: Library name: 32nM_2


title: HeLa_bulk_1D_B_rep2


title: mouse_IN_1k_3D_A_rep4


title: AB18208.txt

description: Library name: Sample 138


title: mouse_IN_1k_1D_B_rep3


title: HeLa_bulk_3D_A_rep2


title: RPB1degron_32nM_dTAGv1_1

description: Library name: 32nM_1


title: AB18207.txt

description: Library name: Sample 137


title: RPB1degron_DMSO_3

description: Library name: DMSO_3

value: DMSO


title: HeLa_bulk_1D_B_rep1


title: AB18206.txt

description: Library name: Sample 136


title: HeLa_bulk_3D_A_rep1


title: mouse_IN_1k_3D_A_rep3


title: mouse_IN_1k_1D_B_rep5


title: mouse_IN_1k_1D_B_rep2


title: RPB1degron_DMSO_2

description: Library name: DMSO_2


title: HeLa_1k_1D_B_rep3


title: RPB1degron_DMSO_1

description: Library name: DMSO_1


title: AB18204.txt

description: Library name: Sample 134


title: mouse_IN_1k_3D_A_rep5


title: HeLa_1k_3D_A_rep3

description: allHela_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: AB18205.txt

description: Library name: Sample 135


title: HeLa_bulk_1D_B_rep3


title: CD4CD25hi015LPL

city: Amsterdam

first: Lisanne

last: Lutter

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam University Medical Center

description:
Library name: Sample 11
column name in combined_raw_counts CD4CD25hi015LPL

data_processing:
Samples were sequenced as 75 bp paired-end on a NextSeq 500 (Illumina).
Quality of the FASTQ files was assessed with FASTQC, and Trimmomatic v0.39 was used to remove low quality reads and adapter contamination.
Reads were aligned using the STAR version 2.3.0 software that permits unique alignments to Human Ensembl genes.
Assembly: GRCh38
Supplementary files format and content: Tab-delimeted file contains raw gene counts per sample.

source_name: colon

growth_protocol: Biopsies were collected in HBSS media (Gibco) containing 2% FCS and 0.2% amphotericin B. The intestinal tissue was transferred to HBSS supplemented with 1 mM DTT (Sigma) and placed on a rolling device for 10 min at 4°C. After discarding the supernatant, the intestinal tissue was transferred to HBSS supplemented with 2% FCS and 5 mM EDTA and shaken (2×) at 180 rpm for 30 min at 37°C. The tissue suspension was passed through a 70 µm cell strainer (Costar) and constituted the intraepithelial population. To obtain lamina propria T cells, the remaining intestinal biopsies were subsequently incubated for 1 h at 37°C with 1 mg/ml collagenase IV (Sigma) in RPMI medium (supplemented with 10% FCS, 100 U/ml penicillin–streptomycin, and 0.2% Fungizone), then forcefully resuspended through a 19G needle, washed and filtered with 70 µm cell strainer (Costar). In preparation for fluorescence-activated cell sorting (FACS) the intestinal cells were incubated with the surface antibodies for 20 min in supplemented RPMI (2% FCS, 1% penicillin and streptomycin, 0.2% Fungizone) at 4°C, and subsequently washed in FACS buffer before sorting on a FACSAria™ III (BD) in TRIzol LS (Thermo Fisher Scientific) and immediately frozen at −80°C. Antibodies used: anti-human EpCAM PerCP-Cy5.5, CD45 PerCP or PE-Cy7, TCRγδ FITC, CD4 BV510, CD8α PB, CD25 APC-Cy7.

extract_protocol:
The sorted cells were thawed in TRIzol LS for TRIzol (Thermo Fisher Scientific) RNA extraction following the manufacturer’s protocol, and stored at −80°C until library preparation.
Sequencing libraries were prepared using the Cel-Seq2 sample preparation protocol.

value: colon

tag: compartment

value: lamina propria

value: Treg (CD25high)

tag: sorted cell_number

tag: diagnosis

value: Crohn's disease


title: mouse_IN_1k_3D_A_rep2

value: wild type


title: mouse_IN_1k_1D_B_rep1


title: HeLa_1k_1D_B_rep2


title: CD4CD25hi015IEL

description:
Library name: Sample 10
column name in combined_raw_counts CD4CD25hi015IEL

value: epithelium


title: AB18203.txt

description: Library name: Sample 133


title: mouse_IN_1k_3D_A_rep1


title: AB18202.txt

description: Library name: Sample 132


title: CD4CD25hi014LPL

description:
Library name: Sample 9
column name in combined_raw_counts CD4CD25hi014LPL


title: HeLa_1k_3D_A_rep2


title: mouse_EN_1k_1D_B_rep6

description: mouseBrain_1k_eN.allMerged.macs2.peaks.narrowPeak

value: excitatory neurons


title: CD4CD25hi014IEL

description:
Library name: Sample 8
column name in combined_raw_counts CD4CD25hi014IEL


title: HeLa_1k_1D_B_rep1


title: AB18201.txt

description: Library name: Sample 131


title: mouse_EN_1k_3D_A_rep6

description: mouse.eN_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: AB18199.txt

description: Library name: Sample 129


title: AB18200.txt

description: Library name: Sample 130


title: CD4CD25hi013LPL

description:
Library name: Sample 7
column name in combined_raw_counts CD4CD25hi013LPL


title: GM12878_1k_1D_B_rep3

source_name: Blood

value: Blood

value: Human B lymphocytes cell line


title: mouse_EN_1k_1D_B_rep5

value: Mouse cerebral cortex

value: Neuron


title: GM12878_1k_3D_A_rep3

description: allGM_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: AB18198.txt

description: Library name: Sample 128


title: CD4CD25hi011LPL

description:
Library name: Sample 4
column name in combined_raw_counts CD4CD25hi011LPL


title: mouse_EN_1k_1D_B_rep4


title: AB18197.txt

description: Library name: Sample 127


title: GM12878_1k_3D_A_rep2


title: mouse_EN_1k_3D_A_rep4


title: CD4CD25hi012IEL

description:
Library name: Sample 5
column name in combined_raw_counts CD4CD25hi012IEL


title: CD4CD25hi011IEL

description:
Library name: Sample 3
column name in combined_raw_counts CD4CD25hi011IEL


title: GM12878_1k_1D_B_rep2


title: AB18196.txt

description: Library name: Sample 126


title: CD4CD25Hi012LPL

description:
Library name: Sample 2
column name in combined_raw_counts CD4CD25Hi012LPL


title: mouse_EN_1k_3D_A_rep3


title: AB18195.txt

description: Library name: Sample 125


title: AB18194.txt

description: Library name: Sample 124


title: GM12878_1k_3D_A_rep1


title: mouse_EN_1k_1D_B_rep3


title: CD4CD25IEL

description:
Library name: Sample 1
column name in combined_raw_counts CD4CD25IEL

value: healthy colon of patient with colorectal cancer


title: mouse_EN_1k_1D_B_rep2


title: AB18193.txt

description: Library name: Sample 123


title: CD4CD25hi013IEL

description:
Library name: Sample 6
column name in combined_raw_counts CD4CD25hi013IEL


title: HeLa_1k_3D_A_rep1

value: cervix adenocarcinoma

value: HeLa


title: mouse_EN_1k_3D_A_rep5


title: mouse_EN_1k_3D_A_rep2


title: LOC_B

city: London

first: Maximiliano

last: Gutierrez

state: --- Select One ---

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: single cell RNA

data_processing:
We used Cell Ranger (version 6.0.1) to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to human transcriptome GRCh38-2020-A (software and data available from 10x genomics).
Assembly: human GRCh38 (GRCh38-2020-A from 10x Genomics)
Supplementary files format and content: Cell ranger output files: 10x counts matrix, features and barcode data

source_name: lung on chip

growth_protocol: iPSC were differentiated in respective culture medium and assembled in the lung on chip, cells were cultured for a total of 22 days prior to cell dissociation. For details, refer to manuscript.

extract_protocol:
Dissociation into single cells, 10x Genomics, CG000315 Chromium Single Cell 3' Reagent Kits
10x Genomics, CG000315 Chromium Single Cell 3' Reagent Kits
10x Chromium Single Cell 3' Capture v3

treatment_protocol: Vascular endothelial cells were/were not seeded on day -1; breathing of lung on chip was achieved using AXBreather maching commencing from day 4. For details, refer to manuscript.

value: lung on chip

value: alveolar epithelial cells, vascular endothelial cells, alveolar macrophages

value: Breathing


title: AB18192.txt

description: Library name: Sample 122


title: mouse_EN_1k_1D_B_rep1


title: LOC_S

description: single cell RNA

value: Control


title: mouse_EN_1k_3D_A_rep1


title: AB15862.txt

description: Library name: Sample 121

value: RunE


city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_5_S29
In vivo CRISPR_PDX.xlsx

data_processing:
To quantify sgRNA reads, 20-nucleotide sequences that matched the sgRNA backbone structure (5’ prime CACCG and 3’ prime GTTT) were extracted and aligned to the sgRNA sequences of the CRISPR screening library using Bowtie2. The frequency for individual sgRNAs was calculated as the read counts of each sgRNA divided by the total read counts matched to the library.
Assembly: The CRISPR library was designed based on GRCh38
Supplementary files format and content: xlsx file, the calculated sgRNA abundance results based on the CRISPR screen.
Library strategy: CRISPR Screen

source_name: PDX

growth_protocol: Human Mono-mac-6 cells were grown in RPMI 1640 media supplemented with 10% FBS ,1% Penicillin-Streptomycin , 2 mM L-glutamine ,1x non-essential amino acids , 1 mM sodium pyruvate , 10 μg /ml human insulin,10mM HEPES and 0.1%Plasmocin™ Prophylactic. The AML PDX cells was cultured in IMDM supplemented with 10% FBS and human cytokines (10 ng/ml IL3, 10 ng/ml IL6, 10 ng/ml FLT3-ligand, 10 ng/ml TPO, 10 ng/ml SCF).

extract_protocol:
Genomic DNA from CRISPR-screened cell samples was extracted using the HotSHOT protocol, a rapid alkaline lysis method.
The CRISPR sgRNA cassette was amplified by PCR using primers DCF01 (5′-CTTGTGGAAAGGACGAAACACCG-3′) and DCR03 (5′-CCTAGGAACAGCGGTTTAAAAAAGC-3′). The PCR product was then prepared for Illumina sequencing by adding P7 and P5 adapters and dual indexes.

treatment_protocol: Mono-mac-6 and PDX cells were infected with the lentiviral library and maintained in fresh culture medium. The medium was replaced every two days, and cells were harvested 3–5 days post-infection as baseline (day 0) samples. For in vivo studies, 1 × 10⁷ PDX cells were injected into each NSGS mouse. The health status of the mice was monitored daily, and bone marrow mononuclear cells (BM MNCs) were collected as endpoint samples when leukemic symptoms became apparent (approximately 28 days post-injection). The AML donor cells were isolated from BM MNCs with hCD45 beads. For in vitro experiments, cells were cultured under optimal growth conditions, with the medium replaced every two days. Cells were collected at day 28 as endpoint samples for DNA extraction and sequencing.

value: PDX

value: AML


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_4_S28
In vivo CRISPR_PDX.xlsx


title: AB15861.txt

description: Library name: Sample 120


title: AM_S

description: single cell RNA

value: alveolar epithelial cells, alveolar macrophages

value: wild type


title: AB15860.txt

description: Library name: Sample 119


title: dliaR, daptomycin-treated, replicate 3

city: Genève

first: Kimberly

last: Kline

address: 1 Rue Michel Servet

country: Switzerland

institute: University of Geneva

description:
Library name: Sample 18
∆liaR 3 treated = dLiaRplus3

data_processing:
Paired-end sequencing (150x150bp) was performed on the Illumina HiSeqX v2.5 system.
The quality of the sequencing data was assessed using FastQC (version 0.11.9).
Adapter and quality trimming were performed using bbduk (BBMap version 38.96)
Assembly: The trimmed reads were mapped to the E. faecalis OG1RF reference genome (GenBank accension CP002621.1) using the BWA-MEM algorithm of Burrows-Wheeler Aligner (version 0.7.17-r1198-dirty) using the default setting.
Supplementary files format and content: Transcript abundance was determined using htseq-count (HTSeq version 2.0.1) with intersection-strict mode. Differential gene expression (DGE) analysis was performed in R (version 4.3.1) using edgeR (version 3.42.4)
Supplementary files format and content: Tab-delimited text file includes new and old gene locus tags, gene name, gene product, operon ID, log2-fold change, logCPM, p value, FDR, and raw counts for each strain/condition,

organism: Enterococcus faecalis

source_name: Planktonic bacteria

growth_protocol: Overnight cultures of strains WT, dliaFSR, and dliaR were sub-cultured 100-fold into fresh BHI supplemented with 50 mg/L CaCl2 and grown at 37°C under static conditions to mid-log phase (OD600 ~0.5).

extract_protocol:
For RNA extraction, cultures were harvested and treated with RNAprotect (Qiagen, USA) to stabilize RNA. Then, cells were lysed with 20 mg/mL lysozyme (Sigma-Aldrich, USA) in lysis buffer (10 mM Tris-HCl at pH 8, 50 mM NaCl, 1 mM EDTA, 0.75 M Sucrose) at 37°C for 1 h. Following centrifugation, the pellet was resuspended in 1 mL of TRIzol and 200 µL of chloroform, and incubated at 4°C for 2 min. After centrifuging at 12,000g at 4°C for 15 min, the top aqueous phase was mixed thoroughly with an equal volume of 80% ethanol. Total RNA was then isolated using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s recommendations. DNA was depleted via on-column DNase I treatment (Qiagen, USA). RNA quality (RINe ≥8) was assessed using the RNA ScreenTape system (Agilent Technologies, USA), while DNA contamination (≤10%) was quantified using the Qubit RNA BR and dsDNA HS Assay kits (Invitrogen, USA).
cDNA library preparation and ribosomal RNA depletion was performed by the in-house sequencing facility using the Illumina Total RNA Prep with Ribo-Zero Plus kit (Illumina, USA).

treatment_protocol: Then, 2 µg/mL of daptomycin was added to the culture and incubated for 15 min. Control cultures were left untreated.

value: Planktonic bacteria

value: OG1RF strain

value: Bacteria

value: dliaR

value: With daptomycin


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_3_S27
In vivo CRISPR_PDX.xlsx


title: GM12878_1k_1D_B_rep1

value: Blood

value: Human B lymphocytes cell line


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_2_S26
In vivo CRISPR_PDX.xlsx


title: mouse_IPC_1k_3D_A_rep1

value: Mouse cerebral cortex

value: Neuron

value: intermediate progenitor cells


title: AB15859.txt

description: Library name: Sample 118


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_6_S30
In vivo CRISPR_PDX.xlsx


title: mouse_IPC_1k_1D_B_rep1


title: AB15858.txt

description: Library name: Sample 117


title: dliaR, daptomycin-treated, replicate 1

description:
Library name: Sample 16
∆liaR 1 treated = dLiaRplus1


title: AM_B

description: single cell RNA

value: lung on chip

value: Breathing


title: dliaR, daptomycin-treated, replicate 2

description:
Library name: Sample 17
∆liaR 2 treated = dLiaRplus2


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_6_S24
In vivo CRISPR_PDX.xlsx


title: mouse_RG_1k_3D_A_rep6

description: mouse.RG_intraOnly.spline_pass1.res25000.significances.loop.bedpe

value: radial glia


title: dliaR, untreated, replicate 3

description:
Library name: Sample 15
∆liaR 3 untreated = dLiaR3

value: No dapromycin


title: AB15857.txt

description: Library name: Sample 116

value: RunE


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_5_S23
In vivo CRISPR_PDX.xlsx

value: PDX

value: AML


title: mouse_RG_1k_1D_B_rep5

description: mouseBrain_1k_RG.allMerged.macs2.peaks.narrowPeak

value: wild type


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_4_S22
In vivo CRISPR_PDX.xlsx


title: AB15856.txt

description: Library name: Sample 115


title: dliaR, untreated, replicate 2

description:
Library name: Sample 14
∆liaR 2 untreated = dLiaR2

value: Planktonic bacteria

value: OG1RF strain


title: mouse_RG_1k_3D_A_rep5


title: mouse_RG_1k_1D_B_rep4


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_3_S21
In vivo CRISPR_PDX.xlsx


title: dliaR, untreated, replicate 1

description:
Library name: Sample 13
∆liaR 1 untreated = dLiaR1

value: Bacteria

value: dliaR


title: AB15855.txt

description: Library name: Sample 114


title: AB15854.txt

description: Library name: Sample 113


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_BM_1_S25
In vivo CRISPR_PDX.xlsx


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_2_S20
In vivo CRISPR_PDX.xlsx


title: dliaFSR, daptomycin-treated, replicate 1

description:
Library name: Sample 10
∆liaFSR 1 treated = dLiaFSRplus1

value: dliaFSR

value: With daptomycin


title: AB15851.txt

description: Library name: Sample 110


title: mouse_RG_1k_1D_B_rep6

value: Mouse cerebral cortex


description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_END2_S14
In vitro CRISPR_PDX.xlsx


title: mouse_RG_1k_3D_A_rep4

value: Neuron


description:
Library name: RS20240507HB_mRNP_PDX148_BM_invivo_Start_1_S19
In vivo CRISPR_PDX.xlsx


title: mouse_RG_1k_1D_B_rep3


title: dliaFSR, daptomycin-treated, replicate 2

description:
Library name: Sample 11
∆liaFSR 2 treated = dLiaFSRplus2


title: dliaFSR, daptomycin-treated, replicate 3

description:
Library name: Sample 12
∆liaFSR 3 treated = dLiaFSRplus3


title: dliaFSR, untreated, replicate 3

description:
Library name: Sample 9
∆liaFSR 3 untreated = dLiaFSR3


description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_END3_S15
In vitro CRISPR_PDX.xlsx


title: mouse_RG_1k_3D_A_rep3

description: mouse.RG_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: AB15853.txt

description: Library name: Sample 112


title: mouse_RG_1k_1D_B_rep2


title: AB15852.txt

description: Library name: Sample 111


title: AB15850.txt

description: Library name: Sample 109


title: AB15849.txt

description: Library name: Sample 108


title: mouse_RG_1k_3D_A_rep2


title: dliaFSR, untreated, replicate 2

description:
Library name: Sample 8
∆liaFSR 2 untreated = dLiaFSR2


description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_END1_S13
In vitro CRISPR_PDX.xlsx


title: mouse_RG_1k_1D_B_rep1

description: mouseBrain_1k_RG.allMerged.macs2.peaks.narrowPeak


title: AB15848.txt

description: Library name: Sample 107


title: WT, daptomycin-treated, replicate 3

description:
Library name: Sample 6
WT 3 treated = WTplus3

value: Wildtype


title: RuiS20231004PDX_mRNP_AML_PDX148_S3_S12

description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_S3_S12
In vitro CRISPR_PDX.xlsx


title: RuiS20231004PDX_mRNP_AML_PDX148_S2_S11

description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_S2_S11
In vitro CRISPR_PDX.xlsx


title: AB15847.txt

description: Library name: Sample 106


title: mouse_RG_1k_3D_A_rep1


title: WT, daptomycin-treated, replicate 2

description:
Library name: Sample 5
WT 2 treated = WTplus2


title: RuiS20231004PDX_mRNP_AML_PDX148_S1_S10

description:
Library name: RuiS20231004PDX_mRNP_AML_PDX148_S1_S10
In vitro CRISPR_PDX.xlsx


title: AB15846.txt

description: Library name: Sample 105


title: WT, untreated, replicate 2

description:
Library name: Sample 2
WT 2 untreated  = WT2


title: mNSC_bulk_1D_B_rep2

description: mNSC.25kb_intraOnly.spline_pass1.res25000.significances.loop.bedpe

source_name: cerebral striatum and mesencephalon

value: cerebral striatum and mesencephalon

value: mNSC

value: Mouse neural stem cells


title: dliaFSR, untreated, replicate 1

description:
Library name: Sample 7
∆liaFSR 1 untreated = dLiaFSR1

value: No dapromycin


title: mNSC_bulk_3D_A_rep3


title: WT, daptomycin-treated, replicate 1

description:
Library name: Sample 4
WT 1 treated = WTplus1


title: AB15844.txt

description: Library name: Sample 103

value: RunE


title: WT, untreated, replicate 3

description:
Library name: Sample 3
WT 3 untreated  = WT3


title: AB15843.txt

description: Library name: Sample 102


title: RuiS20231003MM6_mRNP_AML_MM6_END2_S5

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_END2_S5
In vitro CRISPR_Mono-mac-6.xlsx


title: mNSC_bulk_3D_A_rep2


title: WT, untreated, replicate 1

description:
Library name: Sample 1
WT 1 untreated  = WT1


title: RuiS20231003MM6_mRNP_AML_MM6_END1_S4

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_END1_S4
In vitro CRISPR_Mono-mac-6.xlsx


title: RuiS20231003MM6_mRNP_AML_MM6_S3_S3

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_S3_S3
In vitro CRISPR_Mono-mac-6.xlsx


title: mNSC_bulk_3D_A_rep1


title: AB15842.txt

description: Library name: Sample 101


title: mNSC_bulk_1D_B_rep1


title: RuiS20231003MM6_mRNP_AML_MM6_S1_S1

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_S1_S1
In vitro CRISPR_Mono-mac-6.xlsx


title: AB15841.txt

description: Library name: Sample 100


title: RuiS20231003MM6_mRNP_AML_MM6_S2_S2

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_S2_S2
In vitro CRISPR_Mono-mac-6.xlsx


title: AB15840.txt

description: Library name: Sample 99


title: mNSC_bulk_1D_B_rep3


title: AB15845.txt

description: Library name: Sample 104


title: RuiS20231003MM6_mRNP_AML_MM6_END3_S6

description:
Library name: RuiS20231003MM6_mRNP_AML_MM6_END3_S6
In vitro CRISPR_Mono-mac-6.xlsx


title: OCIAML3_MENi_3

city: Oxford

first: Catherine

last: Chahrour

address: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: Library name: OCIAML3_MENi_3

data_processing:
FASTQ files were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using STAR v2.7.11a with the following parameters: --quantMode TranscriptomeSAM GeneCounts --outSAMunmapped Within --outSAMattributes Standard.
Alignments were quantified using featureCounts v2.0.6 with the following parameters: -s 2 -p --countReadPairs -t exon -g gene_id.
Assembly: hg38
Supplementary files format and content: tsv file containing raw counts

extract_protocol:
RNA was extracted from ~ 5 million cells using the Qiagen RNeasy Kit for RNA (74104) purification following the manufacturer’s instructions. mRNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S) using 1 µg of input RNA.
Library preparation for sequencing was done using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S).


title: AB15839.txt

description: Library name: Sample 98


title: mESC_sc_rep10

source_name: inner cell mass of preimplantation blastocysts

value: mESC

value: Mouse embryonic stem cell line


title: OCIAML3_CONTROL_3

description: Library name: OCIAML3_CONTROL_3

value: vehicle control


title: mESC_sc_rep12

value: inner cell mass of preimplantation blastocysts

value: wild type


title: NIH30, control, snMultiome, ATAC

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St.

institute: The University of Texas Health Science Center at Houston

description:
Library name: NIH30 ATAC
10x Genomics

library_source: other

data_processing:
Cell Ranger ARC (v2.0.2) pipeline was used for aligning the snRNA-seq and snATAC-seq reads from each sample to the GRCh38 genome and quantifying them with ‘cellranger-arc count’.
Assembly: GRCh38
Supplementary files format and content: CellRanger-arc output files: raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

molecule: other

source_name: Hippocampus

extract_protocol:
Samples were stored at -80 °C. The nuclei isolation protocol was modified based on a 10x Genomics protocol (CG000375). Briefly, 30 mg of frozen tissue was finely minced on dry ice to the smallest possible size, and then it was homogenized in homogenization buffer on ice within 20 minutes. The homogenized tissue was filtered through a 35 μm cell strainer. Small cell debris were removed by centrifuging at 300g for 3 minutes at 4 °C. The large cell debris was removed by gradient centrifugation using OptiPrep density gradient medium (Sigma, cat#D1556-250ML) at 7200g for 15 minutes at 4 °C. The nuclei pellet was resuspended in a 0.1x lysis buffer. After washing the isolated nuclei in the wash buffer, the nuclei were resuspended in 1x nuclei buffer before single-nuclei Multiome library construction. (UTHealth Cancer Genomic Core)
Single-nuclei libraries were constructed following the 10x Chromium Single Cell Multiome ATAC + Gene Expression protocol (CG000338).

value: Hippocampus

tag: disease state

value: Control

tag: Sex

value: F

tag: age on_death

tag: pmi (hours)


title: NIH30, control, snMultiome, GEX

description:
Library name: NIH30 GEX
10x Genomics


title: AB15838.txt

description: Library name: Sample 97


title: AB15837.txt

description: Library name: Sample 96


title: mESC_sc_rep8


title: EGR1 DBD

type: protein

first: Yuval

last: Bayer

address: Herzl St 234

hyb_protocol: The probe is designed to form a hairpin-loop structure using loop and clamp sequences and the 25 bp variable part (the partitioned de Bruijn sequence). The hairpin formation was done by incubating the microarray in graduated cooling from 85-celsius degrees degrees Celsius.

scan_protocol: GenePix 4400A array scanner using 720 gain 72 power for ETS1 and 800 gain 80 power for EGR1.

data_processing: For each probe area, calculate median of pixels as intensity. For EGR1, apply linear regression to combine different gain scans. Then using a moving window to remove spatial correlation. Finally, we standradized the normalized values by substracting the mean and dividing by the standrad deviation.

molecule: protein

source_name: E coli

label_protocol: GST-tag mouse mAb Alexa Fluor.

extract_protocol: Expressed in E coli.

tag: tag

value: GST-tagged protein


title: OCIAML3_MENi_1

description: Library name: OCIAML3_MENi_1


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_2

description: Library name: UBC_500nM_2

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.20.0.422) and resultant FASTQ files were quality checked using MultiQC (v1.11). Paired-end reads were aligned to the GRCh38 genome using hisat2 (v2.2.1) with options --no-mixed --no-discordant -p 16 --rna-strandness RF, followed by identification of PCR duplicates using picard Markduplicates (v2.27.3). To perform differential gene expression analysis, reads mapping to genes in the GRCh38 genome (Ensembl release 109) were counted using FeatureCounts from the subread package (v2.0.6; featureCounts -O -M -T 4 -s 2 --fraction -t exon). Differential gene expression was then determined with DESeq2 (alpha=0.01).
Assembly: GRCh38
Supplementary files format and content: text file with gene count information

extract_protocol:
Sixteen hours after treatment with dTAGv-1, media was aspirated and cells were harvested by the addition of 1mL Trizol to the plate. To isolate total RNA, one-fifth of chloroform was added to lysates and shaken well, followed by centrifugation (12000g, 5 minutes at 4C). The upper aqueous phase was transferred to MaXtract high-density phase-lock tubes, that were previously prepared according to manufacturer’s instructions, and an equal volume of chloroform/isoamyl alcohol (24:1) was added. Lysates were then centrifuged again (12000g, 5 minutes at 4C) and the upper aqueous phase was transferred to a new tube. The RNA was then precipitated through the addition of 1.1X volumes of 100% isopropanol, incubation at room temperature for 20 minutes and centrifugation (12000g, 20 minutes at 4C). RNA pellets were washed once with 85% (v/v) ethanol, and air dried at room temperature before resuspension in Ultrapure DNase/RNase-free distilled water.
2ug total RNA was used for oligo(dT) purification. Sequencing libraries were then constructed using a KAPA mRNA HyperPrep Kit

value: RPB1 degron D4; UBC-RPB1-His

value: 500nM dTAGv1


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_3

description: Library name: UBC_500nM_3


title: mESC_sc_rep7

description: merge.sc.mESC.allValidPairs.hic


title: AB15835.txt

description: Library name: Sample 94


title: OCIAML3_CONTROL_1

description: Library name: OCIAML3_CONTROL_1


title: mESC_sc_rep6


title: Full-length human ETS1 W356C


title: OCIAML3_COMBO_3

description: Library name: OCIAML3_COMBO_3

value: ABT-199 plus DS-1594b


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_1

description: Library name: UBC_500nM_1


title: mESC_sc_rep5

description: merge.sc.mESC.allValidPairs.hic


title: mESC_sc_rep11

description: merge.sc.mESC.allValidPairs.hic


title: AB15833.txt

description: Library name: Sample 92


title: OCIAML3_MENi_2

description: Library name: OCIAML3_MENi_2


title: RPB1degron_UBC-RPB1_DMSO_3

description: Library name: UBC_DMSO_3

value: DMSO


title: mESC_sc_rep9

description: merge.sc.mESC.allValidPairs.hic


title: OCIAML3_CONTROL_2

description: Library name: OCIAML3_CONTROL_2


title: OCIAML3_COMBO_2

description: Library name: OCIAML3_COMBO_2


title: AB15831.txt

description: Library name: Sample 90


title: mESC_sc_rep3

description: merge.sc.mESC.allValidPairs.hic


title: AB15832.txt

description: Library name: Sample 91


title: RPB1degron_UBC-RPB1_DMSO_2

description: Library name: UBC_DMSO_2


title: mESC_sc_rep2


title: AB15834.txt

description: Library name: Sample 93


title: mESC_sc_rep4


title: OCIAML3_ABT_3

description: Library name: OCIAML3_ABT_3


title: RPB1degron_UBC-RPB1_DMSO_1

description: Library name: UBC_DMSO_1


title: mESC_sc_rep1

description: merge.sc.mESC.allValidPairs.hic


title: OCIAML3_ABT_2

description: Library name: OCIAML3_ABT_2


title: RPB1degron_500nM_dTAGv1_2

description: Library name: 500nM_2

value: RPB1 degron D4


title: RPB1degron_500nM_dTAGv1_3

description: Library name: 500nM_3


title: OCIAML3_ABT_1

description: Library name: OCIAML3_ABT_1


title: AB15829.txt

description: Library name: Sample 88


title: AB15836.txt

description: Library name: Sample 95


title: RPB1degron_500nM_dTAGv1_1

description: Library name: 500nM_1


title: mESC_bulk_3D_A_rep3

description: mESC.25kb_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: MV411_MENi_3

description: Library name: MV411_MENi_3


title: mESC_bulk_1D_B_rep3


title: OCIAML3_COMBO_1

description: Library name: OCIAML3_COMBO_1


title: AB15830.txt

description: Library name: Sample 89


title: AB15828.txt

description: Library name: Sample 87


title: AB15827.txt

description: Library name: Sample 86


title: MV411_MENi_2

description: Library name: MV411_MENi_2


title: RPB1degron_250nM_dTAGv1_3

description: Library name: 250nM_3

value: 250nM dTAGv1


title: AB15826.txt

description: Library name: Sample 85


title: AB15825.txt

description: Library name: Sample 84


title: Full-length human ETS1 W356C

hyb_protocol: Microarray was double-stranded using Thermo Sequenase polymerase and primers.

data_processing: For each probe area, calculate the median of pixels as intensity. Then, use a moving window to remove spatial correlation. Finally, we standardized the normalized values by subtracting the mean and dividing by the standard deviation.


title: mESC_bulk_1D_B_rep2


title: AB15824.txt

description: Library name: Sample 83


title: RPB1degron_250nM_dTAGv1_2

description: Library name: 250nM_2


title: MV411_MENi_1

description: Library name: MV411_MENi_1


title: MV411_CONTROL_3

description: Library name: MV411_CONTROL_3


title: mESC_bulk_1D_B_rep1


title: RPB1degron_167nM_dTAGv1_3

description: Library name: 167nM_3

value: 167nM dTAGv1


title: RPB1degron_250nM_dTAGv1_1

description: Library name: 250nM_1


title: AB15823.txt

description: Library name: Sample 82

value: RunE


title: mESC_bulk_3D_A_rep2

value: mESC


title: MV411_CONTROL_1

description: Library name: MV411_CONTROL_1


title: MV411_CONTROL_2

description: Library name: MV411_CONTROL_2


title: mESC_1k_1D_B_rep6

description: mESC_1k_intraOnly.spline_pass1.res25000.significances.loop.bedpe

value: Mouse embryonic stem cell line


title: AB15822.txt

description: Library name: Sample 81


title: mESC_bulk_3D_A_rep1


title: EGR1 DBD


title: RPB1degron_167nM_dTAGv1_1

description: Library name: 167nM_1


title: RPB1degron_167nM_dTAGv1_2

description: Library name: 167nM_2


title: AB15821.txt

description: Library name: Sample 80


title: mESC_1k_3D_A_rep6


title: MV411_COMBO_3

description: Library name: MV411_COMBO_3


title: mESC_1k_1D_B_rep5


title: AB15820.txt

description: Library name: Sample 79


title: RPB1degron_125nM_dTAGv1_2

description: Library name: 125nM_2

value: 125nM dTAGv1


title: MV411_COMBO_1

description: Library name: MV411_COMBO_1


title: RPB1degron_125nM_dTAGv1_1

description: Library name: 125nM_1


title: AB15475.txt

description: Library name: Sample 78

value: RunA


title: RPB1degron_83nM_dTAGv1_3

description: Library name: 83nM_3

value: 83nM dTAGv1


title: mESC_1k_1D_B_rep4

value: inner cell mass of preimplantation blastocysts

value: wild type


title: mESC_1k_3D_A_rep5


title: AB15473.txt

description: Library name: Sample 76


title: mESC_1k_3D_A_rep4


title: mESC_1k_3D_A_rep3


title: MV411_ABT_3

description: Library name: MV411_ABT_3


title: AB15472.txt

description: Library name: Sample 75


title: RPB1degron_62nM_dTAGv1_3

description: Library name: 62nM_3

value: 62nM dTAGv1


title: MV411_ABT_1

description: Library name: MV411_ABT_1


title: RPB1degron_125nM_dTAGv1_3

description: Library name: 125nM_3


title: AB15474.txt

description: Library name: Sample 77


title: AB15470.txt

description: Library name: Sample 73


title: RPB1degron_62nM_dTAGv1_2

description: Library name: 62nM_2


title: MV411_ABT_2

description: Library name: MV411_ABT_2


title: PDX_MENi_2

description: Library name: PDX_MENi_2

data_processing:
FASTQ files were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome hg38 using STAR v2.7.11a with the following parameters: --quantMode TranscriptomeSAM GeneCounts --outSAMunmapped Within --outSAMattributes Standard.
Alignments were quantified using featureCounts v2.0.6 with the following parameters: -s 2 -p --countReadPairs -t exon -g gene_id.
Assembly: hg38
Supplementary files format and content: csv file containing raw counts

source_name: PDX spleen cells

value: PDX spleen cells

value: NPM1m PDX/luc/GFP cells


title: RPB1degron_83nM_dTAGv1_1

description: Library name: 83nM_1


title: mESC_1k_1D_B_rep3


title: PDX_MENi_1

description: Library name: PDX_MENi_1


title: AB15471.txt

description: Library name: Sample 74


title: MV411_COMBO_2

description: Library name: MV411_COMBO_2


title: mESC_1k_1D_B_rep2


title: mESC_1k_3D_A_rep2


title: AB15469.txt

description: Library name: Sample 72


title: RPB1degron_62nM_dTAGv1_1

description: Library name: 62nM_1


title: PDX_CONTROL_3

description: Library name: PDX_CONTROL_3

value: vehicle control


title: RPB1degron_83nM_dTAGv1_2

description: Library name: 83nM_2


title: PDX_MENi_3

description: Library name: PDX_MENi_3


title: mESC_1k_1D_B_rep1


title: AB15468.txt

description: Library name: Sample 71


title: RPB1degron_32nM_dTAGv1_3

description: Library name: 32nM_3

value: 32nM dTAGv1


title: AB15467.txt

description: Library name: Sample 70


title: mESC_1k_3D_A_rep1


title: macaque_IN_1k_1D_B_rep6

organism: Macaca mulatta

source_name: Macaque cerebral cortex

value: Macaque cerebral cortex

value: neuron

value: interneurons


title: RPB1degron_32nM_dTAGv1_1

description: Library name: 32nM_1

value: RPB1 degron D4


title: RPB1degron_32nM_dTAGv1_2

description: Library name: 32nM_2


title: PDX_CONTROL_1

description: Library name: PDX_CONTROL_1


title: AB15465.txt

description: Library name: Sample 68


title: RPB1degron_16nM_dTAGv1_3

description: Library name: 16nM_3

value: 16nM dTAGv1


title: macaque_IN_1k_3D_A_rep6

description: macaca.iN_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: PDX_COMBO_2

description: Library name: PDX_COMBO_2

value: ABT-199 plus DS-1594b


title: AB15464.txt

description: Library name: Sample 67


title: RPB1degron_16nM_dTAGv1_2

description: Library name: 16nM_2


title: PDX_COMBO_1

description: Library name: PDX_COMBO_1


title: macaque_IN_1k_1D_B_rep5


title: RPB1degron_16nM_dTAGv1_1

description: Library name: 16nM_1


title: PDX_ABT_3

description: Library name: PDX_ABT_3


title: macaque_IN_1k_3D_A_rep5


title: macaque_IN_1k_1D_B_rep4


title: PDX_CONTROL_2

description: Library name: PDX_CONTROL_2


title: RPB1degron_8nM_dTAGv1_3

description: Library name: 8nM_3

value: 8nM dTAGv1


title: PDX_ABT_2

description: Library name: PDX_ABT_2


title: macaque_IN_1k_3D_A_rep4


title: AB15462.txt

description: Library name: Sample 65


title: AB15461.txt

description: Library name: Sample 64


title: RPB1degron_8nM_dTAGv1_2

description: Library name: 8nM_2


title: AB15466.txt

description: Library name: Sample 69


title: PDX_ABT_1

description: Library name: PDX_ABT_1


title: PDX_COMBO_3

description: Library name: PDX_COMBO_3


title: macaque_IN_1k_3D_A_rep3


title: RPB1degron_8nM_dTAGv1_1

description: Library name: 8nM_1


title: AB15459.txt

description: Library name: Sample 62


title: PDI BIOL REP 6

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

description: Library name: PDI6

data_processing:
RNA paired-end sequencing quality control was assessed through FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) and multiQC (Ewels et al., 2016). Both adapters and low quality bases (QV < 20) were trimmed from reads’ extremities using Trimmomatic (Bolger et al., 2014) with a minimum read length of 30 bp. An average of 23.2 million reads per sample were kept post-trimming for downstream analyses. All libraries were mapped against the bovine ARS-UCD1.2 release-109 reference genome (retrieved from https://ftp.ensembl.org/pub/release-109/fasta/bos_taurus/dna/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa.gz) through STAR aligner (Dobin et al., 2013) with default parameters. STAR-generated sorted BAM output files were used for assigned read counts to gene features with featureCounts (Liao et al., 2014) with the following parameters: -p -B -C -M -O --fraction. We relied on Bos_taurus.ARS-UCD1.2.109.gtf annotation file downloaded from https://ftp.ensembl.org/pub/release-109/gtf/bos_taurus/Bos_taurus.ARS-UCD1.2.109.gtf.gz.
Assembly: Bos_taurus.ARS-UCD1.2.109.gtf
Supplementary files format and content: gene_counts.txt

organism: Bos taurus

source_name: Endometrium

extract_protocol:
Qiagen miRNeasy Micro kit with on-column Qiagen Dnase digestion
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, 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 Novaseq6000 platforms, according to effective library concentration and data amount and using the PE150 sequencing strategy.

value: Endometrium

value: Primary

value: Epithelial

value: Recombinant bovine protein disulphide isomerase (PDI) (1000ng/mL)


title: RPB1degron_4nM_dTAGv1_3

description: Library name: 4nM_3

value: 4nM dTAGv1


title: RPB1degron_4nM_dTAGv1_2

description: Library name: 4nM_2


title: macaque_IN_1k_1D_B_rep2

value: wild type


title: AB15458.txt

description: Library name: Sample 61

value: RunA


title: PDI BIOL REP 5

description: Library name: PDI5


title: AB15463.txt

description: Library name: Sample 66


title: AB15457.txt

description: Library name: Sample 60


title: PDI BIOL REP 3

description: Library name: PDI3


title: AB15456.txt

description: Library name: Sample 59


title: PDI BIOL REP 4

description: Library name: PDI4


title: RPB1degron_4nM_dTAGv1_1

description: Library name: 4nM_1


title: macaque_IN_1k_1D_B_rep1


title: macaque_IN_1k_3D_A_rep1


title: PDI BIOL REP 1

description: Library name: PDI1


title: macaque_IN_1k_1D_B_rep3


title: RPB1degron_2nM_dTAGv1_3

description: Library name: 2nM_3

value: 2nM dTAGv1


title: RPB1degron_2nM_dTAGv1_2

description: Library name: 2nM_2


title: macaque_EN_1k_1D_B_rep6

value: excitatory neurons


title: CAPG BIOL REP 6

description: Library name: CAPG6

value: Recombinant bovine macrophage capping protein (CAPG) (1000ng/mL)


title: AB15454.txt

description: Library name: Sample 57


title: RPB1degron_2nM_dTAGv1_1

description: Library name: 2nM_1


title: macaque_EN_1k_3D_A_rep6

description: macaca.eN_intraOnly.spline_pass1.res25000.significances.loop.bedpe

value: Macaque cerebral cortex


title: AB15460.txt

description: Library name: Sample 63


title: CAPG BIOL REP 5

description: Library name: CAPG5


title: RPB1degron_DMSO_3

description: Library name: DMSO_3

value: DMSO


title: AB15453.txt

description: Library name: Sample 56


title: CAPG BIOL REP 4

description: Library name: CAPG4


title: macaque_EN_1k_1D_B_rep5

value: neuron


title: RPB1degron_DMSO_2

description: Library name: DMSO_2

value: RPB1 degron D4


title: macaque_EN_1k_3D_A_rep5


title: CAPG BIOL REP 3

description: Library name: CAPG3


title: AB15451.txt

description: Library name: Sample 54


title: AB15452.txt

description: Library name: Sample 55


title: macaque_EN_1k_1D_B_rep4


title: macaque_IN_1k_3D_A_rep2

value: interneurons


title: RPB1degron_DMSO_1

description: Library name: DMSO_1


title: macaque_EN_1k_3D_A_rep4


title: IFNT BIOL REP 6

description: Library name: IFNT6

value: Recombinant ovine Interferon Tau (IFNT) (1000ng/ml)


title: Feature-2025-05-23-2-8

description: Library name: Sample36

data_processing:
CellRanger Multi defult parameters using feature_reference.csv
Assembly: GRCh38
Supplementary files format and content: cellranger outputs; barcodes features and matrix for each sample (linked to the corresponding GEX sample records)
Library strategy: CITE-seq

source_name: Renal cell carcinoma patient

extract_protocol:
Fresh tumor samples were obtained from discarded surgical resection specimens collected from consented patients under a Cooperative Human Tissue Network-CHTN IRB approved protocol.  Tumor samples were cut into 1-2mm3 Patient-Derived Tumor Fragments (PDTFs) and cryopreserved in 1ml CryoStor CS10). Cryopreserved PDTFs from five distinct renal cell carcinoma patient tumors were rapidly thawed in a 37°C water bath and immediately placed in RPMI 1640 medium supplemented with 5% fetal bovine serum (FBS). Following thawing, individual tumor fragments were cultured for 48 hours as previously detailed73. For each donor, a total of 16 fragments per treatment condition were allocated to each of the four experimental arms: Isotype Control: anti-Respiratory Syncytial Virus (RSV) IgG1 (10 nM) and anti-Hen Egg Lysozyme (HEL) IgG4 (10 µg/mL), anti-PD-1 Monotherapy: anti-PD-1 (10 µg/mL; Cat: SIM0010) and anti-RSV-IgG1 (10 nM), MiTE144 Monotherapy: MITE144 (1 0nM) and anti-HEL-IgG4 (10 µg/mL), Combination Therapy: MITE144 (10 nM) and anti-PD-1 (10 µg/mL). Upon completion of the 48-hour culture period, 90ul of supernatants were collected and frozen for secreted protein analysis. Next, all fragments from the same donor and treatment arm were pooled and digested into single cell suspensions. Immune cells were enriched from the digested fragments using CD45 magnetic-activated cell sorting (MACS). The resulting CD45-enriched cell fractions were subsequently stained with a custom Immunai CITE-seq antibody panel (see STAR methods) and subjected to fluorescence-activated cell sorting (FACS) to isolate viable CD45 cells.
Single-cell gene expression (GEX) and feature (CITE-seq) libraries were prepared from the sorted cells using the 10x Genomics Chromium Next GEM Single Cell 5' Kit v2. Libraries were sequenced on a Novaseq X Plus sequencer using a 300 cycle kit.

value: Renal cell carcinoma patient

value: Exvivo PDTF

value: Demultiplex by Antibody

tag: library type

value: ADT


title: AB15450.txt

description: Library name: Sample 53


title: AB15455.txt

description: Library name: Sample 58


title: CAPG BIOL REP 1

description: Library name: CAPG1

value: Endometrium

value: Primary

value: Epithelial


title: IFNT BIOL REP 5

description: Library name: IFNT5


title: macaque_EN_1k_1D_B_rep3

value: wild type


title: AB15449.txt

description: Library name: Sample 52

value: RunA


title: Feature-2025-05-23-2-7

description: Library name: Sample34


title: macaque_EN_1k_3D_A_rep3

value: excitatory neurons


title: GEX-2025-05-23-2-8

description: Library name: Sample35

value: mRNA


title: IFNT BIOL REP 4

description: Library name: IFNT4


title: AB15448.txt

description: Library name: Sample 51


title: AB15447.txt

description: Library name: Sample 50


title: GEX-2025-05-23-2-7

description: Library name: Sample33


title: macaque_EN_1k_1D_B_rep2

value: Macaque cerebral cortex


title: IFNT BIOL REP 3

description: Library name: IFNT3


title: Feature-2025-05-23-2-6

description: Library name: Sample32


title: AB15446.txt

description: Library name: Sample 49


title: IFNT BIOL REP 1

description: Library name: IFNT1


title: PBS CONTROL BIOL REP 6

description: Library name: PBS6

value: PBS vehicle control


title: macaque_EN_1k_3D_A_rep2

value: neuron


title: GEX-2025-05-23-2-6

description: Library name: Sample31


title: AB15444.txt

description: Library name: Sample 47


title: Feature-2025-05-23-2-5

description: Library name: Sample30


title: AB15445.txt

description: Library name: Sample 48


title: PBS CONTROL BIOL REP 5

description: Library name: PBS5


title: macaque_EN_1k_3D_A_rep1


title: PBS CONTROL BIOL REP 4

description: Library name: PBS4


title: Feature-2025-05-23-2-4

description: Library name: Sample28


title: AB15442.txt

description: Library name: Sample 45


title: GEX-2025-05-23-2-5

description: Library name: Sample29


title: PBS CONTROL BIOL REP 3

description: Library name: PBS3


title: macaque_IPC_1k_1D_B_rep5

value: intermediate progenitor cells


title: macaque_IPC_1k_3D_A_rep5

description: macaca.iPC_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: AB15441.txt

description: Library name: Sample 44


title: macaque_IPC_1k_1D_B_rep4


title: Feature-2025-05-23-2-3

description: Library name: Sample26


title: GEX-2025-05-23-2-4

description: Library name: Sample27


title: PROGESTERONE BIOL REP 6

description: Library name: P46

value: Progesterone (10 μg/ml)


title: AB15440.txt

description: Library name: Sample 43


title: macaque_IPC_1k_3D_A_rep4


title: AB15437.txt

description: Library name: Sample 42


title: macaque_IPC_1k_1D_B_rep3


title: macaque_EN_1k_1D_B_rep1


title: PROGESTERONE BIOL REP 5

description: Library name: P45


title: Feature-2025-05-23-2-2

description: Library name: Sample24


title: GEX-2025-05-23-2-3

description: Library name: Sample25


title: AB15443.txt

description: Library name: Sample 46


title: PROGESTERONE BIOL REP 4

description: Library name: P44


title: macaque_IPC_1k_3D_A_rep3


title: AB15435.txt

description: Library name: Sample 40


title: GEX-2025-05-23-2-2

description: Library name: Sample23


title: macaque_IPC_1k_1D_B_rep2


title: PROGESTERONE BIOL REP 3

description: Library name: P43


title: AB15434.txt

description: Library name: Sample 39


title: Feature-2025-05-23-2-1

description: Library name: Sample22


title: PBS CONTROL BIOL REP 1

description: Library name: PBS1


title: AB15433.txt

description: Library name: Sample 38


title: PROGESTERONE BIOL REP 1

description: Library name: P41


title: macaque_IPC_1k_3D_A_rep2


title: GEX-2025-05-23-2-1

description: Library name: Sample21


title: Feature-2025-05-22-1-8

description: Library name: Sample20


title: macaque_IPC_1k_1D_B_rep1


title: AB15432.txt

description: Library name: Sample 37


title: VEHICLE CONTROL BIOL REP 5

description: Library name: VC5

value: Vehicle (EtOH) control


title: AB15436.txt

description: Library name: Sample 41


title: AB15431.txt

description: Library name: Sample 36


title: macaque_IPC_1k_3D_A_rep1


title: VEHICLE CONTROL BIOL REP 4

description: Library name: VC4


title: GEX-2025-05-22-1-8

description: Library name: Sample19

value: Renal cell carcinoma patient


title: AB15430.txt

description: Library name: Sample 35


title: macaque_RG_1k_3D_A_rep6

description: macaca.RG_intraOnly.spline_pass1.res25000.significances.loop.bedpe

value: radial glia


title: AB15429.txt

description: Library name: Sample 34


title: VEHICLE CONTROL BIOL REP 3

description: Library name: VC3


title: Feature-2025-05-22-1-7

description: Library name: Sample18

value: Exvivo PDTF

value: Demultiplex by Antibody


title: GEX-2025-05-22-1-7

description: Library name: Sample17


title: AB15428.txt

description: Library name: Sample 33


title: macaque_RG_1k_1D_B_rep5


title: macaque_RG_1k_3D_A_rep5


title: VEHICLE CONTROL BIOL REP 1

description: Library name: VC1

value: Endometrium


title: GEX-2025-05-22-1-6

description: Library name: Sample15


title: AB15427.txt

description: Library name: Sample 32


title: Feature-2025-05-22-1-6

description: Library name: Sample16

value: ADT


title: CONTROL BIOL REP 6

description: Library name: C6

value: Primary

value: Epithelial

value: Media only control


title: macaque_RG_1k_1D_B_rep4

value: wild type


title: AB15426.txt

description: Library name: Sample 31

value: RunA


title: VEHICLE CONTROL BIOL REP 6

description: Library name: VC6


title: CONTROL BIOL REP 5

description: Library name: C5


title: CONTROL BIOL REP 4

description: Library name: C4


title: macaque_RG_1k_3D_A_rep4

value: Macaque cerebral cortex


title: Feature-2025-05-22-1-5

description: Library name: Sample14


title: GEX-2025-05-22-1-5

description: Library name: Sample13

value: mRNA


title: AB15425.txt

description: Library name: Sample 30


title: macaque_RG_1k_1D_B_rep6

value: neuron


title: macaque_RG_1k_1D_B_rep3


title: CONTROL BIOL REP 3

description: Library name: C3


title: Feature-2025-05-22-1-4

description: Library name: Sample12


title: CONTROL BIOL REP 1

description: Library name: C1


title: AB15424.txt

description: Library name: Sample 29


title: macaque_RG_1k_3D_A_rep3


title: zmcryq_Blue1_3

city: Shenzhen

first: Zhao

last: Zhiwei

state: Guangdong

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

description: Library name: Sample 12

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: leaf

growth_protocol: 7 days of B73 and zmcryq seedlings  grown in longday white light

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

treatment_protocol: pretreated with 48h dark, then moved to blue light for 1 hour or kept in dark

value: leaf

tag: developmental stage

value: 7 DAY OLD

value: zmcryq mutant

value: 1 hour Blue light


title: AB15422.txt

description: Library name: Sample 27

tag: tissue


title: Feature-2025-05-22-1-3

description: Library name: Sample10

value: Renal cell carcinoma patient

tag: treatment


title: zmcryq_Blue1_2

description: Library name: Sample 11


title: macaque_RG_1k_3D_A_rep2

tag: cell line

value: radial glia


title: AB15421.txt

description: Library name: Sample 26

tag: cell type


title: GEX-2025-05-22-1-3

description: Library name: Sample9

value: Exvivo PDTF

value: Demultiplex by Antibody


title: AB15420.txt

description: Library name: Sample 25

tag: genotype


title: macaque_RG_1k_1D_B_rep1


title: Feature-2025-05-22-1-2

description: Library name: Sample8

value: ADT


title: macaque_RG_1k_3D_A_rep1


title: GEX-2025-05-22-1-2

description: Library name: Sample7


title: AB15419.txt

description: Library name: Sample 24

tag: mouse id


title: zmcryq_Dark_3

description: Library name: Sample 9

value: Dark


title: zmcryq_Dark_2

description: Library name: Sample 8


title: AB15423.txt

description: Library name: Sample 28

tag: batch


title: AB15418.txt

description: Library name: Sample 23


title: Feature-2025-05-22-1-1

description: Library name: Sample6


title: AB15417.txt

description: Library name: Sample 22


title: GEX-2025-05-22-1-1

description: Library name: Sample5


title: GEX-2025-05-22-1-4

description: Library name: Sample11


title: macaque_RG_1k_1D_B_rep2


title: B73_Blue1_3

description: Library name: Sample 6

value: Wild-type


title: AB15416.txt

description: Library name: Sample 21


title: Feature-2025-05-16-1-2

description: Library name: Sample4


title: strong tumor bio rep3

city: hangzhou

first: qiaoran

last: li

address: Qinchun Road 79

institute: The First Affiliated Hospital, School of Medicine，Zhejiang University

description: Library name: gmrykiSA-3_1.fq.gz

data_processing:
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads(1.0X). And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Assembly: Reads were aligned to the Drosophila melanogaster reference genome (Ensembl_release102)

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Toal RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA) and checked using Rnase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for lumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: head


title: strong tumor bio rep1

description: Library name: gmrykiSA-1_1.fq.gz


title: strong tumor bio rep2

description: Library name: gmrykiSA-2_1.fq.gz


title: B73_Blue1_2

description: Library name: Sample 5


title: weak tumor bio rep3

description: Library name: gmrykiwt-3_1.fq.gz


title: zmcryq_Blue1_1

description: Library name: Sample 10


title: GEX-2025-05-16-1-2

description: Library name: Sample3


title: B73_Blue1_1

description: Library name: Sample 4


title: AB15415.txt

description: Library name: Sample 20

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cell_metadata.csv


title: Feature-2025-05-16-1-1

description: Library name: Sample2


title: AB15414.txt

description: Library name: Sample 19

value: aRSV


title: weak tumor bio rep1

description: Library name: gmrykiwt-1_1.fq.gz


title: B73_Dark_3

description: Library name: Sample 3


title: GEX-2025-05-16-1-1

description: Library name: Sample1


title: zmcryq_Dark_1

description: Library name: Sample 7


title: B73_Dark_2

description: Library name: Sample 2


title: control bio rep3

description: Library name: gmr-control-3_1.fq.gz


title: AB15412.txt

description: Library name: Sample 17

value: RunA


title: B73_Dark_1

description: Library name: Sample 1


title: NIH29, control, snMultiome [GEX]

description: 10x Genomics

source_name: Entorhinal cortex

extract_protocol:
Samples were stored at -80 °C. The nuclei isolation protocol was modified based on a 10x Genomics protocol (CG000375). Briefly, 30 mg of frozen tissue was finely minced on dry ice to the smallest possible size, and then it was homogenized in homogenization buffer on ice within 20 minutes. The homogenized tissue was filtered through a 35 μm cell strainer. Small cell debris were removed by centrifuging at 300g for 3 minutes at 4 °C. The large cell debris was removed by gradient centrifugation using OptiPrep density gradient medium (Sigma, cat#D1556-250ML) at 7200g for 15 minutes at 4 °C. The nuclei pellet was resuspended in a 0.1x lysis buffer. After washing the isolated nuclei in the wash buffer, the nuclei were resuspended in 1x nuclei buffer before single-nuclei Multiome library construction. (UTHealth Cancer Genomic Core)
single-nuclei Multiome sequencing; Single-nuclei libraries were constructed following the 10x Chromium Single Cell Multiome ATAC + Gene Expression protocol (CG000338).

value: Entorhinal cortex

value: Control

value: F


title: AB15411.txt

description: Library name: Sample 16


title: NIH28, control, snMultiome [GEX]

description: 10x Genomics

source_name: Prefrontal cortex

value: Prefrontal cortex


title: 4EHP_mutant_adar_3

city: New York

first: Hyung Don

last: Ryoo

state: NY

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

description:
Library name: Sample 18
Predicted_TRIBE_sites.csv
ADARM3

data_processing:
Seq-N-Slide automated workflow (https://github.com/igordot/sns) was sued to process fastq files.
For read mapping to the Drosophila reference genome, dm6, STAR was used.
Fastq Screen was used to check for contaminating sequences.
featureCounts was used to generate matrices of read counts.
DESeq2 package was used for differential gene statistical comparisons.
Assembly: dm6
Supplementary files format and content: csv

source_name: larval fat body

growth_protocol: Larvae were grown in standard cornmeal food.

extract_protocol:
Trizol extraction of RNA following the manufacturer's protocol
The cDNA library was prepared from polyA-containing mRNA

treatment_protocol: No treatment

value: larval fat body

value: tissue

value: adipose cells


title: control bio rep1

description: Library name: gmr-control-1_1.fq.gz


title: NIH17, sEOAD, snMultiome [GEX]

description: 10x Genomics

value: sEOAD

value: M


title: 4EHP_mutant_adar_1

description:
Library name: Sample 16
Predicted_TRIBE_sites.csv
ADARM1


title: AB15409.txt

description: Library name: Sample 14

extract_protocol:
Tumors were minced into small pieces on ice and digested using RPMI supplemented with 1mg/ml Collagenase IV (LS004188, Enco) and 0.05mg/ml DnaseI (DnaseI, Sigma Aldrich) at 37 degrees for three times 8 min. In between the incubation steps, the tissue was further dissociated using a gentleMACS dissociator (130-093-235, Miltenyi Biotec). After digestion, the cells were filtered trough a 100um cell strainer and washed with ice cold PBS.  Cells were stained with FACS antibodies and viability dye for 30min on ice. After washing them again with ice cold PBS, cells were sorted and acquired on a BD FACS Symphony 6 flow cytometer. After excluding doublets and dead cells, two 384-well plates of CD45+ cells and CD90.2+ and/or NK1.1+ (=T/NKT/NK/ILCs) were sorted per sample The 384-well plates contained a lysis solution, mineral oil and barcoded poly(T) reverse transciption primers enabeling scRNA sequencing.
SPID-seq92, an adapted version of the MARS-seq pipeline93, was used to generate scRNA-seq libraries. In short, polyadenylated mRNA from individual cells that had been sorted into 384-well plates was captured, followed by a barcoding step of the mRNA during reverse transcription into cDNA. cDNA of each plate was pooled into a single tube, and was fragmented and amplified to generate sequencing-ready libraries for NovaSeq X plus (Illumina) sequencing. Quality control was performed on each library created from a plate.


title: M1404 spleen 4

city: Clayton

first: Thomas

middle: R

last: Smallman

state: Victoria

address: 19 Innovation walk

department: Microbiology

country: Australia

institute: Monash University

description: Library name: L32_M1404_s4_S32_L001_R1_001.fastq.gz

data_processing:
Reads quality control checked using FastQC v0.11.9. Checked for presence of the transposon tag in the first 10 bases, and then random genomic DNA afterwars.
Reads were trimmed to remove any adapter sequences using Trimmomatic v0.39
TraDIS data analysis was performed using the Bio-TraDIS toolkit (v1.4.5) (https://github.com/sanger-pathogens/Bio-Tradis). Reads were mapped to the genome using the bacteria_tradis using smalt as the mapper and allowing multimapping reads to be mapped randomly. Insertion site data was combined with the annotation using the tradis_gene_insert_sites, trimming reads in the final 10% of the gene for the rich media analysis, and essential genes identified using tradis_essentiality.R.
Genes important for fitness were identified using tradis_comparison.R (github.com/francesca-short/tradis_scripts).
Assembly: GCF_011390865.1 for VP161 and GCA_002083265.2 for M1404
Supplementary files format and content: Table containing all output data from the Bio-TraDIS pipeline and tradis_comparison.R scripts, shows the number of unique and total insertions per gene, as well as essentiality and fitness calls for all genes.

organism: Pasteurella multocida

source_name: Spleen

growth_protocol: Cells were grown in heart infusion broth overnight, then subcultured into fresh heart infusion broth and grown until mid-exponential phase. Cells were then injected intrapertioneally into BALB/c mice, and when mice reached the humane end point, cells were recovered from the bloodstream by heart puncture, or recovered from the liver and spleen by crushing the tissues in 1 x PBS. Cells were then plated onto heart infusion agar plates and grown overnight.

extract_protocol:
Genomic DNA was extracted using the HiYield Genomic DNA Mini Kit (Real Biotech Corporation) as per the manufacturer's instructions for extraction from Gram-negative bacteria
Genomic DNA was fragmented to ~300 bp using Covaris sonication. The fragment DNA was end-repaired and A-tailed before adapters were ligated onto all fragments. Amplification of transposon-chromosome junctions was performed using Kapa HiFi HotStart ReadyMix, a transposon-specific primer and an adapter-specific primer.

treatment_protocol: No additional treatments

value: Spleen

value: Systemic infection in BALB/c mice


title: AB15410.txt

description: Library name: Sample 15


title: NIH18, sEOAD, snMultiome [GEX]

description: 10x Genomics

value: Hippocampus


title: weak tumor bio rep2

description: Library name: gmrykiwt-2_1.fq.gz


title: M1404 spleen 3

description: Library name: L31_M1404_s3_S31_L001_R1_001.fastq.gz


title: M1404 spleen 2

description: Library name: L30_M1404_s2_S30_L001_R1_001.fastq.gz


title: AB15408.txt

description: Library name: Sample 13


title: 4EHP_adar_3

description:
Library name: Sample 15
Predicted_TRIBE_sites.csv
ADARWT3


title: AB15407.txt

description: Library name: Sample 12


title: M1404 spleen 1

description: Library name: L29_M1404_s1_S29_L001_R1_001.fastq.gz


title: AB15413.txt

description: Library name: Sample 18


title: 4EHP_adar_2

description:
Library name: Sample 14
Predicted_TRIBE_sites.csv
ADARWT2


title: AB15406.txt

description: Library name: Sample 11


title: 4EHP_adar_1

description:
Library name: Sample 13
Predicted_TRIBE_sites.csv
ADARWT1


title: NIH14, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: control bio rep2

description: Library name: gmr-control-2_1.fq.gz


title: AB15405.txt

description: Library name: Sample 10


title: M1404 liver 3

description: Library name: L27_M1404_l3_S27_L001_R1_001.fastq.gz

source_name: Liver

value: Liver


title: NIH13, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: AB15404.txt

description: Library name: Sample 9


title: 4EHP_mutant_adar_2

description:
Library name: Sample 17
Predicted_TRIBE_sites.csv
ADARM2


title: NELFE_Rnai_3

description:
Library name: Sample 12
nelfe_counts.cpm.csv
Nelf-EIR-3

value: dcg-Gal4/uas-NELF-E RNAi


title: NIH16, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: NIH12, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: AB15403.txt

description: Library name: Sample 8


title: NIH15, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: NIH11, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: NELFE_Rnai_1

description:
Library name: Sample 10
nelfe_counts.cpm.csv
Nelf-EIR-1


title: NELFE_Rnai_2

description:
Library name: Sample 11
nelfe_counts.cpm.csv
Nelf-EIR-2


title: M1404 blood 4

description: Library name: L24_M1404_b4_S24_L001_R1_001.fastq.gz

source_name: Blood

value: Blood


title: M1404 liver 2

description: Library name: L26_M1404_l2_S26_L001_R1_001.fastq.gz


title: NIH10, sEOAD, snMultiome [GEX]

description: 10x Genomics


title: M1404 liver 1

description: Library name: L25_M1404_l1_S25_L001_R1_001.fastq.gz


title: NIH06, control, snMultiome [GEX]

description: 10x Genomics


title: AB15402.txt

description: Library name: Sample 7

value: aRSV


title: M1404 liver 4

description: Library name: L28_M1404_l4_S28_L001_R1_001.fastq.gz


title: lacZi_3

description:
Library name: Sample 9
nelfe_counts.cpm.csv
LacZIR-3

value: dcg-Gal4/uas-lacZ RNAi


title: M1404 blood 3

description: Library name: L23_M1404_b3_S23_L001_R1_001.fastq.gz


title: NIH05, control, snMultiome [GEX]

description: 10x Genomics

value: Entorhinal cortex


title: lacZi_1

description:
Library name: Sample 7
nelfe_counts.cpm.csv
LacZIR-1


title: lacZi_2

description:
Library name: Sample 8
nelfe_counts.cpm.csv
LacZIR-2


title: AB15401.txt

description: Library name: Sample 6

value: RunA


title: AB15400.txt

description: Library name: Sample 5


title: M1404 blood 2

description: Library name: L22_M1404_b2_S22_L001_R1_001.fastq.gz


title: NIH04, control, snMultiome [GEX]

description: 10x Genomics

value: Control


title: 4EHP_RNAi_3

description:
Library name: Sample 6
4ehp_counts.cpm.csv
4EHP_IR-3

value: dcg-Gal4/uas-4EHP RNAi


title: M1404 blood 1

description: Library name: L21_M1404_b1_S21_L001_R1_001.fastq.gz


title: AB15399.txt

description: Library name: Sample 4


title: NIH03, control, snMultiome [GEX]

description: 10x Genomics


title: M1404 rich media 4

description: Library name: L20_M1404_in4_S20_L001_R1_001.fastq.gz

source_name: Rich media

value: Rich media


title: AB15398.txt

description: Library name: Sample 3


title: 4EHP_RNAi_2

description:
Library name: Sample 5
4ehp_counts.cpm.csv
4EHP_IR-2

value: larval fat body

value: tissue


title: AB15397.txt

description: Library name: Sample 2


title: 4EHP_RNAi_1

description:
Library name: Sample 4
4ehp_counts.cpm.csv
4EHP_IR-1

value: adipose cells


title: NIH02, control, snMultiome [GEX]

description: 10x Genomics

value: M


title: control_for_4EHP_3

description:
Library name: Sample 3
4ehp_counts.cpm.csv
w1118-3


title: M1404 rich media 2

description: Library name: L18_M1404_in2_S18_L001_R1_001.fastq.gz


title: NIH01, control, snMultiome [GEX]

description: 10x Genomics

value: Prefrontal cortex


title: WT c-kit+ bone marrow cells, RE, rep-3

city: Shanghai

first: jiaying

last: xie

address: Dongfang Road

institute: Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: WT3RE

data_processing:
Raw sequencing reads were quality checked using FastQC (v0.11.9). Adapter and low-quality bases were trimmed using fastp (v0.23.2) with default parameters.
Reads were aligned to the Mouse reference genome (GRCm39) using HISAT2 (v2.1.0) with default settings.
Gene-level counts were obtained using featureCounts (v2.0.3) from the Subread package and TPM was calculated. Only uniquely mapped reads were counted. Raw counts were used for downstream differential expression analysis with DESeq2. No additional normalization was performed for the deposited data.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA extraction was performed by the sequencing service provider (Geneplus technology) using their standard protocols. RNA quality control metrics  were confirmed prior to library construction
RNA-seq library preparation and sequencing were performed by  the sequencing service provider (Geneplus technology, Gene+) following their in-house protocols for MGI platforms

value: Bone marrow

value: cKit+ bone marrow

value: WT

value: RE


title: AB15396.txt

description: Library name: Sample 1


title: M1404 rich media 3

description: Library name: L19_M1404_in3_S19_L001_R1_001.fastq.gz

value: Systemic infection in BALB/c mice


title: VP161 spleen 4

description: Library name: L16_VP161_s4_S16_L001_R1_001.fastq.gz

value: Spleen


title: NIH29, control, snMultiome [ATAC]

description: 10x Genomics

library_source: genomic single cell

value: F


title: control_for_4EHP_2

description:
Library name: Sample 2
4ehp_counts.cpm.csv
w1118-2


title: VP161 spleen 3

description: Library name: L15_VP161_s3_S15_L001_R1_001.fastq.gz


title: WT c-kit+ bone marrow cells, C16, rep-3

description: Library name: WT3C16


title: NIH28, control, snMultiome [ATAC]

description: 10x Genomics


title: WT c-kit+ bone marrow cells, RE, rep-2

description: Library name: WT2RE


title: control_for_4EHP_1

description:
Library name: Sample 1
4ehp_counts.cpm.csv
w1118-1


title: NIH18, sEOAD, snMultiome [ATAC]

description: 10x Genomics

value: Hippocampus

value: sEOAD


title: WT c-kit+ bone marrow cells, DMSO, rep-3

description: Library name: WT3Ctrl

value: DMSO


title: NIH17, sEOAD, snMultiome [ATAC]

description: 10x Genomics

value: Entorhinal cortex


title: WT c-kit+ bone marrow cells, DMSO, rep-2

description: Library name: WT2Ctrl


title: NIH16, sEOAD, snMultiome [ATAC]

description: 10x Genomics


title: PD032_2

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

data_processing:
RNA sequencing reads were aligned to the mouse genome mm10 with STAR aligner with input parameters “--outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts”. Raw counts were extracted from the STAR output using customed script. Principal component analysis and differential expression analysis was performed with raw counts using the R package DESeq2. Genes were considered as deregulated if |log2FC|> 1 and FDR < 0.01 using Benjamini-Hochberge multiple test adjustment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts for each samples
Supplementary files format and content: tab-delimited text files with normalized counts for each samples

source_name: cell line

growth_protocol: ES cell lines were maintained in the presence of 2i/Lif (0.4 µM PD0325901, 3 µM CHIR99021 and 4 ng/ml Lif), on plastic dishes coated with 0.2% gelatin and passaged at 1:6 ratio using 0.25% Trypsin-EDTA

extract_protocol:
RNA was isolated from cells using the NucleoSpin RNA isolation kit following the manufacturer’s protocol. Samples with RNA integrity number (RIN) above 7 from 1 μg of total RNA were used further.
The mRNA enrichment performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and cDNA library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: ES cells were resuspended in matrigel (2000 cells per 1 µl of matrigel) and plated on petri dishes. To solidify the hydrogel, the plate was placed for 5-10 min in a cell culture incubator at 37°C, 5% CO2 atmosphere in air. After that, each well was filled with N2B27 medium supplemented with single or combination of inhibitors inhibitors, 2iLif, FAK, Aurka inh, PD032 or PD032+ Aurka inh.  To isolate ESCs cultured in Matrigel, the Matrigel was incubated in a 1:2 (v/v) mixture of 0.25% trypsin-EDTA and Accutase for 20 min in a cell culture incubator at 37°C, 5% CO2 atmosphere in air. The Matrigel was then broken into pieces by twice manual pipetting. Cells were pelleted by centrifugation (1000rpm/5 min), and the pellet was washed once with PBS.

value: cell line

value: embryonic stem cells

value: E14 ES cells grown in growth factor reduced matrigel


title: VP161 spleen 1

description: Library name: L13_VP161_s1_S13_L001_R1_001.fastq.gz


title: WT c-kit+ bone marrow cells, C16, rep-2

description: Library name: WT2C16


title: NIH15, sEOAD, snMultiome [ATAC]

description: 10x Genomics

source_name: Hippocampus


title: PD032+ Aurka inh_3


title: VP161 spleen 2

description: Library name: L14_VP161_s2_S14_L001_R1_001.fastq.gz


title: M1404 rich media 1

description: Library name: L17_M1404_in1_S17_L001_R1_001.fastq.gz

value: Rich media


title: WT c-kit+ bone marrow cells, RE, rep-1

description: Library name: WT1RE


title: VP161 liver 4

description: Library name: L12_VP161_l4_S12_L001_R1_001.fastq.gz

value: Liver


title: PD032_3


title: VP161 liver 3

description: Library name: L11_VP161_l3_S11_L001_R1_001.fastq.gz


title: WT c-kit+ bone marrow cells, DMSO, rep-1

description: Library name: WT1Ctrl


title: PD032+ Aurka inh_2


title: VP161 liver 2

description: Library name: L10_VP161_l2_S10_L001_R1_001.fastq.gz


title: PD032+ Aurka inh_1


title: NIH14, sEOAD, snMultiome [ATAC]

description: 10x Genomics


title: NIH13, sEOAD, snMultiome [ATAC]

description: 10x Genomics

value: Prefrontal cortex


title: VP161 liver 1

description: Library name: L09_VP161_l1_S9_L001_R1_001.fastq.gz


title: AE9a c-kit+ bone marrow cells, RE, rep-3

description: Library name: AE3RE

value: Bone marrow


title: NIH11, sEOAD, snMultiome [ATAC]

description: 10x Genomics


title: WT c-kit+ bone marrow cells, C16, rep-1

description: Library name: WT1C16

value: cKit+ bone marrow


title: FGF2/Activin_2

value: WT


title: FGF2/Activin_3


title: AE9a c-kit+ bone marrow cells, DMSO, rep-3

description: Library name: AE3Ctrl


title: PD032_1


title: NIH10, sEOAD, snMultiome [ATAC]

description: 10x Genomics


title: VP161 blood 4

description: Library name: L08_VP161_b4_S8_L001_R1_001.fastq.gz

value: Blood


title: FGF2/Activin_1


title: VP161 blood 3

description: Library name: L07_VP161_b3_S7_L001_R1_001.fastq.gz

value: Systemic infection in BALB/c mice


title: AE9a c-kit+ bone marrow cells, C16, rep-3

description: Library name: AE3C16


title: NIH06, control, snMultiome [ATAC]

description: 10x Genomics

value: Control

value: M


title: Aurka inh_3


title: VP161 blood 2

description: Library name: L06_VP161_b2_S6_L001_R1_001.fastq.gz


title: AE9a c-kit+ bone marrow cells, RE, rep-2

description: Library name: AE2RE

value: RE


title: Aurka inh_2


title: NIH05, control, snMultiome [ATAC]

description: 10x Genomics


title: NIH12, sEOAD, snMultiome [ATAC]

description: 10x Genomics

value: Hippocampus

value: sEOAD

value: F


title: VP161 blood 1

description: Library name: L05_VP161_b1_S5_L001_R1_001.fastq.gz


title: NIH04, control, snMultiome [ATAC]

description: 10x Genomics


title: AE9a c-kit+ bone marrow cells, DMSO, rep-2

description: Library name: AE2Ctrl

value: DMSO


title: VP161 rich media 4

description: Library name: L04_VP161_in4_S4_L001_R1_001.fastq.gz


title: 2iLif_3

value: cell line

value: embryonic stem cells


title: AE9a c-kit+ bone marrow cells, C16, rep-2

description: Library name: AE2C16


title: VP161 rich media 3

description: Library name: L03_VP161_in3_S3_L001_R1_001.fastq.gz

value: Rich media


title: AE9a c-kit+ bone marrow cells, DMSO, rep-1

description: Library name: AE1Ctrl


title: 2iLif_2

value: E14 ES cells grown in growth factor reduced matrigel


title: 2iLif_1


title: VP161 rich media 2

description: Library name: L02_VP161_in2_S2_L001_R1_001.fastq.gz


title: NIH02, control, snMultiome [ATAC]

description: 10x Genomics

value: Entorhinal cortex


title: NIH01, control, snMultiome [ATAC]

description: 10x Genomics

value: Prefrontal cortex