title: Con-2

description: Primary control (TNFR1-/+) CMFs - mouse 2


title: RNA_pRB8c_rep3

status: Public on Jul 01 2025

type: SRA

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

description: Library name: RNA_pRB8c_rep3

library_source: transcriptomic

data_processing:
The quality of the obtained footprint reads was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were removed using cutadapt.
All alignments were performed with STAR aligner v2.7.1a, using a sequential mapping approach where unmapped reads were used as input for the proceeding alignment. The alignment order is as follows: 1) rRNA and tRNA contaminants; 2) chloroplast genome; 3) mitochondrial genome; and 4) nuclear genome. The following sequences were obtained from NCBI (with following annotation): 5.8S rRNA (AJ300215.1), 5S rRNA (AJ222659.1), 18S rRNA (AJ236016.1), and 26S rRNA (AF479172.1), chloroplast genome (Z00044.2), mitochondrial genome (NC_006581.1). Sequences for the nuclear genome and tRNAs were obtained from solgenomics (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/).
Additional processing and sorting of alignment data were done using samtools and bedtools.
Assembly: Z00044.2
Supplementary files format and content: xlsx file including total reads, RPKM from each sample for chloroplast transcripts

molecule: total RNA

organism: Nicotiana tabacum

source_name: Petit Havana

growth_protocol: Knockout tobacco mutants of essential photosynthetic genes were grown heterotrophically in Magenta boxes containing solidified Murashige and Skoog (MS) medium supplemented with 3% sucrose. Tissue was harvested once equivalent developmental stage of a four leaf old tobacco seedling was reached.

extract_protocol:
For Ribo-Seq, the ribosome footprints were generated using 250 U RNase I per 1 ml of plant lysate (derived from 100 mg of plant fresh weight). The lysate was then layered on a sucrose cushion to purify monosomes. Ribosome footprints from ~20 nt to ~39 nt were size-selected from polyacrylamide gels. For total RNA samples, RNA was isolated with the TRIzol® Reagent (Thermo Fisher Scientific) according to manufacturer’s instructions, gDNA was removed using TURBO™ DNase.
For Ribo-seq, cDNA was synthesized by using NEXTflex™ Small RNA-Seq Kit v3. For RNA-seq, cDNA libraries were generated using Zymo-Seq RiboFree total RNA library kit. The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

tag: cell line

value: Petit Havana

tag: genotype


title: A. rectalis, glucose, R3

city: Jouy-en-Josas

first: Paul

last: Biscarrat

address: 78352 Rue de la Manufacture,

country: France

institute: INRAE

description: Library name: AR_G_R3

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779/A.rectalis NZ_AP012325.1 / B.adolescentis NC_008618.1 / B.uniformis RefSeq GCF_000154205.1/A.rectalis NC_012781
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison

organism: Agathobacter rectalis

source_name: Bacteria

growth_protocol: Bacteria were cultured in Hungate tubes with a containing 90 % N2, 5 % CO2, 5 % H2 atmosphere. Cultures were performed in a minimum medium adapted from YCFA medium supplemented with 0.5 % carbohydrate. Cultures were stopped 12 h after inoculation.

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.

value: Bacteria

tag: cell type

tag: treatment

value: Glucose


title: label_NC_2

city: Shanghai

first: Rui

last: Cheng

state: Shanghai

address: No. 1630 East Road, Pudong New Area

country: China

institute: Shanghai Jiao Tong University

description: Library name: SAMPLES 14

data_processing:
FASTQ files were processed using the DynamicST pipeline to extract UMIs (47–58 bp) and spatial barcodes (X: 1–8 bp, Y: 39–46 bp) from Read 1 for spatial location identification. cDNA from Read 2 was aligned to the mouse genome (mm10, Gencode vM13) using STAR 2.7.11a. Spots outside tissue regions, defined by H&E staining, were excluded.
Assembly: mm10
Supplementary files format and content: The spatial transcriptomics file in .h5ad format, including the raw matrices of both new and old total RNA.

organism: Mus musculus

source_name: kidney

extract_protocol:
First, the nucleoside analog 4sU is administered to mice via tail vein injection. 4sU is rapidly diffused throughout the body via blood flow and is incorporated into new RNA during transcription. After labeling, the tissue is sectioned and attached to a DNA coordinate barcoding array for spatial transcriptome indexing. Following hematoxyling and eosin (H&E) and permeabilization, the released RNAs with poly (A) tails from the tissue are in situ captured by the spatial barcoding oligo(dT) sequence in each spot. By iodoacetamide (IAA)-based alkylation treatment, the 4sU in mRNA is transformed into a cytosine analog by covalently attaching a carboxyamidomethyl group, altering its hydrogen-bonding properties. During reverse transcription, this chemical modification leads to T-to-C substitutions at single-base resolution, marking the newly synthesized RNAs, while the spatial barcoding sequences added to the cDNAs record the coordinate of captured mRNAs. Subsequently, second-strand cDNA synthesis, library construction, and next-generation sequencing are performed.
RNA-Seq

treatment_protocol: To induce renal ischemia, mice were first anesthetized via intraperitoneal injection of 30 mg/ml pentobarbital sodium. Ischemia was initiated by clamping the renal artery, thereby obstructing blood flow to the kidney. After a 50-minute ischemic period, reperfusion was initiated by releasing the clamp, allowing blood flow to return to the kidney. The renal artery remained clamped for 50 minutes during the ischemic phase, and following the release of the clamp, blood circulation was restored. Kidneys were harvested at three different time points following reperfusion: 4.5 hours, 12 hours, and 24.8 hours.

tag: tissue

value: kidney


title: A. rectalis, glucose, R2

description: Library name: AR_G_R2


title: 2317TGP-NEG, Low Serum #2

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

institute: Institut Curie

description: Library name: 231_N2

data_processing:
Raw counts were generated using Star (v2.6.1a) gene quantification mode (--quantMode GeneCounts) on the Gencode v19 gene database.
Raw counts were normalized using  the TMM method using EdgeR (v3.22.5) and Limma's voom function (v3.36.5).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM for each sample

organism: Homo sapiens

growth_protocol: MDA-MB-2317TGP-POS and MDA-MB-2317TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2. MDA-MB-4367TGP-POS and MDA-MB-4367TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Extraction was performed using the RNAeasy Mini Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions
TruSeq Stranded mRNA

treatment_protocol: WNT activity reporter cell lines were generated by liposome-mediated transfection of the 7TGP plasmid, followed by stable selection with puromycin (3 μg/mL) for a minimum of five passages. The 7TGP reporter vector contains seven copies of TCF-binding sites upstream of a minimal promoter that drives eGFP expression in response to WNT pathway activation. Upon nuclear translocation of β-catenin and subsequent binding to TCF/LEF1 transcription factors, eGFP is expressed. Reporter activity (7TGP/eGFP status) was assessed by flow cytometry and fluorescence microscopy under optimal growth conditions. Sequential FACS sorting was performed on the stably transfected lines to enrich for either 7TGP-positive or 7TGP-negative subpopulations.

value: Mesenchymal Cell line

value: Wnt-negative cell line

value: 7TGP vector transfected MDA-MB-2317TGP-NEG


title: RNA_pRB8c_rep2

description: Library name: RNA_pRB8c_rep2


title: RNA_∆3'psbD_rep2

description: Library name: RNA_dpsbD_rep2

value: delta 3'psbD


title: label_NC_1

description: Library name: SAMPLES 13


title: 2317TGP-NEG, Low Serum #1

description: Library name: 231_N1


title: 4367TGP-POS, Low Serum #2

description: Library name: 436_P2

value: Wnt-positive cell Line

value: 7TGP vector transfected MDA-MB-4367TGP-POS


title: RNA_pRB8c_rep1

description: Library name: RNA_pRB8c_rep1


title: A. rectalis, glucose, R1

description: Library name: AR_G_R1


title: HD-unlabel_NC

description: Library name: SAMPLES 12


title: B. catenulatum, raffinose, R3

description: Library name: BC_R_R3

organism: Bifidobacterium catenulatum

value: Raffinose


title: WT_Day9_P8_2nd

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: WT_Day9_P8_2nd

data_processing:
Adapter Trimming
Quality control using prinseq, FastQC
Bismark mapping, duplicate removal
Methylation call, methylation level comparison using methylkit
Assembly: hg38
Supplementary files format and content: bedGraph files, read count files

source_name: WT

growth_protocol: Hematopoietic differentiation was induced using the STEMdiff™ Hematopoietic Kit. 610B1 cells were seeded at a density of 40-60 aggregates/well, and differentiation was induced by switching from mTeSR+ medium to A medium on day 0. Medium changes were performed on days 2,3, and every other day thereafter.

extract_protocol:
DNA was extracted using the NucleoSpin tissue kit (Macherey-Nagel, Cat# 740952).
Libraries were prepared using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs, Cat# E7120S) and sequenced on the Illumina HiSeqX-Ten system. Bismark and Bowtie2 were used for mapping, and the methylKit R package was used to identify differential methylation regions.

treatment_protocol: The Alt-R™ S.p. Cas9 Nuclease 3NLS (Integrated DNA Technologies, Cat#1081060) was diluted to 36 µM in Resuspension Buffer from the Neon™ Transfection System (Invitrogen, MPK1096), and added to the crRNA:tracrRNA mixture. The complex was incubated at room temperature for 20 minutes before transfection into cells with single-strand donor DNA via electroporation (1400 mV, 20 ms pulse width, 1 pulse). Genome editing was confirmed via T7E1 assay for TAD truncated lines and PCR for Runt-VP64 lines.

value: WT

value: iPS


title: RFP_∆atpB_rep3

description: Library name: RFP_datpB_rep3

library_source: other

data_processing:
The quality of the obtained footprint reads was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were removed using cutadapt.
All alignments were performed with STAR aligner v2.7.1a, using a sequential mapping approach where unmapped reads were used as input for the proceeding alignment. The alignment order is as follows: 1) rRNA and tRNA contaminants; 2) chloroplast genome; 3) mitochondrial genome; and 4) nuclear genome. The following sequences were obtained from NCBI (with following annotation): 5.8S rRNA (AJ300215.1), 5S rRNA (AJ222659.1), 18S rRNA (AJ236016.1), and 26S rRNA (AF479172.1), chloroplast genome (Z00044.2), mitochondrial genome (NC_006581.1). Sequences for the nuclear genome and tRNAs were obtained from solgenomics (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/).
Additional processing and sorting of alignment data were done using samtools and bedtools.
Assembly: Z00044.2
Supplementary files format and content: xlsx file including total reads, RPKM from each sample for chloroplast transcripts
Library strategy: Ribo-Seq

molecule: other

value: delta atpB


title: RFP_∆atpB_rep2

description: Library name: RFP_datpB_rep2


title: B. catenulatum, raffinose, R2

description: Library name: BC_R_R2


title: WT_Day9_P6_2nd

description: Library name: WT_Day9_P6_2nd


title: WT_Day9_P8_1st

description: Library name: WT_Day9_P8_1st


title: Stomach

description: Library name: SAMPLES 10

source_name: stomach

value: stomach


title: RFP_∆atpB_rep1

description: Library name: RFP_datpB_rep1


title: Heart

description: Library name: SAMPLES 9

source_name: heart

value: heart


title: B. catenulatum, raffinose, R1

description: Library name: BC_R_R1


title: RFP_WT_SNN_rep3

description: Library name: RFP_WT_SNN_rep3


title: B. catenulatum, glucose, R3

description: Library name: BC_G_R3


title: IR_24.8h_2

description: Library name: SAMPLES 8


title: WT_Day9_P6_1st

description: Library name: WT_Day9_P6_1st


title: WT_Day6_2nd

description: Library name: WT_Day6_2nd


title: RFP_WT_SNN_rep2

description: Library name: RFP_WT_SNN_rep2


title: B. catenulatum, glucose, R1

description: Library name: BC_G_R1


title: RFP_WT_SNN_rep1

description: Library name: RFP_WT_SNN_rep1


title: IR_24.8h_1

description: Library name: SAMPLES 7


title: IR_12.8h_2

description: Library name: SAMPLES 6


title: IR_12.8h_1

description: Library name: SAMPLES 5


title: Zea mays non-exposed, 10 day, replicate 3

city: Auburn

first: Emily

last: Roggenkamp

state: AL

address: 209 Rouse Life Science Bldg

country: USA

institute: Auburn University

description:
Library name: PM02_mRNA12
early_control_rep3

data_processing:
Trimmed adapters and low quality reads with cutadapt
Aligned to the Phyllachora maydis PM02 genome and performed contaminant analysis with diamond blastx and megan
Aligned to the B73 reference genome version 5 with hisat2
Read alignments counted at genic regions using Htseq
Differential expression analysis with DEseq2
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: Read count file supplied to Deseq. Rows are the respective maize B73 genes for version 5. Columns are each sample. Tab separated.

molecule: polyA RNA

organism:
Zea mays
Phyllachora maydis

source_name: leaf

growth_protocol: 30 days grown in outdoor greenhouse courtyard space

extract_protocol:
For each sample, five leaf disks were sampled to extract RNA. RNA was extracted using the Plant Rneasy minikit from Qiagen
Illumina stranded mRNA library using ligation kit and IDT for Illumina TruSeq RNA Unique Dual indexes.

treatment_protocol: 10 days exposure to a corn field with high loads of tar spot inoculum

value: leaf

value: not exposed

tag: time

value: 10 day

tag: batch


title: HD-label_NC

description: Library name: SAMPLES 11


title: B. catenulatum, glucose, R2

description: Library name: BC_G_R2

value: Bacteria

value: Glucose


title: Zea mays non-exposed, 10 day, replicate 2

description:
Library name: PM02_mRNA11
early_control_rep2


title: RFP_as_ATPC_rep3

description: Library name: RFP_as_ATPC_rep3

value: Petit Havana


title: VP_Day9_P8_2nd

description: Library name: VP_Day9_P8_2nd


title: Zea mays non-exposed, 10 day, replicate 1

description:
Library name: PM02_mRNA10
early_control_rep1


title: RFP_as_ATPC_rep1

description: Library name: RFP_as_ATPC_rep1


title: RFP_∆psaB_rep3

description: Library name: RFP_dpsaB_rep3

value: delta psaB


title: IR_5.3h_1

description: Library name: SAMPLES 3

value: kidney


title: IR_0h_2

description: Library name: SAMPLES 2


title: RFP_as_ATPC_rep2

description: Library name: RFP_as_ATPC_rep2


title: WT_Day0_2nd

description: Library name: WT_Day0_2nd


title: Zea mays exposed to Phyllachora maydis environment, 10 day, replicate 3

description:
Library name: PM02_mRNA9
early_infected_rep3

value: tar spot environmental exposure


title: WT_Day0_1st

description: Library name: WT_Day0_1st


title: VP_Day9_P6_2nd

description: Library name: VP_Day9_P6_2nd


title: IR_0h_1

description: Library name: SAMPLES 1


title: VP_Day9_P6_1st

description: Library name: VP_Day9_P6_1st


title: RFP_∆psaB_rep1

description: Library name: RFP_dpsaB_rep1


title: Zea mays exposed to Phyllachora maydis environment, 10 day, replicate 2

description:
Library name: PM02_mRNA8
early_infected_rep2


title: Zea mays exposed to Phyllachora maydis environment, 10 day, replicate 1

description:
Library name: PM02_mRNA7
early_infected_rep1


title: WT_Day6_1st

description: Library name: WT_Day6_1st


title: IR_5.3h_2

description: Library name: SAMPLES 4


title: Zea mays non-exposed, 24 day, replicate 3

description:
Library name: PM02_mRNA6
late_control_rep3

value: 24 day


title: RFP_∆petN_rep3

description: Library name: RFP_dpetN_rep3

value: delta petN


title: VP64_Day6_2nd

description: Library name: VP64_Day6_2nd


title: mOocyte, FloxDelCre, rep3

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

institute: Kyushu University

description: Library name: m918_B3

data_processing:
Sequence reads were trimmed adaptor and low-quality bases using fastp with the option '-3 -q 15 -l 15'.
Hisat2 v2.2.1 was used to align the reads to the mouse genome (GRCm38).
The featureCounts v2.0.3 tool implemented in the Subread software was used to generate counts of reads uniquely mapped to annotated genes using the Ensembl (release 93) annotation gtf file.
In order to quantify the first exon of Kif11, as proxy for the full-length mRNA, reads were counted using the custom annotation gtf file with all Kif11 exons removed except for the exon 1.
Assembly: mouse genome GRCm38
Supplementary files format and content: tab-delimited text file including raw count or TPM for each sample.

source_name: oocytes

extract_protocol:
The isolated full-grown oocytes at the germinal vesicle (GV) stage were washed in washing medium [0.1% PBA in PBS] and collected manually with 0.5 μL of the washing medium in 2.125 μl cell lysis buffer [10X Lysis Buffer (TAKARA), RNase Inhibitor (TAKARA), and RNase-free water (Nacalai)] in 0.2 mL 8-strip tubes. Three oocytes were collected in each tube with one or two replicates from each mouse.
The SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) was used to reverse transcribe poly(A) RNA and amplify full-length cDNA. Samples were amplified for 13 cycles in 8-strip tubes. After the cDNA was adjusted to 0.5 ng in 1.25 μL of elution buffer [10mM Tris-HCl, pH8.5], Tn5 tagmentation-based reaction was performed with 1/4 volume of the Nextera XT DNA Library Preparation Kit (Illumina) with Nextera XT Index Kit (Illumina) according to manufacturer's protocol. Library DNA was amplified with 12 cycles of PCR and purified using 1.8× volume of SPRISelect (Beckman Coulter) and eluted into 12 μL of the elution buffer [10mM Tris-HCl, pH8.5].

value: oocytes

value: FloxDel, Spo11-Cre


title: VP64_Day6_1st

description: Library name: VP64_Day6_1st

value: iPS


title: RFP_∆petN_rep2

description: Library name: RFP_dpetN_rep2


title: Zea mays non-exposed, 24 day, replicate 2

description:
Library name: PM02_mRNA5
late_control_rep2


title: mOocyte, FloxDelCre, rep2

description: Library name: m910_B2


title: VP_Day9_P8_1st

description: Library name: VP_Day9_P8_1st


title: VP64_Day0_2nd

description: Library name: VP64_Day0_2nd


title: Zea mays non-exposed, 24 day, replicate 1

description:
Library name: PM02_mRNA4
late_control_rep1


title: RFP_∆petN_rep1

description: Library name: RFP_dpetN_rep1


title: VP64_Day0_1st

description: Library name: VP64_Day0_1st


title: RFP_∆psaB_rep2

description: Library name: RFP_dpsaB_rep2


title: mOocyte, FloxDelCre, rep1

description: Library name: m910_B1


title: RFP_∆petB/D_rep3

description: Library name: RFP_dpetB_D_rep3

value: delta petB/D


title: RFP_∆petB/D_rep2

description: Library name: RFP_dpetB_D_rep2


title: Zea mays exposed to Phyllachora maydis environment, 24 day, replicate 2

description:
Library name: PM02_mRNA2
late_infected_rep2


title: mOocyte, FloxDel, rep3

description: Library name: m921_A7

value: FloxDel


title: KO_Day9_2nd

description: Library name: KO_Day9_2nd

source_name: TAD

value: TAD


title: Zea mays exposed to Phyllachora maydis environment, 24 day, replicate 1

description:
Library name: PM02_mRNA1
late_infected_rep1

value: leaf


title: KO_Day6_1st

description: Library name: KO_Day6_1st


title: KO_Day6_2nd

description: Library name: KO_Day6_2nd


title: RFP_∆petB/D_rep1

description: Library name: RFP_dpetB_D_rep1


title: mOocyte, FloxDelCre, rep4

description: Library name: m918_B4


title: RFP_∆psbJ_rep3

description: Library name: RFP_dpsbJ_rep3

value: delta psbJ


title: mOocyte, FloxDel, rep2

description: Library name: m919_A6


title: FFA-100uM-180-ExpB_03

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

description: Library name: Sample12

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397) using STAR2.7.1a and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 and/or Limma-Voom in the R statistical computing environment.
Assembly: Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397)
Supplementary files format and content: tab-delimitated text (.txt) files include raw counts for each Sample

organism: Mycobacteroides abscessus

growth_protocol: M. abscessus ATCC19977 was cultured in cation-adjusted mueller hinton broth shaking at 225 rpm at 37 °C.

extract_protocol:
After treatment, 5 mL of Bacterial RNAprotect (Qiagen) was added for 5 minutes at room temperature. The culture was then centrifuged at 3214 xg for 10 minutes at 4 °C and the supernatant discarded. An RNAeasy Plus Mini Kit (Qiagen; Cat. No. 74134) was used to extract the RNA following the manufacturer’s instructions utilizing mechanical lysis for Gram-positive bacteria.
Libraries were prepared from ribosomal RNA-depleted total RNA using Illumina Stranded Total RNA Prep, ligation with Ribo-Zero Plus mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20037135). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Paired-end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).

treatment_protocol: Five mL of mid-log cultures (OD600 0.4-0.6) were 100µM of florfenicol amine for 30 minutes and 3 hours, or equilalent vehicle control (DMSO) for 30 minutes or 3 hours shaking at 225 rpm at 37 °C.

value: Planktonic

value: Florfenicol amine-0.1 mM-3 hours


title: RFP_∆psbJ_rep2

description: Library name: RFP_dpsbJ_rep2


title: KO_Day0_2nd

description: Library name: KO_Day0_2nd


title: mOocyte, FloxDel, rep1

description: Library name: m919_A5


title: mOocyte, WtFloxCre, rep5

description: Library name: m922_C1

value: WtFlox, Spo11-Cre


title: KO_Day0_1st

description: Library name: KO_Day0_1st


title: RFP_∆psbJ_rep1

description: Library name: RFP_dpsbJ_rep1

value: Petit Havana


title: FFA-100uM-180-ExpB_01

description: Library name: Sample10


title: Zea mays exposed to Phyllachora maydis environment, 24 day, replicate 3

description:
Library name: PM02_mRNA3
late_infected_rep3


title: mOocyte, FloxDel, rep4

description: Library name: m921_A8


title: mOocyte, WtFloxCre, rep4

description: Library name: m917_B8


title: VP64_Day9_P6

description: Library name: Lib8

library_source: genomic

data_processing:
Adapter Trimming
Quality control using prinseq, FastQC
Bismark mapping, duplicate removal
Methylation call, methylation level comparison using methylkit
Assembly: hg38
Supplementary files format and content: bedGraph files, read count files
Library strategy: EM-Seq

molecule: genomic DNA


title: RFP_∆3'psbD_rep3

description: Library name: RFP_dpsbD_rep3

value: delta 3'psbD


title: WT_Day9_P6

description: Library name: Lib7

source_name: Wild-type

value: Wild-type


title: Control-180-ExpB_02

description: Library name: Sample8

value: DMSO-3 hours


title: RFP_∆3'psbD_rep2

description: Library name: RFP_dpsbD_rep2


title: VP64_Day9

description: Library name: Lib6


title: Control-180-ExpB_01

description: Library name: Sample7


title: mOocyte, WtFloxCre, rep2

description: Library name: m916_B6


title: VP64_Day6

description: Library name: Lib5


title: RFP_RB70_rep3

description: Library name: RFP_RB70_rep3


title: FFA-100uM-30-ExpB_03

description: Library name: Sample6

value: Florfenicol amine-0.1 mM-30 minutes


title: mOocyte, WtFloxCre, rep1

description: Library name: m916_B5


title: mOocyte, WtFlox, rep4

description: Library name: m923_A4

value: WtFlox


title: KO_Day9

description: Library name: Lib4


title: FFA-100uM-30-ExpB_02

description: Library name: Sample5


title: RFP_RB70_rep2

description: Library name: RFP_RB70_rep2


title: KO_Day6

description: Library name: Lib3


title: FFA-100uM-180-ExpB_02

description: Library name: Sample11


title: RFP_RB70_rep1

description: Library name: RFP_RB70_rep1


title: mOocyte, WtFlox, rep2

description: Library name: m920_A2

value: oocytes


title: FFA-100uM-30-ExpB_01

description: Library name: Sample4


title: mOocyte, WtFlox, rep1

description: Library name: m920_A1


title: mOocyte, WtFloxCre, rep3

description: Library name: m917_B7


title: Control-30-ExpB_03

description: Library name: Sample3

value: DMSO-30 minutes


title: Control-180-ExpB_03

description: Library name: Sample9


title: WT_Day6

description: Library name: Lib1

value: iPS


title: WT_Day9

description: Library name: Lib2


title: RFP_pRB8c_rep2

description: Library name: RFP_pRB8c_rep2


title: N354

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using the Cell Ranger pipeline
Assembly: Dog10K_Boxer_Tasha/canFam6
Supplementary files format and content: Compressed Tab-separated value files and matrix market exchange format files

organism: Canis lupus familiaris

source_name: Neuroretina

extract_protocol:
Five mm diameter neuretinal punches were collected within the injection bleb and pretreated with 0.25% trypsin for 10 min at 37°C. The tissue was then dissociated into single cells using the Miltenyi Biotec Neural Tissue Dissociation kit - Postnatal neurons. Cells were washed in PBS and resuspended in PBS supplemented 0.5% BSA.
Libraries were prepared using the 10X Single Cell 3' v3.1 following manufacterer's protocol.

treatment_protocol: Dogs were subretially injected with a pool of AAV5-promoter-GFP vectors for Massively Parallel Reporter Assays. Neuroretina was collected 5-6 weeks post injection.

value: Neuroretina

tag: age (in_weeks)

tag: gender

value: M

value: Subretinal injection of canine promoter-GFP pool


title: RFP_∆3'psbD_rep1

description: Library name: RFP_dpsbD_rep1


title: RFP_pRB8c_rep1

description: Library name: RFP_pRB8c_rep1


title: Control-30-ExpB_01

description: Library name: Sample1


title: Control-30-ExpB_02

description: Library name: Sample2


title: PbAP2-TR_D3_DIP

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

description: Library name: Sample2

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: text, Peak-calling

organism: Plasmodium berghei ANKA

source_name: ANKA

extract_protocol:
Recombinant AP2 domains fused with MBP  was incubated with P. berghei ANKA genomic DNA fragments in binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol) for 30 min. The protein/DNA solution was further mixed with amylose resin and incubated for 30 min. After incubation, the resin was washed three times with binding/washing buffer, and bound protein-DNA complexes were eluted with 10 mM maltose solution.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),

value: ANKA


title: mOocyte, WtFlox, rep3

description: Library name: m923_A3


title: leaves, bzip53 mutant, 78h extended night, replicate 2

status: Public on Jun 30 2025

city: Wuerzburg

first: Christoph

last: Weiste

address: Julius-von-Sachs Platz 2

department: Pharmaceutical Biology

institute: University of Wuerzburg

description: Library name: Nr56_bzip53_78_h_D.fq

data_processing:
Reads were mapped to the Arabidopsis thaliana genome (Col-0 TAIR10 genome release) using Bowtie2. Between 78% and 91% of all reads could be unambiguosly aligned and were used for further analysis. The resulting SAM files were converted to BAM files using Samtools. DEGs were analysed using Rstudio (packages: GenomicRanges, Rtracklayer, Rsamtools and EdgeR).
Assembly: Arabidopsis TAIR10 release
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: whole rosettes

growth_protocol: Plants were grown in a 12 h light / 12 h dark regime at a light intensity of around 100 µmol photons m-2 s-1 during the light period. Temperature was set to 21°C during the respective day and 18°C during the night. Relative humidity was set to 60%

extract_protocol:
RNA was extracted using a Trizol based extraction protocol. RNA quality was checked using a 2100 Bioanalyzer with a RNA 6000 Nano kit.
Libraries were prepared using the TruSeq Stranded mRNA library preparation kit from Illumina following the manufacturers instructions

treatment_protocol: Plants were grown in a 12 h light / 12 h dark regime for 4 weeks. At ZT0 plants were either kept in light or transferred to darkness. At ZT6 plants were harvested in light or after 6h, 30h or 78h of extended darkness.

value: whole rosettes

value: bzip53 mutant

value: 78h extended night


title: leaves, bzip1/53 mutant, 78h extended night, replicate 1

description: Library name: Nr52_bzip1_53_78_h_D.fq

value: bzip1/53 mutant


title: leaves, bzip53 mutant, 78h extended night, replicate 1

description: Library name: Nr55_bzip53_78_h_D.fq


title: leaves, bzip1/53 mutant, 78h extended night, replicate 3

description: Library name: Nr54_bzip1_53_78_h_D.fq


title: leaves, bzip53 mutant, 78h extended night, replicate 3

description: Library name: Nr57_bzip53_78_h_D.fq


title: leaves, bzip1 mutant, 78h extended night, replicate 2

description: Library name: Nr59_bzip1_78_h_D.fq

value: bzip1 mutant


title: leaves, bzip2/11/44 mutant, 78h extended night, replicate 3

description: Library name: Nr51_bzip2_11_44_78_h_D.fq

value: bzip2/11/44 mutant


title: leaves, bzip1 mutant, 78h extended night, replicate 1

description: Library name: Nr58_bzip1_78_h_D.fq


title: RFP_pRB8c_rep3

description: Library name: RFP_pRB8c_rep3

value: Petit Havana


title: leaves, bzip2/11/44 mutant, 78h extended night, replicate 2

description: Library name: Nr50_bzip2_11_44_78_h_D.fq


title: leaves, bzip2/11/44 mutant, 78h extended night, replicate 1

description: Library name: Nr49_bzip2_11_44_78_h_D.fq


title: leaves, WT control, 78h extended night, replicate 2

description: Library name: Nr47_WT_78_h_D.fq

value: wildtype


title: leaves, WT control, 78h extended night, replicate 3

description: Library name: Nr48_WT_78_h_D.fq


title: leaves, WT control, 78h extended night, replicate 1

description: Library name: Nr46_WT_78_h_D.fq


title: leaves, bzip1 mutant, 30h extended night, replicate 2

description: Library name: Nr44_bzip1_30_h_D.fq

value: 30h extended night


title: leaves, bzip1 mutant, 30h extended night, replicate 1

description: Library name: Nr43_bzip1_30_h_D.fq


title: leaves, bzip53 mutant, 30h extended night, replicate 3

description: Library name: Nr42_bzip53_30_h_D.fq


title: leaves, bzip53 mutant, 30h extended night, replicate 2

description: Library name: Nr41_bzip53_30_h_D.fq


title: leaves, bzip1 mutant, 30h extended night, replicate 3

description: Library name: Nr45_bzip1_30_h_D.fq


title: PbAP2-TR_D1D2_DIP

description: Library name: Sample1


title: leaves, bzip1 mutant, 78h extended night, replicate 3

description: Library name: Nr60_bzip1_78_h_D.fq


title: leaves, bzip1/53 mutant, 30h extended night, replicate 3

description: Library name: Nr39_bzip1_53_30_h_D.fq


title: leaves, bzip1/53 mutant, 30h extended night, replicate 2

description: Library name: Nr38_bzip1_53_30_h_D.fq


title: leaves, bzip2/11/44 mutant, 30h extended night, replicate 1

description: Library name: Nr34_bzip2_11_44_30_h_D.fq


title: leaves, bzip2/11/44 mutant, 30h extended night, replicate 3

description: Library name: Nr36_bzip2_11_44_30_h_D.fq


title: leaves, bzip1/53 mutant, 78h extended night, replicate 2

description: Library name: Nr53_bzip1_53_78_h_D.fq


title: leaves, WT control, 30h extended night, replicate 3

description: Library name: Nr33_WT_30_h_D.fq


title: leaves, bzip53 mutant, 6h extended night, replicate 3

description: Library name: Nr27_bzip53_6_h_D.fq

value: 6h extended night


title: leaves, WT control, 30h extended night, replicate 2

description: Library name: Nr32_WT_30_h_D.fq


title: leaves, bzip1 mutant, 6h extended night, replicate 3

description: Library name: Nr30_bzip1_6_h_D.fq


title: leaves, bzip1 mutant, 6h extended night, replicate 1

description: Library name: Nr28_bzip1_6_h_D.fq


title: leaves, WT control, 30h extended night, replicate 1

description: Library name: Nr31_WT_30_h_D.fq


title: leaves, bzip1 mutant, 6h extended night, replicate 2

description: Library name: Nr29_bzip1_6_h_D.fq


title: leaves, bzip53 mutant, 6h extended night, replicate 2

description: Library name: Nr26_bzip53_6_h_D.fq


title: leaves, bzip53 mutant, 6h extended night, replicate 1

description: Library name: Nr25_bzip53_6_h_D.fq


title: leaves, bzip1/53 mutant, 6h extended night, replicate 2

description: Library name: Nr23_bzip1_53_6_h_D.fq


title: leaves, bzip2/11/44 mutant, 6h extended night, replicate 2

description: Library name: Nr20_bzip2_11_44_6_h_D.fq


title: leaves, bzip1/53 mutant, 6h extended night, replicate 1

description: Library name: Nr22_bzip1_53_6_h_D.fq


title: leaves, bzip1/53 mutant, 6h extended night, replicate 3

description: Library name: Nr24_bzip1_53_6_h_D.fq


title: leaves, bzip2/11/44 mutant, 6h extended night, replicate 3

description: Library name: Nr21_bzip2_11_44_6_h_D.fq


title: leaves, bzip2/11/44 mutant, 6h extended night, replicate 1

description: Library name: Nr19_bzip2_11_44_6_h_D.fq


title: leaves, bzip1 mutant, 6h light, replicate 3

description: Library name: Nr15_bzip1_6_h_L.fq

value: 6h light (Zeitgeber time 6)


title: leaves, WT control, 6h extended night, replicate 3

description: Library name: Nr18_WT_6_h_D.fq


title: leaves, bzip1/53 mutant, 30h extended night, replicate 1

description: Library name: Nr37_bzip1_53_30_h_D.fq


title: leaves, WT control, 6h extended night, replicate 1

description: Library name: Nr16_WT_6_h_D.fq


title: leaves, bzip53 mutant, 30h extended night, replicate 1

description: Library name: Nr40_bzip53_30_h_D.fq


title: leaves, bzip1 mutant, 6h light, replicate 1

description: Library name: Nr13_bzip1_6_h_L.fq


title: leaves, WT control, 6h extended night, replicate 2

description: Library name: Nr17_WT_6_h_D.fq


title: leaves, bzip53 mutant, 6h light, replicate 3

description: Library name: Nr12_bzip53_6_h_L.fq


title: leaves, bzip2/11/44 mutant, 30h extended night, replicate 2

description: Library name: Nr35_bzip2_11_44_30_h_D.fq


title: leaves, bzip1 mutant, 6h light, replicate 2

description: Library name: Nr14_bzip1_6_h_L.fq


title: leaves, bzip1/53 mutant, 6h light, replicate 3

description: Library name: Nr9_bzip1_53_6_h_L.fq


title: leaves, bzip53 mutant, 6h light, replicate 1

description: Library name: Nr10_bzip53_6_h_L.fq


title: leaves, bzip1/53 mutant, 6h light, replicate 1

description: Library name: Nr7_bzip1_53_6_h_L.fq


title: leaves, bzip2/11/44 mutant, 6h light, replicate 3

description: Library name: Nr6_bzip2_11_44_6_h_L.fq


title: leaves, bzip2/11/44 mutant, 6h light, replicate 2

description: Library name: Nr5_bzip2_11_44_6_h_L.fq


title: leaves, WT control, 6h light, replicate 3

description: Library name: Nr3_WT_6_h_L.fq


title: leaves, WT control, 6h light, replicate 2

description: Library name: Nr2_WT_6_h_L.fq


title: leaves, bzip2/11/44 mutant, 6h light, replicate 1

description: Library name: Nr4_bzip2_11_44_6_h_L.fq


title: Ly6C-hi monocyte blood LLC tumor-bearing IgG control CUT&Run Rep 1

status: Public on Jun 25 2025

city: Saint Petersburg

first: Laszlo

last: Halasz

state: Florida

address: 600 5th Ave S

department: Institute for Fundamental Biomedical Research

institute: Johns Hopkins University

description: mm_CUTRUN_LLC_Ly6C_high_Monocyte_IgG_Rep1

data_processing:
*library strategy: CUT&RUN
RNA-seq: Raw sequencing reads were processed by the nfcore RNA-seq pipeline (v3.10.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.7) and cutadapt (v3.4) then mapped to the mm10 genome using STAR (v2.6.1d) and quantified with Salmon (v1.9.0). Genes with low counts were removed using edgeR’s filterByExpr function (min.count = 3).  ATAC-seq: Raw sequencing reads were processed by the nfcore ATAC-seq pipeline (v1.2.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.4_dev) then mapped to the mm10 genome using BWA (v0.7.17-r1188). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged. CUT&Run and CUT&Tag: Raw sequencing reads were processed by the nfcore cutandrun pipeline (v3.0.0) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.6) then mapped to the mm10 genome using Bowtie2 (v2.4.4). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged.
Assembly: mm10
Supplementary files format and content: RNA-seq: Raw and normalized count table ATAC-seq/CUT&Run/CUT&Tag: bigwig coverage file

source_name: Blood

growth_protocol: CD11b+ Ly6G- Ly6Chi MHC-II- monocytes were sorted from the blood of healthy mice, the blood of subcutaneous LLC tumor-bearing mice or from LLC tumors.

extract_protocol:
RNA-seq: RNA from sorted cells was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA-Seq library was prepared using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol. Libraries were sequenced with Illumina HiScanSQ sequencer. ATAC-seq: ATAC-seq was carried out as described earlier with minor modifications (Buenrostro et al. Nature Methods, 2013). Monocytes were sorted into ice-cold PBS in three biological replicates. After centrifugation, the cell pellet was resuspended in ATAC lysis buffer (10 mmol/L Tris-HCl pH7.4, 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.1% IGEPAL). After centrifugation, cell nuclei were tagmented using Nextera DNA Library Preparation Kit (Illumina). After tagmentation, DNA was purified with MinElute PCR Purification Kit (QIAGEN). Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 9 PCR cycles. Amplified libraries were purified again with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform. CUT&Run: The CUT&RUN protocol was performed using the Epicypher CUTANA CUT&RUN kit according to the manufacturer's instructions with some minor modifications. Briefly, monocytes were recovered from freezing media by quickly thawing samples at 37°C. Cells were spun down at 600g for 3 minutes at room temperature. Cells were then resuspended in 105uL of room temperature wash buffer and cell viability was confirmed. Cells were then incubated with concavilin A beads for 10 minutes at room temperature. 0.5ug of antibodies for target proteins were then added and incubated overnight on nutator at 4°C. The following day, cells were washed with cell permeabilization buffer, before the addition of the pAG-MNase. Cells were incubated with the pAG-MNase for 10 minutes at room temperature. To digest and release target chromatin, 100mM Calcium Chloride was added to the reaction. After a 2-hour incubation on nutator at 4°C, the reaction was halted by the addition of a stop mastermix. Reactions were placed on a thermocycler at 37°C for 10 minutes. DNA was purified using SPRISelect beads (1.4X volume). Libraries were then prepared with Epicypher’s CUT&RUN Library Prep Kit according to the manufacturer’s protocol and then subjected to pair-end sequencing on a NextSeq2000 machine (1x50bp reads). CUT&Tag: Sorted Ly6C-hi monocytes were cryopreserved in ice cold cryopreservation solution consisting of 50% FBS, 40% RPMI and 10%DMSO. Cryopreserved samples were sent to Active Motif for CUT&Tag in two replicates. Briefly, cells were incubated overnight with Concanavalin A beads and 1 µl of the primary anti-H3K4me1 antibody per reaction (Active Motif, catalog number 39297) and 1 µl of the primary anti-H3K27ac antibody per reaction (Active Motif, catalog number 39135). After incubation with the secondary anti-rabbit antibody (1:100), cells were washed and tagmentation was performed at 37℃ using protein-A-Tn5. Tagmentation was halted by the addition of EDTA, SDS and proteinase K at 55℃, after which DNA extraction and ethanol purification was performed, followed by PCR amplification and barcoding (see Active Motif CUT&Tag kit, catalog number 53160 for recommended conditions and indexes). Following SPRI bead cleanup (Beckman Coulter), the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 550 (PE38).
RNA-seq: RNA-Seq library was prepared using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol. Libraries were sequenced with Illumina HiScanSQ sequencer. ATAC-seq: Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 9 PCR cycles. Amplified libraries were purified with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform. CUT&Run: Libraries were prepared with Epicypher’s CUT&RUN Library Prep Kit according to the manufacturer’s protocol and then subjected to pair-end sequencing on a NextSeq2000 machine (1x50bp reads). CUT&Tag: PCR amplification and barcoding of tagmented DNA were performed according to the Active Motif CUT&Tag kit (catalog number 53160). Following SPRI bead cleanup (Beckman Coulter), the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 550 (PE38).

value: Blood

value: Ly6C-hi monocyte

tag: strain


title: Ly6C-hi monocyte blood LLC tumor-bearing IgG control CUT&Run Rep 2

description: mm_CUTRUN_LLC_Ly6C_high_Monocyte_IgG_Rep2


title: Ly6C-hi monocyte blood healthy IgG control CUT&Run Rep 2

description: mm_CUTRUN_Naive_Ly6C_high_Monocyte_IgG_Rep2


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K4me3 CUT&Run Rep 2

description: mm_CUTRUN_LLC_Ly6C_high_Monocyte_H3K4me3_Rep2


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K4me3 CUT&Run Rep 1

description: mm_CUTRUN_LLC_Ly6C_high_Monocyte_H3K4me3_Rep1


title: Ly6C-hi monocyte blood healthy IgG control CUT&Run Rep 1

description: mm_CUTRUN_Naive_Ly6C_high_Monocyte_IgG_Rep1


title: leaves, bzip53 mutant, 6h light, replicate 2

description: Library name: Nr11_bzip53_6_h_L.fq


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K27ac CUT&Tag Rep 2

description: mm_CUTTAG_LLC_Ly6C_high_Monocyte_H3K27ac_Rep2

data_processing:
*library strategy: CUT&TAG
RNA-seq: Raw sequencing reads were processed by the nfcore RNA-seq pipeline (v3.10.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.7) and cutadapt (v3.4) then mapped to the mm10 genome using STAR (v2.6.1d) and quantified with Salmon (v1.9.0). Genes with low counts were removed using edgeR’s filterByExpr function (min.count = 3).  ATAC-seq: Raw sequencing reads were processed by the nfcore ATAC-seq pipeline (v1.2.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.4_dev) then mapped to the mm10 genome using BWA (v0.7.17-r1188). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged. CUT&Run and CUT&Tag: Raw sequencing reads were processed by the nfcore cutandrun pipeline (v3.0.0) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.6) then mapped to the mm10 genome using Bowtie2 (v2.4.4). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged.
Assembly: mm10
Supplementary files format and content: RNA-seq: Raw and normalized count table ATAC-seq/CUT&Run/CUT&Tag: bigwig coverage file


title: Ly6C-hi monocyte blood healthy H3K4me3 CUT&Run Rep 2

description: mm_CUTRUN_Naive_Ly6C_high_Monocyte_H3K4me3_Rep2


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K27ac CUT&Tag Rep 1

description: mm_CUTTAG_LLC_Ly6C_high_Monocyte_H3K27ac_Rep1


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K4me1 CUT&Tag Rep 2

description: mm_CUTTAG_LLC_Ly6C_high_Monocyte_H3K4me1_Rep2


title: Ly6C-hi monocyte blood healthy H3K4me3 CUT&Run Rep 1

description: mm_CUTRUN_Naive_Ly6C_high_Monocyte_H3K4me3_Rep1


title: Ly6C-hi monocyte blood healthy H3K27ac CUT&Tag Rep 1

description: mm_CUTTAG_Naive_Ly6C_high_Monocyte_H3K27ac_Rep1


title: Ly6C-hi monocyte blood healthy H3K27ac CUT&Tag Rep 2

description: mm_CUTTAG_Naive_Ly6C_high_Monocyte_H3K27ac_Rep2


title: Ly6C-hi monocyte blood LLC tumor-bearing H3K4me1 CUT&Tag Rep 1

description: mm_CUTTAG_LLC_Ly6C_high_Monocyte_H3K4me1_Rep1


title: Ly6C-hi monocyte blood healthy H3K4me1 CUT&Tag Rep 2

description: mm_CUTTAG_Naive_Ly6C_high_Monocyte_H3K4me1_Rep2


title: Ly6C-hi monocyte LLC tumor RNA-seq Rep 3

data_processing:
RNA-seq: Raw sequencing reads were processed by the nfcore RNA-seq pipeline (v3.10.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.7) and cutadapt (v3.4) then mapped to the mm10 genome using STAR (v2.6.1d) and quantified with Salmon (v1.9.0). Genes with low counts were removed using edgeR’s filterByExpr function (min.count = 3).  ATAC-seq: Raw sequencing reads were processed by the nfcore ATAC-seq pipeline (v1.2.1) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.4_dev) then mapped to the mm10 genome using BWA (v0.7.17-r1188). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged. CUT&Run and CUT&Tag: Raw sequencing reads were processed by the nfcore cutandrun pipeline (v3.0.0) with default parameters. Briefly, the reads were trimmed with trimgalore (v0.6.6) then mapped to the mm10 genome using Bowtie2 (v2.4.4). Low quality reads and reads mapping to blacklisted regions were discarded. Duplicated reads were merged.
Assembly: mm10
Supplementary files format and content: RNA-seq: Raw and normalized count table ATAC-seq/CUT&Run/CUT&Tag: bigwig coverage file

source_name: LLC tumor

value: LLC tumor


title: Ly6C-hi monocyte blood LLC tumor-bearing RNA-seq Rep 3


title: leaves, bzip1/53 mutant, 6h light, replicate 2

description: Library name: Nr8_bzip1_53_6_h_L.fq


title: leaves, WT control, 6h light, replicate 1

description: Library name: Nr1_WT_6_h_L.fq


title: Ly6C-hi monocyte blood healthy H3K4me1 CUT&Tag Rep 1

description: mm_CUTTAG_Naive_Ly6C_high_Monocyte_H3K4me1_Rep1


title: Ly6C-hi monocyte LLC tumor RNA-seq Rep 1


title: Ly6C-hi monocyte LLC tumor RNA-seq Rep 2


title: Ly6C-hi monocyte blood LLC tumor-bearing RNA-seq Rep 2


title: Ly6C-hi monocyte blood LLC tumor-bearing RNA-seq Rep 1


title: Ly6C-hi monocyte blood healthy RNA-seq Rep 3


title: Ly6C-hi monocyte blood healthy RNA-seq Rep 1


title: Ly6C-hi monocyte blood healthy ATAC-seq Rep 3


title: Ly6C-hi monocyte blood LLC tumor-bearing ATAC-seq Rep 2


title: Ly6C-hi monocyte blood healthy RNA-seq Rep 2


title: Ly6C-hi monocyte blood LLC tumor-bearing ATAC-seq Rep 3


title: WT_HS_MicroC_t2_biol_rep2

status: Public on Jun 24 2025

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description: Library name: ag10

data_processing:
The raw reads were processed with distiller-nf pipeline using NC_000913.3 E.coli reference genome and BWA as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: cooler (.cool, a contact matrix) file for each sample

organism: Escherichia coli

growth_protocol: E. coli K-12 MG1655 strain was grown in Luria-Bertani broth at 37 °C and 200 rpm until reaching an OD600 of ~ 0.6.

extract_protocol: Cells were fixed with 3% formaldehyde and 2 mM DSG followed by treatment with lysozyme. DNA was digested with MNase. DNA ends were labeled with biotin and ligated followed by removal of biotin from non-ligated ends by Exonuclease III. The sample was de-crosslinked at 65 °C in the presence of Proteinase K followed by phenol-chloroform extraction and ethanol precipitation. RNA was removed by RNase A treatment and DNA was further purified with AMpure XP beads. Downstream steps included sonication, biotin pull down, end repair, A-tailing, ligation of Illumina Y adapters, and PCR amplification.

treatment_protocol: For heat shock treatment, cells were incubated in a water bath at 44 °C for 10 min. For transcription inhibition, cells were treated with 25 or 750 µg/mL rifampicin for 40 min at 37 °C and 200 rpm. To induce DNA damage, cells were exposed to 70 µg/mL bleomycin for 10 min at 37 °C and 200 rpm. For DNA gyrase inhibition, cells were treated with 0.025 or 0.25 µg/mL ciprofloxacin or 25 or 250 µg/mL novobiocin for 15 min at 37 °C and 200 rpm. For netropsin treatment, cells were grown to an OD600 ~ 0.4, followed by the addition of netropsin to a final concentration of 20 or 200 µg/mL and incubation for 30 min at 37 °C and 200 rpm.

value: bacteria

value: WT

value: heat shock


title: WT_MicroC_t2_biol_rep2

description: Library name: ag09


title: WT_HS_MicroC_t2_biol_rep1

description: Library name: ag08


title: WT_Netro200_RNASeq_biol_rep5

description: Library name: ag60

data_processing:
Data was processed using nf-core/rnaseq pipeline
Assembly: NC_000913.3
Supplementary files format and content: .csv,  gene counts  matrix

source_name: bacteria

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini RNA isolation kit according to the manufacturer's instructions. Ribosomal RNA was removed from 200 ng of the starting material using the NEBNext rRNA depletion kit (bacteria) and the libraries were prepared using NEBNext Ultra II Directional RNA-Seq library preparation kit.

value: netropsin


title: WT_MicroC_t2_biol_rep1

description: Library name: ag07


title: WT_Netro200_RNASeq_biol_rep3

description: Library name: ag58


title: WT_Netro200_RNASeq_biol_rep2

description: Library name: ag57


title: Ly6C-hi monocyte blood healthy ATAC-seq Rep 1


title: WT_Netro200_RNASeq_biol_rep1

description: Library name: ag56


title: deltaStpA_RNASeq_biol_rep5

description: Library name: ag55

value: delta stpA


title: deltaStpA_RNASeq_biol_rep1

description: Library name: ag51


title: deltaStpA_RNASeq_biol_rep3

description: Library name: ag53


title: deltaStpA_RNASeq_biol_rep4

description: Library name: ag54


title: deltaStpA_RNASeq_biol_rep2

description: Library name: ag52


title: deltaStpAdeltaHNS_RNASeq_biol_rep5

description: Library name: ag50

value: delta stpA delta HNS


title: deltaStpAdeltaHNS_RNASeq_biol_rep4

description: Library name: ag49


title: deltaStpAdeltaHNS_RNASeq_biol_rep3

description: Library name: ag48


title: deltaStpAdeltaHNS_RNASeq_biol_rep1

description: Library name: ag46


title: Ly6C-hi monocyte blood LLC tumor-bearing ATAC-seq Rep 1


title: deltaMuk_MicroC_biol_rep1

description: Library name: ag44

value: delta muk


title: deltaMuk_MicroC_biol_rep2

description: Library name: ag45


title: WT_netro200_MicroC

description: Library name: ag43

value: netropsin 200 ug/ml


title: Ly6C-hi monocyte blood healthy ATAC-seq Rep 2


title: deltaStpAdeltaHNS_RNASeq_biol_rep2

description: Library name: ag47


title: WT_cipro025_MicroC

description: Library name: ag41

value: ciprofloxacin 0.25 ug/ml


title: WT_cipro0025_MicroC

description: Library name: ag40

value: ciprofloxacin 0.025 ug/ml


title: WT_netro20_MicroC

description: Library name: ag42

value: netropsin 20 ug/ml


title: WT_novo25_MicroC

description: Library name: ag38

value: novobiocin 25 ug/ml


title: WT_bleo_MicroC_biol_rep1

description: Library name: ag36

value: bleomycin 70 ug/ml


title: WT_37Cgrowth-37Cfix_MicroC

description: Library name: ag34


title: WT_bleo_MicroC_biol_rep2

description: Library name: ag37


title: WT_RTgrowth-RTfix_MicroC

description: Library name: ag35


title: WT_Netro200_RNASeq_biol_rep4

description: Library name: ag59


title: WT_noligase_MicroC

description: Library name: ag33


title: deltaHNS_MicroC_biol_rep1

description: Library name: ag31

value: delta HNS


title: deltaHNS_MicroC_biol_rep2

description: Library name: ag32


title: deltaStpA_MicroC_biol_rep1

description: Library name: ag29


title: deltaHNS_RNASeq_biol_rep5

description: Library name: ag28

data_processing:
Data was processed using nf-core/rnaseq v3.16.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects.
Assembly: NC_000913.3
Supplementary files format and content: .csv,  gene counts  matrix

value: deltaHNS


title: deltaStpA_MicroC_biol_rep2

description: Library name: ag30


title: deltaHNS_RNASeq_biol_rep2

description: Library name: ag25


title: deltaHNS_RNASeq_biol_rep1

description: Library name: ag24


title: deltaHNS_RNASeq_biol_rep4

description: Library name: ag27


title: deltaHNS_RNASeq_biol_rep3

description: Library name: ag26


title: WT_RNASeq_biol_rep5

description: Library name: ag23


title: WT_RNASeq_biol_rep4

description: Library name: ag22


title: WT_RNASeq_biol_rep3

description: Library name: ag21


title: WT_RNASeq_biol_rep2

description: Library name: ag20


title: WT_RNASeq_biol_rep1

description: Library name: ag19


title: WT_RedC_biol_rep1

description: Library name: ag15

data_processing:
The raw reads were processed with redc pipeline using NC_000913.3 E.coli reference genome and hisat2 as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: tab-delimited redc contacts file for each condition

extract_protocol: Cells were fixed with 3% formaldehyde followed by treatment with lysozyme, SDS, and Triton X-100. DNA was digested with NlaIII. Downstream steps included RNA-to-DNA bridge ligation, reverse transcription, and library construction. Red-C uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.


title: WT_RedC_biol_rep2

description: Library name: ag17


title: WT_HS_RedC_biol_rep1

description: Library name: ag16


title: WT_novo250_MicroC

description: Library name: ag39

value: novobiocin 250 ug/ml


title: WT_rif750_MicorC_biol_rep2

description: Library name: ag14

value: rif 750 ug/ml


title: WT_HS_RedC_biol_rep2

description: Library name: ag18

value: bacteria


title: WT_rif25_MicroC_biol_rep2

description: Library name: ag12

value: WT

value: rif 25 ug/ml


title: WT_rif750_MicroC_biol_rep1

description: Library name: ag13


title: WT_MicroC_t1_biol_rep2

description: Library name: ag05


title: WT_rif25_MicroC_biol_rep1

description: Library name: ag11


title: WT_HS_MicroC_t1_biol_rep1

description: Library name: ag04

value: heat shock


title: WT_HiC_biol_rep1

description: Library name: ag01

extract_protocol: Cells were fixed with 3% formaldehyde followed by treatment with lysozyme, SDS, and Triton X-100. DNA was digested with HpaII. DNA ends were labeled with biotin and ligated. The sample was de-crosslinked at 65 °C in the presence of Proteinase K followed by phenol-chloroform extraction and ethanol precipitation. RNA was removed by RNase A treatment and DNA was further purified with AMpure XP beads. Downstream steps included sonication, biotin pull down, end repair, A-tailing, ligation of Illumina Y adapters, and PCR amplification.


title: WT_HiC_biol_rep2

description: Library name: ag02


title: WT_MicroC_t1_biol_rep1

description: Library name: ag03


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP-, #6a

status: Public on Jun 19 2025

city: Bern

first: Sven

last: Rottenberg

address: Länggassstrasse 122

country: Switzerland

institute: University of Bern

description:
Library name: 185_2_mic
Chromium single-cell

data_processing:
For scRNA-seq, FastQ files were processed using the Cell Ranger (10x Genomics) pipeline. For ST, FastQ files were processed using the Space Ranger (10x Genomics) pipeline. Manual alignment to the fiducial frame and identification of tissue-covered spots was performed using Loupe Browser (10x Genomics).
Assembly: Mus musculus: mm10, Homo sapiens: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying capture spots
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and capture spots
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue

source_name: KB1P mammary tumor

growth_protocol: Two different parental tumors (T1, T2.1-2.2) were derived from the K14cre;Brca1F/F;Trp53F/F (KB1P) mouse mammary tumor model. The DMSO-frozen tumor pieces were thawed, washed with PBS and cut into small pieces. The pieces were transplanted in the fourth mammary fat pad (on the right side or both sides) of 2-4 months FVB/NJ mice.

extract_protocol:
The mammary tumors were harvested at different experimental endpoints and processed either for tissue collection and fixation or for scRNA-seq. For ST and IMC, the tissue was fixed in 4% paraformaldehyde immediately after harvesting. The fixed samples were trimmed, embedded in paraffin and stained with H&E for a first histological assessment.
For scRNA-seq, the 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v3.1 was used according to the manufacturer’s standard protocol (cDNA amplification in 14 cycles). A targeted cell recovery of 8’000 cells per sample was aimed. The sequencing of the library was performed on the NovaSeq 6000 platform (Illumina) using a S4 flow cell. For ST, 5 μm thick tissue sections were placed on Visium slides with the ROI within the capture area and manually H&E stained and scanned with an S360 Nanozoomer (Hamamatsu) using a 40x magnification. cDNA libraries were constructed according to the Visium Gene Expression User Guide (10X Genomics) and sequenced by the Next Generation Sequencing Platform at the University of Bern on an Illumina NovaSeq 6000 System on different flow cells with 100-300 cycles.

treatment_protocol: Animals were randomly assigned to the treatment groups. When the tumors reached a size of approximately 8 × 6 mm, the tumor-bearing mice were either sacrificed to collect the primary tumors or treated with a single dose of TAC therapy as a combination of 2.5 mg/kg doxorubicin (Teva, Pharmacode 4439164) injected intravenously, 12.5 mg/kg docetaxel (Teva, Pharmacode 6984902) and 120 mg/kg cyclophosphamide (Baxter, Pharmacode 2731162), both injected intraperitoneally or with a single dose of cisplatin 6 mg/kg (Teva, Pharmacode 4333164) injected intravenously. The residual tumors were collected 7 or 12 days after treatment and the recurrent tumors were collected once they reached the size of approximately 8 × 6 mm again. Some cisplatin-treated tumors were collected 4 or 24 hours after treatment for profiling with IMC.

value: KB1P mammary tumor

tag: library type

value: mRNA

value: no treatment


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP-, #2b

description:
Library name: 183_3_micb
Chromium single-cell


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP+, #6b

description:
Library name: 185_2_tumb
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP+, #5a

description:
Library name: 187_1_tum
Chromium single-cell

value: TAC regimen


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP-, #4a

description:
Library name: 188_4_mic
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP-, #5a

description:
Library name: 187_1_mic
Chromium single-cell


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP+, #4a

description:
Library name: 188_4_tum
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP+, #3a

description:
Library name: 183_1_tum
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP-, #3a

description:
Library name: 183_1_mic
Chromium single-cell


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP-, #2a

description:
Library name: 183_3_mic
Chromium single-cell


title: Mouse, scRNA-seq, Primary tumor, TAC, GFP+, #2a

description:
Library name: 183_3_tum
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP-, #1a

description:
Library name: 185_5_mic
Chromium single-cell


title: Mouse, scRNA-seq, Residual tumor, TAC, GFP+, #1a

description:
Library name: 185_5_tum
Chromium single-cell


title: Mouse, Visium ST, Cisplatin 12dpt, #28

description:
Library name: 20230607-2_8
FFPE Visium V1

data_processing:
For scRNA-seq, FastQ files were processed using the Cell Ranger (10x Genomics) pipeline. For ST, FastQ files were processed using the Space Ranger (10x Genomics) pipeline. Manual alignment to the fiducial frame and identification of tissue-covered spots was performed using Loupe Browser (10x Genomics).
Assembly: Mus musculus: mm10, Homo sapiens: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying capture spots
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and capture spots
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue
Library strategy: Spatial Transcriptomics

value: cisplatin 6mg/kg


title: Mouse, Visium ST, Cisplatin 24hpt, #27

description:
Library name: 20230607-2_7
FFPE Visium V1


title: WT_HS_MicroC_t1_biol_rep2

description: Library name: ag06


title: Mouse, Visium ST, Primary tumor, #25

description:
Library name: 20230607-2_5
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 24hpt 12mg/kg, #24

description:
Library name: 20230607-1_4
FFPE Visium V1

value: cisplatin 12mg/kg


title: Mouse, Visium ST, Cisplatin 4hpt, #26

description:
Library name: 20230607-2_6
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 12dpt, #19

description:
Library name: 20221010-4_15
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #21

description:
Library name: 20230607-1_1
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 4hpt, #22

description:
Library name: 20230607-1_2
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #17b

description:
Library name: 20221010-4_13
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 24hpt, #23

description:
Library name: 20230607-1_3
FFPE Visium V1


title: Mouse, Visium ST, TAC 12dpt, #3b

description:
Library name: 20221010-3_11
FFPE Visium V1


title: Mouse, Visium ST, TAC Recurrent, #16

description:
Library name: 20221010-3_12
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #17a

description:
Library name: 20221010-3_9
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 7dpt, #18

description:
Library name: 20221010-4_14
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #9b

description:
Library name: 20221010-2_5
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin Recurrent, #12

description:
Library name: 20221010-1_4
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 12dpt, #11

description:
Library name: 20221010-1_3
FFPE Visium V1


title: Mouse, Visium ST, TAC 7dpt, #13

description:
Library name: 20221010-2_6
FFPE Visium V1


title: Mouse, Visium ST, TAC Recurrent, #14

description:
Library name: 20221010-2_8
FFPE Visium V1


title: Mouse, Visium ST, TAC 12dpt, #8a

description:
Library name: 20220401-2_8
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #6

description:
Library name: 20220401-2_6
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin 7dpt, #10

description:
Library name: 20221010-1_2
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #9a

description:
Library name: 20221010-1_1
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #7

description:
Library name: 20220401-2_7
FFPE Visium V1


title: Mouse, Visium ST, Cisplatin Recurrent, #20

description:
Library name: 20221010-4_16
FFPE Visium V1


title: Mouse, Visium ST, Mammary gland, #5

description:
Library name: 20220401-2_5
FFPE Visium V1

source_name: Mammary gland

value: Mammary gland


title: Human, Visium ST, Residual tumor, #5

description:
Library name: T1212
FFPE Visium V2

source_name: Triple-negative breast cancer

value: Triple-negative breast cancer

value: neoadjuvant chemotherapy


title: Human, Visium ST, Primary tumor, #4

description:
Library name: T23_48
FFPE Visium V1


title: Mouse, Visium ST, Primary tumor, #2

description:
Library name: 20220401-1_2
FFPE Visium V1


title: Mouse, Visium ST, TAC 12dpt, #3a

description:
Library name: 20220401-1_3
FFPE Visium V1


title: kidney, 51_POD_PCK1_WT

status: Public on Jun 18 2025

city: Bellinzona

first: Anna

last: Rinaldi

address: Zorzi

institute: EOC

data_processing:
The sequencing data were processed using CellRanger (version 5.0.1), with reads aligned to the murine reference genome (mm10-2020-A).
The Cell Ranger cellranger count function output filtered gene–cell expression matrices, removing cell barcodes not represented in cells.
UMI count table utilizing both exonic and intronic reads was generated for downstream analysis.
Assembly: mm10-2020-A
Supplementary files format and content: RDS files

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Mice were perfused with ice-cold PBS and kidney halves collected for snRNA-seq analysis. Half kidney was cut into small pieces (>25) and transferred into a 2-ml Dounce homogenizer (Sigma, Cat#D8938) loaded with 1 ml of NEZ Lysis Buffer (Sigma, Cat#N3408) with RNase inhibitor (NEB, Cat#M0314) at final concentration of 0.4U/µl) on ice. Samples were then Dounce homogenized on ice with five strokes of the looser pestle every 2 min for 8 min (25 strokes in total). Samples were then slowly Dounce homogenized 25 times with the tighter pestle on ice. The  homogenized sample was filtered through a 40-μm Falcon Nylon Cell Strainer, then the filter was washed with 8 ml of 1% BSA PBS, and the nuclear suspension spun in a precooled (4 °C) centrifuge at 650g for 8 min. Supernatant was removed and the pellet resuspended in 1% BSA PBS (plus RNase inhibitor) and moved to a low-bind Eppendorf tube. Nuclear quality and number were assessed with trypan blue staining. Nuclei were sorted as DAPI positive on a BD Aria into 2% BSA solution with RNA inhibitor.
Barcoded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions

value: kidney

value: POD-ATTAC mice on a C57BL/6 background

value: PCK1 WT

tag: age

value: At 8 weeks-old

tag: Sex

value: Male

value: euthanized at 14

value: Dimerizer


title: Mouse, Visium ST, Primary tumor, #1

description:
Library name: 20220401-1_1
FFPE Visium V1


title: Mouse, Visium ST, TAC 7dpt, #15

description:
Library name: 20221010-3_10
FFPE Visium V1


title: Mouse, Visium ST, Mammary gland, #4

description:
Library name: 20220401-1_4
FFPE Visium V1


title: Human, Visium ST, Residual tumor, #2

description:
Library name: T23_42
FFPE Visium V1


title: Mouse, Visium ST, TAC 12dpt, #8b

description:
Library name: 20221010-2_7
FFPE Visium V1


title: Human, Visium ST, Residual tumor, #1

description:
Library name: T23_41
FFPE Visium V1


title: kidney, 31_POD_PCK1_WT


title: AOSN.B.COSN123_clone5A.6_rep2_L

status: Public on Jun 17 2025

city: San Diego

first: David

middle: M

last: Gilbert

state: California

address: 3525 John Hopkins Ct Ste 200

institute: San Diego Biomedical Research Institute

description:
Library name: AOSN.B.COSN123_clone5A.6_rep2_L
hom_AOSN_B_C3OSN_5A_6_Rep2_L

data_processing:
Sequence reads were trimmed using Trim_Galore/cutadapt and aligned to a custom N-masked mm10 reference genome where N replaces 129 or Castaneus SNPs relative to the standard mm10 reference genome.
Aligned reads were haplotype phased using SNP-split and split into 129- or Cas-specific files
Phased reads were counted in 50kb genomic bins using bedtools intersect
Log2 ratio of Early and Late read counts from corresponding sample and genome files is taken to calculate raw replication timing in each bin
Raw replication timing data is then quantile normalized across all datasets and loess-smoothed in 300kb genomic windows
Assembly: mm10
Supplementary files format and content: bedgraph file containing all datasets, where columns 1-3 are the genomic coordinates of each bin and columns 4-n contain the normalized and smoothed replication timing values. Each column contains a header, with columns 1-3 containing the chromosome, coordinate of bin start, and coordinate of bin end. Columns 4-n contain headers indentifying the cell line, clone, replicate, and parental genome of the dataset (the Zenododata can be found at DOI 10.5281/zenodo.15678081). Additionally, code to repeat our processing and analysis can be found at the following github repositories: https://github.com/jlt3/ERCEs_2023, https://github.com/ay-lab/SignifRT

growth_protocol: F121-9 Hybrid mESCs were grown in 2i + LIF

extract_protocol:
DNA from ~20k cells was extracted using the Quick-gDNA Microprep kit (Zymo)
Sequencing libraries were prepared according to Marchal et al 2018 Nat Protoc (PMID: 29599440). Briefly, DNA was sheared to an average size of 200bp using ultrasonication. Fragmented DNA was end repaired and adaptor-ligated using the NEBNext Ultra II DNA Library prep kit (NEB) following manufacturer instructions. BrdU-labeled DNA was immunoprecipitated using an anti-BrdU antibody and then purified. Purified BrdU-labeled DNA was then amplified using NEBNext Multiplex Oligos for Illumina (NEB). Libraries were pooled and sequenced on a Novaseq6000 machine.

treatment_protocol: Cells were engineered with various CRISPR-mediated deletions. Cells were labeled with BrdU for 2 hours, fixed in ethanol, and sorted for DNA content using flow cytometry into Early and Late S phase fractions.

value: Embryonic stem cell

value: CRISPR-mediated deletion(s)


title: AOSN.B.COSN123_clone5A.6_rep2_E

description:
Library name: AOSN.B.COSN123_clone5A.6_rep2_E
hom_AOSN_B_C3OSN_5A_6_Rep2_E


title: AOSN.B.COSN123_clone5A.6_rep1_L

description:
Library name: AOSN.B.COSN123_clone5A.6_rep1_L
hom_AOSN_B_C3OSN_5A_6_Rep1_L


title: Human, Visium ST, Primary tumor, #3

description:
Library name: T23_47
FFPE Visium V1

value: mRNA


title: kidney, 4_POD_PCK1_KI

value: PCK1 KI


title: kidney, 29_POD_PCK1_KI


title: AOSN.B.COSN123_clone5A.6_rep1_E

description:
Library name: AOSN.B.COSN123_clone5A.6_rep1_E
hom_AOSN_B_C3OSN_5A_6_Rep1_E


title: AOSN.B.COSN123_clone3C.4_rep1_L

description:
Library name: AOSN.B.COSN123_clone3C.4_rep1_L
hom_AOSN_B_C3OSN_3C_4_Rep1_L


title: AOSN.B.COSN123_clone3C.4_rep2_E

description:
Library name: AOSN.B.COSN123_clone3C.4_rep2_E
hom_AOSN_B_C3OSN_3C_4_Rep2_E


title: AOSN.B.COSN123_clone3C.4_rep1_E

description:
Library name: AOSN.B.COSN123_clone3C.4_rep1_E
hom_AOSN_B_C3OSN_3C_4_Rep1_E


title: AOSN.B.COSN123_clone2A.2_rep2_L

description:
Library name: AOSN.B.COSN123_clone2A.2_rep2_L
hom_AOSN_B_C3OSN_2A_2_Rep2_L


title: AOSN.B.COSN123_clone2A.2_rep2_E

description:
Library name: AOSN.B.COSN123_clone2A.2_rep2_E
hom_AOSN_B_C3OSN_2A_2_Rep2_E


title: AOSN.B.COSN123_clone2A.2_rep1_L

description:
Library name: AOSN.B.COSN123_clone2A.2_rep1_L
hom_AOSN_B_C3OSN_2A_2_Rep1_L


title: A.B.COSN123_clone5A.7_rep2_L

description:
Library name: A.B.COSN123_clone5A.7_rep2_L
hom_A_B_C3OSN_5A_7_Rep2_L


title: AOSN.B.COSN123_clone2A.2_rep1_E

description:
Library name: AOSN.B.COSN123_clone2A.2_rep1_E
hom_AOSN_B_C3OSN_2A_2_Rep1_E


title: A.B.COSN123_clone5A.7_rep2_E

description:
Library name: A.B.COSN123_clone5A.7_rep2_E
hom_A_B_C3OSN_5A_7_Rep2_E


title: A.B.COSN123_clone5A.7_rep1_L

description:
Library name: A.B.COSN123_clone5A.7_rep1_L
hom_A_B_C3OSN_5A_7_Rep1_L


title: A.B.COSN123_clone5A.7_rep1_E

description:
Library name: A.B.COSN123_clone5A.7_rep1_E
hom_A_B_C3OSN_5A_7_Rep1_E


title: AOSN.B.COSN123_clone5A.2_rep1_L

description:
Library name: AOSN.B.COSN123_clone5A.2_rep1_L
het_AOSN_B_C3OSN_5A_2_Rep1_L


title: AOSN.B.COSN123_clone5A.2_rep2_L

description:
Library name: AOSN.B.COSN123_clone5A.2_rep2_L
het_AOSN_B_C3OSN_5A_2_Rep2_L


title: AOSN.B.COSN123_clone3C.4_rep2_L

description:
Library name: AOSN.B.COSN123_clone3C.4_rep2_L
hom_AOSN_B_C3OSN_3C_4_Rep2_L


title: AOSN.B.COSN123_clone1A.4_rep2_L

description:
Library name: AOSN.B.COSN123_clone1A.4_rep2_L
het_AOSN_B_C3OSN_1A_4_Rep2_L


title: AOSN.B.COSN123_clone5A.2_rep2_E

description:
Library name: AOSN.B.COSN123_clone5A.2_rep2_E
het_AOSN_B_C3OSN_5A_2_Rep2_E


title: AOSN.B.COSN123_clone1A.4_rep1_L

description:
Library name: AOSN.B.COSN123_clone1A.4_rep1_L
het_AOSN_B_C3OSN_1A_4_Rep1_L


title: AOSN.B.COSN123_clone5A.2_rep1_E

description:
Library name: AOSN.B.COSN123_clone5A.2_rep1_E
het_AOSN_B_C3OSN_5A_2_Rep1_E


title: COSN12_cloneD3_L

description:
Library name: COSN12_cloneD3_L
F121-9-Dppa-del-C2OSN-129_ESC_cloneD3_L


title: A.B.COSN123_clone2E.1_rep2_E

description:
Library name: A.B.COSN123_clone2E.1_rep2_E
het_A_B_C3OSN_2E_1_Rep2_E


title: A.B.COSN123_clone2E.1_rep1_L

description:
Library name: A.B.COSN123_clone2E.1_rep1_L
het_A_B_C3OSN_2E_1_Rep1_L


title: A.B.COSN123_clone2E.1_rep2_L

description:
Library name: A.B.COSN123_clone2E.1_rep2_L
het_A_B_C3OSN_2E_1_Rep2_L


title: AOSN.B.COSN123_clone1A.4_rep2_E

description:
Library name: AOSN.B.COSN123_clone1A.4_rep2_E
het_AOSN_B_C3OSN_1A_4_Rep2_E


title: COSN12_cloneD3_E

description:
Library name: COSN12_cloneD3_E
F121-9-Dppa-del-C2OSN-129_ESC_cloneD3_E


title: COSN12_cloneB6_L

description:
Library name: COSN12_cloneB6_L
F121-9-Dppa-del-C2OSN-129_ESC_cloneB6_L


title: A.B.COSN123_clone2E.1_rep1_E

description:
Library name: A.B.COSN123_clone2E.1_rep1_E
het_A_B_C3OSN_2E_1_Rep1_E


title: BTSS.CTSS_cloneH11_E

description:
Library name: BTSS.CTSS_cloneH11_E
F121-9-Dppa-del-BTSS-CTSS_cloneH11_E


title: COSN12_cloneC6_E

description:
Library name: COSN12_cloneC6_E
F121-9-Dppa-del-C2OSN-129_ESC_cloneC6_E


title: COSN12_cloneC6_L

description:
Library name: COSN12_cloneC6_L
F121-9-Dppa-del-C2OSN-129_ESC_cloneC6_L


title: COSN12_cloneB6_E

description:
Library name: COSN12_cloneB6_E
F121-9-Dppa-del-C2OSN-129_ESC_cloneB6_E


title: BTSS.CTSS_cloneH11_L

description:
Library name: BTSS.CTSS_cloneH11_L
F121-9-Dppa-del-BTSS-CTSS_cloneH11_L


title: BTSS.CTSS_cloneG3_E

description:
Library name: BTSS.CTSS_cloneG3_E
F121-9-Dppa-del-BTSS-CTSS_cloneG3_E


title: BTSS.CTSS_cloneC11_L

description:
Library name: BTSS.CTSS_cloneC11_L
F121-9-Dppa-del-BTSS-CTSS_cloneC11_L


title: BTSS_cloneA10_L

description:
Library name: BTSS_cloneA10_L
F121-9-Dppa-del-BTSS_cloneA10_L


title: BTSS.CTSS_cloneC11_E

description:
Library name: BTSS.CTSS_cloneC11_E
F121-9-Dppa-del-BTSS-CTSS_cloneC11_E


title: AOSN.COSN12_cloneG2_L

description:
Library name: AOSN.COSN12_cloneG2_L
F121-9-Dppa-del-AOSN-C2OSN-129_ESC_cloneG2_L


title: AOSN.COSN12_cloneG2_E

description:
Library name: AOSN.COSN12_cloneG2_E
F121-9-Dppa-del-AOSN-C2OSN-129_ESC_cloneG2_E


title: AOSN.B.COSN123_clone1A.4_rep1_E

description:
Library name: AOSN.B.COSN123_clone1A.4_rep1_E
het_AOSN_B_C3OSN_1A_4_Rep1_E


title: A.CTSS_cloneA8_L

description:
Library name: A.CTSS_cloneA8_L
F121-9-Dppa-del-A-CTSS-cas_ESC_cloneA8_L


title: AOSN.COSN12_cloneF3_E

description:
Library name: AOSN.COSN12_cloneF3_E
F121-9-Dppa-del-AOSN-C2OSN-129_ESC_cloneF3_E


title: AOSN.COSN12_cloneF3_L

description:
Library name: AOSN.COSN12_cloneF3_L
F121-9-Dppa-del-AOSN-C2OSN-129_ESC_cloneF3_L


title: A.CTSS_cloneA8_E

description:
Library name: A.CTSS_cloneA8_E
F121-9-Dppa-del-A-CTSS-cas_ESC_cloneA8_E


title: A.CTSS_cloneA10_L

description:
Library name: A.CTSS_cloneA10_L
F121-9-Dppa-del-A-CTSS-cas_ESC_cloneA10_L


title: A.COSN12_cloneD6_E

description:
Library name: A.COSN12_cloneD6_E
F121-9-Dppa-del-A-C2OSN-129_ESC_cloneD6_E


title: A.CTSS_cloneA10_E

description:
Library name: A.CTSS_cloneA10_E
F121-9-Dppa-del-A-CTSS-cas_ESC_cloneA10_E


title: A.COSN12_cloneD6_L

description:
Library name: A.COSN12_cloneD6_L
F121-9-Dppa-del-A-C2OSN-129_ESC_cloneD6_L


title: A.COSN12_cloneA3_E

description:
Library name: A.COSN12_cloneA3_E
F121-9-Dppa-del-A-C2OSN-129_ESC_cloneA3_E


title: CTSS_cloneC12_rep1_L

description:
Library name: CTSS_cloneC12_rep1_L
Dppadel_CTSS_cloneC12_rep1_L_


title: CTSS_cloneC4_rep1_E

description:
Library name: CTSS_cloneC4_rep1_E
Dppadel_CTSS_cloneC4_rep1_E_


title: Z.AOSN.COSN123_cloneB4_L

description:
Library name: Z.AOSN.COSN123_cloneB4_L
delZAOSNCOSN123_cloneB4_L


title: Z.AOSN.COSN123_cloneA9_L

description:
Library name: Z.AOSN.COSN123_cloneA9_L
delZAOSNCOSN123_cloneA9_L


title: COSN123_cloneA10_rep4_L

description:
Library name: COSN123_cloneA10_rep4_L
COSN123_cloneA10_rep4_L


title: BTSS_cloneA10_E

description:
Library name: BTSS_cloneA10_E
F121-9-Dppa-del-BTSS_cloneA10_E


title: CTSS_cloneC12_rep1_E

description:
Library name: CTSS_cloneC12_rep1_E
Dppadel_CTSS_cloneC12_rep1_E_


title: A.COSN12_cloneA3_L

description:
Library name: A.COSN12_cloneA3_L
F121-9-Dppa-del-A-C2OSN-129_ESC_cloneA3_L


title: COSN123_cloneA10_rep2_L

description:
Library name: COSN123_cloneA10_rep2_L
COSN123_cloneA10_rep2_L


title: COSN123_cloneA10_rep3_E

description:
Library name: COSN123_cloneA10_rep3_E
COSN123_cloneA10_rep3_E


title: COSN123_cloneA10_rep1_L

description:
Library name: COSN123_cloneA10_rep1_L
COSN123_cloneA10_rep1_L


title: BTSS.CTSS_cloneG3_L

description:
Library name: BTSS.CTSS_cloneG3_L
F121-9-Dppa-del-BTSS-CTSS_cloneG3_L


title: Z.AOSN.COSN123_cloneB4_E

description:
Library name: Z.AOSN.COSN123_cloneB4_E
delZAOSNCOSN123_cloneB4_E


title: COSN123_cloneA10_rep1_E

description:
Library name: COSN123_cloneA10_rep1_E
COSN123_cloneA10_rep1_E


title: COSN123_cloneA10_rep2_E

description:
Library name: COSN123_cloneA10_rep2_E
COSN123_cloneA10_rep2_E


title: Full_Length_Rep3

city: Brighton

first: Leinal

last: Sejour

state: MA

address: 63 Nonantum St.

department: Vlachos - Non Coding RNA Lab

institute: BIDMC

data_processing:
Sequencing reads were trimmed for adapters/low quality read sequence at 3' end/ and read length with cutadapt (Parameters: --minimum-length 17, --quality-check 10)
Trimmed reads were mapped to GRCh38 Ensembl v98 using STAR (Parameters:         --minimum distance allowed to other junctions 10 10 5 10 \         --max number of loci anchors 100 \         --max number of allowed multiple alignments  20 \         --minimum overhang for unannotated junctions 8 \         --minimum overhang for annotated junctions 1 \         --maximum number of mismatches per pair 999 \         --max number of mismatches per pair relative to read length 0.1 \         --alignIntronMin 20 \         --minimum intron length 1000000 \         --maximum genomic distance between mates 1000000 \         --outSJfilterCountUniqueMin 10 3 3 3 \         --outSJfilterCountTotalMin 10 3 3 3 \)
Differential expression was performed with DESeq2, version 1.24.07
Transcription factor binding site analysis was performed the DIANA-mirRxTra (v2.0) online suite. Differentially expressed transcription factors and potential targets were collected, using annotated transcription factor binding sites (TFBS) from DNAse-Seq datasets and OregAnno v 3.0. Targets within these TFBS were collected and used for a Fisher exact test to determine statistically significance based on proximity. Targets were annotated using GRCh38, Ensembl v80
Assembly: GRCh38 Ensembl v98
Assembly: GRCh38 Ensembl v80
Supplementary files format and content: tab-delimited file including the raw counts for each sample

source_name: A375 cells

growth_protocol: A375 cells (purchased from ATCC) were cultured as adherent cells in Dulbecco’s modified eagle medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was isolated using RNeasy® plus Mini Kit (Qiagen, 74134) following manufacturer’s protocol. cDNA was generated using SuperScript III (Invitrogen, 18080093) reverse transcriptase following manufacturer’s protocol.
Extracted RNA was submitted to Genewiz (Azenta) for library preparation and rRNA depletion using Illumina library prep kit. Sequencing was performed on Illumina HiSeq 2x150bp configuration, single index, per lane.

treatment_protocol: A375 cells overexpressing SLNCR were generated by transfecting cells with pcDNA3.1 plasmid consisting of puromycin resistant gene and CAG promoter. After 48 hrs of growth in complete DMEM media consisting of 2 μg/mL puromycin, RNA was extracted. Lipofectamine® 2000 (Life Technologies, 11668027) was used for all plasmid transfections and following manufacturer’s protocol.

value: Epithelial

value: wild type SLNCR

value: transfection with pcDNA3.1


title: Z.AOSN.COSN123_cloneA9_E

description:
Library name: Z.AOSN.COSN123_cloneA9_E
delZAOSNCOSN123_cloneA9_E


title: BOSN1.COSN123_cloneE6_L

description:
Library name: BOSN1.COSN123_cloneE6_L
BOSN1-C3OSN_cloneE6_L


title: CTSS_cloneC4_rep1_L

description:
Library name: CTSS_cloneC4_rep1_L
Dppadel_CTSS_cloneC4_rep1_L_


title: BOSN1.COSN123_cloneE6_E

description:
Library name: BOSN1.COSN123_cloneE6_E
BOSN1-C3OSN_cloneE6_E


title: COSN123_cloneA10_rep3_L

description:
Library name: COSN123_cloneA10_rep3_L
COSN123_cloneA10_rep3_L


title: Full_Length_Rep2


title: COSN123_cloneA10_rep4_E

description:
Library name: COSN123_cloneA10_rep4_E
COSN123_cloneA10_rep4_E


title: BOSN1.COSN123_cloneC4_L

description:
Library name: BOSN1.COSN123_cloneC4_L
BOSN1-C3OSN_cloneC4_L


title: Full_Length_Rep1


title: Empty_Rep3

value: Vector backbone control


title: BOSN12.COSN123_cloneB1_L

description:
Library name: BOSN12.COSN123_cloneB1_L
B2OSN-C3OSN_cloneB1_L


title: BOSN1.COSN123_cloneC4_E

description:
Library name: BOSN1.COSN123_cloneC4_E
BOSN1-C3OSN_cloneC4_E


title: Empty_Rep2


title: ATSS.BTSS.CTSS_cloneC4_L

description:
Library name: ATSS.BTSS.CTSS_cloneC4_L
ATSS-BTSS-CTSS_cloneC4_L


title: BOSN12.COSN123_cloneB1_E

description:
Library name: BOSN12.COSN123_cloneB1_E
B2OSN-C3OSN_cloneB1_E


title: BOSN12.COSN123_cloneA2_L

description:
Library name: BOSN12.COSN123_cloneA2_L
B2OSN-C3OSN_cloneA2_L


title: Empty_Rep1


title: BOSN12.COSN123_cloneA2_E

description:
Library name: BOSN12.COSN123_cloneA2_E
B2OSN-C3OSN_cloneA2_E


title: ATSS.BTSS.CTSS_cloneA8_L

description:
Library name: ATSS.BTSS.CTSS_cloneA8_L
ATSS-BTSS-CTSS_cloneA8_L


title: ATSS.BTSS.CTSS_cloneA1_L

description:
Library name: ATSS.BTSS.CTSS_cloneA1_L
ATSS-BTSS-CTSS_cloneA1_L


title: Z.B.C_cloneE5_E

description:
Library name: Z.B.C_cloneE5_E
AOSN2-B-C_cloneE5_E


title: Z.B.C_cloneE5_L

description:
Library name: Z.B.C_cloneE5_L
AOSN2-B-C_cloneE5_L


title: Z.B.C_cloneA6_L

description:
Library name: Z.B.C_cloneA6_L
AOSN2-B-C_cloneA6_L


title: ATSS.BTSS.CTSS_cloneC4_E

description:
Library name: ATSS.BTSS.CTSS_cloneC4_E
ATSS-BTSS-CTSS_cloneC4_E


title: Z.B.C_cloneA6_E

description:
Library name: Z.B.C_cloneA6_E
AOSN2-B-C_cloneA6_E


title: AOSN.COSN123_cloneF4_L

description:
Library name: AOSN.COSN123_cloneF4_L
AOSN_C3OSN_F4_03152022_L_S4_cat


title: ATSS.BTSS.CTSS_cloneA1_E

description:
Library name: ATSS.BTSS.CTSS_cloneA1_E
ATSS-BTSS-CTSS_cloneA1_E


title: AOSN.COSN123_cloneB6_L

description:
Library name: AOSN.COSN123_cloneB6_L
AOSN_C3OSN_B6_03152022_L_S2_cat


title: AOSN.COSN123_cloneF4_E

description:
Library name: AOSN.COSN123_cloneF4_E
AOSN_C3OSN_F4_03152022_E_S3_cat


title: AOSN.COSN123_cloneA6_L

description:
Library name: AOSN.COSN123_cloneA6_L
AOSN_C3OSN_A6_L_S104_cat


title: AOSN.COSN123_cloneB6_E

description:
Library name: AOSN.COSN123_cloneB6_E
AOSN_C3OSN_B6_03152022_E_S1_cat


title: AOSN.COSN123_cloneA6_E

description:
Library name: AOSN.COSN123_cloneA6_E
AOSN_C3OSN_A6_E_S103_cat


title: A.BOSN1.COSN123_cloneB1_L

description:
Library name: A.BOSN1.COSN123_cloneB1_L
A-BOSN1-C3OSN_cloneB1_L


title: A.BOSN1.COSN123_cloneB1_E

description:
Library name: A.BOSN1.COSN123_cloneB1_E
A-BOSN1-C3OSN_cloneB1_E


title: A.BOSN12.COSN123_cloneA6_L

description:
Library name: A.BOSN12.COSN123_cloneA6_L
A-B2OSN-C3OSN_cloneA6_L


title: A.BOSN12.COSN123_cloneC11_E

description:
Library name: A.BOSN12.COSN123_cloneC11_E
A-B2OSN-C3OSN_cloneC11_E


title: A.COSN123_cloneH10_L

description:
Library name: A.COSN123_cloneH10_L
A_C3OSN_H10_03152022_L_S8_cat


title: ATSS.BTSS.CTSS_cloneA8_E

description:
Library name: ATSS.BTSS.CTSS_cloneA8_E
ATSS-BTSS-CTSS_cloneA8_E


title: A.COSN123_cloneD8_E

description:
Library name: A.COSN123_cloneD8_E
A_C3OSN_D8_03152022_E_S5_cat


title: A.COSN123_cloneC9_E

description:
Library name: A.COSN123_cloneC9_E
A_C3OSN_C9_E_S107_cat


title: A.COSN123_cloneB7_L

description:
Library name: A.COSN123_cloneB7_L
A_C3OSN_B7_L_S106_cat


title: A.COSN123_cloneC9_L

description:
Library name: A.COSN123_cloneC9_L
A_C3OSN_C9_L_S108_cat


title: CTSS_cloneC4_rep2_L

description:
Library name: CTSS_cloneC4_rep2_L
Dppadel_CTSS_cloneC4_rep2_L


title: CTSS_cloneC4_rep2_E

description:
Library name: CTSS_cloneC4_rep2_E
Dppadel_CTSS_cloneC4_rep2_E


title: A.COSN123_cloneB7_E

description:
Library name: A.COSN123_cloneB7_E
A_C3OSN_B7_E_S105_cat


title: CTSS_cloneC12_rep2_E

description:
Library name: CTSS_cloneC12_rep2_E
Dppadel_CTSS_cloneC12_rep2_E


title: CR13.4k_clone2-12_E

description:
Library name: CR13.4k_clone2-12_E
Dppadel_C6_clone2-12_E


title: COSN1.2.8k_clone18_L

description:
Library name: COSN1.2.8k_clone18_L
Dppadel_C5_clone18_L


title: COSN1.2.8k_clone4_E

description:
Library name: COSN1.2.8k_clone4_E
Dppadel_C5_clone4_E


title: COSN1.2.8k_clone4_L

description:
Library name: COSN1.2.8k_clone4_L
Dppadel_C5_clone4_L


title: COSN1_clone2-28_L

description:
Library name: COSN1_clone2-28_L
Dppadel_C3_clone2-28_L


title: CR13.4k_clone2-49_E

description:
Library name: CR13.4k_clone2-49_E
Dppadel_C6_clone2-49_E


title: COSN1_clone2-33_L

description:
Library name: COSN1_clone2-33_L
Dppadel_C3_clone2-33_L


title: CR13.4k_clone2-12_L

description:
Library name: CR13.4k_clone2-12_L
Dppadel_C6_clone2-12_L


title: COSN1_clone2-33_E

description:
Library name: COSN1_clone2-33_E
Dppadel_C3_clone2-33_E


title: A.BOSN12.COSN123_cloneC11_L

description:
Library name: A.BOSN12.COSN123_cloneC11_L
A-B2OSN-C3OSN_cloneC11_L


title: A.BOSN12.COSN123_cloneA6_E

description:
Library name: A.BOSN12.COSN123_cloneA6_E
A-B2OSN-C3OSN_cloneA6_E


title: COSN1_clone2-28_E

description:
Library name: COSN1_clone2-28_E
Dppadel_C3_clone2-28_E


title: A.COSN123_cloneH10_E

description:
Library name: A.COSN123_cloneH10_E
A_C3OSN_H10_03152022_E_S7_cat


title: A.COSN123_cloneD8_L

description:
Library name: A.COSN123_cloneD8_L
A_C3OSN_D8_03152022_L_S6_cat


title: CL20k_clone85_L

description:
Library name: CL20k_clone85_L
Dppadel_C2_clone85_L


title: CL20k_clone49_L

description:
Library name: CL20k_clone49_L
Dppadel_C2_clone49_L


title: CL20k_clone85_E

description:
Library name: CL20k_clone85_E
Dppadel_C2_clone85_E


title: CL20k_clone49_E

description:
Library name: CL20k_clone49_E
Dppadel_C2_clone49_E


title: CR14.6k_clone53_L

description:
Library name: CR14.6k_clone53_L
Dppadel_C1_clone53_L


title: CR13.4k_clone2-49_L

description:
Library name: CR13.4k_clone2-49_L
Dppadel_C6_clone2-49_L


title: CR14.6k_clone53_E

description:
Library name: CR14.6k_clone53_E
Dppadel_C1_clone53_E


title: CR14.6k_clone16_L

description:
Library name: CR14.6k_clone16_L
Dppadel_C1_clone16_L


title: CR14.6k_clone16_E

description:
Library name: CR14.6k_clone16_E
Dppadel_C1_clone16_E


title: COSN1.2.8k_clone18_E

description:
Library name: COSN1.2.8k_clone18_E
Dppadel_C5_clone18_E


title: CR11.8k_clone50_E

description:
Library name: CR11.8k_clone50_E
dCR11_8_E


title: AOSN.BOSN12.COSN123_cloneD6_L

description:
Library name: AOSN.BOSN12.COSN123_cloneD6_L
dAOSN-dBOSN12-dCOSN123_D6_L


title: A.BOSN12.BTSS.COSN123_cloneC4_rep2_L

description:
Library name: A.BOSN12.BTSS.COSN123_cloneC4_rep2_L
A-BOSN12-BTSS-COSN123_cloneC4-Rep2_L


title: A.BOSN12.BTSS.COSN123_cloneC4_rep2_E

description:
Library name: A.BOSN12.BTSS.COSN123_cloneC4_rep2_E
A-BOSN12-BTSS-COSN123_cloneC4-Rep2_E


title: ILC2, mes ln, infected 3

status: Public on Jun 12 2025

city: Denver

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

description: Library name: 5C Mes

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ files with Illumina DRAGEN bcl2fastq (v4.2.7). Quality check, adapter trimming, and alignment to the murine genome reference sequence mm10 (UCSC) was performed using CellRanger (v6.1.2) to generate a gene expression matrix for each sample containing the number of UMIs for each gene associated with each cell barcode.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Bone marrow

extract_protocol:
Intestine draining mesenteric lymph nodes, lung, and bone marrow were collected 5 days post infection with Nippostrongylus brasiliensis. ILC2 and ILC progenitors were enriched using EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit (Stemcell, 19856) prior to cell sorting. Bone marrow cells were sorted for progenitor cell markers CD45+Lin- CD127+ a4b7+ Flt3-. These markers account for both the common helper-like ILC progenitors (CHILP) and ILC2 progenitors (ILC2p). Mesenteric lymph nodes and lung cells were sorted for conventional ILC2 markers CD45+ Lin- CD127+ and KLRG1low/+. Lung, mesenteric lymph node, and bone marrow cell suspensions from three mice were treated as 9 separate samples for scRNA-seq. Sorted cells were resuspended in 0.04% BSA in PBS and counted prior to GEM encapsulation using the 10x Genomics Chromium controller with a targeted cell recovery of 5,000 cells.
3′ mRNA-seq gene expression libraries were prepared per the Chromium Single Cell 3' User Guide (10x Genomics, CG000204). Library quality was verified using TapeStation 4200 (Agilent) and libraries were quantified by Qubit fluorometer (Thermo Fisher) prior to pooling. Library pools were sequenced at the National Jewish Health Genomics Facility on an Illumina NEXTSEQ 2000, 28x10x10x90 bp, paired-end sequencing.

treatment_protocol: Nippostrongylus brasiliensis infection

value: Bone marrow

value: CHILP, ILC2p


title: A.BOSN12.BTSS.COSN123_cloneC4_rep1_L

description:
Library name: A.BOSN12.BTSS.COSN123_cloneC4_rep1_L
A-BOSN12-BTSS-COSN123_cloneC4-Rep1_L


title: ILC2, bm, infected 3

description: Library name: 5B BM

source_name: Mesenteric lymph node

value: Mesenteric lymph node


title: A.BOSN12.BTSS.COSN123_cloneC4_rep1_E

description:
Library name: A.BOSN12.BTSS.COSN123_cloneC4_rep1_E
A-BOSN12-BTSS-COSN123_cloneC4-Rep1_E


title: AOSN.BOSN12.COSN123_cloneB8_E

description:
Library name: AOSN.BOSN12.COSN123_cloneB8_E
dAOSN-dBOSN12-dCOSN123_B8_E


title: ILC2, mes ln, infected 1

description: Library name: 2C Mes


title: ILC2, bm, infected 1

description: Library name: 2B BM


title: ILC2, mes ln, infected 2

description: Library name: 4C Mes


title: ILC2, bm, infected 2

description: Library name: 4B BM


title: ILC2, lung, infected 2

description: Library name: 4A Lung

source_name: Lung

value: Lung


title: Subject_C17_Blood

status: Public on Jun 11 2025

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample_Fq_18
GEX

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 (10x Genomics)
Assembly: GRCH38
Supplementary files format and content: Compressed tab-separated values files, unfiltered single cell barcode gene expression matrix

extract_protocol:
Nasal tissue samples were minced, digested in a DNAse/Liberase solution for 30 minutes, strained and washed to create a single cell suspension. Paired whole blood was centrifuged layered on Histopaque 1077, with PBMC layer extracted and washed. Nasal and PBMC samples were loaded as single cell suspensions without sorting
ScRNAseq gene expression libraries were contructed in accordance with the manufacturer protocol (Single cell 5' v2 protocol, 10x Genomics)

value: Blood

value: Healthy control


title: Subject_C17_Nasal

description:
Library name: Sample_Fq_19
GEX

source_name: Nasal

value: Nasal


title: ILC2, lung, infected 1

description: Library name: 2A Lung


title: Subject_C21_Nasal

description:
Library name: Sample_Fq_15
GEX


title: Subject_C26_Nasal

description:
Library name: Sample_Fq_38
GEX


title: Subject_C21_Blood

description:
Library name: Sample_Fq_14
GEX


title: AOSN.BOSN12.COSN123_cloneB8_L

description:
Library name: AOSN.BOSN12.COSN123_cloneB8_L
dAOSN-dBOSN12-dCOSN123_B8_L


title: CR11.8k_clone50_L

description:
Library name: CR11.8k_clone50_L
dCR11_8_L


title: Subject_C24_Nasal

description:
Library name: Sample_Fq_11
GEX


title: Subject_C19_Nasal

description:
Library name: Sample_Fq_9
GEX


title: AOSN.BOSN12.COSN123_cloneD6_E

description:
Library name: AOSN.BOSN12.COSN123_cloneD6_E
dAOSN-dBOSN12-dCOSN123_D6_E


title: Subject_C24_Blood

description:
Library name: Sample_Fq_10
GEX