title: BAL, Saline D7, rep 2

status: Public on Apr 28 2025

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

institute: University of Oxford

data_processing:
FASTQs were aligned to the human reference genome GRCh38 (GENCODE version 32/Ensembl 98).
All analysis was performed on R version 4.1.2 and Python version 3.8.19. Barcode assignment, Unique Molecular Identifier (UMI) tagging, and sequence alignment for the BAL samples were conducted using the Cell Ranger count pipeline (v6.0.1), employing the human reference genome GRCh38 (GENCODE version 32/Ensembl 98) provided by 10x Genomics. Potential contamination by ambient RNA was removed using the SoupX package (v1.6.1). Data processing and doublet exclusion were then executed using the Scanpy toolkit (v1.9.8). Cells were excluded if they had fewer than 200 genes detected, more than 10% mitochondrial gene expression, or if their doublet score surpassed the 0.75 quantile by 1.5 times of the interquartile range (IQR), as determined by the Scrublet (v0.2.3). After filtering, a total of 91,958 cells were left for downstream analysis.
Assembly: GRCh38 (GENCODE version 32/Ensembl 98)
Supplementary files format and content: The processed data file is an h5ad file, which contains all of the metadata of filtered cells and their expression matrix.

source_name: BAL

extract_protocol:
BAL cells from three BCG-infected from each group and all control volunteers were processed for scRNA-seq. Cells in Group 1 (Bronchoscopy on D2) were first incubated with CD3+ microbeads (Miltenyi Biotec), to enrich for CD3+ cells to ensure there were sufficient cells to describe T cell subsets. However as the BAL was sufficiently enriched for T cells to detect T cell subsets without the need for CD3+ enrichment, Group 2 (Bronchoscopy on D7) cells were not incubated with CD3+ microbeads to minimise cell handling. Incubation results in 30% epitope “light-touch” attachment per cell, allowing ongoing functionality and availability for TCR sequencing and therefore sequencing results between the two groups should not have been affected. Furthermore, a head-to-head comparison was made to compare sequencing by both methods, which found no difference in cell proportions. Despite this, cell proportions identified by scRNA-seq have not been reported here, with results from scRNA-seq limited to reporting detection of cell types and differential gene expression analysis.
Single cell RNA-seq libraries were created from BAL cells as per manufacturer’s instructions using 10x Genomics single cell RNA 5 prime kits (v1.1). The target number of cells per channel was 5000 and two channels were used per sample (with the pooled count of 10,000 cells sequenced). Libraries were sequenced on a Novaseq 6000 S4 flowcell (150 paired-end configuration). Accepted minimum sequencing depth was 30,000 mean reads per cell and 50% sequencing saturation.

value: BAL

value: Saline D7


title: Astro-NT_NN.9mo

status: Public on Apr 30 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description:
Library name: sample 2
read length: 151

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (CONTACT files) describing the raw contact number between two genome regions . Columns are: 1. Strand1 (0 for forward, anything else for reverse), 2. Chromosome1, 3. Position1, 4. restriction site fragments, 5. Strand2 (0 for forward, anything else for reverse), 6.  Chromosome2, 7. Position2, 8. restriction site fragments, 9. the score imputed to this read
Library strategy: snm3C-seq

molecule: genomic DNA

organism: Mus musculus

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: tissue

value: brain

tag: Sex

value: female

tag: cell type


title: Astro-TE_NN.18mo

description:
Library name: sample 3
read length: 151


title: BAL, Saline D7, rep 1

country: United Kingdom

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: treatment


title: BAL, Saline D7, rep 3


title: BAL, BCG D7, rep 3

value: BCG D7


title: BAL, BCG D2, rep 3

value: BCG D2


title: BAL, BCG D7, rep 1


title: BAL, BCG D7, rep 2


title: BAL, Saline D2, rep 3

value: Saline D2


title: BAL, BCG D2, rep 2


title: BAL, BCG D2, rep 1


title: BAL, Saline D2, rep 2


title: BAL, Saline D2, rep 1


title: Murine prostate VP

status: Public on Apr 24 2025

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: VP1

data_processing:
Adaptor sequences were removed with TrimmomaticPE using options ‘HEADCROP:10 CROP:70 ILLUMINACLIP:adaptor_file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’.
ATAC–seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (v.2.2.6) using options ‘-X 2000 –fr –very-sensitive –no-discordant –no-unal –no-mixed –non-deterministic’.
Mitochondrial reads, reads from unmapped or random counting and reads with a mapping quality < 20 were removed using SAMtools.
Duplicate reads were removed by Picard MarkDuplicates module.
Peak calling was performed on each individual sample by MACS2 (v.2.1.0.20151222) using options ‘-f BAMPE -g mm –nomodel– --shift 0 -q 0.01.
Reads counts of each merged peak for each individual sample were calculated by HTSeq-count using options ‘-f bam -r pos -m intersection-nonempty’.
These counts were normalized for one million mapped reads in merged peaks and fold-change was calculated compared to control. Peaks were associated to genes with GREAT software (v.4.0.4) with the following parameters: 5.0 kb in proximal upstream, 1.0 kb in proximal downstream and 100.0 kb in distal.
De novo motif search was performed using findMotifsGenome.pl program in HOMER software searching for motifs of 6 to 12 bp in a region of 250 bp up-stream and down-stream from the center of peak.
Assembly: mm10
Supplementary files format and content: .csv / normalised gene expression

source_name: Murine prostate

extract_protocol:
Cells were collected in 1 ml PBS supplemented with 3% FBS at 4 °C. Cells were centrifuged and cell pellets were resuspended in 100 μl lysis buffer (TrisHCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0.1%) and centrifuged at 500g for 25 min at 4 °C.
Supernatant was carefully discarded and nuclei were resuspended in 50μl reaction buffer (Tn5 transposase 2.5μl, TD buffer 22.5μl, from Nextera DNA sample preparation kit, Illumina, and 25μl H20). The reaction was performed at 37 °C for 30 min and was stopped by adding 5μl clean up buffer (NaCl 900 mM, EDTA 300 mM). DNA was purified using the MiniElute purification kit (QIAGEN) following the manufacturer’s protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800 bp (BluePippin, Sage Sciences), following the manufacturer’s recommendations.

value: Murine prostate

value: Ventral lobe


title: Luminal cells derived from Luminal cells on Anterial-Dorsal prostate, replicate 2

description: Library name: LC_derived_LC_AD_2

library_source: transcriptomic

data_processing:
Quality of each raw dataset was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by Trimmomatic.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v. 2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .xlsx / normalised gene expression

source_name: murine prostate

extract_protocol:
RNA extraction from FACS-isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations.
Indexed complementary DNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: murine prostate


title: Murine prostate AP

description: Library name: AP1

value: Antero-dorsal lobe


title: Luminal cells derived from Basal cells on Ventral prostate, replicate 2

description: Library name: BC_derived_LC_VP_2


title: Luminal cells derived from Basal cells on Anterial-Dorsal prostate, replicate 3

description: Library name: BC_derived_LC_AD_3


title: L5_IT_CTX_Glut.18mo

description:
Library name: sample 33
read length: 151


title: Luminal cells derived from Basal cells on Anterial-Dorsal prostate, replicate 2

description: Library name: BC_derived_LC_AD_2


title: Luminal cells derived from Basal cells on Anterial-Dorsal prostate, replicate 1

description: Library name: BC_derived_LC_AD_1


title: R_D54

status: Public on Apr 16 2025

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

country: China

institute: southwest medical university

description: 10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

molecule: total RNA

source_name: hHPLCs

extract_protocol:
Cells at indicated time points were digested and resuspended at 1 × 106 cells per milliliter in 1 × PBS with 0.04% BSA. Then, cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit (10x Genomics). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Invitrogen).
According to the manufacturer’s instructions, scRNA-seq libraries were constructed using the Single Cell 3′ Library and Gel Bead Kit V3.1.

tag: cell line

value: hHPLCs

value: hepatocytes


title: R_D38

description: 10X Genomics


title: R_D63

description: 10X Genomics


title: M-D4

description: 10X Genomics

source_name: hiHeps

value: hiHeps


title: M-D0

description: 10X Genomics


title: Murine prostate DLP

description: Library name: DLP1

value: Distal lobe


title: Control_6mA_rep2

status: Public on Apr 10 2025

city: Fukuoka

first: Yoshiki

last: Hayashi

state: Fukuoka

address: 744, Moto-oka, Nishi-ku

department: Department of Biology

country: Japan

institute: Kyushu University

description:
Library name: MeDIP_Control_6mA_rep2
6-methyladenine antibody was used for library selection.

data_processing:
Mapping of the reads to the Drosophila genome or each transposon sequence was done with bowtie2 softwere .
The Peak detection was done with MACS.
The detecton of the nearest genes was done with ChiPpeakAnno.
Assembly: dmel_r6.45
Supplementary files format and content: Excel file include peak regions detected in each sample.

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Drosophila standard culture condition.

extract_protocol:
Ovarian genome is extracted with Wizard genomic DNA purification kit (Promega) with two-times treatments of Rnase A.
Library preparation was performed with NEB Next Ultra DNA library prep kit (NEB) following manufacture’s instruction.

treatment_protocol: UASp-Sam-S was overexpressed in germline using nanos-gal4.

value: Ovary

tag: genotype

value: control

tag: sample type

tag: medip antibody

value: 6mA (Synaptic Systems)

tag: batch


title: SamS_6mA_rep1

description:
Library name: MeDIP_SamS_6mA_rep1
6-methyladenine antibody was used for library selection.


title: M-D2

description: 10X Genomics


title: Luminal cells derived from Luminal cells on Anterial-Dorsal prostate, replicate 3

description: Library name: LC_derived_LC_AD_3


title: Control_input_rep1

description:
Library name: MeDIP_Control_input_rep1
6-methyladenine antibody was used for library selection.

value: Input


title: Luminal cells derived from Luminal cells on Anterial-Dorsal prostate, replicate 1

description: Library name: LC_derived_LC_AD_1


title: Control_6mA_rep1

description:
Library name: MeDIP_Control_6mA_rep1
6-methyladenine antibody was used for library selection.


title: Control_input_rep2

description:
Library name: MeDIP_Control_input_rep2
6-methyladenine antibody was used for library selection.


title: SamS_input_rep2

description:
Library name: MeDIP_SamS_input_rep2
6-methyladenine antibody was used for library selection.


title: SamS_input_rep1

description:
Library name: MeDIP_SamS_input_rep1
6-methyladenine antibody was used for library selection.


title: Sam-S_overexpressing ovary_rep1

description:
Library name: RNASeq_SamS_rep1
TPM_Exp1

data_processing:
Mapping of the reads to the Drosophila genome was done with STAR softwere .
The extraction of DEGs was done with DE-Seq2.
Assembly: dmel_r6.27
Supplementary files format and content: Excel file includeTPM for each sample.

extract_protocol:
Total RNA was extracted by Trizol (Thermo) following the manufacture's instruction.
Library preparation was performed with TruSeq Stranded mRNA Library kit (Illumima) following manufacture’s instruction.

value: Flies that have UASp-Sam-S construct were crossed with nanos-gal4 flies


title: Control_ovary_rep2

description:
Library name: RNASeq_Control_rep2
TPM_Cont2

value: nanos-gal4 flies crossed with flies that have empty docking sites for the UASp-Sam-S construct


title: Luminal cells derived from Basal cells on Ventral prostate, replicate 1

description: Library name: BC_derived_LC_VP_1


title: Control_ovary_rep1

description:
Library name: RNASeq_Control_rep1
TPM_Cont1


title: CA3_Glut.8wk

description:
Library name: sample 10
read length: 151

value: brain

value: female


title: M-D7

description: 10X Genomics


title: 0013717_asthma_healthy

status: Public on Apr 08 2025

type: RNA

city: London

first: Regis

last: Joulia

address: South Kensington, SAF 3rd floor

department: NHLI

institute: Imperial College

hyb_protocol: 5 µm tissue sections from FFPE blocks were sectioned and place on the Xenium slide. For the KIA samples, tissue sections were deparaffinized using xylene for ~10 minutes at room temperature. A drop of DPX mounting reagent (Merck) was paced on top of each section and left to dry at room temperature overnight. Using a razor blade, sections were gently lift off the slide and transfer to the Xenium slide. Up to 9 transferred sections were placed on the Xenium slide and the slide was left in a slide oven for 4 hours at 56ºC. Processing was done per manufacturer’s protocols.

scan_protocol: Xenium slides were processed using 10X genomic recommended protocols (https://www.10xgenomics.com/in-situ-technology)

data_processing:
Date were processed as indicated in 10X genomic support documents (https://www.10xgenomics.com/in-situ-technology).
barcodes.tsv.gz: list of spatial barcodes
features.tsv.gz: list of gene IDs
cells.csv.gz: list of cells information
matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
transcripts.csv.gz: list of transcript information
morphology.ome.tif: image of tissue
gene_panel.json: store and transmit information about gene testing panels

label: Xenium Human Probe Set

source_name: Lung endobronchial biopsies

label_protocol: Not applicable

growth_protocol: Not applicable

extract_protocol: Endo bronchoscopy were performed at the Royal Brompton hospital. Biopsies were preserved in cell media (DMEM, ThermoFisher), then swiftly transfer into 4% paraformaldehyde for 1 hour at room temperature and finally kept in 70% ethanol until embedding in paraffin.

treatment_protocol: Not applicable

value: Lung endobronchial biopsies


title: SamS_6mA_rep2

description:
Library name: MeDIP_SamS_6mA_rep2
6-methyladenine antibody was used for library selection.


title: Cut & Tag, Proliferating iMOPs, IgG (Control), CUT&Tag,biol 2

status: Public on Apr 07 2025

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Library name: P_IgG_Set 2

data_processing:
Paired-end CUT&Tag reads were aligned to the mm10 genome assembly with bowtie2.
deepTools bamCoverage was used to remove duplicate reads and generate normalized bigwig files into reads per kilobase per million (RPKM) from individual samples.
Replicate bigwig files were merged to generate the averaged bigwig files using deepTools bigwigCompare.
Peaks were called using SEACR under stringent conditions using IgG sample as the empirical background
Peaks for H3K36me3 were called using SEACR under stringent conditions using IgG set2 sample as the empirical background.
Assembly: mm10
Supplementary files format and content: bigwig, averaged bigwig signals from two replicates
Supplementary files format and content: SEACR peaks (except for IgG control), consensus SEACR peaks from two replicates
Library strategy: CUT&Tag

source_name: iMOPs

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XB27, 25 µg/ml carbenicillin and 20 ng/ml bFGF. iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
500,000 cells were used for each CUT&Tag library prepration. Cells were incubated with primary antibodies against CHD7, H3K4me3, p300, CTCF, H3K36me3, and IgG (control). DNA libraries were amplified using PCR and purified using SPRI beads. Libraries were sequenced on illumina Hiseq 3000 platform (2X150bp).
pA-Tn5-transposomes mediated tagmentation using CUT&Tag-IT Assay kit (Active Motif).

value: iMOPs

value: Proliferating iMOPs

value: wild-type


title: Cut & Tag, iMOP-derived neurons, CTCF, CUT&Tag

description: Library name: N_CTCF

value: iMOP-derived neurons


title: Cut & Tag, iMOP-derived neurons, IgG (Control), CUT&Tag

description: Library name: N_IgG


title: Cut & Tag, iMOP-derived neurons, IgG (Control), CUT&Tag,biol 2

description: Library name: N_IgG_Set2


title: Cut & Tag, iMOP-derived neurons, H3K36me3, CUT&Tag

description: Library name: N_H3K36me3


title: Sam-S_overexpressing ovary_rep2

description:
Library name: RNASeq_SamS_rep2
TPM_Exp2


title: Cut & Tag, Proliferating iMOPs, IgG (Control), CUT&Tag

description: Library name: P_IgG


title: Cut & Tag, Proliferating iMOPs, H3K36me3, CUT&Tag

description: Library name: P_H3K36me3


title: Cut & Tag, Proliferating iMOPs, p300, CUT&Tag

description: Library name: P_p300


title: K562, 3Flag FOXK1-7A, ChIP

status: Public on Apr 06 2025

city: Montreal

first: Louis

last: Masclef

state: QC

address: 5415 Boulevard de l'Assomption

department: Biochemistry

country: Canada

institute: University of Montreal

data_processing:
For ChIP-seq and ATAC-seq reads were aligned on UCSC hg38 genome using bowtie2 v2.3.1 using per-end settings. Optical and PCR duplicates reads were removed using picard v2.9.0. Peak calling was performed with MACS2 v2.1.1. ChIP-seq and ATAC-seq coverage were generated with deeptools bamcoverage using CPM normalization. ChIPseq coverage for K562 were generated using deeptools using bamcoverage FPKM normalization. Cut&Run were analyzed using nf-core/cutandrun (v3.2.2). Highly correlated technical replicates were merged. Normalization was performed with spike-in mode using aligned reads from E.Coli (K-12), expect for the analysis of FOXK1 and FOXK2 recruitment following U2OS cell synchronization, CPM normalization was applied.
For RNA-seq, the quality of the raw reads was assessed with FASTQC v0.11.8. After examining the quality of the raw reads, no trimming was deemed necessary. The human samples were spiked-in with drosophila S2 cells. A hybrid reference genome and annotation concatenating both species were used for the alignment. The GRCh38 (release 102) reference genome and BDGP6.32 (release 107) reference genome were used and downloaded from Ensembl. The reads were aligned to the hybrid reference genome with STAR v2.7.6a. The raw counts were calculated with HTseq v0.11.2 based on the hybrid reference genome. Differential expression was performed using DESeq2 v1.30.0 R package.
Assembly: hg38
Supplementary files format and content: gene counts, narrowPeaks

growth_protocol: IMR90 cells were grown in DMEM supplemented with 10% FBS, 4mM glutamine and penicilin streptomycin. U2OS were grown in DMEM supplemented with 5% NBS + 2% FBS, 4mM glutamine and penicilin streptomycin. K562 cells were grow in RPMI 1640 supplemented with 5% NBS, 4mM glutamine and penicilin streptomycin. Cells were cultured at 37C in 5% CO2.

extract_protocol:
For ChIPseq, cells were fixed in 1% formaldehyde for 10 min at room temperature. Cells were quenched in ice cold PBS with 125 mM glycine. Chromatin was then sonicated using probe sonicator. Samples preparation for Cut&Run were done following manufacturer (Epycipher CUTANA™). For RNAseq, IMR90 cells were infected with retroviruses coding for empty vector, FOXK1 or FOXK2. 48h following the end of antibiotic selection, cells were harvested in TRIzol and RNA was extracted. For ATAC-seq, transposition was performed directly on nuclei following manufacturer recommendations (Tn5 Illumina).
For ChIP-Seq samples, size distribution and molarity of immunoprecipitated and input samples were evaluated on a 2100 bioanalyzer (Agilent Technologies). ChIP-seq libraries and CUT&RUN librairies were prepared using the KAPA hyperprep library kit (Roche Diagnostics). The number of PCR cycles was calculated based on the quantification of the ligation products (Illumina adapters) by qPCR. Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired end reads (PE100), on a Novaseq 6000 system or HiSeq 4000 for K562 ChIP-Seq (Illumina), with a S4 flowcell and a coverage of 50M for ChIP-Seq and H2AUb Cut&Run library. 10M fragments were sequenced for BAP1 and H3K4me1 Cut&Run per library. For RNAseq, libraries were prepared using ribosomal RNA depletion (KAPA RNA HyperPrep kit) with a sequencing depth of a minimum of 50 million reads.

treatment_protocol: For Cut&Run and ATACseq, cells were treated twice with siRNA against FOXK1. 72h after the first transfection cells were harvested for Cut&Run or ATACseq. For FOXK1 and FOXK2 Cut&Run following realse into the cell cycle, fibroblasts were grown to confluence and further cultured for 3 days. The cells were then serum starved for two days, trypsinized and replated in fresh medium before being harvested. For RNAseq, IMR90 cells were infected with retroviruses coding for empty vector, FOXK1 or FOXK2. 48h following the end of antibiotic selection, cells were harvested in TRIzol and RNA was extracted.

value: Human chronic myelogenous leukemia


title: K562, 3Flag FOXK1, ChIP


title: Control_ovary_rep3

description:
Library name: RNASeq_Control_rep3
TPM_Cont3


title: Sam-S_overexpressing ovary_rep3

description:
Library name: RNASeq_SamS_rep3
TPM_Exp3


title: K562, 3Flag FOXK2, ChIP


title: Cut & Tag, iMOP-derived neurons, CHD7, CUT&Tag

description: Library name: N_CHD7


title: Cut & Tag, iMOP-derived neurons, H3K4me3, CUT&Tag

description: Library name: N_H3K4me3


title: K562, Input, ChIP


title: U2OS, M_FOXK1, Cut&Run

description: Library name: U2OS_M_FOXK1

value: Human osteosarcoma


title: K562, vector, ChIP


title: Cut & Tag, Proliferating iMOPs, CHD7, CUT&Tag

description: Library name: P_CHD7


title: U2OS, G2_FOXK2, Cut&Run

description: Library name: U2OS_G2_FOXK2


title: Cut & Tag, Proliferating iMOPs, H3K4me3, CUT&Tag

description: Library name: P_H3K4me3


title: U2OS, M_FOXK2, Cut&Run

description: Library name: U2OS_M_FOXK2


title: 0013532_resections_all


title: U2OS, G2_FOXK1, Cut&Run

description: Library name: U2OS_G2_FOXK1


title: Cut & Tag, iMOP-derived neurons, p300, CUT&Tag

description: Library name: N_p300


title: U2OS, endogenous FOXK1, ChIP


title: U2OS, 3Flag FOXK1-7A, ChIP


title: U2OS, S_FOXK1, Cut&Run

description: Library name: U2OS_S_FOXK1


title: U2OS, S_FOXK2, Cut&Run

description: Library name: U2OS_S_FOXK2


title: Cut & Tag, Proliferating iMOPs, CTCF, CUT&Tag

description: Library name: P_CTCF


title: U2OS, G1_S_FOXK1, Cut&Run

description: Library name: U2OS_G1_S_FOXK1


title: U2OS, G1_S_FOXK2, Cut&Run

description: Library name: U2OS_G1_S_FOXK2


title: U2OS, 3Flag FOXK1, ChIP


title: U2OS, EG1_FOXK1, Cut&Run

description: Library name: U2OS_EG1_FOXK1


title: U2OS, input, ChIP


title: U2OS, EG1_FOXK2, Cut&Run

description: Library name: U2OS_EG1_FOXK2


title: U2OS, BAP1_empty_KOFOXK1, Cut&Run

description: Library name: U2OS_BAP1_empty_KOFOXK1


title: U2OS, BAP1_FOXK1_KOFOXK1, Cut&Run

description: Library name: U2OS_BAP1_FOXK1_KOFOXK1


title: U2OS, IgG_synchro, Cut&Run

description: Library name: U2OS_synchro_IgG


title: U2OS, IgG_forBAP1, Cut&Run

description: Library name: U2OS_IgG_forBAP1


title: U2OS, vector, ChIP


title: IMR90, SIN3A_11A_siFOXK1, Cut&Run, merge

description: Library name: IMR90_SIN3A_11A_siFOXK1_merged

value: Human lung fibroblast


title: IMR90, IgG_forSIN3A, Cut&Run

description: Library name: IMR90_IgG_forSIN3A


title: IMR90, SIN3A_vector_siFOXK1, Cut&Run, merge

description: Library name: IMR90_SIN3A_vector_siFOXK1_merged


title: IMR90, FOXK2_G0, Cut&Run, merge

description: Library name: IMR90_FOXK2_G0_merged


title: IMR90, IgG_synchro, Cut&Run

description: Library name: IMR90_synchro_IgG


title: IMR90, FOXK1_T18, Cut&Run, merge

description: Library name: IMR90_FOXK1_T18_merged


title: IMR90, FOXK2_T18, Cut&Run, merge

description: Library name: IMR90_FOXK2_T18_merged


title: IMR90, FOXK1_G0, Cut&Run, merge

description: Library name: IMR90_FOXK1_G0_merged


title: IMR90, FOXK1-7A, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge


title: IMR90, FOXK1-11A, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge


title: IMR90, FOXK1, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge


title: IMR90, FOXK1-11A, siRNA anti-FOXK1, H2AUb, Cut&Run, merge


title: IMR90, vector, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge


title: IMR90, FOXK1-7A, siRNA anti-FOXK1, H2AUb, Cut&Run, merge


title: IMR90, FOXK1, siRNA anti-FOXK1, H2AUb, Cut&Run, merge


title: U2OS, BAP1_11A_KOFOXK1, Cut&Run

description: Library name: U2OS_BAP1_11A_KOFOXK1


title: IMR90, IgG_170723, Cut&Run


title: IMR90, vector, siRNA anti-FOXK1, H2AUb, Cut&Run, merge


title: IMR90, SIN3A_FOXK1_siFOXK1, Cut&Run, merge

description: Library name: IMR90_SIN3A_K1_siFOXK1_merged


title: IMR90, FOXK1-11A, siRNA anti-FOXK1, BAP1, Cut&Run, merge


title: IMR90, IgG_300523, Cut&Run, merge


title: IMR90, vector, siRNA anti-FOXK1, BAP1, Cut&Run, merge


title: IMR90, 3Flag FOXK1-11A, ChIP


title: IMR90, FOXK1-7A, siRNA anti-FOXK1, BAP1, Cut&Run, merge


title: IMR90, 3Flag FOXK1-7A, ChIP


title: IMR90, FOXK1, siRNA anti-FOXK1, BAP1, Cut&Run, merge


title: L23_IT_PPP_Glut.8wk

description:
Library name: sample 25
read length: 151


title: ATAC_rep16

status: Public on Apr 02 2025

city: Boston

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

description: demultiplexed with BCL Convert

data_processing:
Files were demultiplexed with BCL convert then aligned with Cellranger with GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: h5 matrix, gene expression counts stored in $`Gene Expression`
Supplementary files format and content: h5 matrix, peak counts stored in $`Peaks`
Supplementary files format and content: h5 matrix, CROPseq counts
Library strategy: 10x ATAC + GEX Multiome

source_name: Hematopoietic cells

growth_protocol: Erythroid media

extract_protocol: Chromium Single Cell Multiome ATAC + Gene Expression

value: Hematopoietic cells

value: erythroid cells


title: IMR90, 3Flag FOXK1, ChIP


title: IMR90, endogenous FOXK2, ChIP


title: ATAC_rep13

description: demultiplexed with BCL Convert


title: IMR90, vector, ChIP


title: IMR90, input, ChIP


title: ATAC_rep14

description: demultiplexed with BCL Convert


title: ATAC_rep12

description: demultiplexed with BCL Convert


title: ATAC_rep10

description: demultiplexed with BCL Convert


title: ATAC_rep7

description: demultiplexed with BCL Convert


title: ATAC_rep6

description: demultiplexed with BCL Convert


title: ATAC_rep5

description: demultiplexed with BCL Convert


title: ATAC_rep4

description: demultiplexed with BCL Convert


title: ATAC_rep8

description: demultiplexed with BCL Convert


title: ATAC_rep3

description: demultiplexed with BCL Convert


title: IMR90, 3Flag FOXK2, ChIP


title: ATAC_rep1

description: demultiplexed with BCL Convert


title: L5_ET_CTX_Glut.18mo

description:
Library name: sample 30
read length: 151


title: RNA_rep14

description: demultiplexed with BCL Convert


title: RNA_rep13

description: demultiplexed with BCL Convert


title: RNA_rep12

description: demultiplexed with BCL Convert


title: IMR90, endogenous FOXK1, ChIP


title: RNA_rep9

description: demultiplexed with BCL Convert


title: RNA_rep10

description: demultiplexed with BCL Convert


title: RNA_rep8

description: demultiplexed with BCL Convert


title: RNA_rep7

description: demultiplexed with BCL Convert


title: RNA_rep6

description: demultiplexed with BCL Convert


title: RNA_rep2

description: demultiplexed with BCL Convert


title: RNA_rep4

description: demultiplexed with BCL Convert


title: RNA_rep5

description: demultiplexed with BCL Convert


title: RNA_rep1

description: demultiplexed with BCL Convert


title: F1_.5_rep4

status: Public on Mar 20 2025

city: Durham

first: Kinsey

middle: C

last: Fisher

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

description:
Library name: Sample 9
F1

data_processing:
Paired-end reads were mapped with bowtie with the following settings: bowtie -I 0 -X 500 --chunkmbs 256 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset. Count data was restricted to include only protein-coding genes (20,127), and then further restricted to include only genes with CPM>1 in at least 4 libraries (14,426 genes).
Differential expression analysis was then performed using edgeR version 3.24.3
Assembly: WS273
Supplementary files format and content: One data file is a spreadhseet that consists of raw counts for all samples (Bergemann2025_preconception_counts.xlsx). The second data file (Bergemann2025_preconception_analysis.xlsx) is a spreadsheet that consists of one sheet with counts per million for each gene in each condition, and other sheets showing logFC, logCPM, P-value and FDR for each gene in comparisons between each condition using edgeR

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: All C. elegans strains used were grown and maintained at 20 °C on K-agar plates (51 mM sodium chloride, 32 mM potassium chloride, 1 mM calcium chloride, 1 mM magnesium sulfate, 10 µg/mL cholesterol, 0.25 % peptone, 2 % agar) seeded with OP50 E. coli bacteria.

extract_protocol:
After 52 hrs for control groups and 0.03uM rotenon exposure, or 74 hours for 0.5uM rotenone-exposed groups worms were harvested for sample collection. Samples containing approximately 1,000 nematodes from each group were rinsed several times with K medium  until most of the bacteria were cleared out, then flash-frozen and maintained at -80°C.
Nematode samples were used for RNA extraction using 1 ml TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol with the exception that approximately 100 µL of acid-washed sand (Sigma-Aldrich), measured with a graduated 1.7 mL microcentrifuge tube, was added to each sample at the beginning of the protocol to aid homogenization. RNA was eluted in nuclease-free water and stored at -80ºC until further use. A nanodrop spectrophotometer (ThermoFisher) was used to assess the purity of the extracted RNA and the Qubit RNA HS Assay kit (ThermoFisher) was used to determine concentration. All RNA samples used for mRNA-Seq library preparation had a 260/280 absorbance ratio over 1.8. Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) starting with 500 ng total RNA per library and 9 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000 to obtain 50 bp paired-end reads.

treatment_protocol: Mixed stage plates were washed and bleached with hydroxide bleach solution to obtain synchronized embryos. Embryos were added to Erlenmeyer flasks with complete K-medium and HB101 at a density of 1 embryo/uL. 0.03uM, 0.5uM of rotenone or 0.125% DMSO (control vehicle solution) were added to the cultures at the start. Rotenone was re-added after 24 and 48 h of exposure, while DMSO was only added after 24h of exposure.

value: Whole worm

value: Wild Type (N2)


title: F1_.03_rep4

description:
Library name: Sample 8
F1


title: P0_.5_rep4

description:
Library name: Sample 6
P0


title: F1_ctrl_rep4

description:
Library name: Sample 7
F1

value: Control


title: RNA_rep16

description: demultiplexed with BCL Convert


title: P0_ctrl_rep4

description:
Library name: Sample 4
P0


title: ATAC_rep2

description: demultiplexed with BCL Convert


title: F1_.03_rep3

description:
Library name: Sample 24
F1


title: F1_ctrl_rep3

description:
Library name: Sample 23
F1


title: P0_.03_rep3

description:
Library name: Sample 21
P0


title: P0_.5_rep3

description:
Library name: Sample 22
P0


title: ATAC_rep9

description: demultiplexed with BCL Convert


title: F1_.5_rep2

description:
Library name: Sample 2
F1


title: F1_ctrl_rep2

description:
Library name: Sample 18
F1


title: P0_ctrl_rep3

description:
Library name: Sample 20
P0


title: P0_ctrl_rep2

description:
Library name: Sample 15
P0


title: F1_.03_rep2

description:
Library name: Sample 19
F1


title: F1_ctrl_rep1

description:
Library name: Sample 12
F1


title: F1_.5_rep1

description:
Library name: Sample 14
F1


title: P0_ctrl_rep1

description:
Library name: Sample 1
P0


title: P0_.03_rep1

description:
Library name: Sample 10
P0


title: P0_.03_rep2

description:
Library name: Sample 16
P0


title: P0_.5_rep1

description:
Library name: Sample 11
P0


title: Male E13.5, ATAC, replicate 2

status: Public on Mar 19 2025

first: Humphrey

middle: Hung-Chang

last: Yao

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description: Library name: E13-M-R2-ATAC

library_source: genomic single cell

data_processing:
All libraries demulitplexed using cellranger-arc mkfastq
Demultiplexed data was processed using cellranger-arc mkfastq
Assembly: mm10
Supplementary files format and content: cellranger-arc count atac output files: E11-F-R1.atac_fragments.tsv.gz E11-F-R2.atac_fragments.tsv.gz E11-M-R1.atac_fragments.tsv.gz E11-M-R2.atac_fragments.tsv.gz E12-F-R1.atac_fragments.tsv.gz E12-F-R2.atac_fragments.tsv.gz E12-M-R1.atac_fragments.tsv.gz E12-M-R2.atac_fragments.tsv.gz E13-F-R1.atac_fragments.tsv.gz E13-F-R2.atac_fragments.tsv.gz E13-M-R1.atac_fragments.tsv.gz E13-M-R2.atac_fragments.tsv.gz
Supplementary files format and content: cellranger-arc count matrix output files: E11-F-R1.barcodes.tsv.gz E11-F-R1.features.tsv.gz E11-F-R1.matrix.mtx.gz E11-F-R2.barcodes.tsv.gz E11-F-R2.features.tsv.gz E11-F-R2.matrix.mtx.gz E11-M-R1.barcodes.tsv.gz E11-M-R1.features.tsv.gz E11-M-R1.matrix.mtx.gz E11-M-R2.barcodes.tsv.gz E11-M-R2.features.tsv.gz E11-M-R2.matrix.mtx.gz

source_name: gonad

extract_protocol:
Whole ovaries and testes were collected at E11.5, E11.5, and E12.5. The sexes of the embryos were determined using amnion staining, as previously published20, to identify the presence (XX) or absence (XY) of the Barr body and confirmed with PCR using primers that recognize the Y chromosome. Tomato fluorescence was used to facilitate the dissection of the gonad away from the mesonephros, which was done using needles. Isolated fetal mouse gonads were isolated in PBS, and pairs of gonads or groups pooled between fetuses of the same sex and age were immediately frozen in liquid nitrogen for storage. Nuclei isolation was performed using the 10X Genomics Chromium Nuclei Isolation Kit (catalog #1000494) following the manufacturer’s protocol.
The 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library Preparation Kit (catalog #1000284) was used to generate a 10X barcoded library of mRNA and transposed DNA from individual nuclei. The 10X barcoded single-nuclei RNA and ATAC-seq libraries were obtained from 8,687 average (1,555-20,000) nuclei per sample and sequenced with Illumina NOVAseq to a minimum sequencing depth of 129,120,442 raw reads and 22,406 read pairs/nucleus

value: gonad

value: gonadal cell populations

tag: library type

value: ATAC


title: F1_.5_rep3

description:
Library name: Sample 3
F1


title: P0_.03_rep4

description:
Library name: Sample 5
P0


title: Female E13.5, ATAC, replicate 1

description: Library name: E13-F-R1-ATAC


title: Male E12.5, ATAC, replicate 1

description: Library name: E12-M-R1-ATAC


title: Male E12.5, ATAC, replicate 2

description: Library name: E12-M-R2-ATAC


title: Female E12.5, ATAC, replicate 1

description: Library name: E12-F-R1-ATAC


title: Male E11.5, ATAC, replicate 2

description: Library name: E11-M-R2-ATAC


title: Female E12.5, ATAC, replicate 2

description: Library name: E12-F-R2-ATAC


title: Female E11.5, ATAC, replicate 2

description: Library name: E11-F-R2-ATAC


title: PB-postDexa, peripheral blood (PB) sample obtained one month after dexamethasone treatment (month 13), BCR

status: Public on Mar 12 2025

city: Cologne

first: Till

last: Braun

address: Kerpener Strasse 62

department: Clinic I for Internal Medicine

country: Germany

institute: University Hospital of Cologne

description:
Library name: P2264_bcr
No processed data files provided, because cellranger output was empty

library_source: other

data_processing:
The CAR nucleotide sequence for the cilta-cel vector was obtained from the respective patent. A custom human reference genome was created by adding the CAR nucleotide sequence to the human reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cell Ranger v7.1.0.
The Cell Ranger multi pipeline was used to process the single-cell gene expression, cell surface protein, and V(D)J libraries. The feature reference CSV file, declaring antibody capture constructs and associated barcodes is provided at https://github.com/fraunhofer-izi/Braun_et_al_2024 (data/feature_reference.csv). The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes of cells
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data for cells
Supplementary files format and content: cellranger output: vdj_t-filtered_contig_annotations.csv
Supplementary files format and content: cellranger output: vdj_b-filtered_contig_annotations.csv:
Library strategy: BCR-Seq

molecule: other

source_name: Peripheral blood

extract_protocol:
Samples were thawed and quality was assessed by acridine orange and propidium iodide (AO/PI) staining using automated cell counting. Samples with initial viability <80% were subjected to dead cell removal using ViahanceTM dead-cell removal kit (BioPAL, Inc., United States).
The cells were stained with a custom panel of 70 TotalSeqTM-C antibodies (BioLegend, United States), optimized, and prepared by Singleron Biotechnologies, Singapore. These TotalSeqTM-C antibodies are oligonucleotide-coupled antibodies directed against selected cell surface proteins. The antibodies are conjugated via a linker to oligonucleotides, which consist of a polymerase chain reaction (PCR) handle, an antibody-specific barcode, and a capture sequence. These antibody-bound oligonucleotides can be captured during single-cell library preparation, allowing simultaneous surface protein and gene expression profiling. The single-cell gene expression, surface protein expression, and T-cell receptor (TCR) libraries were constructed using Chromium single-cell 5’ reagent kits (v2 chemistry; 10x Genomics, Inc., United States), as per the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq X platform using a 10B flow cell and PE150 chemistry.

value: Peripheral blood

value: BCR

tag: time point

value: 13 months post CAR-T


title: Female E13.5, ATAC, replicate 2

description: Library name: E13-F-R2-ATAC


title: F1_.03_rep1

description:
Library name: Sample 13
F1


title: PB-postDexa, peripheral blood (PB) sample obtained one month after dexamethasone treatment (month 13), ADT

description: Library name: P2264_adt

data_processing:
The CAR nucleotide sequence for the cilta-cel vector was obtained from the respective patent. A custom human reference genome was created by adding the CAR nucleotide sequence to the human reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cell Ranger v7.1.0.
The Cell Ranger multi pipeline was used to process the single-cell gene expression, cell surface protein, and V(D)J libraries. The feature reference CSV file, declaring antibody capture constructs and associated barcodes is provided at https://github.com/fraunhofer-izi/Braun_et_al_2024 (data/feature_reference.csv). The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes of cells
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data for cells
Supplementary files format and content: cellranger output: vdj_t-filtered_contig_annotations.csv
Supplementary files format and content: cellranger output: vdj_b-filtered_contig_annotations.csv:

molecule: protein

value: ADT


title: Male E11.5, ATAC, replicate 1

description: Library name: E11-M-R1-ATAC


title: P0_.5_rep2

description:
Library name: Sample 17
P0


title: Female E11.5, ATAC, replicate 1

description: Library name: E11-F-R1-ATAC


title: PB-postDexa, peripheral blood (PB) sample obtained one month after dexamethasone treatment (month 13), TCR

description: Library name: P2264_tcr

data_processing:
The CAR nucleotide sequence for the cilta-cel vector was obtained from the respective patent. A custom human reference genome was created by adding the CAR nucleotide sequence to the human reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cell Ranger v7.1.0.
The Cell Ranger multi pipeline was used to process the single-cell gene expression, cell surface protein, and V(D)J libraries. The feature reference CSV file, declaring antibody capture constructs and associated barcodes is provided at https://github.com/fraunhofer-izi/Braun_et_al_2024 (data/feature_reference.csv). The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes of cells
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data for cells
Supplementary files format and content: cellranger output: vdj_t-filtered_contig_annotations.csv
Supplementary files format and content: cellranger output: vdj_b-filtered_contig_annotations.csv:
Library strategy: TCR-Seq

value: TCR


title: PB-postDexa, peripheral blood (PB) sample obtained one month after dexamethasone treatment (month 13), GEX

description: Library name: P2264_mRNA

value: mRNA


title: Male E13.5, ATAC, replicate 1

description: Library name: E13-M-R1-ATAC


title: PB-preDexa, peripheral blood (PB) sample collected and cryopreserved 12 months after CAR T-cell infusion, BCR

description:
Library name: P2249_bcr
No processed data files provided, because cellranger output was empty

value: 12 months post CAR-T


title: PB-preDexa, peripheral blood (PB) sample collected and cryopreserved 12 months after CAR T-cell infusion, TCR

description: Library name: P2249_tcr


title: PB-preDexa, peripheral blood (PB) sample collected and cryopreserved 12 months after CAR T-cell infusion, ADT

description: Library name: P2249_adt


title: PB-preDexa, peripheral blood (PB) sample collected and cryopreserved 12 months after CAR T-cell infusion, GEX

description: Library name: P2249_mRNA


title: BM-preDexa, bone marrow (BM) sample collected and cryopreserved 12 months after CAR T-cell infusion, TCR

description: Library name: P2248_tcr

source_name: Bone marrow

value: Bone marrow


title: BM-preDexa, bone marrow (BM) sample collected and cryopreserved 12 months after CAR T-cell infusion, ADT

description: Library name: P2248_adt


title: BM-preDexa, bone marrow (BM) sample collected and cryopreserved 12 months after CAR T-cell infusion, BCR

description:
Library name: P2248_bcr
No processed data files provided, because cellranger output was empty.


title: Aph, peripheral blood (PB) stem cell apheresis products collected three years prior to CAR-T infusion, TCR

description: Library name: AphNB_tcr

value: 3 years prior CAR-T


title: BM-preDexa, bone marrow (BM) sample collected and cryopreserved 12 months after CAR T-cell infusion, GEX

description: Library name: P2248_mRNA


title: Aph, peripheral blood (PB) stem cell apheresis products collected three years prior to CAR-T infusion, GEX

description: Library name: AphNB_mRNA


title: Aph, peripheral blood (PB) stem cell apheresis products collected three years prior to CAR-T infusion, ADT

description: Library name: AphNB_adt


title: P047_ST

status: Public on Feb 26 2025

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: P047
Visium (10X)

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
Raw reads were processed utilizing the spaceranger command line tool (version 2.1.0, 10x Genomics) and mapped to the human reference genome (Homo sapiens, GRCh38-2020-A).
Assembly: Homo sapiens, GRCh38-2020-A
Supplementary files format and content: Gzipped tar archives containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions as well as a svg file with the manual annotation of morphology.
Supplementary files format and content: metadata file with relevant metadat for each sample
Supplementary files format and content: Gzip RDS file with Seurat object containing all samples and metadata

source_name: Ectocervix

extract_protocol:
Fresh frozen tisue were sliced to a thickness of 10 μm using a pre-cooled cryostat.
Library preparation for sequencing adhered to the manufacturer’s instructions (10x Genomics, Visium Spatial Transcriptomic). Sequencing was conducted on a NovaSeq6000 (NovaSeq Control Software 1.8.1/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell.

value: Ectocervix

tag: group

value: HIV

value: female


title: RNA_rep3

description: demultiplexed with BCL Convert

value: Hematopoietic cells

value: erythroid cells


title: P028_ST

description:
Library name: P028
Visium (10X)


title: P007_ST

description:
Library name: P007
Visium (10X)


title: P016_ST

description:
Library name: P016
Visium (10X)


title: P023_ST

description:
Library name: P023
Visium (10X)


title: P067_ST

description:
Library name: P067
Visium (10X)

value: Control


title: P044_ST

description:
Library name: P044
Visium (10X)


title: P008_ST

description:
Library name: P008
Visium (10X)


title: P026_ST

description:
Library name: P026
Visium (10X)


title: P004_ST

description:
Library name: P004
Visium (10X)


title: Pt-10_PDX

status: Public on Feb 21 2025

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description:
Library name: Pt-10_PDX
FFPE Visium CytAssist ST sequencing

data_processing:
The demultiplexed reads were processed using Space Ranger (v.1.3.1 or 2.1.0) from 10x Genomics, aligned to the GRCh38 reference genome with default parameters. The resulting unique molecular identifier (UMI) count matrices were then analysed using Seurat (v.4.3) 47 in the R platform (v.4.2.0). Detailed quality control (QC) metrics were generated and evaluated, and spots were carefully filtered to obtain high-quality SRT data for downstream analyses. Briefly, for basic quality filtering, spots with low complexity libraries (UMI count below 100) were filtered out to eliminate low-quality spots. Additionally, spots located within acellular stromal interfaces were excluded and samples with more than 40% low-quality spots were also excluded from subsequent analyses.
Assembly: GRCh38 reference genome
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Library strategy: Spatial Transcriptomics

source_name: PDX for primary PDAC

extract_protocol:
The frozen tissue samples were embedded in OCT, and then cryo-sectioned to a thickness of 10μm using a cryostat. FFPE tissue sections from PDX models were cut to a thickness of 5μm using a microtome. Subsequently, these sections were stained with Hematoxylin and Eosin (H&E) for histological examination. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time) or the Visium CytAssist Spatial Gene Expression protocol for FFPE tissue samples.
Library preparation for frozen tissue samples was performed as described in  the Visium Spatial Gene Expression Reagent Kit (PN-1000189), Library Construction Kit (PN-1000196), and Dual Index Plate TT Set A (PN-3000431) as described in the Visium protocol for fresh frozen tissue samples (CG000239). FFPE tissue sections for PDX models were prepared following the 6.5 x 6.5 mm Visium CytAssist Spatial Gene Expression protocol (CG000518 for tissue preparation, CG000520 for deparaffinization and H&E staining, and CG000495 for library construction, 10X Genomics).

value: PDX for primary PDAC

tag: age

value: male


title: Pt-13_PDX

description:
Library name: Pt-13_PDX
FFPE Visium CytAssist ST sequencing

value: FOLFIRINOX, Capecitabine, gemcitabine/abraxane/ denosumab


title: Pt-13_Pri3

description:
Library name: Pt-13_Pri3
Fresh frozen Visium ST sequencing

source_name: Primary PDAC

value: Primary PDAC


title: Pt-8_Pri2

description:
Library name: Pt-8_Pri2
Fresh frozen Visium ST sequencing


title: Pt-13_Pri2

description:
Library name: Pt-13_Pri2
Fresh frozen Visium ST sequencing


title: Aph, peripheral blood (PB) stem cell apheresis products collected three years prior to CAR-T infusion, BCR

description: Library name: AphNB_bcr

value: Peripheral blood

value: BCR


title: Pt-6_Pri2

description:
Library name: Pt-6_Pri2
Fresh frozen Visium ST sequencing

value: gemcitabine, AVN944, erlotinib


title: Pt-13A

description: Fresh frozen Visium ST sequencing

data_processing:
The demultiplexed reads were processed using Space Ranger (v.1.3.1) from 10x Genomics, aligned to the GRCh38 reference genome with default parameters. The resulting unique molecular identifier (UMI) count matrices were then analysed using Seurat (v.4.3) 47 in the R platform (v.4.2.0). Detailed quality control (QC) metrics were generated and evaluated, and spots were carefully filtered to obtain high-quality SRT data for downstream analyses. Briefly, for basic quality filtering, spots with low complexity libraries (UMI count below 100) were filtered out to eliminate low-quality spots. Additionally, spots located within acellular stromal interfaces were excluded and samples with more than 40% low-quality spots were also excluded from subsequent analyses.
Assembly: GRCh38 reference genome
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Library strategy: Spatial Transcriptomics

extract_protocol:
Samples were flash frozen in liquid nitrogen, cryo-sectioned and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time).
Library preparation was performed as described in  the Visium Spatial Gene Expression Reagent Kit (PN-1000189), Library Construction Kit (PN-1000196), and Dual Index Plate TT Set A (PN-3000431) as described in the Visium protocol for fresh frozen tissue samples (CG000239).

value: F


title: Pt-13E

description: Fresh frozen Visium ST sequencing

source_name: Peritoneal metastasis

value: Peritoneal metastasis


title: Pt-13D

description: Fresh frozen Visium ST sequencing


title: Pt-13C

description: Fresh frozen Visium ST sequencing

source_name: Lung metastasis

value: Lung metastasis


title: Pt-11C

description: Fresh frozen Visium ST sequencing

value: M

value: gemcitabine, Oxaliplatin, leucovorin-modulated 5-FU, irinotecan,


title: Pt-12A

description: Fresh frozen Visium ST sequencing

value: gemcitabine


title: Pt-12C

description: Fresh frozen Visium ST sequencing


title: Pt-11A

description: Fresh frozen Visium ST sequencing


title: Pt-12D

description: Fresh frozen Visium ST sequencing


title: Pt-12B

description: Fresh frozen Visium ST sequencing

source_name: Liver metastasis

value: Liver metastasis


title: Pt-10D

description: Fresh frozen Visium ST sequencing


title: Pt-10A

description: Fresh frozen Visium ST sequencing


title: Pt-10B

description: Fresh frozen Visium ST sequencing


title: Pt-9B

description: Fresh frozen Visium ST sequencing

value: Cisplatin, gemcitabine, ADH-1, 5-FU (Clinical trial)


title: Pt-9C

description: Fresh frozen Visium ST sequencing


title: Pt-13B

description: Fresh frozen Visium ST sequencing


title: Pt-9D

description: Fresh frozen Visium ST sequencing


title: Pt-11D

description: Fresh frozen Visium ST sequencing


title: Pt-11B

description: Fresh frozen Visium ST sequencing


title: Pt-8D

description: Fresh frozen Visium ST sequencing


title: Pt-6_Pri3

description:
Library name: Pt-6_Pri3
Fresh frozen Visium ST sequencing


title: Pt-8B

description: Fresh frozen Visium ST sequencing


title: Pt-8C

description: Fresh frozen Visium ST sequencing


title: Pt-7D

description: Fresh frozen Visium ST sequencing

value: gemcitabine, ADH1, cisplatin


title: Pt-7C

description: Fresh frozen Visium ST sequencing


title: Pt-3_Pri2

description:
Library name: Pt-3_Pri2
Fresh frozen Visium ST sequencing

value: female

value: No treatment


title: Pt-9A

description: Fresh frozen Visium ST sequencing


title: Pt-7B

description: Fresh frozen Visium ST sequencing


title: Pt-7A

description: Fresh frozen Visium ST sequencing


title: C elegans, Glia, Herm, Rep2

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

description:
10X Genomics
Day1_Herm_mir228GFP_Rep2

data_processing:
Count matrices for the two samples were generated using CellRanger-5.0.1
The 3’ untranslated regions (UTRs) in the reference transcriptome (WormBase WS280) have been previously reported to be too short for reliable gene assignment. Therefore, following the previously published approaches, we extended 3’ UTRs in the WS280 genome. Specifically, for genes not overlapping with a downstream gene, we extended their 3’ UTRs by 50, 100, 150, 200, 250, 300, 400 and 500bp. In case the extended sequence collided with a downstream gene, it was trimmed back to the base next to the gene. The unmodified and eight modified GTF files were each used to build a reference genome. Protein-coding genes and non-coding RNA genes (lincRNAs, ncRNAs and antisense RNAs) were included for gene expression count determination. Cellranger was used to generate a count matrix for each sample relative to each reference and the optimal 3’ UTR extension was defined as follows: 20 reads were considered as a significant gain by an extension interval. For each gene, the cumulative sums from 3’ (the longest extension) to 5’ was calculated after subtracting 20 from read increment in each extension interval. The optimal extension for a given sample was set to the point which had the smallest cumulative sum of less than 0. If cumulative sums were all greater than zero, the optimal extension was set to 500bp. The final extension of a gene was set to the point supported by most samples and by at least two samples. Prior work has suggested low UMIs for C. elegans single-cell RNAseq data59. We thus evaluated multiple cut-offs and empirically selected 200 UMIs as empty droplet cut-off. Cell-containing droplets by 10X Cellranger were used for downstream analysis
Data processing was performed using the scanpy package with default parameters unless specified. Count matrices from all samples were concatenated. Raw counts were normalized by dividing the counts by total counts per cell. The normalized data was multiplied by the median of total counts across cells to avoid numerical issues and log-transformed with a pseudo count of 1. Feature selection was then performed to select the top 2500 most highly variable genes (using scanpy.pp.highly_variable_genes), which was used as input for principal component analysis with 50 components. The PCs were used as input for generating UMAPs (with min_dist=0.2) and clustering with Leiden.
Assembly: WormBase WS280
Supplementary files format and content: Scanpy anndata objects containing counts, normalized data and cell-types

molecule: nuclear RNA

source_name: 1 day old whole hermaphrodite worm

growth_protocol: Preparation of adults for dissociation: Worms were grown on 10 cm, standard 1% NGM agar plates seeded with E.coli strain OP50. To obtain synchronized day 1 adult worms, we first obtained embryos by performing hypochlorite treatment (1M NaOH + 4% NaOCl freshly made) on adult hermaphrodites. The embryos hatched overnight (16-20 hours) on unseeded NGM agar plates and starved L1 arrested worms were recovered on 10 cm OP50-seeded plates at 20C for 64-68 hours. For each hermaphrodite sample, about 50,000 day 1 adult worms were washed off plates with M9 into 50 ml conical tubes that were fitted with a 50um pluriStrainer® filter to separate day 1 adults from embryos or hatched L1s. The pure day 1 adult hermaphrodite population was transferred to 15 ml conical tubes and further washed 3x with M9 with centrifugation at 1200 rcf for 1 min.  For each male sample, about 150,000 day 1 adult worms were washed off plates with M9 into 50 ml conical tubes that were fitted with stacked 50 um, 40 um, and 30 um pluriStrainer® filters to separate adult males from hermaphrodites. The stacked filtration was repeated one more time. The worms from the 30 um filter were mix of about 80-90% males, plus young day 1 adult hermaphrodites. To further enrich for a male only population, we used the COPAS worm sorter to select animals based on size and lack of Pmig-24: mVenus staining and recovered 50,000 males. After sorting, 5x10ul aliquots of worms were visualized under a light microscope for counting and each aliquot contained 100% males. The males were further washed 3x with M9 with centrifugation at 1200 rcf for 1 min.

extract_protocol:
Dissociation: Single nuclei suspensions were obtained as described in Kalestky R et al., 2018 for cells, with some modifications to further dissociate the cell membranes. After removing most of the M9 solution, worms were quickly washed once in 500ul lysis buffer (200mM DTT, 0.25% SDS, 20mM Hepes pH 8.0, 3% sucrose), and then lysed with 750ul lysis buffer for 5 min for hermaphrodites and 3 minutes for males. Lysis was shorter for males because longer lysis time caused the males to rupture during the downstream M9 washing steps. Cuticle disruption was monitored by examining 1μL of sample under a microscope. When lysis was complete, worms had a slightly blunt head, but were not ruptured. Reaction was stopped by adding 500ul M9 and then did 6 quick washed in M9. Worms were then dissociated by adding 500 ul freshly made 20mg/ml Pronase (resuspended in water) to the worm pellet for 15-20 minutes depending on the lot of Pronase. Males were dissociated in 15 mg/ml Pronase. During the Pronase incubation, worms were dissociated by pipetting vigorously with a P1000 pipette set to 400ul every 45 seconds, rotating between samples for the first 10 minutes, followed by trituration with a P200 pipette set to 200 ul for remaining 5-10 minutes. Worms were quickly spun down between triturations so that the worm pellet size could be monitored. Between pipetting, 2ul of worms were examined on a dissecting scope to assess level of dissociation. Dissociation was continued until large fragments were gone and the pellet of worms was less than 20 ul when quickly centrifuged. We noticed that during this over digestion step, the cell membranes would also digest. To stop the digestion, 750μL of ice-cold 1xPBS/10%FBS was added to the tube. The dissociated nuclei were transferred to a 1ml syringe using a 27-gauge needle. The needle was replaced by a 5uM syringe filter that was pre-wetted with ice cold PBS. The cells were gently passed through the syringe filter directly into the FACS collection tube on ice. Protector RNAse Inhibitor was added to the following solutions: Pronase, PBS-FBS, and PBS-L15-FBS to get final concentration of 2U/ul inhibitor.   Cell sorting and preparation for RNA sequencing: The nuclei were sorted with a Sony SH800S cell sorter fitted with the 100µm nozzle running at a speed of 10-12k events per second using the PE filter set. Nuclei were sorted into 1:1 1xPBS:L15+30%FBS 2U/µl Protector RNAse inhibitor, transferred to a low bind 2 ml tube and centrifuged 9600xg for 5 min at 4C. Once an RFP+ pellet was confirmed under a fluorescent dissection scope, the nuclei were gently resuspended in 1xPBS10%FBS buffer aiming for a final concentration of 1000 nuclei/uL based on the number of nuclei sorted.
We targeted 10,000 cells per sample and used the 10X Chromium platform using 10X NextGem v3.1 chemistry. cDNA was amplified for 12 cycles and the index PCR was cycled 12 times. Final libraries were brought to 10 nM concentration.
Next-generation sequencing libraries were constructed following the User Guide, which were sequenced on an Illumina NovaSeq 2500 system.

value: 1 day old whole hermaphrodite worm

value: glia


title: Pt-5B

description: Fresh frozen Visium ST sequencing


title: Pt-5A

description: Fresh frozen Visium ST sequencing

value: Primary PDAC


title: C elegans, Glia, Herm, Rep1

description:
10X Genomics
Day1_Herm_mir228GFP_Rep1


title: Pt-10C

description: Fresh frozen Visium ST sequencing


title: Pt-4D

description: Fresh frozen Visium ST sequencing


title: Pt-4C

description: Fresh frozen Visium ST sequencing


title: Pt-3A

description: Fresh frozen Visium ST sequencing


title: Pt-4B

description: Fresh frozen Visium ST sequencing


title: Pt-6C

description: Fresh frozen Visium ST sequencing


title: Pt-2B

description: Fresh frozen Visium ST sequencing


title: Pt-8A

description: Fresh frozen Visium ST sequencing


title: Pt-3B

description: Fresh frozen Visium ST sequencing


title: Pt-3C

description: Fresh frozen Visium ST sequencing


title: Pt-2A

description: Fresh frozen Visium ST sequencing


title: Pt-1C

description: Fresh frozen Visium ST sequencing


title: Pt-2C

description: Fresh frozen Visium ST sequencing


title: Pt-4A

description: Fresh frozen Visium ST sequencing


title: Pt-5C

description: Fresh frozen Visium ST sequencing


title: Pt-1B

description: Fresh frozen Visium ST sequencing


title: Pt-6A

description: Fresh frozen Visium ST sequencing


title: TUBO_1

status: Public on Feb 12 2025

city: Tampa

first: Brian

middle: J

last: Czerniecki

state: FL

address: 12902 Magnolia Drive

department: Breast Oncology

institute: Moffitt Cancer Center

description: RNA sequecing

data_processing:
RNAseq reads were subjected to a series of QC measures before mapped against mouse reference genome mm10 using Tophat #2.0.13.
Gene quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region associated with each gene.
Assembly: mm10
Supplementary files format and content: Gene expression data are provided as raw read counts.

source_name: Breast cancer

growth_protocol: standard animal cell culture methods were used

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
Nugen Ovation Mouse RNAseq Kit

treatment_protocol: Disseminated cancer cells isolated from bone marrow of breast cancer patients and transgenic mouse breast cancer model and breast cancer cell lines were treated with or without IFN-𝛾 or TNF-⍺ or anti-HER2 antibodies or in combination

value: Breast cancer

value: TUBO

value: Breast cancer cell line

value: WT

value: control, biological rep1


title: EL_tumor_neuT_1

description: RNA sequecing

value: Primay isolated cancer cells

value: Cancer cells from early mammary tumor lesion


title: EL_tumor_neuT_2

description: RNA sequecing

value: control, biological rep2


title: Pt-1A

description: Fresh frozen Visium ST sequencing

value: F


title: DCCs_IFN_2

description: RNA sequecing

value: disseminated cancer cells

value: Disseminated cancer cells isolated from bone marrow of spontaneous breast cancer metastasis mice

value: IFN-𝛾 treated, biological rep2


title: DCCs_IFN_1

description: RNA sequecing

value: IFN-𝛾 treated, biological rep1


title: DCCs_Control_2

description: RNA sequecing


title: S04_HCC1954_1_10092023

data_processing:
RNAseq reads were aligned against the human genome hg19 using STAR-2.5.3a. Gene expression quantification was performed by calculating the read count at the gene level with RSEM.
Assembly: hg19
Supplementary files format and content: Gene expression data are provided as raw read counts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
Followed Nugen Universal RNAseq Human Kit protocol


title: S06_HCC1954_3_10092023

value: control, biological rep3


title: S05_HCC1954_2_10092023


title: Pt-6D

description: Fresh frozen Visium ST sequencing

value: Peritoneal metastasis

value: M

value: gemcitabine, AVN944, erlotinib


title: S01_BT474_1_10092023

value: Breast cancer


title: S02_BT474_2_10092023


title: S012_JIMT_1IFNγ_3

value: IFN-𝛾 treated, biological rep3


title: S08_JIMT_1control_2

value: Breast cancer cell line


title: S03_BT474_3_10092023

value: WT


title: S011_JIMT_1IFNγ_2


title: TUBO_2

description: RNA sequecing

value: TUBO


title: S010_JIMT_1IFNγ_1


title: S09_JIMT_1contro_3


title: PRD, AL foamy, s090

status: Public on Jan 02 2025

city: Amsterdam

first: Alida

last: Chen

address: Meibergdreef 47, 1105 BA

country: Netherlands

institute: Netherlands Institute for Neuroscience

description:
Library name: 104898-001-090
104898-001-090

data_processing:
Adapter sequences were trimmed using Trimmomatic (version 0.39).
Trimmed reads were mapped to the human GRCh38 genome using HISAT2 (version 2.2.1) on default settings
Feature counts of reads mapped to genes were determined using HTSeq (version 1.99.2) with the ‘Homo_sapiens.CRCh38.105.gtf’ file (options: -m union -f bam -r name -s no -a 10 -t exon -i gene_id)
Resulting counts of both datasets were analyzed separately using R (version 4.1.0) and Bioconductor (version 3.13)
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing raw, unnormalised counts for each sample

source_name: AL foamy

extract_protocol:
All samples were collected in TRIsure and stored at -80°C until further processing. Total RNA was isolated with the RNeasy micro kit (QIAGEN) according to the manufacturers’ instructions.
rRNA depletion using QIAseq FastSelect kit (Qiagen)

treatment_protocol: MS lesions and NAWM samples were isolated from frozen post-mortem brain tissue

tag: donor

value: PRD

value: AL foamy

tag: diagnosis

value: Multiple Sclerosis

value: female

tag: ms type

value: SP

tag: rin value


title: PRD, AL foamy_NAWM, s096

description:
Library name: 104898-001-096
104898-001-096

source_name: AL foamy_NAWM

tag: tissue

value: AL foamy_NAWM


title: PRD, AL foamy_NAWM, s091

description:
Library name: 104898-001-091
104898-001-091

tag: Sex


title: PRD, AL foamy_NAWM, s095

description:
Library name: 104898-001-095
104898-001-095


title: Pt-6B

description: Fresh frozen Visium ST sequencing

value: Liver metastasis


title: PRD, AL foamy_NAWM, s092

description:
Library name: 104898-001-092
104898-001-092

value: PP


title: PRD, AL foamy_NAWM, s094

description:
Library name: 104898-001-094
104898-001-094


title: PRD, AL foamy, s089

description:
Library name: 104898-001-089
104898-001-089


title: PRD, AL foamy, s088

description:
Library name: 104898-001-088
104898-001-088


title: PRD, AL foamy, s085

description:
Library name: 104898-001-085
104898-001-085


title: PRD, AL foamy, s086

description:
Library name: 104898-001-086
104898-001-086


title: PRD, AL foamy, s084

description:
Library name: 104898-001-084
104898-001-084


title: ERD, AL foamy, s075

description:
Library name: 104898-001-075
104898-001-075

value: ERD

value: RR


title: ERD, AL foamy_NAWM, s077

description:
Library name: 104898-001-077
104898-001-077

value: PR


title: DCCs_Control_1

description: RNA sequecing

value: disseminated cancer cells

tag: cell type

value: Disseminated cancer cells isolated from bone marrow of spontaneous breast cancer metastasis mice

value: control, biological rep1


title: PRD, AL ram-amo_NAWM, s067

description:
Library name: 104898-001-067
104898-001-067

source_name: AL ram-amo_NAWM

value: AL ram-amo_NAWM


title: PRD, AL ram-amo_NAWM, s064

description:
Library name: 104898-001-064
104898-001-064


title: PRD, AL ram-amo, s060

description:
Library name: 104898-001-060
104898-001-060

source_name: AL ram-amo

value: AL ram-amo


title: PRD, AL ram-amo_NAWM, s065

description:
Library name: 104898-001-065
104898-001-065


title: PRD, AL ram-amo_NAWM, s063

description:
Library name: 104898-001-063
104898-001-063


title: ERD, AL foamy_NAWM, s082

description:
Library name: 104898-001-082
104898-001-082


title: PRD, AL ram-amo, s058

description:
Library name: 104898-001-058
104898-001-058


title: PRD, AL ram-amo, s057

description:
Library name: 104898-001-057
104898-001-057


title: S07_JIMT_1control_1

value: Breast cancer

value: Breast cancer cell line

value: WT

tag: treatment


title: ERD, AL ram-amo, s047

description:
Library name: 104898-001-047
104898-001-047

value: Multiple Sclerosis


title: ERD, AL ram-amo_NAWM, s052

description:
Library name: 104898-001-052
104898-001-052

value: female


title: ERD, AL foamy, s070

description:
Library name: 104898-001-070
104898-001-070

value: AL foamy


title: ERD, AL ram-amo, s045

description:
Library name: 104898-001-045
104898-001-045

value: SP


title: PRD, RL_NAWM, s042

description:
Library name: 104898-001-042
104898-001-042

value: PRD


title: PRD, RL_NAWM, s037

description:
Library name: 104898-001-037
104898-001-037


title: ERD, AL ram-amo, s043

description:
Library name: 104898-001-043
104898-001-043

value: PP


title: ERD, AL ram-amo_NAWM, s050

description:
Library name: 104898-001-050
104898-001-050

value: ERD


title: PRD, RL, s035

description:
Library name: 104898-001-035
104898-001-035

source_name: RL

value: RL


title: PRD, RL, s031

description:
Library name: 104898-001-031
104898-001-031


title: PRD, RL, s032

description:
Library name: 104898-001-032
104898-001-032


title: PRD, RL, s030

description:
Library name: 104898-001-030
104898-001-030


title: PRD, RL_NAWM, AL foamy_NAWM, s039

description:
Library name: 104898-001-039
104898-001-039

source_name: RL_NAWM/AL foamy_NAWM

value: RL_NAWM/AL foamy_NAWM


title: PRD, RL_NAWM, s038

description:
Library name: 104898-001-038
104898-001-038


title: PRD, AL ram-amo, s056

description:
Library name: 104898-001-056
104898-001-056


title: ERD, RL_NAWM, s024

description:
Library name: 104898-001-024
104898-001-024


title: ERD, RL_NAWM, s022

description:
Library name: 104898-001-022
104898-001-022


title: ERD, RL_NAWM, s025

description:
Library name: 104898-001-025
104898-001-025


title: ERD, AL ram-amo_NAWM, s054

description:
Library name: 104898-001-054
104898-001-054


title: ERD, RL_NAWM, s023

description:
Library name: 104898-001-023
104898-001-023


title: ERD, RL, s018

description:
Library name: 104898-001-018
104898-001-018


title: ERD, RL, s016

description:
Library name: 104898-001-016
104898-001-016


title: ERD, RL, s017

description:
Library name: 104898-001-017
104898-001-017


title: ERD, RL, s015

description:
Library name: 104898-001-015
104898-001-015


title: ERD, RL_NAWM, s010

description:
Library name: 104898-001-010
104898-001-010

value: RR


title: ERD, RL_NAWM, s009

description:
Library name: 104898-001-009
104898-001-009

value: PR


title: ERD, RL, s006

description:
Library name: 104898-001-006
104898-001-006


title: ERD, RL, s005

description:
Library name: 104898-001-005
104898-001-005


title: ERD, RL, s004

description:
Library name: 104898-001-004
104898-001-004


title: ERD, RL, s003

description:
Library name: 104898-001-003
104898-001-003


title: 007i SYN + WNTi

status: Public on Dec 24 2024

city: Los Angeles

first: Dmitriy

last: Sheyn

address: 127 S. San Vicente Blvd

institute: Cedars-Sinai Medical Center

description:
Library name: 007i
007i

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20.  Cell Ranger (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the human reference genome GRCh38. Cell Ranger versions v6.0.0 was used for A-E  and v7.0.0 for 83i and 007i.
Assembly: GRCh38_2020_A
Supplementary files format and content: tsv and mtx files

extract_protocol:
Single cell suspensions were stained with Trypan Blue (Invitrogen, Waltham, CA) to determine cell suspension quality and cell viability.  Cell suspensions were partitioned (5000 cells target capture) into Gel Beads-in-emulsion (GEMs) on the Chromium Connect (10x Genomics, Pleasanton, CA) per the Chromium Automated Single Cell 3’ Reagent Kits User Guide (v3.1).  Reverse transcription, cDNA amplification, and library construction were performed on the Chromium Connect.
Barcoded libraries were quantified by quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific, Waltham, CA) and library size was measured via the 4200 TapeStation (Agilent Technologies, Santa Clara, CA).  Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) with sequencing configuration 28 x 10 x 10 x 90 bp, and a sequencing depth of 36,000 reads/cell.

tag: cell line

value: iPSC


title: 83i SYN + WNTi

description:
Library name: 83i
83i


title: 007i SYN

description:
Library name: E
E


title: 007i SM

description:
Library name: C
C


title: RNA-seq of E. coli cells, 30 min post-shift to 10°C, control

status: Public on Dec 14 2024

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

description: Library name: RNA-seq_cold-shock_30min_noDMS

data_processing:
Following sequencing, reads were clipped of sequencing adapters using Cutadapt v4.4 (parameters: -a AGATCGGAAG -m 100 -O 1). Reads were then mapped to a reference containing all E. coli genes using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local --nofw" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed to calculate gene TPMs.
processed data files format and content: TSV table of TPMs across DMS treated/untreated cells at 2 min and 30 min post-cold shock

molecule: cytoplasmic RNA

organism: Escherichia coli

source_name: bacteria

growth_protocol: E. coli K-12 MG1655 derivative strain DH5α was streaked on LB plates, and a single colony was picked, inoculated in 4 mL LB broth, and grown overnight at 37°C with shaking. The day after, the culture was diluted to an OD600 = 0.05 in 25 mL LB broth and grown at 37°C until OD600 ≈ 0.5 (~2 h). For cold-shock, 2 mL of this culture were mixed with 2 mL of LB broth pre-chilled to 0°C in a water-ice slurry, then incubated at 10°C.

extract_protocol:
Cell pellets were resuspended in 62.5 μl Resuspension Buffer [20 mM Tris-HCl pH 8.0; 80 mM NaCl; 10 mM EDTA pH 8.0], supplemented with 100 μg/mL final Lysozyme (cat. L6876, Merck) and 20 U SUPERase•In™ RNase Inhibitor (cat. A2696, ThermoFisher Scientific), by vigorous vortexing. Samples were incubated at room temperature for 1 min, followed by addition of 62.5 μl Lysis Buffer [0.5% Tween-20; 0.4% Sodium deoxycholate; 2 M NaCl; 10 mM EDTA]. Samples were then inverted 5-10 times and incubated at room temperature for 2 min, followed by additional 2 min on ice. 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific) was then added, samples were vigorously vortexed for 15 sec, and RNA was extracted as per manufacturer instructions.
Prior to library preparation, highly abundant short RNA species, such as tRNAs, were depleted on Monarch® RNA Cleanup columns by loading a 1:1:1 mixture of total RNA in nuclease-free water, RNA binding buffer and 100% ethanol. rRNA depletion was performed on 1.1 μg total RNA using the RiboCop for Bacteria kit (cat. 126, Lexogen), with two minor changes to the manufacturer’s protocol: denaturation temperature was increased to 95°C, and probe annealing temperature was lowered to 55°C. Following rRNA depletion, RNA was cleaned up on Monarch® RNA Cleanup columns, eluted in 8 μl nuclease-free water, and supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50) and 25 ng/μl Actinomycin D (to increase strand-specificity; cat. A1410, Merck), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: Dimethyl sulfate (DMS; cat. D186309, Merck) from a fresh 1:4 dilution in ethanol (~2.64 M) was added to the bacteria at a final concentration of 200 mM. Probing was conducted for 2 min or 30 min at 10°C. eactions were then quenched by addition of 1 volume 1 M DTT. For in cell treatments, bacteria were collected by centrifugation at 17,000g for 1 min. Supernatant was discarded, the pellet was washed twice with 0.5 M DTT, and then immediately subjected to RNA extraction.

value: bacteria

tag: strain


title: 007i SCL

description:
Library name: D
D


title: 007i PS

description:
Library name: B
B


title: RNA-seq of E. coli cells, 2 min post-shift to 10°C, DMS-modified

description: Library name: RNA-seq_cold-shock_2min_DMS


title: 007i iPSC

description:
Library name: A
A


title: RNA-seq of E. coli cells, 30 min post-shift to 10°C, DMS-modified

description: Library name: RNA-seq_cold-shock_30min_DMS


title: DMS-MaPseq of lpxP mutant (37°C)

description: Library name: lpxP_mutant

data_processing:
Following sequencing, reads were clipped of sequencing adapters using Cutadapt v4.4 (parameters: -a AGATCGGAAG -m 100 -O 1). Reads were then mapped to a reference containing the sequence of the lpxP mutant using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local --nofw" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt of a transcript, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -wl 2000 -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1 -mpr 2).
processed data files format and content: Wiggle files of bulk normalized DMS-MaPseq mutation frequencies

growth_protocol: T7 template of mutant lpxP, including both 5′ UTR and CDS, was generated by PCR from DH5α gDNA using Q5® High-Fidelity 2X Master Mix (cat. M0492L, New England Biolabs). In vitro transcription reaction was performed using the HiScribe® T7 High Yield RNA Synthesis Kit (cat. E2040L, New England Biolabs) in 20 μl, using 1 μg of template. Reaction was incubated for 4 h at 37°C.

extract_protocol:
RNA was cleaned up on Monarch® RNA Cleanup column as per manufacturer instructions. Template DNA was then removed by digestion with TURBO DNase I (cat. AM2239, ThermoFisher Scientific) at 37°C for 30 min, and RNA sample wAS again cleaned up on Monarch® RNA Cleanup column.
8 μl RNA, supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: RNA was probed by directly adding 200 mM final DMS to the IVT reaction and incubating at 37°C for 2 min, or at 10°C for 30 min. Reaction were then quenched by addition of 1 volume 1 M DTT


title: RNA-seq of E. coli cells, 2 min post-shift to 10°C, control

description: Library name: RNA-seq_cold-shock_2min_noDMS


title: ERD, RL_NAWM, s012

description:
Library name: 104898-001-012
104898-001-012


title: DMS-MaPseq of in vitro transcribed RNA for candidate thermometers (37°C), replicate 1

description: Library name: Thermometers_IVT_37C_rep1

data_processing:
Following sequencing, reads were clipped of sequencing adapters using Cutadapt v4.4 (parameters: -a AGATCGGAAG -m 100 -O 1). Reads were then mapped to a reference containing the analyzed thermometers using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local --nofw" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt of a transcript, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -wl 2000 -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1 -mpr 2).
processed data files format and content: Wiggle files of bulk normalized DMS-MaPseq mutation frequencies

growth_protocol: T7 templates of cspB, cspG, cspI, cpxP and lpxP, including both 5′ UTR and CDS, were generated by PCR from DH5α gDNA using Q5® High-Fidelity 2X Master Mix (cat. M0492L, New England Biolabs). In vitro transcription reactions were performed using the HiScribe® T7 High Yield RNA Synthesis Kit (cat. E2040L, New England Biolabs) in 20 μl, using 1 μg of an equimolar pool of all templates. Reactions were incubated for 4 h at either 37°C or 10°C.

extract_protocol:
RNA was cleaned up on Monarch® RNA Cleanup columns as per manufacturer instructions. Template DNA was then removed by digestion with TURBO DNase I (cat. AM2239, ThermoFisher Scientific) at 37°C for 30 min, and RNA samples were again cleaned up on Monarch® RNA Cleanup columns.
8 μl RNA, supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: RNA was probed by directly adding 200 mM final DMS to the IVT reactions and incubating at 37°C for 2 min, or at 10°C for 30 min. Reactions were then quenched by addition of 1 volume 1 M DTT


title: ERD, RL_NAWM, s013

description:
Library name: 104898-001-013
104898-001-013


title: DMS-MaPseq of in vitro transcribed RNA for candidate thermometers (10°C), replicate 1

description: Library name: Thermometers_IVT_10C_rep1


title: ERD, RL_NAWM, s011

description:
Library name: 104898-001-011
104898-001-011


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 4

status: Public on Nov 25 2024

first: James

middle: L

last: Warner

state: MA

address: 77 Avenue Louis Pasteur, Room 358

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to the S.cerevisiae and S. pombe genomes using Bowtie2 (Langmead and Salzburg 2012) and sorted using samtools (Danecek et al. 2021).
Spike-in normalization factors were calculated using a custom python script (https://github.com/winston-lab/warner_chip_seq) using the number of reads mapping to the S. pombe genome.
Spike-in normalized coverage tracks were generated using deeptools bamCoverage (Ramirez et al 2016).
ChIP enrichment over input samples for ratio coverage tracks was calculated using deeptools bigwigCompare (Ramirez et al 2016).
Assembly: S. cerevisiae R64.2.1/sacCer3
Supplementary files format and content: Spike-in normalized coverage tracks generated using deeptools (Ramirez et al 2016) are provided in BIGWIG format (files ending _si.bw).
Supplementary files format and content: ChIP enrichment over input coverage tracks are provided in BIGWIG format (files ending _ratio.bw).

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in SC-Trp at 30°C wth shaking to an OD600 of ≈ 0.6 prior to treament.

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. Quenching, cell lysis, and chromatin extraction were performed as previously described (Gopalakrishnan et al 2019). Chromatin was sonicated using a Covaris E220e sonicator for 450 seconds per sample with a peak power of 140, a duty factor of 5, and 200 cycles per burst. Sonication was confirmed by agarose gel electrophoresis. Each chromatin sample was mixed with 10% S. pombe chromatin (strain FWP570) by protein mass for spike-in normalization.
Libraries were constructed using the NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) following manufacturer specifications.

treatment_protocol: Cultures were diluted in SC-Trp to OD600 = 0.3 and treated with either DMSO (final concentration 0.05% v/v) or 3-indoleacetic acid (IAA, final concentration 25 μM) for 90 minutes at 30°C with shaking.

tag: plasmid

tag: chip antibody

value: a-Rpb1 8WG16 (EMD Millipore 05-952-I)

tag: genotype

value: spt6delta2-238-3xFLAG, SPT6-V5-AID

value: 3-indoleacetic acid


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 2


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 4

value: DMSO


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA, rep 3

value: SPT6-3xFLAG, SPT6-V5-AID


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA, rep 2


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA, rep 4


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 4


title: DMS-MaPseq of in vitro transcribed RNA for candidate thermometers (10°C), replicate 2

description: Library name: Thermometers_IVT_10C_rep2


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 2


title: DMS-MaPseq of in vitro transcribed RNA for candidate thermometers (37°C), replicate 2

description: Library name: Thermometers_IVT_37C_rep2


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 2

value: a-V5 (Invitrogen 46-0705)


title: V5 ChIP-seq, ChIP DNA: wild-type, IAA, rep 4


title: V5 ChIP-seq, ChIP DNA: wild-type, IAA, rep 3


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 3


title: ERD, RL, s002

description:
Library name: 104898-001-002
104898-001-002

value: Multiple Sclerosis

value: female


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 4


title: V5 ChIP-seq, ChIP DNA: wild-type, IAA, rep 2


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 3


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 3


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 2


title: V5 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 4


title: V5 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 2


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 3

value: a-FLAG M2 (Sigma F3165)


title: V5 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 3


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 3


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 3


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 4


title: Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 2


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 2


title: Flag ChIP-seq, ChIP DNA: wild-type, IAA, rep 4


title: Flag ChIP-seq, ChIP DNA: wild-type, IAA, rep 3


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 2


title: Rpb1 ChIP-seq, ChIP DNA: wild-type, DMSO, rep 3


title: V5 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA, rep 4


title: Flag ChIP-seq, ChIP DNA: wild-type, DMSO, rep 4


title: Flag ChIP-seq, ChIP DNA: wild-type, DMSO, rep 3


title: ChIP-seq input DNA: spt6Δ2-238, IAA, rep 4


title: ChIP-seq input DNA: spt6Δ2-238, IAA, rep 2


title: ChIP-seq input DNA: spt6Δ2-238, IAA, rep 3


title: ChIP-seq input DNA: spt6Δ2-238, DMSO, rep 4


title: ChIP-seq input DNA: spt6Δ2-238, DMSO, rep 2


title: Flag ChIP-seq, ChIP DNA: spt6Δ2-238, DMSO, rep 4


title: ChIP-seq input DNA: spt6Δ2-238, DMSO, rep 3


title: ChIP-seq input DNA: wild-type, IAA, rep 4


title: ChIP-seq input DNA: wild-type, DMSO, rep 3


title: ChIP-seq input DNA: wild-type, DMSO, rep 2


title: MNase-seq: spt6Δ2-238, pob3-E154K, IAA, rep 2

data_processing:
Reads were aligned to the S.cerevisiae and S. pombe genomes using Bowtie2 (Langmead and Salzburg 2012) and sorted using samtools (Danecek et al. 2021).
Spike-in normalization factors were calculated using a custom python script (https://github.com/winston-lab/warner_mnase_seq) using the number of reads mapping to the S. pombe genome.
Spike-in normalized nucleosome dyad postion coverage tracks were generated using deeptools bamCoverage (Ramirez et al 2016) and the '--MNase' optional argument.
Assembly: S. cerevisiae R64.2.1/sacCer3
Supplementary files format and content: Spike-in normalized coverage tracks generated using deeptools (Ramirez et al 2016) are provided in BIGWIG format (files ending .bw).

extract_protocol:
Cell pellets were processed for MNase digestion as described in (McKnight et al 2021). Briefly, cells were fixed with 1% formaldehyde for 15 minutes and quenched with glycine. Cells were spheroplasted using Zymolyase 100T until >90% of the cells were spheroplasts as assessed by microscopy. Micrococcal nuclease and Exonucelase III were added to each sample and the reactions were incubated at 37°C for exactly 15 minutes. Digestion was halted by the addition of EDTA and EGTA. Each sample was mixed mith S. pombe mononucleosomal DNA (strain FWP570) at a ratio of 1 ng S. pobe DNA / 1.5 x 10^7 S. cerevisiae cells. Mononucleosomal DNA was isolated and used to construct libraries.
Libraries were constructed using the NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) following manufacturer specifications.


title: ChIP-seq input DNA: wild-type, DMSO, rep 4


title: MNase-seq: spt6Δ2-238, pob3-E154K, DMSO, rep 3


title: MNase-seq: spt6Δ2-238, pob3-E154K, IAA, rep 3


title: MNase-seq: spt6Δ2-238, pob3-E154K, DMSO, rep 2


title: ChIP-seq input DNA: wild-type, IAA, rep 2


title: MNase-seq: spt6Δ2-238, pob3-E154K, IAA, rep 1


title: MNase-seq: wild-type, pob3-E154K, IAA, rep 2

value: SPT6-3xFLAG, SPT6-V5-AID, pob3-E154K


title: MNase-seq: wild-type, pob3-E154K, IAA, rep 3


title: MNase-seq: wild-type, pob3-E154K, IAA, rep 1


title: MNase-seq: wild-type, pob3-E154K, DMSO, rep 3


title: MNase-seq: spt6Δ2-238, pob3-E154K, DMSO, rep 1


title: MNase-seq: empty vector, pob3-E154K, IAA, rep 3

value: empty vector, SPT6-V5-AID, pob3-E154K


title: MNase-seq: wild-type, pob3-E154K, DMSO, rep 1


title: Flag ChIP-seq, ChIP DNA: wild-type, DMSO, rep 2


title: MNase-seq: empty vector, pob3-E154K, IAA, rep 1


title: MNase-seq: empty vector, pob3-E154K, IAA, rep 2


title: ChIP-seq input DNA: wild-type, IAA, rep 3


title: MNase-seq: empty vector, pob3-E154K, DMSO, rep 3


title: MNase-seq: spt6Δ2-238, IAA, rep 3


title: MNase-seq: empty vector, pob3-E154K, DMSO, rep 2


title: MNase-seq: spt6Δ2-238, IAA, rep 1


title: MNase-seq: spt6Δ2-238, DMSO, rep 3


title: MNase-seq: spt6Δ2-238, DMSO, rep 2


title: Flag ChIP-seq, ChIP DNA: wild-type, IAA, rep 2


title: MNase-seq: empty vector, pob3-E154K, DMSO, rep 1


title: MNase-seq: wild-type, pob3-E154K, DMSO, rep 2


title: MNase-seq: empty vector, IAA, rep 3

value: empty vector, SPT6-V5-AID, POB3


title: MNase-seq: spt6Δ2-238, DMSO, rep 1