title: Photoreceptor nuclei, dsRNA targets at Set1, ZT20, rep3

value: Male


status: Public on Jan 27 2026

type: SRA

city: Shanghai

first: Li

last: Zhixue

address: 320 Yueyang Road, Xuhui District

country: China

institute: CAS Center for Excellence in Molecular Cell Science

description: Library name: uSpyCLIP-seq of PTBP1 with 10,000,000 cells, rep2

library_source: transcriptomic

data_processing:
Reads were trimmed using Trim-Galore (v.0.0.6) and the 10-nucleotides unique molecular identifier (UMI) at the 5′end of the reads were removed and used as the read identity for further deduplication.
The remaining reads were mapped to the human genome (v.hg38) using the STAR program (v.2.7.9a)53 with the parameter (--twopassMode Basic --outFilterMultimapNmax 1 –alignEndsType Extend5pofRead1).
PCR duplicates were collapsed into a single read using the de-duplication function of umitools (v.1.0.1)
The remaining usable reads were used for identification of clusters using the iCount program with 7-nt clustering window (v2.0.0).
Assembly: hg38
Supplementary files format and content: bed

molecule: total RNA

organism: Homo sapiens

source_name: Human embryonic kidney

growth_protocol: RBP-expressing Lenti-X 293T stable cell lines were maintained in DMEM supplemented with 10% Fetal Bovine Serum at 37℃ with 5% CO2.

extract_protocol:
The crosslinked cell pellets were resuspended with lysis buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, 1×Protease Inhibitor Cocktail) using 1 ml per 10 million cells and lysed on ice for 10 min. RNA was rationally fragmented using RNase I.
uSpyCLIP libraries were constructed using the uSpyCLIP method developed in-house

treatment_protocol: RBP-expressing Lenti-X 293T cells were rinsed with ice-cold PBS and irradiated on ice with UV-C light at 400 mJ/cm2 in a UV Crosslinker

tag: tissue

value: Human embryonic kidney

tag: cell line

tag: cell type

value: Epithelial cell


title: cll_7, IBR, timepoint 1, bcr library

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

country: USA

institute: Ohio State University

description:
Library name: cll_7_baseline_bcr
10X Genomics

data_processing:
Cell barcode/gene matrices, TCRA/TCRB, and IGH/IGL CDR3 cell clonotypes were generated using CellRanger v3.1.0.
Assembly: GRCh38
Supplementary files format and content: cellular barcodes:  tab separated values; feature ids:  tab separated values; count matrices:  sparse matrix format

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
PBMC were collected by density gradient centrifugation and cryopreserved.  Samples were thawed, counted and immediately processed for single cell capture using the 10X Genomics immune profiling platform.
Gene expression, TCR, and BCR libraries were made according to the manufacturer's instructions.

treatment_protocol: All patients were treated with ibrutinib

value: peripheral blood

tag: patient

tag: patient type

value: IBR

tag: timepoint

tag: library type

value: bcr


title: KD1

city: Guangzhou

first: Yiming

last: Zhu

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
FastQC (v0.11.9) package was used to check the quality of raw data, and the Trim-Galore (v0.6.7) for trimming the adapter sequence and filter reads with low quality.
Paired-end sequencing reads were aligned to the mouse genome (GRCm38.primary_assembly.genome) using Spliced Transcripts Alignment to a Reference (STAR) 2.7.10a.
Package featureCounts v.2.0.1 was used to count the read numbers mapped of each gene.
Assembly: mouse genome(GRCm38.primary_assembly.genome)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Total RNA from 10,000 sorted PCs was extracted using the EZ-press RNA Purification Kit PLUS (EZB, B0004-PLUS-S).
Reverse transcription, PCR preamplification, and purification of PCR products were conducted using the Discover-sc WTA Kit V2 (Vazyme Biotech). The RNA-seq library was generated by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) using 10 ng amplified cDNAs as input following the manufacturer's protocols.

treatment_protocol: Mice were provided with regular diet or ketoenic diet for three weeks, respectively. Then 10,000 plasma cells(CD138high CD267high) in bone marrow of these mice were sorted using BD FACSAria Ⅲ.

value: Bone marrow

value: not applicable

value: Plasma cells

tag: stain

tag: treatment

value: ketogenic diet


title: uSpyCLIP-seq SpyCatcher1.0, 20ug

description: Library name: uSpyCLIP-seq SpyCatcher1.0, 20ug


title: cll_7, IBR, timepoint 1, gex library

description:
Library name: cll_7_baseline_gex
10X Genomics

library_source: transcriptomic single cell

value: gex


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT12, rep1

city: WEST LAFAYETTE

first: Weake

middle: Marie

last: Vikki

state: IN

address: 175 S University st

department: Biochemistry

institute: Purdue University

data_processing:
Raw fq.gz files are acquired from Novogene. The first 5bp from the 5' end of the forward read is cut using Cutadapt version 3.7 as suggested by Ovation SoLo RNAseq system kit. Trimmomatic version 0.39 is used to trim the paired-end reads with the following condition: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Trimmed reads are aligned to Drosophila melanogaster genome dm6 by hisat2 version 2.2.1 with the following seeting --rna-strandness FR. Samtools version 1.17 is used to convert sam files to bam files, and to sort, index bam files.
FeatureCounts function in Subread version 2.0.1 is used to count mapped reads using the following setting: -p -t exon ig gene_id
Assembly: dm6
Supplementary files format and content: Processed data files are txt files that contain quantification results of mapped reads for genes using featureCounts. Drosophila_melanogaster.BDGP6.46.111.gtf from Ensembl is used as a reference.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Photoreceptor cells

growth_protocol: Flies are raised in 12 hour light and 12 hour dark, 25 °C, 80% humidity incubators to Day 10 post-eclosion.

extract_protocol:
400 flies are decapitated by vortexing after being flash frozen in liquid nitrogen. Fly heads are separated using pre-chilled sieves of different sizes. The fly heads are then homogenized using glass homogenizer and the homogenate (cell debris and intact nuclei) are incubated with Anti-GFP-attached beads to enrich GFP-tagged photoreceptor nuclei.
Photoreceptor nuclear RNA are extracted using ZYMO Direct-zol RNA Microprep Kits (#R2061). cRNA library is prepared using Ovation® SoLo RNA-Seq System (#0502-32) that has Drosophila ribosomal RNA depletion built into the protocol.

treatment_protocol: KD F1 flies are generated by crossing Rh1-Gal4 flies and UAS-RNAi flies.

value: Photoreceptor cells

tag: genotype

value: Trr KD

tag: time

tag: Sex


title: AdLib2

treatment_protocol: Mice were subjected to a prolonged fasting treatment (72 hours)  or had free access to food, respectively. Then 10,000 plasma cells (CD138high CD267high) in bone marrow of these mice were sorted using BD FACSAria Ⅲ.

value: Ad Lib


title: cll_7, IBR, timepoint 2, tcr library

description:
Library name: cll_7_btk_clone_tcr
10X Genomics

value: tcr


title: Fasted1

value: Fasting


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT20, rep2

value: Set1 KD


description: Library name: uSpyCLIP-seq of PTBP1 with 100,000 cells, rep2


title: cll_6, IBR, timepoint 3, tcr library

description:
Library name: cll_6_relapse_tcr
10X Genomics


title: HSkM cells, wt, siDMD/UTRN, biol rep 2

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description:
Library name: HSkM D12 wt siDMD/UTRN_rep 2
Column name in All_samples_raw_counts.csv; HSkM-siDU-2_htseq

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parametr quality q 25, minimal read lenght m 20)
Trimmed sequence reads were mapped to GRCh38.p14 using Hisat2 (–rna-strandness FR)
Read count extraction and normalization were performed using Htseq
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HSkM

growth_protocol: HeLa cells were maintained in DMEM supplement with 10% fetal bovine serum (FBS) and 1% antibiotics. HSkM cells were maintained in Nutrient Mixture F-10 Ham medium supplement with 20% fetal bovine serum (FBS), 10 ug/ul epidermal growth factor (EGF), 1 mg/ul dexamethasone, and 1% antibiotics. Differentiation of HSkM cells were maintained in DMEM-HA with 2% horse serum and 1% antibiotics. All cells were grown at 37 °C in a humidified incubator containing 5% CO2

extract_protocol:
RNA was extracted using the Total RNA Zol-Out™ (A&A Biotechnology) kit and RNA Clean & Concentrator™-5 with DNase I (ZYMO Research). 1000 ng/ul of total RNA was used for rRNA depletion. 2 ng/ul depleted RNA was used for the construcion of sequencing librabies.
RNA libraries for RNA-seq were prepared using RiboCop rRNA Depletion Kit V2 (Lexogen) and RNA-Seq V2 Library Prep Kit with UDIs (Lexogen) following the Long Insert Sizes (RTL) manufacturer's protocols.

treatment_protocol:
The DMD ko cell line was derived from HeLa cells. Lipofectamine CRISPRMAX Cas9 Transfection Reagent (Thermo Fisher) was used to transfect the cells with TrueGuide sgRNA (Thermo Fisher) and TrueCut Cas9 Protein v2 (Thermo Fisher). HeLa cells were transfected with UTRN siRNA using Silence Select siRNA (Thermo Fisher) and Lipofectamine RNAiMAX Transfection Reagent, following the manufacturer's protocol. The final concentration of each siRNA was 25 nM. In the case of double siRNA transfection, the final concentration of the negative control siRNA was 50 nM. For differentiation, siRNA was added simultaneously with the induction of differentiation.
HSkM cells were transfected with DMD and UTRN siRNA using Silence Select siRNA (Thermo Fisher) and Lipofectamine RNAiMAX Transfection Reagent, following the manufacturer's protocol. The final concentration of each siRNA was 25 nM. In the case of double siRNA transfection, the final concentration of the negative control siRNA was 50 nM.

value: HSkM

value: human skeletal myoblasts

value: wild-type

value: differentiation, siDMD/UTRN

value: Day 12


title: cll_7, IBR, timepoint 2, bcr library

description:
Library name: cll_7_btk_clone_bcr
10X Genomics

value: peripheral blood

value: IBR

value: bcr


title: HSkM cells, wt, siCtrl, biol rep 3

description:
Library name: HSkM D12 wt siCtrl_rep 3
Column name in All_samples_raw_counts.csv; HSkM-si-3_htseq

value: differentiation, siCtrl


title: cll_6, IBR, timepoint 1, tcr library

description:
Library name: cll_6_baseline_tcr
10X Genomics


title: PT Sample 4

type: genomic

city: Palma

first: Diego

middle: M.

last: Marzese

state: Balearic Islands

address: Carretera de Valldemossa 79

department: Department of Cancer Epigenetics

country: Spain

institute: IdISBa

description: DNA from cell line-derived xenografts FFPE tissue

hyb_protocol: DNAm patterns from our XEN models were assessed using the Infinium Methylation EPIC v2.0 array. Bisulfite conversion, amplification, and hybridization on the beadchip were performed by Diagenode Inc. following the manufacturer’s protocol.

scan_protocol: The array was scanned with the iScan system from Illumina according to the manufacturer's guidelines.

data_processing:
Data import, quality control, and normalization were performed using the R package ChAMP (v2.36.0). Beta-Mixture Quantile (BMIQ) normalization was applied, and batch effects were tested and corrected using the ‘champ.runCombat’ function. Probes with a detection P-value above 0.01 were excluded. Probes targeting non-CG dinucleotides, single-nucleotide polymorphisms, and chromosome Y were also removed, with a total of 868,873 CpG sites analyzed for downstream analyses.
Normalized Beta-values PT, LU and LN.txt; Beta-values, corrected for batch effects arising from different sample origins and technical variations across arrays, were used to quantify DNA methylation levels at each CpG site.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Primary tumor

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from 8 μm tissue sections. Tumor and metastatic regions were microdissected with a needle, avoiding mouse tissue contamination. DNA was isolated using Quick-DNA FFPE Kit (ZYMO Research Cat. No: D3067) according to the manufacturer´s instructions. DNA concentration and purity were determined by Qubit 3.0 (Q33216; Thermo Fisher Scientific, CA) fluorometric quantification.

tag: animal

value: Primary tumor

tag: tissue type


title: AdLib1

value: Bone marrow

value: Plasma cells


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT16, rep3

value: Photoreceptor cells

value: Male


description: Library name: uSpyCLIP-seq of PTBP1 with 100,000 cells, rep1

value: Human embryonic kidney

value: Epithelial cell


title: LU Sample 3

source_name: Lung

value: Lung

value: cell line-derived xenografts FFPE tissue


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT16, rep1

value: Set1 KD


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT4, rep2


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT4, rep3


title: LN Sample 4

source_name: Lymph node

value: Lymph node


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT8, rep1


title: HeLa cells, DMD ko, siUTRN, biol rep 3

description:
Library name: HeLa DMDko siUTRN_rep 3
Column name in All_samples_raw_counts.csv; HeLa-KO-siU3_htseq

source_name: HeLa

value: HeLa

value: human epithelial carcinoma cells

value: DMD knock-out

value: proliferating, siUTRN

value: Day 0


description: Library name: uSpyCLIP-seq of PTBP1 with 10,000,000 cells, rep1


title: HeLa cells, DMD ko, siUTRN, biol rep 2

description:
Library name: HeLa DMDko siUTRN_rep 2
Column name in All_samples_raw_counts.csv; HeLa-KO-siU2_htseq


title: AdLib3

value: Ad Lib


title: cll_5, IBR, timepoint 3, tcr library

description:
Library name: cll_5_relapse_tcr
10X Genomics

value: peripheral blood

value: IBR

value: tcr


title: KD3

value: Bone marrow

value: not applicable

value: Plasma cells

value: ketogenic diet


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT20, rep1

value: Photoreceptor cells

value: Male


title: cll_6, IBR, timepoint 3, bcr library

description:
Library name: cll_6_relapse_bcr
10X Genomics

value: bcr


title: Control2

value: regular diet


title: HSkM cells, wt, siDMD/UTRN, biol rep 3

description:
Library name: HSkM D12 wt siDMD/UTRN_rep 3
Column name in All_samples_raw_counts.csv; HSkM-siDU-2_htseq

value: HSkM

value: human skeletal myoblasts

value: wild-type

value: differentiation, siDMD/UTRN

value: Day 12


title: HeLa cells, DMD ko, siUTRN, biol rep 1

description:
Library name: HeLa DMDko siUTRN_rep 1
Column name in All_samples_raw_counts.csv; HeLa-KO-siU1_htseq

value: HeLa

value: human epithelial carcinoma cells

value: DMD knock-out

value: proliferating, siUTRN

value: Day 0


title: Control3

value: Bone marrow

value: not applicable


title: cll_5, IBR, timepoint 3, bcr library

description:
Library name: cll_5_relapse_bcr
10X Genomics

value: peripheral blood

value: IBR


title: cll_5, IBR, timepoint 3, gex library

description:
Library name: cll_5_relapse_gex
10X Genomics

value: gex


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT0, rep2

value: Photoreceptor cells

value: Set1 KD

value: Male


title: HeLa cells, wt, siCtrl, biol rep 3

description:
Library name: HeLa wt siCtrl_rep 3
Column name in All_samples_raw_counts.csv; HeLa-WT-si-3_htseq

value: proliferating, siCtrl


title: LN Sample 2

value: Lymph node

value: cell line-derived xenografts FFPE tissue


title: Control1

value: Plasma cells

value: regular diet


title: cll_6, IBR, timepoint 3, gex library

description:
Library name: cll_6_relapse_gex
10X Genomics


title: cll_5, IBR, timepoint 2, tcr library

description:
Library name: cll_5_btk_clone_tcr
10X Genomics

value: tcr


title: HSkM cells, wt, siDMD/UTRN, biol rep 1

description:
Library name: HSkM D12 wt siDMD/UTRN_rep 1
Column name in All_samples_raw_counts.csv; HSkM-siDU-1_htseq

value: HSkM

value: human skeletal myoblasts

value: wild-type

value: differentiation, siDMD/UTRN

value: Day 12


title: LN Sample 1


title: HeLa cells, wt, siCtrl, biol rep 2

description:
Library name: HeLa wt siCtrl_rep 2
Column name in All_samples_raw_counts.csv; HeLa-WT-si-2_htseq

value: HeLa

value: human epithelial carcinoma cells

value: Day 0


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT0, rep1

value: Photoreceptor cells


title: HeLa cells, wt, siCtrl, biol rep 1

description:
Library name: HeLa wt siCtrl_rep 1
Column name in All_samples_raw_counts.csv; HeLa-WT-si-1_htseq


title: cll_6, IBR, timepoint 1, gex library

description:
Library name: cll_6_baseline_gex
10X Genomics

value: peripheral blood

value: IBR

value: gex


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT16, rep2

value: Set1 KD

value: Male


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT12, rep2


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT12, rep1


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT12, rep3


title: HSkM cells, wt, siCtrl, biol rep 2

description:
Library name: HSkM D12 wt siCtrl_rep 2
Column name in All_samples_raw_counts.csv; HSkM-si-2_htseq

value: differentiation, siCtrl


title: cll_5, IBR, timepoint 2, gex library

description:
Library name: cll_5_btk_clone_gex
10X Genomics


title: ligament, acl, acl22f

city: San Francisco

first: Brian

middle: T

last: Feeley

state: CA

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

description:
Library name: acl22f
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: integrated metadata and matrix files

source_name: ligament

extract_protocol:
ACL samples were obtained during ACL reconstruction. All samples were transferred from the operating room on ice and stored in 30% FBS (fetal bovine serum, Gibco, #10437028) in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, #11965084) until processing. Samples were then mechanically and enzymatically digested in 1 mg/ml collagenase III (Worthington Biochemical Corporation, #NC0021929) in DMEM with 10% FBS and 1% Penicillin/Streptomycin (Gibco, #15140122) at 37°C for 70 minutes with intermittent manual needle trituration with an 18-gauge needle. Digests were washed with PBS (Gibco, #10010023) and further digested with 0.25% trypsin-EDTA (Gibco, #25200056) at 37°C for 12–15 min. Suspensions were passed through 40 µm nylon mesh (Corning, #431750), erythrocytes were lysed with ACK lysing buffer (Quality Biological, #188-156-101) for 5–7 minutes on ice and washed in PBS with 2% FBS. Cells were then resuspended in 100 µl flow cytometry buffer (PBS with 2% FBS, 5 mM EDTA (Corning, #MT-46034CI), 2 mM HEPES (Quality Biological, #118-089-721)) per 1 gram of starting tissue weight. Cells were then frozen in 10% Dimethyl sulfoxide (DMSO, Sigma Aldrich, #276855) in FBS (fetal bovine serum, Gibco, #10437028) before flow cytometry and single cell sequencing. Cells were thawed, washed, and resuspended in flow cytometry buffer with 1:1000 SYTOX Blue (ThermoFisher, #S34857). Cells were resuspended in 0.04% BSA in PBS at 1000 cells per μl to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: ligament

tag: location

value: anterior cruciate ligament

value: All Live Cells


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT8, rep2

value: mCherry KD


title: LU Sample 1

description: DNA from cell line-derived xenografts FFPE tissue

value: Lung


title: LU Sample 2

value: cell line-derived xenografts FFPE tissue


title: cll_5, IBR, timepoint 1, tcr library

description:
Library name: cll_5_baseline_tcr
10X Genomics

value: tcr


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT0, rep3


title: ligament, acl, acl23m

description:
Library name: acl23m
10x Genomics


title: PT Sample 1

value: Primary tumor


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT8, rep1


title: ligament, acl, acl26f

description:
Library name: acl26f
10x Genomics


title: cll_6, IBR, timepoint 1, bcr library

description:
Library name: cll_6_baseline_bcr
10X Genomics

value: bcr


title: cll_5, IBR, timepoint 1, gex library

description:
Library name: cll_5_baseline_gex
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT4, rep1


title: HSkM cells, wt, siCtrl, biol rep 1

description:
Library name: HSkM D12 wt siCtrl_rep 1
Column name in All_samples_raw_counts.csv; HSkM-si-1_htseq

value: HSkM

value: human skeletal myoblasts

value: wild-type

value: Day 12


title: ligament, acl, aclfirstfive

description:
Library name: aclfirstfive
10x Genomics


title: ligament, acl, acl30f

description:
Library name: acl30f
10x Genomics


title: LN Sample 3


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT4, rep2

value: Photoreceptor cells


title: PT Sample 3


title: cll_5, IBR, timepoint 1, bcr library

description:
Library name: cll_5_baseline_bcr
10X Genomics

value: peripheral blood

value: IBR


title: cll_4, IBS, timepoint 2, tcr library

description:
Library name: cll_4_3yrs_tcr
10X Genomics

value: IBS


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT8, rep3

value: Male


title: PT Sample 2


title: cll_5, IBR, timepoint 2, bcr library

description:
Library name: cll_5_btk_clone_bcr
10X Genomics


title: BA9,Non-deletion Batch

city: Parkville

first: Shokouh

last: Shahrokhi Sabzevar

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

description: Nuclei from four non-deletion PWS tissue samples were pooled in non-deletion batch

data_processing:
Sequenced reads were processed, aligned to the human genome (GRCh38-3.0.0), counted, and filtered using Cell Ranger (v6.0.2). Soupx was used for ambient RNA removal. Samples in each pool were demultiplexed using Demuxafy and a combination of four built-in methods including Demuxlet, Vireo, Souporcell, and SCDS.
Assembly: GRCh38-3.0.0
Supplementary files format and content: filtered counts of sequencing reads

source_name: Dorsolateral Prefrontal cortex (Brodmann area 9), left hemisphere

extract_protocol:
Dissected PFC tissue was incubated in 2.5 ml lysis buffer [10 mM Tris-HCl (PH:8), 3 mM MgCl2, 10 mM NaCl, Nonidet P40, and 0.2 U/ul RNase inhibitor]. 2.5 ml of ice-cold 1x dPBS was then added to the lysis buffer, and the tissue was homogenized and filtered through a 30 µm strainer and spun at 2000 x g for 5 minutes at 4˚C. nuclei pellet resuspended in 400 µl of staining buffer (1x dPBS, 1% UltraPure BSA, 0.2 U/ul RNase inhibitor, and 1:10,000 DAPI), and sorted using FACS. The sorted samples were centrifuged at 500 x g for 15 minutes at 4˚C and the nuclei pellet was resuspended in 50 ul of nuclei EZ storage buffer.
Libraries were made according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol.
10x Chromium single nuclei RNA-seq


title: WT,D40,ZT12,IgG,rep3

description:
PE150
MM_039

library_source: genomic

data_processing:
We obatined at least 7 million reads for each CUT&RUN library. Data was trimmed using trimmomatic for paired-end reads, and aligned to the D. melanogaster genome (BDGP6.46) using bowtie2 with the --very-sensitive and --dovetail arguments. SAM files were processed using SAMtools to generate sorted BAM files. CPM-normalized bigWig files were generated using deepTools.
Assembly: BDGP6.46
Supplementary files format and content: CPM normalized bigWig files were provided for each of the CUT&RUN library.
Library strategy: CUT&RUN

source_name: Outer photoreceptor cells

growth_protocol: Drosophila were maintained on standard fly food at 25°C under 12-h:12-h light:dark conditions. Male flies were collected at indicated age (days post-eclosion, D) ± 1 day and ZT12 ± 15 minutes.

extract_protocol:
Rh1-Gal4>UAS-GFPKASH flies that express GFP on the photoreceptor nuclei membrane were used in this study. Photoreceptor nuclei were immuno-enriched (NIE) by anti-GFP coated magnetic beads (Jauregui-Lozano et al., 2021). CUT&RUN was performed on bead-bound photoreceptor nuclei as described in (Meers et al., 2019).  Detailed protocols for NIE-based CUT&RUN are available: dx.doi.org/10.17504/protocols.io.kxygxp1d4l8j/v2.
CUT&RUN libraries were prepared following the instructions of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit.

treatment_protocol: For D10/D40 CUT&RUN, Rh1-Gal4>UAS-GFPKASH flies were collected on either D10 or D40 in quadruplicates, 400 flies per replicate. Antibodies used are: anti-H3K4me2/3 (Abcam #ab8580), anti-H3K36me3 (Abcam #ab9050), anti-H3K9me3 (Abcam #ab176916) and anti-H3K27me3 (Epicypher #13-0055) and anti-IgG negative control (Epicypher #13-0042). pAG-MNase activation/ cleavage was performed for 20 minutes upon the addition of CaCl2.  Antibodies used are: anti-H3K4me2/3 (Abcam #ab8580), anti-H3K36me3 (Abcam #ab9050), anti-H3K9me3 (Abcam #ab176916) and anti-H3K27me3 (Epicypher #13-0055) and anti-IgG negative control (Epicypher #13-0042). pAG-MNase activation/ cleavage was performed for 20 minutes upon the addition of CaCl2.

value: Outer photoreceptor cells

value: Nuclei


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT20, rep2

value: mCherry KD


title: WT,D40,ZT12,IgG,rep4

description:
PE150
MM_040


title: WT,D40,ZT12,H3K9me3,rep2

description:
PE150
MM_034


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT4, rep3


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT16, rep3


title: ligament, acl, acl29f

description:
Library name: acl29f
10x Genomics

value: ligament

value: anterior cruciate ligament

value: All Live Cells


title: WT,D40,ZT12,H3K9me3,rep3

description:
PE150
MM_035


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT16, rep2


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT20, rep3


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT16, rep1


title: cll_4, IBS, timepoint 1, bcr library

description:
Library name: cll_4_baseline_bcr
10X Genomics


title: ligament, acl, acl26m

description:
Library name: acl26m
10x Genomics


title: cll_4, IBS, timepoint 3, bcr library

description:
Library name: cll_4_5yrs_bcr
10X Genomics


title: cll_4, IBS, timepoint 3, tcr library

description:
Library name: cll_4_5yrs_tcr
10X Genomics

value: tcr


title: WT,D40,ZT12,IgG,rep1

description:
PE150
MM_037


title: WT,D40,ZT12,H3K4me3,rep3

description:
PE150
MM_031


title: WT,D40,ZT12,H3K9me3,rep4

description:
PE150
MM_036


title: cll_4, IBS, timepoint 1, gex library

description:
Library name: cll_4_baseline_gex
10X Genomics

value: gex


title: WT,D40,ZT12,IgG,rep2

description:
PE150
MM_038


title: emf2 H3K4me3 (ChIP) rep2

city: Rehovot

first: Leor

middle: Eshed

last: Eshed Williams

address: P.O.Box 12

department: Faculty of Agriculture

country: Israel

institute: Hebrew university

description: Library name: Sample 14 emf2 Callus H3K4me3 biol rep2

data_processing:
Each NGS analysis included quality control using FastQC
adaptor trimming using cutadapt
NGS reads were mapped to the Arabidopsis thaliana reference transcriptome TAIR10 using Bowtie2
ChIP-Seq alignment accepted only reads that were mapped to one location for better accuracy. Integrative Genomics Viewer (IGV) was used for the visualization of the data (Robinson et al. 2011; Thorvaldsdóttir et al. 2013). Biological replications consistency was measured using spearman correlation of BAM files in deepTools (Ramírez et al. 2016).  ChIP-Seq samples with p>0.88 were merged.
Assembly: TAIR10
Supplementary files format and content: norm10M.bigwig

organism: Arabidopsis

source_name: Callus

growth_protocol: For all experiments, seeds were surface sterilized for 10 minutes in 3% Sodium Hypochlorite containing 0.1% Triton X-100 and washed 4 times with DDW before sowing. seeds were sown on Murashige and Skoog (MS) basal medium 87, and kept under continuous light at 23°C for one week.

extract_protocol:
ChIP-seq was performed according to the protocol described by Kaufmann et al., 2010 (Kaufmann et al., 2010a).
Sequencing was done at the Technion Genome Centre (TGC) according to Illumina's protocols. The TruSeq Nano DNA Library Prep Kit (FC-121) was used for library preparation. ChIP-enriched DNA fragments were size-selected on an agarose gel to isolate fragments approximately 200 bp in size. Indexed adapters, diluted 1:10, were added, and the library was amplified using PCR with 14 cycles (instead of the standard 8 cycles). Groups of 7–10 indexed libraries were loaded onto individual lanes of the Illumina HiSeq 2500 system. All samples were processed using the standard 50 bp single-end sequencing protocol.

treatment_protocol: To generate callus from Col-0 and emf2 cotyledons, sterilized seeds were sown directly on callus-inducing medium (CIM): Gamborg B5 medium with 0.5g/L MES, 2% dextrose, 0.9% phytagel, supplemented with 2.2μM 2,4-dichlorophenoxyacetic acid and 0.46μM kinetin. Following two days at 4°C, plates were transferred to a continuous light growth room at 23°C. After seven days, cotyledons were trimmed and transferred to a new CIM plate placed in the dark. During the next 5-6 weeks, calli were re-cultured to new CIM plates every 7-10 days. All analyses were done on 6-8 weeks-old calli.

value: Callus

tag: chip abs

value: Anti-Histone H3K4me3, Abcam, ab8584


title: cll_4, IBS, timepoint 2, bcr library

description:
Library name: cll_4_3yrs_bcr
10X Genomics

value: bcr


title: cll_4, IBS, timepoint 3, gex library

description:
Library name: cll_4_5yrs_gex
10X Genomics


title: BA9,Deletion Batch

description: Nuclei from four deletion PWS tissue samples were pooled in deletion batch

value: Dorsolateral Prefrontal cortex (Brodmann area 9), left hemisphere


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT12, rep1

value: Photoreceptor cells


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT20, rep1


title: BA9,Control Batch

description: Nuclei from four control tissue samples were pooled in control batch


title: cll_3, IBS, timepoint 3, tcr library

description:
Library name: cll_3_5yrs_tcr
10X Genomics

value: peripheral blood


title: cll_4, IBS, timepoint 2, gex library

description:
Library name: cll_4_3yrs_gex
10X Genomics


title: WT,D40,ZT12,H3K9me3,rep1

description:
PE150
MM_033


title: cll_4, IBS, timepoint 1, tcr library

description:
Library name: cll_4_baseline_tcr
10X Genomics


title: cll_3, IBS, timepoint 3, bcr library

description:
Library name: cll_3_5yrs_bcr
10X Genomics


title: WT,D40,ZT12,H3K4me3,rep4

description:
PE150
MM_032


title: WT H3K27me3 rep2

description: Library name: Sample 17 WT Callus H3K27me3  biol rep2

value: Anti-Histone H3K27me3, Abcam, ab6003


title: WT H3K4me3 (ChIP) rep 3

description: Library name: Sample 12 WT Callus H3K4me3 biol rep3

value: Anti-Histone H3K4me3, Abcam, ab8582


title: emf2 H3K4me3 (ChIP) rep1

description: Library name: Sample 13 emf2 Callus H3K4me3  biol rep1

value: Anti-Histone H3K4me3, Abcam, ab8583


title: WT,D40,ZT12,H3K4me3,rep1

description:
PE150
MM_029

value: Outer photoreceptor cells


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT12, rep3

value: Male


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT0, rep3

value: mCherry KD


title: WT H3K27me3 rep1

description: Library name: Sample 16 WT Callus H3K27me3  biol rep1

value: Anti-Histone H3K27me3, Abcam, ab6002


title: WT H3K4me3 (ChIP) rep2

description: Library name: Sample 11 WT Callus H3K4me3 biol rep2

value: Anti-Histone H3K4me3, Abcam, ab8581


title: WT,D40,ZT12,H3K36me3,rep4

description:
PE150
MM_028

value: Nuclei


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT0, rep2


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT0, rep1


title: cll_3, IBS, timepoint 3, gex library

description:
Library name: cll_3_5yrs_gex
10X Genomics

value: IBS


title: Photoreceptor nuclei, dsRNA targets at mCherry, ZT12, rep2


title: cll_3, IBS, timepoint 2, bcr library

description:
Library name: cll_3_3yrs_bcr
10X Genomics


title: K562 circPCMTD1 Knockdown 3_3

city: Salt Lake City

first: Ramiro

last: Garzon

state: UT

address: 2000 Circle of Hope

department: Division of Hematology and Hematologic Malignancies

institute: Huntsman Cancer Institute

description:
Library name: K562_KD3_3
K562 circPCMTD1 siRNA

data_processing:
Paired Fastq files were trimmed to remove adapter sequences using Trimgalore
Assembly: Trimmed fastq files were aligned to the reference human genome GRCh38 using STAR tool
Supplementary files format and content: Gene counts were generated from aligned files using featureCounts. Raw counts for all samples submitted as a matrix file

growth_protocol: K562 cells were maintained in Iscove's Modified Dulbecco's Medium supplemented with 10% FBS

extract_protocol:
RNA was extracted using the Zymo Research RNA Clean and Concentrator Kit
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit

treatment_protocol: K562 cells were transfected with antisense gapmers targeting the backsplice junction of circPCMTD1 or with scrambled (control) antisense gapmers, and cells were harvested 48 hours post-transfection using TRIzol.

value: lymphoblast cells

value: circPCMTD1 antisense gapmer


title: WT,D40,ZT12,H3K4me3,rep2

description:
PE150
MM_030


title: WT,D40,ZT12,H3K36me3,rep3

description:
PE150
MM_027


title: K562 circPCMTD1 Knockdown 3_2

description:
Library name: K562_KD3_2
K562 circPCMTD1 siRNA


title: cll_3, IBS, timepoint 1, tcr library

description:
Library name: cll_3_baseline_tcr
10X Genomics

value: tcr


title: cll_3, IBS, timepoint 2, tcr library

description:
Library name: cll_3_3yrs_tcr
10X Genomics


title: R22301095-R22050074LR01-HF100-1

city: wenzhou

first: bin

last: zhou

address: Nanbaixiang, Ouhai District, Wenzhou, Zhejiang Province

institute: Affiliated Hospital of Weifang Medical University

description: Library name: Sample 5

data_processing:
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Read count extraction and normalization were performed using CLC genomic benchwork
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: csv files include RPKM values for each Sample

source_name: cell line

growth_protocol: MOLM13 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
centrifuge to remove supernatant, add about 2ML PBS (2% FBS), with a total amount of about 2.5mL, Add cells to trizol
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Comparative gene expression profiling analysis of RNA-seq data for MOLM13  cells treated with halofuginone  .

value: cell line

value: adipogenic differentiation

value: Separate ribosomal RNA

tag: batch

value: Day 0


title: WT,D40,ZT12,H3K36me3,rep1

description:
PE150
MM_025

tag: tissue


title: WT,D40,ZT12,H3K27me3,rep2

description:
PE150
MM_022


title: K562 circPCMTD1 Knockdown 3_1

description:
Library name: K562_KD3_1
K562 circPCMTD1 siRNA

tag: cell line


title: WT H3K4me3 (ChIP) rep1

description: Library name: Sample 10 WT Callus H3K4me3  biol rep1

value: Callus

value: Anti-Histone H3K4me3, Abcam, ab8580


title: cll_3, IBS, timepoint 1, bcr library

description:
Library name: cll_3_baseline_bcr
10X Genomics

value: peripheral blood

value: bcr


title: cll_3, IBS, timepoint 1, gex library

description:
Library name: cll_3_baseline_gex
10X Genomics

value: gex


title: WT,D40,ZT12,H3K36me3,rep2

description:
PE150
MM_026

value: Outer photoreceptor cells

tag: cell type


title: R22301096-R22050075LR01-HF100-2

description: Library name: Sample 6


title: WT,D40,ZT12,H3K27me3,rep1

description:
PE150
MM_021


title: R22301093-R22050072LR01-HF50-1

description: Library name: Sample 3


title: WT,D40,ZT12,H3K27me3,rep4

description:
PE150
MM_024


title: WT,D10, ZT12,IgG,rep4

description:
PE150
MM_020


title: cll_2, IBS, timepoint 3, bcr library

description:
Library name: cll_2_5yrs_bcr
10X Genomics

tag: patient


title: cll_3, IBS, timepoint 2, gex library

description:
Library name: cll_3_3yrs_gex
10X Genomics

tag: patient type


title: R22301094-R22050073LR01-HF50-2

description: Library name: Sample 4


title: K562 circPCMTD1 Knockdown 2_2

description:
Library name: K562_KD2_2
K562 circPCMTD1 siRNA


title: cll_2, IBS, timepoint 3, tcr library

description:
Library name: cll_2_5yrs_tcr
10X Genomics

tag: timepoint


title: K562 circPCMTD1 Knockdown 2_1

description:
Library name: K562_KD2_1
K562 circPCMTD1 siRNA


title: WT,D10, ZT12,IgG,rep3

description:
PE150
MM_019


title: K562 circPCMTD1 Knockdown 1_3

description:
Library name: K562_KD1_3
K562 circPCMTD1 siRNA


title: S2pct_6h_Replica_4_S28_R1

city: St Louis

first: Sara

last: Pietroforte

state: Missouri

address: 425 S. Euclid Avenue

department: Ob&Gyn

institute: Washington University in St Louis

description:
Library name: S2pct_6h_Replica_4_S28_R1.fastq.gz
Column name in processed data.xlsx

data_processing:
aligment by STAR 2.7.0a
count by SummarizeOverlap of Bioconductor/R package Genomic Features
Differentially gene expression by DESeq2
Assembly: mm10 genome
Supplementary files format and content: csv data table including normalized counts

source_name: secondary follicles

extract_protocol:
Direct cell were used for library prep
SMART-seq mRNA kit (Takara) used according to manufacturer's protocol

value: secondary follicles

value: WT

value: 2% alginate


title: R22301091-R22050070LR01-ctrl-1

description: Library name: Sample 1

value: CON


title: K562 circPCMTD1 Knockdown 2_3

description:
Library name: K562_KD2_3
K562 circPCMTD1 siRNA

value: lymphoblast cells


title: R22301092-R22050071LR01-ctrl-2

description: Library name: Sample 2


title: WT,D40,ZT12,H3K27me3,rep3

description:
PE150
MM_023

value: Nuclei


title: S2pct_6h_Replica_2_S12_R1

description:
Library name: S2pct_6h_Replica_2_S12_R1.fastq.gz
Column name in processed data.xlsx


title: cll_2, IBS, timepoint 2, bcr library

description:
Library name: cll_2_3yrs_bcr
10X Genomics

value: IBS

tag: library type


title: cll_2, IBS, timepoint 3, gex library

description:
Library name: cll_2_5yrs_gex
10X Genomics


title: K562 circPCMTD1 Knockdown 1_1

description:
Library name: K562_KD1_1
K562 circPCMTD1 siRNA

value: circPCMTD1 antisense gapmer


title: cll_2, IBS, timepoint 2, tcr library

description:
Library name: cll_2_3yrs_tcr
10X Genomics

value: tcr


title: K562 Scrambled 3_3

description:
Library name: K562_Scr3_3
K562 scrambled siRNA

value: scrambled antisense gapmers


title: WT,D10,ZT12,H3K9me3,rep3

description:
PE150
MM_015


title: S2pct_6h_Replica_3_S20_R1

description:
Library name: S2pct_6h_Replica_3_S20_R1.fastq.gz
Column name in processed data.xlsx


title: K562 circPCMTD1 Knockdown 1_2

description:
Library name: K562_KD1_2
K562 circPCMTD1 siRNA


title: S2pct_6h_Replica_1_S4_R1

description:
Library name: S2pct_6h_Replica_1_S4_R1.fastq.gz
Column name in processed data.xlsx


title: cll_2, IBS, timepoint 2, gex library

description:
Library name: cll_2_3yrs_gex
10X Genomics


title: K562 Scrambled 3_1

description:
Library name: K562_Scr3_1
K562 scrambled siRNA


title: WT,D10, ZT12,IgG,rep2

description:
PE150
MM_018


title: S2pct_3h_Replica_3_S18_R1

description:
Library name: S2pct_3h_Replica_3_S18_R1.fastq.gz
Column name in processed data.xlsx


title: K562 Scrambled 3_2

description:
Library name: K562_Scr3_2
K562 scrambled siRNA


title: cll_2, IBS, timepoint 1, tcr library

description:
Library name: cll_2_baseline_tcr
10X Genomics


title: WT,D10, ZT12,IgG,rep1

description:
PE150
MM_017


title: cll_2, IBS, timepoint 1, bcr library

description:
Library name: cll_2_baseline_bcr
10X Genomics


title: K562 Scrambled 2_2

description:
Library name: K562_Scr2_2
K562 scrambled siRNA


title: WT,D10,ZT12,H3K9me3,rep1

description:
PE150
MM_013


title: WT,D10,ZT12,H3K4me3,rep4

description:
PE150
MM_012


title: S2pct_3h_Replica_4_S26_R1

description:
Library name: S2pct_3h_Replica_4_S26_R1.fastq.gz
Column name in processed data.xlsx


title: S2pct_3h_Replica_1_S2_R1

description:
Library name: S2pct_3h_Replica_1_S2_R1.fastq.gz
Column name in processed data.xlsx


title: cll_1, IBS, timepoint 3, tcr library

description:
Library name: cll_1_5yrs_tcr
10X Genomics


title: S2pct_3h_Replica_2_S10_R1

description:
Library name: S2pct_3h_Replica_2_S10_R1.fastq.gz
Column name in processed data.xlsx


title: K562 Scrambled 2_3

description:
Library name: K562_Scr2_3
K562 scrambled siRNA


title: K562 Scrambled 2_1

description:
Library name: K562_Scr2_1
K562 scrambled siRNA


title: S2pct_24h_Replica_4_S32_R1

description:
Library name: S2pct_24h_Replica_4_S32_R1.fastq.gz
Column name in processed data.xlsx


title: WT,D10,ZT12,H3K4me3,rep3

description:
PE150
MM_011


title: K562 Scrambled 1_3

description:
Library name: K562_Scr1_3
K562 scrambled siRNA


title: WT,D10,ZT12,H3K9me3,rep4

description:
PE150
MM_016


title: S2pct_24h_Replica_3_S24_R1

description:
Library name: S2pct_24h_Replica_3_S24_R1.fastq.gz
Column name in processed data.xlsx


title: cll_1, IBS, timepoint 3, gex library

description:
Library name: cll_1_5yrs_gex
10X Genomics


title: cll_2, IBS, timepoint 1, gex library

description:
Library name: cll_2_baseline_gex
10X Genomics


title: cll_1, IBS, timepoint 2, tcr library

description:
Library name: cll_1_3yrs_tcr
10X Genomics


title: K562 Scrambled 1_1

description:
Library name: K562_Scr1_1
K562 scrambled siRNA


title: WT,D10,ZT12,H3K9me3,rep2

description:
PE150
MM_014


title: WT,D10, ZT12,H3K36me3,rep3

description:
PE150
MM_007


title: Ethmoid sinus tissue, Control, UC_9_S53_L002

city: La Jolla

first: Yung-An

last: Huang

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

description:
Library name: UCSD009
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

data_processing:
Raw sequence reads were quality- and adapter-trimmed using the Rfastp package. Reads were filtered for quality by requiring a minimum length of 25 bp and a mean quality score of 20 (Q20).
Clean reads were subsequently mapped to the GRCh38/hg38 reference genome using Rsubread's subjunc function, retaining only uniquely mapped reads (unique=TRUE).
Feature counts were extracted using Rsubread's featureCounts function against the GENCODE v49 GTF annotation. The primary feature used for quantification was the gene_name (Gene Symbol), as specified by GTF.attrType="gene_name", while gene_id and gene_type were included as extra attributes.
Gene-level raw counts were derived from FeatureCounts and imported into edgeR. Library sizes were normalized using the TMM method. Final processed data consists of two supplementary files: the Raw Counts Matrix and the log2(CPM+0.5) Normalized Expression Matrix.
Assembly: GRCh38/hg38
Supplementary files format and content: txt file includes raw integer counts per gene for each Sample, used as DE input.
Supplementary files format and content: txt file includes TMM-normalized log2(CPM+0.5) values per gene for each Sample, used for visualization.

source_name: Ethmoid sinus tissue

growth_protocol: N/A, primary clinical tissue samples

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
RNA sequencing libraries were generated using the Illumina Ribo-Zero Plus rRNA Depletion Kit with Illumina DNA/RNA UD Indexes (Illumina). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 50 million reads per sample on an Illumina NovaSeq X Plus. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: N/A, primary clinical tissue samples

value: Ethmoid sinus tissue

tag: condition

value: CRSsNP

value: Control


title: K562 Scrambled 1_2

description:
Library name: K562_Scr1_2
K562 scrambled siRNA

tag: treatment


title: S2pct_24h_Replica_2_S16_R1

description:
Library name: S2pct_24h_Replica_2_S16_R1.fastq.gz
Column name in processed data.xlsx

tag: genotype


title: WT,D10, ZT12,H3K36me3,rep2

description:
PE150
MM_006


title: cll_1, IBS, timepoint 1, tcr library

description:
Library name: cll_1_baseline_tcr
10X Genomics

value: peripheral blood


title: WT,D10,ZT12,H3K4me3,rep1

description:
PE150
MM_009


title: cll_1, IBS, timepoint 3, bcr library

description:
Library name: cll_1_5yrs_bcr
10X Genomics

value: bcr


title: cll_1, IBS, timepoint 1, bcr library

description:
Library name: cll_1_baseline_bcr
10X Genomics


title: WT,D10, ZT12,H3K36me3,rep4

description:
PE150
MM_008


title: cll_1, IBS, timepoint 2, bcr library

description:
Library name: cll_1_3yrs_bcr
10X Genomics


title: WT,D10,ZT12,H3K4me3,rep2

description:
PE150
MM_010


title: S2pct_24h_Replica_1_S8_R1

description:
Library name: S2pct_24h_Replica_1_S8_R1.fastq.gz
Column name in processed data.xlsx

tag: time


title: Ethmoid sinus tissue, Control, UC_8_S52_L002

description:
Library name: UCSD008
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: cll_1, IBS, timepoint 2, gex library

description:
Library name: cll_1_3yrs_gex
10X Genomics

value: gex


title: S2pct_12h_Replica_2_S14_R1

description:
Library name: S2pct_12h_Replica_2_S14_R1.fastq.gz
Column name in processed data.xlsx


title: S0_5pct_6h_Replica_4_S27_R1

description:
Library name: S0_5pct_6h_Replica_4_S27_R1.fastq.gz
Column name in processed data.xlsx

value: 0.5% alginate


title: Ethmoid sinus tissue, Control, UC_5_S49_L002

description:
Library name: UCSD005
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

value: CRSwNP


title: WT,D10, ZT12,H3K27me3,rep3

description:
PE150
MM_003

value: Outer photoreceptor cells


title: WT,D10, ZT12,H3K36me3,rep1

description:
PE150
MM_005


title: WT,D10, ZT12,H3K27me3,rep4

description:
PE150
MM_004


title: S0_5pct_6h_Replica_3_S19_R1

description:
Library name: S0_5pct_6h_Replica_3_S19_R1.fastq.gz
Column name in processed data.xlsx

value: secondary follicles

value: WT


title: S2pct_12h_Replica_3_S22_R1

description:
Library name: S2pct_12h_Replica_3_S22_R1.fastq.gz
Column name in processed data.xlsx

value: 2% alginate


title: Ethmoid sinus tissue, Control, UC_4_S48_L002

description:
Library name: UCSD004
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: Ethmoid sinus tissue, Control, UC_7_S51_L002

description:
Library name: UCSD007
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: cll_1, IBS, timepoint 1, gex library

description:
Library name: cll_1_baseline_gex
10X Genomics


title: S2pct_12h_Replica_1_S6_R1

description:
Library name: S2pct_12h_Replica_1_S6_R1.fastq.gz
Column name in processed data.xlsx


title: mda-mb-231_IDB-003_10mpk_rep7

city: SOUTH SAN FRANCISCO

first: Paige

middle: D

last: Diamond

state: California

address: 201 HASKINS WAY

institute: Interdict Bio

description: Library name: EXP037_O7

data_processing:
Paired-end sequencing reads were aligned to the human RefSeq MANE v1.3 transcriptome using HISAT2 with default parameters. Transcript-level read counts were generated across RefSeq MANE annotations.
Differential expression analysis was performed between treatment and control groups with DESeq2. To assess, pathway-level changes, significantly regulated genes (adjusted p-value < 0.05) were subjected to gene set enrichment analysis (GSEA) using the MSigDB Hallmark gene sets.
Assembly: H. sapiens genomic annotations were from GRCh38 and transcript annotations from NCBI RefSeq MANE v.1.3.
Supplementary files format and content: Transcript-level count table.

growth_protocol: Efficacy study for IDB-003 in human TNBC MDA-MB-231 tumor bearing, female BALB/c nude mice was performed at Pharmaron (Beijing, China). The MDA-MB231 tumor cell lines were be maintained in vitro as monolayer in L-15 medium supplemented with 10% heat inactivated fetal bovine serum at 37 °C in an atmosphere of 100% air. The tumor cells were routinely sub-cultured before confluence by trypsin-EDTA treatment, not to exceed 4-5 passages. The cells growing in an exponential growth phase were harvested and counted for tumor inoculation. Each mouse was inoculated subcutaneously on the right flank with MDA-MB-231 tumor cells (1 × 107) in 0.1 mL medium and matrigel mixture (1:1 ratio) for tumor development.

extract_protocol:
Tumor samples were first flash frozen with liquid nitrogen and pulverized to ensure thorough disruption. Total RNA and protein were extracted using the AllPrep RNA/Protein kit (Qiagen), following the manufacturer’s protocol. RNA fractions were subsequently subjected to additional purification and DNase treatment with the RNA Clean and Concentrator kit (Zymo Research) to remove residual genomic DNA and improve RNA integrity.
Strand-specific cDNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Total RNA was depleted of rRNA with the NEBNext rRNA Depletion Kit v2 (New England Biolabs). Libraries were PCR-amplified with NEBNext Multiplex Oligos for Illumina and size-selected with AMPure XP beads (Beckman Coulter).

treatment_protocol: Mice were provided with vehicle (5% DMSO/95% (20% HP-β-CD in water)) or IDB-003 dissolved in vehicle by oral gavage. For the group dosed with 3 mg/kg IDB-003, the mice received treatments twice daily for 28 days. The mice dosed at 10 mg/kg were given a 2-day dosing holiday after 11 days of treatment (11 days on, 2 days off) for the 28-day period.

value: epithelial cell

value: IDB-003, 10mpk, BID, 28days


title: mda-mb-231_IDB-003_10mpk_rep6

description: Library name: EXP037_O6


title: Ethmoid sinus tissue, Control, UC_10_S54_L002

description:
Library name: UCSD010
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: WT,D10, ZT12,H3K27me3,rep2

description:
PE150
MM_002

value: Nuclei


title: S0_5pct_6h_Replica_1_S3_R1

description:
Library name: S0_5pct_6h_Replica_1_S3_R1.fastq.gz
Column name in processed data.xlsx


title: S0_5pct_3h_Replica_4_S25_R1

description:
Library name: S0_5pct_3h_Replica_4_S25_R1.fastq.gz
Column name in processed data.xlsx


title: S2pct_12h_Replica_4_S30_R1

description:
Library name: S2pct_12h_Replica_4_S30_R1.fastq.gz
Column name in processed data.xlsx


title: mda-mb-231_IDB-003_10mpk_rep3

description: Library name: EXP037_O3


title: mda-mb-231_IDB-003_10mpk_rep4

description: Library name: EXP037_O4


title: mda-mb-231_IDB-003_10mpk_rep8

description: Library name: EXP037_O8


title: shRNA targets at trx, D10, ZT12,IgG, rep3

description:
PE150
GM_045

value: trxKD


title: Ethmoid sinus tissue, Exposed, BP_20_S59_L002

description:
Library name: BP020
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

value: Exposed


title: shRNA targets at trx, D10, ZT12,me3, rep3

description:
PE150
GM_048


title: WT,D10, ZT12,H3K27me3,rep1

description:
PE150
MM_001


title: Ethmoid sinus tissue, Control, UC_2_S46_L002

description:
Library name: UCSD002
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

value: Ethmoid sinus tissue


title: Ethmoid sinus tissue, Exposed, BP_18_S57_L002

description:
Library name: BP018
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

value: CRSsNP


title: S0_5pct_6h_Replica_2_S11_R1

description:
Library name: S0_5pct_6h_Replica_2_S11_R1.fastq.gz
Column name in processed data.xlsx


title: Ethmoid sinus tissue, Control, UC_3_S47_L002

description:
Library name: UCSD003
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name

value: Control


title: shRNA targets at trr, D10, ZT12,me2, rep3

description:
PE150
GM_043

value: trrKD


title: Ethmoid sinus tissue, Exposed, BP_17_S56_L002

description:
Library name: BP017
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: Ethmoid sinus tissue, Control, UC_6_S50_L002

description:
Library name: UCSD006
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: shRNA targets at trx, D10, ZT12,me2, rep3

description:
PE150
GM_047


title: Ethmoid sinus tissue, Exposed, BP_19_S58_L002

description:
Library name: BP019
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: S0_5pct_24h_Replica_4_S31_R1

description:
Library name: S0_5pct_24h_Replica_4_S31_R1.fastq.gz
Column name in processed data.xlsx


title: shRNA targets at trx, D10, ZT12,me1, rep3

description:
PE150
GM_046


title: mda-mb-231_vehicle_rep5

description: Library name: EXP037_K6

value: Vehicle


title: S0_5pct_3h_Replica_3_S17_R1

description:
Library name: S0_5pct_3h_Replica_3_S17_R1.fastq.gz
Column name in processed data.xlsx


title: Ethmoid sinus tissue, Exposed, BP_16_S55_L002

description:
Library name: BP016
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: mda-mb-231_IDB-003_10mpk_rep1

description: Library name: EXP037_O1


title: shRNA targets at trr, D10, ZT12,me3, rep3

description:
PE150
GM_044


title: S0_5pct_24h_Replica_3_S23_R1

description:
Library name: S0_5pct_24h_Replica_3_S23_R1.fastq.gz
Column name in processed data.xlsx


title: mda-mb-231_IDB-003_10mpk_rep2

description: Library name: EXP037_O2


title: mda-mb-231_IDB-003_10mpk_rep5

description: Library name: EXP037_O5


title: S0_5pct_3h_Replica_1_S1_R1

description:
Library name: S0_5pct_3h_Replica_1_S1_R1.fastq.gz
Column name in processed data.xlsx


title: S0_5pct_3h_Replica_2_S9_R1

description:
Library name: S0_5pct_3h_Replica_2_S9_R1.fastq.gz
Column name in processed data.xlsx


title: S0_5pct_24hh_Replica_1_S7_R1

description:
Library name: S0_5pct_24hh_Replica_1_S7_R1.fastq.gz
Column name in processed data.xlsx


title: mda-mb-231_vehicle_rep4

description: Library name: EXP037_K5


title: S0_5pct_24hh_Replica_2_S15_R1

description:
Library name: S0_5pct_24hh_Replica_2_S15_R1.fastq.gz
Column name in processed data.xlsx


title: shRNA targets at trr, D10, ZT12,me1, rep3

description:
PE150
GM_042


title: shRNA targets at mCherry, D10, ZT12,me1, rep3

description:
PE150
GM_034

value: mCherryKD


title: Ethmoid sinus tissue, Exposed, BP007_S53_L008

description:
Library name: BP007
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: shRNA targets at mCherry, D10, ZT12,me2, rep3

description:
PE150
GM_035


title: mda-mb-231_vehicle_rep2

description: Library name: EXP037_K3


title: shRNA targets at trr, D10, ZT12,IgG, rep3

description:
PE150
GM_041


title: Ethmoid sinus tissue, Control, UCSD0001_S55_L008

description:
Library name: UCSD001
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: mda-mb-231_vehicle_rep3

description: Library name: EXP037_K4


title: mda-mb-231_vehicle_rep1

description: Library name: EXP037_K2


title: S0_5pct_12h_Replica_3_S21_R1

description:
Library name: S0_5pct_12h_Replica_3_S21_R1.fastq.gz
Column name in processed data.xlsx

value: 0.5% alginate


title: S0_5pct_12h_Replica_4_S29_R1

description:
Library name: S0_5pct_12h_Replica_4_S29_R1.fastq.gz
Column name in processed data.xlsx


title: Ethmoid sinus tissue, Exposed, BP010_S54_L008

description:
Library name: BP010
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: Ethmoid sinus tissue, Exposed, BP006_S52_L008

description:
Library name: BP006
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: hcc1143_IDB-001_10uM_rep3

description: Library name: EXP018_A11_B

data_processing:
Raw ribosome profiling sequencing reads were first trimmed to remove adapter sequences using Cutadapt, discarding any reads shorter than 16 nucleotides. The trimmed reads were then mapped sequentially to rRNA, cytoplasmic and mitochondrial tRNA references, followed by alignment to mitochondrial mRNA, mitochondrial DNA, and various noncoding RNA references with Bowtie and Bowtie2. Next, any remaining reads were aligned to human mRNA (RefSeq MANE v1.3) and processed through RSEM for transcript quantification. RSEM quantifications of mRNA-aligned RFPs were used for all downstream analyses. Using the length of each ribosome footprint and the reading frame identified at the 5’ end of the ribosome-protected fragment, the A-site codon was inferred and subsequently used to determine the corresponding peptide sequence in the nascent polypeptide chain.
The position-weighted matrix analysis was performed by extracting amino acid identities from ribosome footprints and corresponding nascent peptide sequences from nascent chain position (-7 to 0). After filtering for coverage threshold (genes with > 0.1 read/codon) and normalizing to library size, log2 fold-change was calculated by comparing each treatment condition to DMSO for every residue at each position.
Assembly: H. sapiens genomic annotations were from GRCh38 and transcript annotations from NCBI RefSeq MANE v.1.3.
Supplementary files format and content: Position-weighted frequency matrix is included for amino acid positions -7 to 0. Identity and position columns correspond to amino acid residue and position within the nascent chain, respectively. All other column names correspond to library names and values correspond to frequency of that identity at that position.
Library strategy: Ribo-Seq

growth_protocol: HCC1143 breast cancer cells (ATCC) were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 1% GlutaMax (Gibco).

extract_protocol:
Cells were washed with ice-cold phosphate-buffered saline and lysed in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1mM DTT, 1% v/v Trizon X-100, 25 U/mL Turbo DNase I). Lysates were incubated on ice for 30 minutes to allow for DNase digestion and clarified by centrifugation at 20,000 × g for 30 minutes at 4 °C. Lysates were digested with 3.33 U/µg RNase I (Ambion) for 45 minutes at room temperature with gentle agitation. Resulting monosomes were isolated by sucrose cushion, using 450 µL 1M sucrose in polysome buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1mM DTT) for 400 µL of digested lysate material. Sucrose cushions were performed with MLA-130 rotor in an Optima Max-XP ultracentrifuge (Beckman Coulter) at 100,000 × g for 90 minutes at 4 °C. Pellet were resuspended in resuspension buffer (150 mM NaCl, 20 mM EDTA, 1% Triton X-100, 20 mM pH 7.5 Tris-HCl) and incubated at room temperature for at least 10 minutes. RNA was extracted using Direct-zol RNA miniprep kit (Zymo), according to manufacturer’s instructions. Ribosome footprint RNA size selection was performed as previously described (McGlincy & Ingolia 2017, Methods) with minor modifications, including the use of 10% TBE-urea gel (Biorad) and custom sizing markers (oIB188-190, 17nt-34nt). Following overnight gel extraction and ethanol precipitation, RNA was dephosphorylated with T4 PNK (NEB) at 37C for 1 hour.
Ribosome footprint cDNA libraries were subsequently constructed with Ordered Two-Template Relay kits (Karnateq) according to manufacturer’s recommendations (Ferguson et al. (2023), Nat. Methods). cDNA libraries were indexed and amplified with NEBNext Indexing Primers (NEB).

treatment_protocol: When cells reached 70-80% confluency, they were treated with anisomycin (ANS) or Interdictor for 60 minutes at noted concentrations.


title: S0_5pct_12h_Replica_2_S13_R1

description:
Library name: S0_5pct_12h_Replica_2_S13_R1.fastq.gz
Column name in processed data.xlsx


title: shRNA targets at mCherry, D10, ZT12,IgG, rep3

description:
PE150
GM_033


title: Ethmoid sinus tissue, Exposed, BP001_S49_L008

description:
Library name: BP001
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: shRNA targets at mCherry, D10, ZT12,me3, rep3

description:
PE150
GM_036


title: S0_5pct_12h_Replica_1_S5_R1

description:
Library name: S0_5pct_12h_Replica_1_S5_R1.fastq.gz
Column name in processed data.xlsx


title: hcc1143_IDB-001_10uM_rep1

description: Library name: EXP018_A10_B


title: shRNA targets at trx, D10, ZT12,me3, rep2

description:
PE150
GM_032


title: hcc1143_IDB-001_10uM_rep2

description: Library name: EXP018_B10_B


title: Ethmoid sinus tissue, Exposed, BP005_S51_L008

description:
Library name: BP005
Column name in Clinical_nasal_BPC_raw_featurecounts_matrix.txt and Clinical_nasal_BPC_logCPM_matrix.txt: the same as library name


title: HUVEC with Listeria monocytogenes infected PMA differentiated U937 cells, 8 h, rep2

city: Tübingen

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

country: Germany

institute: University of Tübingen

description:
Library name: Sample 13
10 × Genomics

data_processing:
Demultiplexing, barcoded processing and read alignment was performed with Cell Ranger v9.0.1 and the reference genome GRCh38 (10x refdata-gex-GRCh38-2024-A).
Quality Check (QC) analysis was performed using Seurat R package V5.3.0. (https://satijalab.org/seurat/, https://github.com/satijalab/seurat). As filtering criteria cells with a mitochondrial gene ratio above 10% and ribosomal gene ratio below 5% were filtered out to exclude contamination from dead or dying cells and cells with degraded RNA respectively. Cells with less than 500 UMI and 300 genes were excluded to ensure that only high quality cells are included in the next steps. Environmental contamination and doublet removal were performed using SoupX 1.6.2 and DoubletFinder V2.0.4, repectively.
Gene counting, normalization and scaling and sample clustering was performed using Seurat R package V5.3.0. Sample anotation was performed using celldex V1.12.0  with references celldex::ManoImmuneData and celldex::Human PrimaryCellsAtlasData.
Differential expression analysis on selected sample clusters was performed using Seurat R package V5.3.0.
KEGG pathway enrichment analysis of differentially expressed genes was performed using clusterProfiler V4.16.0.
Assembly: GRCh38
Supplementary files format and content: DE_analysis_SingleCellRNAseq.xlsx file contains the differentially expressed genes (DEGs) between different conditions and different populations in sheets 1 to 4. Specifically: sheet 1 compares HUVEC from co-cultures with infected U937 (MF) versus unexposed HUVEC controls; sheet 2  compares HUVEC from co-cultures with uninfected U937 (MF) versus unexposed HUVEC controls; sheet 3  compares HUVEC from co-cultures with infected U937 (MF) versus HUVEC from co-cultures with uninfected U937 (MF); sheet 4 compares infected U937 (MF) from co-cultures with HUVEC versus uninfected U937 (MF) from co-cultures with HUVEC. In each of these sheets the following are shown in: column A, name of the differentially expressed (DE) gene; column B, p-value for DE; column C, log2 of average fold change value; column D, ptc.1 value; column E, ptc.2 value; column F, adjusted p_value for DE. Sheets 5 to 8 show the results of the KEGG pathway enrichment analysis for the same comparisons as in sheets 1-4. In each of these sheets the following are shown in: column A, ID for pathway identifier in KEGG database; column B, name of the pathway; column C, number of DE associated with that pathway; column D, p_value for the pathway enrichment  with hypergeometric distribution test; column E, false discovery rate for the pathway; column F, value of enrichment score for the pathway (equal to "-log10(p_value)"); column G, list of DEGs associated with the specific pathway.
Supplementary files format and content: Sample_XX_raw_feature_bc_matrix.h5 files contain the number of counts(data) per feature (genes) and barcodes (detected cells) resulting from Cell Ranger.
Supplementary files format and content: Sample_XX_web_summary.html files contain the summary of the quality control measures (number of reads, percentages of valid barcodes, valid UMIs, sequence saturation, Q30 bases in barcode, Q30 bases in RNA read, Q30 bases in UMI), mapping measures (percentages for reads mapped to genome, reads mapped confidently to genome, reads mapped confidently to intergenic regions, reads mapped confidently to intronic regions, reads mapped confidently to exonic regions, reads mapped confidently to transcriptome, reads mapped antisense to gene), statistics for detected cells (estimated number of single cells per sample, fraction reads in cells, mean reads per cell, median UMI counts per cell, median genes per cell, total genes detected). The files also contains summary information of the gene expresion including t-SNE projections, calculated clusters (from 2 to 11) overlaid in t-SNE projection, table of features (genes) and differential expression per cluster, and plots for sequence saturation vs mean reads per cell and median genes per cell vs mean reads per cell.

growth_protocol: U937 monocyte cells were differentiated to macrophage-like cells prior to infection by addition of 500 ng/ml phorbol 12-myristate 13-acetate (PMA) (Sigma, P1585-1MG) in RPMI 1640 medium, HEPES (Gibco) supplemented with 10% FBS (referred to as RPMI from now on) and antibiotic-antimycotic solution. The cells were incubated for 48 h at 37°C and 5% CO2. GFP expressing Listeria monocytogenes (LM) strain JAT606 was streaked from a glycerol stock on a BHI agar plate (10006334, Fisher) containing 7.5 µg/mL chloramphenicol (15353771, Fisher Scientific) and 200 µg/mL streptomycin (15424871, Fisher Scientific), and incubated for 3 days at 37°C. The evening before infection a single colony was picked and incubated at room temperature overnight in BHI (53286, Sigma) supplemented with 7.5 µg/mL chloramphenicol and 200 µg/ml streptomycin. The next morning the liquid cultures, were centrifuged at 2000xg for 5 min at room temperature. The pellet was washed 1x with PBS (10010023, Thermofisher) and 5x the original volume of RPMI, then diluted to a concentration of approximately 1.6x10^3 bacteria per U937 cell and added to the differentiated U937 cells (12 mL per T175 flask). U937 were incubated for 40 min at 37°C. Afterwards, the bacterial suspension was removed, cells were washed 1x with PBS and resuspended in RPMI supplemented with 20 µg/mL gentamycin (15820243, Fisher). U937 were then incubated for 2.5-3.5 h. Prior to flow sorting, cells were washed 1x with PBS, detached using 0.25% trypsin EDTA (25200056, Thermofischer), and suspended in Leibovitz's L-15 CO2 independent medium (21083027, Thermofisher) during flow sorting with the multi-application cell sorter MA 900 (Sony Biotechnology). GFP positive cells were collected for further experiments.

extract_protocol:
Cell samples were then gently washed 1x with PBS, followed by the addition of 200 µL per well of 0.05% Trypsin-EDTA for 5 min to allow cell detachment. Next, 800 µL of cell culture medium containing 5% DMSO was added. Cells were frozen overnight at –80°C and subsequently transferred to –120 °C until shipment on dry ice to the company carying out the scRNA-seq.
GEM generation, library preparation and sequencing were performed by Lexogen NGS Services, Lexogen GmBH, Austria. In brief, cell viability and counting were performed with AO/PI staining and LUNA FX7 cell counter (Logos Biosystems). Approximately 8000 cells per sample were subjected to single-cell RNA sequencing (scRNA-seq) on the 10X Chromium platform. Single nuclei were loaded onto a Chromium Next GEM Chip G Single Cell Kit (10 × Genomics) and processed through a Chromium Controller to generate GEMs (Gel Beads in Emulsion). The sequencing libraries were prepared with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10 × Genomics) following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq X platform, at 20000 reads per cell per sample. Sequencing read mode applied was: Read 1 28bp; Read 2 90bp; Index Reads 1 and 2 10 bp each.

treatment_protocol: HUVEC were placed at a concentration of 2.5x10^5 cells/well on glass collagen I-coated coverslips of 24-well plates for 24 h so that confluent monolayer are formed. Subsequently PMA-differentiated U937 cells infected or not with LM were added at a concentration of 2.5x10^4 cells/well (or not for unexposed HUVEC control samples). Co-cultured cells were incubated for additional 8 h together.

value: HUVEC

tag: bacterial strain

value: 10403S expressing GFP

value: Human umbilical vein endothelial cells with PMA-differentiated infected human, pro-monocytic U937 cells (cell line)

value: HUVEC co-cultured for 8 h with Listeria monocytogenes-infected U937 cells


title: HUVEC with Listeria monocytogenes infected PMA differentiated U937 cells, 8 h, rep3

description:
Library name: Sample 14
10 × Genomics

value: WT


title: Mid DOX-treated in-vitro BMP4 treated sample 3

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
Library name: DV53-12wB-midDOX
normalized_counts_BMP.txt

data_processing:
alignment to hg38; Salmon version 1.2.1; default parameters for hg38 alignment
RNA-seq read mapping; Salmon version 1.8.0; salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization; DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: normalized_counts_BMP: Normalized abundance counts across BMP4-treated RNA-seq datasets generated
Supplementary files format and content: CTRL_TvB_Log2FC_normcounts: Normalized abundance counts between CTRL TGF-beta and BMP4 RNA-seq datasets generated

source_name: H9 HESC

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol:
Collagenase digestion
Samples were prepared using HiSeq Illumina RNA library preparation

value: H9 HESC

value: chondrocytes


title: hcc1143_IDB-002_10uM_rep2

description: Library name: EXP018_A9_B

value: epithelial cell


title: Mid DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV49-12wB-midDOX
normalized_counts_BMP.txt


title: shRNA targets at trx, D10, ZT12,me2, rep2

description:
PE150
GM_031

value: Outer photoreceptor cells

value: Nuclei

value: trxKD


title: Mid DOX-treated in-vitro BMP4 treated sample 1

description:
Library name: DV48-12wB-midDOX
normalized_counts_BMP.txt


title: hcc1143_ANS_10uM_rep3

description: Library name: EXP018_D12_B

value: Anisomycin, 10uM


title: hcc1143_IDB-002_10uM_rep1

description: Library name: EXP018_H12_B


title: shRNA targets at trx, D10, ZT12,me1, rep2

description:
PE150
GM_030


title: shRNA targets at trr, D10, ZT12,me3, rep2

description:
PE150
GM_028


title: HUVEC with Listeria monocytogenes infected PMA differentiated U937 cells, 8 h, rep1

description:
Library name: Sample 04
10 × Genomics


title: HUVEC with uninfected PMA-differentiated U937 cells, 8 h, rep2

description:
Library name: Sample 15
10 × Genomics

value: Human umbilical vein endothelial cells with PMA-differentiated human, pro-monocytic U937 cells (cell line)

value: HUVEC co-cultured for 8 h with uninfected U937 cells


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-earDOX
CREB5_normalized_counts.txt

data_processing:
alignment to hg38
Salmon version 1.2.1; default parameters for hg38 alignment
RNA-seq read mapping
Salmon version 1.8.0; salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization
DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: CREB5_normalized_counts.txt' file contains all normalized counts for each sample

tag: sample group


title: HUVEC with uninfected PMA-differentiated U937 cells, 8 h, rep1

description:
Library name: Sample 11
10 × Genomics


title: shRNA targets at trr, D10, ZT12,me2, rep2

description:
PE150
GM_027

value: trrKD


title: shRNA targets at trx, D10, ZT12,IgG, rep2

description:
PE150
GM_029


title: HUVEC, 8 h, rep3

description:
Library name: Sample 18
10 × Genomics

source_name: HUVEC

value: Human umbilical vein endothelial cells

value: none (HUVEC alone)


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-earDOX
CREB5_normalized_counts.txt


title: shRNA targets at trr, D10, ZT12,me1, rep2

description:
PE150
GM_026


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-midDOX
CREB5_normalized_counts.txt


title: hcc1143_DMSO_exp018_rep1

description: Library name: EXP018_E11_B

value: DMSO


title: hcc1143_DMSO_exp018_rep2

description: Library name: EXP018_F11_C


title: HUVEC, 8 h, rep1

description:
Library name: Sample 01
10 × Genomics

value: HUVEC


title: hcc1143_ANS_10uM_rep1

description: Library name: EXP018_H11_B


title: HUVEC, 8 h, rep2

description:
Library name: Sample 17
10 × Genomics


title: shRNA targets at trr, D10, ZT12,IgG, rep2

description:
PE150
GM_025


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-CTRL
CREB5_normalized_counts.txt


title: shRNA targets at mCherry, D10, ZT12,me1, rep2

description:
PE150
GM_018

value: mCherryKD


title: hcc1143_DMSO_exp018_rep3

description: Library name: EXP018_G11_B


title: HUVEC with uninfected PMA-differentiated U937 cells, 8 h, rep3

description:
Library name: Sample 16
10 × Genomics


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-midDOX
CREB5_normalized_counts.txt


title: shRNA targets at mCherry, D10, ZT12,me2, rep2

description:
PE150
GM_019


title: shRNA targets at mCherry, D10, ZT12,me3, rep2

description:
PE150
GM_020


title: hcc1143_ANS_10uM_rep2

description: Library name: EXP018_C12_B


title: hcc1143_DMSO_exp025_rep2

description: Library name: EXP025_C7


title: shRNA targets at mCherry, D10, ZT12,IgG, rep2

description:
PE150
GM_017


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-midDOX
CREB5_normalized_counts.txt


title: hcc1143_DMSO_exp025_rep1

description: Library name: EXP025_B7


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-midDOX
CREB5_normalized_counts.txt


title: Cells from PBMC from patient #492

city: Philadelphia

first: Julia Han

last: Noll

state: Pennsylvania

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

description:
Library name: HTS_SO188_08_492_PBMC
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger software (v8.0.0). Reads were aligned to the human reference genome (GRCh38), augmented with a custom reference to detect the Cilta-cel transgene.
Assembly: GRCh38
Supplementary files format and content: Tab seperated values files and matrix files

source_name: PBMC

extract_protocol:
Samples were cryopreserved in R10 medium. Upon thawing, cells were washed, resuspended, and counted, and viability was assessed. CAR positivity was evaluated by flow cytometry.
10x Genomics Chromium GEM-X Single Cell 3' v4 Gene Expression assay following the manufacturer’s protocol (10x Genomics, Pleasanton, CA). Briefly, single-cell suspensions derived from PBMC and CSF were evaluated for viability and concentration prior to loading onto the Chromium X instrument for Gel Beads-in-Emulsion (GEM) generation, enabling the barcoding of individual cells and their transcripts. Reverse transcription and cDNA amplification were carried out within the GEMs, followed by library construction, using the Chromium GEM-X Single Cell 3' Kit (PN-1000691), Chromium GEM-X Single Cell 3' Chip Kit (PN-1000690), and the Dual Index Kit TT Set A (PN-1000215). Final libraries were quantified, pooled, and sequenced on an Illumina NovaSeq X system using the 10B Reagent Kit (100 cycles) to a depth of 100K reads per cell.

value: PBMC

value: ciltacel


title: Cells from PBMC from patient #251

description:
Library name: HTS_SO188_05_251_PBMC
10x Genomics


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-CTRL
CREB5_normalized_counts.txt

value: H9 HESC


title: hcc1143_IDB-002_0.5uM_rep1

description: Library name: EXP025_E6

value: WT


title: hcc1143_IDB-002_0.5uM_rep2

description: Library name: EXP025_F6

value: epithelial cell


title: Cells from PBMC from patient #470

description:
Library name: HTS_SO188_07_470_PBMC
10x Genomics


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-earDOX
CREB5_normalized_counts.txt

value: chondrocytes


title: Cells from PMBC from patient #439

description:
Library name: HTS_SO188_06_439_PBMC
10x Genomics


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-CTRL
CREB5_normalized_counts.txt


title: shRNA targets at trx, D10, ZT12,me2, rep1

description:
PE150
GM_015

value: Outer photoreceptor cells

value: Nuclei


title: hcc1143_IDB-002_2.5uM_rep1

description: Library name: EXP025_G6


title: Cells from CSF liquor from patient #470

description:
Library name: HTS_SO188_03_470_CSF
10x Genomics

source_name: CSF

value: CSF


title: Cells from CSF liquor from patient #492

description:
Library name: HTS_SO188_04_492_CSF
10x Genomics


title: shRNA targets at trx, D10, ZT12,me3, rep1

description:
PE150
GM_016

value: trxKD


title: shRNA targets at trx, D10, ZT12,me1, rep1

description:
PE150
GM_014


title: hcc1143_IDB-002_2.5uM_rep2

description: Library name: EXP025_H6


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-earDOX
CREB5_normalized_counts.txt


title: Brain, Control, rep4

city: Tallinn

first: Tõnis

last: Timmusk

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

data_processing:
The original raw data from Illumina platform are transformed to Sequenced Reads, known as Raw Data or RAW Reads, by base calling. Raw data are recorded in a FASTQ file, which contains sequencing reads and corresponding sequencing quality. Every read in FASTQ format is stored in four lines (Cock P.J.A. et al. 2010).
RNA-seq adapter and quality trimming were performed using BBDuk (part of BBMap version 38.90) with the following parameters: ktrim=r k=23 mink=11 hdist=1 tbo qtrim=lr trimq=10 maq=10 minlen=25.
RNA-seq reads were mapped to BDGP6.32 using STAR aligner version 2.7.4a with default parameters.
To increase sensitivity for unannotated splice junctions, splice junctions obtained from the 1st pass were combined per dataset and filtered as follows: junctions on non-canonical intron motifs were removed; only junctions detected in at least 2 samples (10 % rounded up to the nearest integer) in the whole dataset were kept. Filtered junctions were added to the 2nd pass mapping using STAR aligner.
RNA sequencing reads were assigned to features using FeatureCounts version 2.0.1. The following parameters were used for paired end RNA-seq data: -p –B –C –J.
Assembly: BDGP6.32
Supplementary files format and content: tab-delimited text file of raw counts for all samples from FeatureCounts

source_name: Brain

growth_protocol: Drosophila lines and crosses were fed with malt and semolina-based food with 12 h light and dark daily rhythms at 25°C with 60% humidity.

extract_protocol:
RNA from  0 to 1 day old adult Drosophila brains was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Flies were collected as follows: 0 to 1 day old adult elavC155>emc or elavC155/+ Drosophila brains (pooled male and female) were dissected.

value: Brain

tag: Sex

value: pooled male and female

tag: age

value: 0 to 1 day old


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-CTRL
CREB5_normalized_counts.txt


title: Cells from CSF liquor from patient #439

description:
Library name: HTS_SO188_02_439_CSF
10x Genomics


title: Brain, emcOE, rep4


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-midDOX
CREB5_normalized_counts.txt


title: shRNA targets at trx, D10, ZT12,IgG, rep1

description:
PE150
GM_013


title: Cells from CSF liquor from patient #251

description:
Library name: HTS_SO188_01_251_CSF
10x Genomics


title: shRNA targets at trr, D10, ZT12,me3, rep1

description:
PE150
GM_012

value: trrKD


title: shRNA targets at trr, D10, ZT12,me2, rep1

description:
PE150
GM_011


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-earDOX
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-CTRL
CREB5_normalized_counts.txt


title: Brain, emcOE, rep3


title: Brain, Control, rep3


title: M42022110348_MCC26_Combo

city: Seattle

first: Daniel

last: Jones

state: WA

institute: Fred Hutchinson Cancer Center

description: Library name: M42022110348

data_processing:
Reads aligned with Bowtie 2
Genes with counts less than 10 across all samples were filtered out
The subsequent raw RNA-Seq count data were normalized using TMM-FPKM, followed by log2 transformation with a pseudocount of 2, as implemented in the edgeR R/Bioconductor package
Assembly: GRCh38
Supplementary files format and content: Log FPKM expression estimates in csv format

extract_protocol:
Sample QC was performed with Agilent Tapestation 4200 to identify samples with RIN>7. 200ng qualified RNA from each sample was processed for library preparation. In brief, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads.
RNA fragment and reverse transcription: Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP.  End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments.   PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer.  Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.  DNA nanoball synthesis.

value: ATRi + Radiation


title: M42022110347_MCC26_Combo

description: Library name: M42022110347


title: M42022110346_MCC26_Combo

description: Library name: M42022110346


title: shRNA targets at trr, D10, ZT12,IgG, rep1

description:
PE150
GM_009


title: shRNA targets at trr, D10, ZT12,me1, rep1

description:
PE150
GM_010


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-earDOX
CREB5_normalized_counts.txt


title: Brain, Control, rep2


title: shRNA targets at mCherry, D10, ZT12,me3, rep1

description:
PE150
GM_004


title: M42022110345_MCC26_RT

description: Library name: M42022110345

value: Radiation


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-midDOX
CREB5_normalized_counts.txt


title: Brain, emcOE, rep2


title: Vehicle treated in-vitro TGF-beta treated sample 3

data_processing:
alignment to hg38: Salmon version 1.2.1 (default parameters for hg38 alignment)
RNA-seq read mapping: Salmon version 1.8.0 (salmon -l A --numBootstraps 100 --gcBias –validateMappings)
Read abundance normalization : DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: Normalized abundance counts across BMP4-treated RNA-seq datasets generated
Supplementary files format and content: Normalized abundance counts between CTRL TGF-beta and BMP4 RNA-seq datasets generated


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-CTRL
CREB5_normalized_counts.txt


title: M42022110344_MCC26_RT

description: Library name: M42022110344


title: Brain, Control, rep1


title: M42022110343_MCC26_RT

description: Library name: M42022110343


title: shRNA targets at mCherry, D10, ZT12,me1, rep1

description:
PE150
GM_002

value: mCherryKD


title: Brain, emcOE, rep1


title: shRNA targets at mCherry, D10, ZT12,IgG, rep1

description:
PE150
GM_001


title: shRNA targets at mCherry, D10, ZT12,me2, rep1

description:
PE150
GM_003


title: M42022110342_MCC26_ATRi

description: Library name: M42022110342

value: ATRi


title: Vehicle treated in-vitro TGF-beta treated sample 2


title: Vehicle treated in-vitro BMP4 treated sample 3

value: Vehicle treated in-vitro BMP4 treated


title: 5%_HD_Miosis

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

description: Library name: mitosis_wHD_R1

data_processing:
In situ Hi-C data were processed using the rfy_hic2 package (https://github.com/rafysta/rfy_hic2)
Processed HiC data were converted to juicer format using the pre command of JUICER program (version 1.22.01)
Assembly: S.pombe (2018)
Supplementary files format and content: Juicer format

organism: Schizosaccharomyces pombe

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 10 minutes and disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in lysis buffer [50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  After washing with 1 ml PBS solution, the cells were further fixed with 3 mM disuccinimidyl glutarate (Thermo Fisher Scientific) in 2.5 ml PBS solution at 30°C for 40 minutes.  The fixed cells were incubated at 62°C for 7 minutes with 0.1% SDS and subsequently with 1% Triton-X 100.  The permeabilized cells were incubated with 25 units of MboI, HinfI, and MluCI at 37°C overnight.  The pellet containing restriction enzyme-digested DNA fragments was treated with 150 μM biotin-14-dATP, dCTP, dGTP, and dTTP and incubated with 20 units of Klenow fragment (NEB) at 37°C for 45 minutes, followed by proximity ligation using 2,500 units of T4 DNA ligase (NEB) at room temperature for 4 hours with a gentle rotation.  After ligation, the pellet was subjected to proteinase K treatment at 68°C overnight in the presence of 0.5 M NaCl.
DNA was purified by phenol/chloroform extraction and ethanol precipitation.  The purified DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode).  Biotin-labeled DNA was purified using Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific).  Sequencing adapters were ligated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) while DNA was bound to the beads.  Sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).

tag: strain

tag: restriction enzyme

value: MboI, HinfI, MluCI


title: no_HD_Miosis

description: Library name: mitosis_woHD_R1


title: mTSC, IAP CRISPRi, rep 3

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description: Library name: KRAB_IAP_RNA-3

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Hisat2 v2.0.5 with --no-softclip.
Reads with MAPQ < 2 were removed.
Raw read counts per gene were extracted using Seqmonk.
Assembly: mm10 (Mus musculus); GCF_900095145 (Mus pahari)
Supplementary files format and content: txt, table of raw counts

source_name: Rs26 mTSCs

growth_protocol: TS conditioned medium (TS-CM) was prepared by incubating TS base medium (TS-BM; RMPI 1640 supplemented with 20% FBS, 1X antibiotic-antimycotic, 1 mM sodium pyruvate and 50 µM 2-mercaptoethanol) on confluent, mitomycin-treated primary mouse embryonic fibroblast (PMEF) feeders for 72 h, followed by filtration through a 0.45 µm PES membrane. Blastocysts from C57BL/6 mice were plated individually onto gelatin-coated wells containing mitomycin-treated PMEF feeders in medium consisting of 70% TS-CM and 30% TS-BM, supplemented with 50 ng/ml bFGF, 2 μg/ml heparin and 100 µM Y-27632 (ROCK inhibitor). Following hatching, once 3-4 layers of TSCs formed around the blastocyst, outgrowths were dissociated using 0.5% trypsin-EDTA. TSCs were passaged at sub-confluency until feeder cells were eliminated and subsequently cryopreserved in liquid nitrogen in freezing medium containing 90% culture medium and 10% DMSO. For regular passaging of established lines (B6 TSCs, GFP TSCs and Rs26 TSCs), medium with no ROCK inhibitor and reduced bFGF (25 ng/ml) and heparin (1 µg/ml) was used. Cells were kept in humidified atmosphere with 5% CO2 at 37 ˚C.

extract_protocol:
Total RNA was isolated using a commercial RNA extraction kit (Qiagen) and treated with DNase I (Ambion) to remove residual genomic DNA.
500 ng of total RNA was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2. Strand-specific libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Rs26 KRAB sgIAP TSCs were treated with 8 µg/ml doxycycline hydrochloride to induce CRISPR interference.

value: Rs26 mTSCs

value: Trophoblast stem cells

value: dCas9-KRAB; IAP-sgRNA

value: doxycycline hydrochloride


title: mTSC, IAP CRISPRi, rep 2

description: Library name: KRAB_IAP_RNA-2


title: mTSC, IAP CRISPRi, rep 1

description: Library name: KRAB_IAP_RNA-1


title: M42022110341_MCC26_ATRi

description: Library name: M42022110341


title: Cnd1_Pmc4_degron

description: Library name: Cnd1_Pmc4_degron_mitosis


title: M42022110340_MCC26_ATRi

description: Library name: M42022110340


title: Vehicle treated in-vitro BMP4 treated sample 1

value: H9 HESC

value: chondrocytes


title: M42022110339_MCC26_Untx

description: Library name: M42022110339

value: Untreated


title: M42022110338_MCC26_Untx

description: Library name: M42022110338


title: Vehicle treated in-vitro TGF-beta treated sample 1


title: Pmc4_degron

description: Library name: Pmc4_degron_mitosis


title: Cnd1_degron

description: Library name: Cnd1_degron_mitosis


title: EA-23

type: RNA

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

description: European-Amercian Stroma -23

hyb_protocol: Affymetrix Human Gene 1.0 ST Array fluidics script FS450-0001

scan_protocol: GenChipTM Scanner 3000 System

data_processing: Bioconductor Affy package

label: biotin

source_name: Laser-capture microdissected prostate stroma

label_protocol: Ensore Biotin Module (NuGEN)

growth_protocol: not applicable

extract_protocol: RNAaqueous-Micro Kit (Thermo Fisher AM1931) and Affymetrix Gene Chip Pico Reagent Kit (Thermo Fisher 902622)

treatment_protocol: not applicable

tag: tissue

value: Stroma around benign epithelium

tag: ethnicity

value: EA


title: mTSC CRISPRi control, rep 2

description: Library name: KRAB_control_RNA-2

tag: cell line

tag: cell type


title: WT_control

description: Library name: WT_control_mitosis


title: B6 mTSCs

description: Library name: bTSCs_musculus_RNA

source_name: B6 mTSCs

value: B6 mTSCs


title: Vehicle treated in-vitro BMP4 treated sample 2


title: M32022110336_MCC13_Combo

description: Library name: M32022110336


title: M32022110335_MCC13_Combo

description: Library name: M32022110335


title: Mus musculus placenta, rep 3

description: Library name: Placenta_musculus_RNA-3

source_name: Placenta

value: Placenta


title: Cnd1_K658E_Myc

description: Library name: Cnd1_K658E_Myc_R2


title: mTSC CRISPRi control, rep 3

description: Library name: KRAB_control_RNA-3


title: Pmc4_WT

description: Library name: pmc4_60_w_HiC_Double-MHM


title: EA-20

description: European-Amercian Stroma -20


title: mTSC CRISPRi control, rep 1

description: Library name: KRAB_control_RNA-1


title: EA-18

description: European-Amercian Stroma -18


title: Cnd1_WT2

description: Library name: Cnd1_WT_Myc_R2


title: Mus musculus placenta, rep 2

description: Library name: Placenta_musculus_RNA-2


title: M42022110337_MCC26_Untx

description: Library name: M42022110337


title: GFP mTSCs

description: Library name: GFPTSCs_musculus_RNA

source_name: GFP mTSCs

value: GFP mTSCs


title: M32022110332_MCC13_RT

description: Library name: M32022110332

value: Radiation


title: EA-21

description: European-Amercian Stroma -21


title: M32022110334_MCC13_Combo

description: Library name: M32022110334

value: ATRi + Radiation


title: PolII_ChIP_5%_HD

description: Library name: PolII_mitosis_HD

data_processing:
ChIP-seq reads were aligned to S.pombe genome (2018) using Bowtie2 version 2.4.4
bigWig files were generated using deeptools version 3.5.1 with subcommand "bamCoverage" and the options --ignoreForNormalization III --normalizeUsing RPGC --effectiveGenomeSize 10118937 or --scaleFactor for spike-in normalization.
Spike-in normalization was performed
Scores represent subtraction of control read density from treatment read density.
Assembly: S.pombe (2018)
Supplementary files format and content: bigWig

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 30 minutes, washed twice with 1´ PBS, and further fixed with 10 mM dimethyl adipimidate (Sigma Aldrich) at room temperature for 45 minutes.  After two washes with 1´ PBS, the cells were disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in ChIP lysis buffer [50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  Chromatin DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode), and the soluble fraction was collected by centrifugation at 13,000 rpm for 15 minutes.  A total of 50 μl ChIP lysis buffer containing 5 µl antibody and 15 µl Dynabeads protein G (Thermo Fisher Scientific) was added to the soluble fraction, and the bead suspension was incubated at 4°C for 2 hours with a gentle rotation.  The beads were washed twice with ChIP lysis buffer, once with ChIP lysis buffer containing 0.65 M NaCl, once with washing buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and 1 mM EDTA), and once with TE (10 mM Tris-HCl pH 8.0, and 1 mM EDTA) for 5 minutes each with a gentle rotation.  The protein-DNA mixture was eluted by incubating the beads with TES (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 1% SDS) at 65°C for 30 minutes with harsh agitation at 1,000 rpm using ThermoMixer (Eppendorf) and subjected to reverse crosslinking at 68°C overnight in the presence of 0.5 M NaCl.  DNA was purified using QIAquick PCR purification kit (Qiagen)
The recovered DNA was subjected to library construction using NEBNext Ultra DNA library prep kit (NEB).  The sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).  The libraries were sequenced by NextSeq 2000 (Illumina) to obtain paired-end reads.

tag: chip antibody

value: Abcam Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody; ab5408