title: Digested control cells, macrophages from CMFBMF, replicate 2

description:
CM+FB+MF2_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx

value: 40 min digestion


title: SCMp, IAA, rep1

status: Public on Apr 02 2024

type: SRA

city: Québec

first: Pierre-Marc

last: Frédérick

state: Québec

address: 9 Rue McMahon

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

description: small RNA analysis

library_source: transcriptomic

data_processing:
The samples or debarcoded
The adaptors are removed and only >16nt are kept
Small RNAs are mapped to the genome and cDNA using Bowtie 0.12.7 (maximum of 3 seed mismatches)
The samples were normalized to total gene expression (geex) reads excluding structural RNA (struc) and transformed in RPM (read per million).
Assembly: C. elegans WS215
Supplementary files format and content: (PMF1-18) The raw reads were individually normalized on the total gene expression reads (geex) minus the structural reads (struct) and converted to RPM. (PMF19-PMF24) The raw reads were individually normalized on the level of ALG-1 protein immunoprecipitated.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Seam cells

growth_protocol: Worms were grown on NGM plates supplemented with EtOH 0.4% or IAA 4mM at 20°C.

extract_protocol:
TRIzol extraction.
Total RNA was used with NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (E7560S) and size selected on a gel (approximatively 140bp)

treatment_protocol: 2mL of IAA 1M  (or EtOH 100%) was added to 500mL of cooling NGM (between 40°C and 45°C).

tag: tissue

value: Seam cells

tag: developmental stage

value: Young adults

tag: treatment

value: IAA 4mM


title: D39 CEP:rr10, OD 0.4, Rep3 [RR10-3]

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

data_processing:
Raw reads from the fastq files were mapped to the genome with bowtie2 using local alignment. Samtools was used for SAM-to-BAM conversion and sorting.
Raw reads were counted at a feature level with featureCounts. Multimapping reads were counted and fractionally assigned to their features. Reads overlapping several features were assigned by largest overlap.
Parameters used with featureCounts (example): featureCounts -p -M --fraction -O --largestOverlap -t gene -f -g  Name  --extraAttributes locus_tag,gene_biotype -a CP027540.1.gff3 -s 2 -o featureCounts_report FILENAMES
Assembly: CP027540.1 (several sRNA features identified in D39W were manually added to the General Feature Format (GFF)-file)
Supplementary files format and content: File contains read counts for all features of S. pneumoniae D39V in all samples (file format: csv). In addition to feature coordinates, the file also contains locus_tags, names, gene_biotypes.

organism: Streptococcus pneumoniae

source_name: Bacterial cell

growth_protocol: Streptococcus pneumoniae D39V and overexpression mutant derivatives were grown in the rich C+Y medium in triplicate cultures at 37°C with 5% CO2 to an OD600 0.4.

extract_protocol:
RNA was extracted from Streptococcus pneumoniae by a phenol-chloroform extraction.
1 µg RNA was depleted for ribosomal RNA using the NEBNext® rRNA Depletion Kit (Bacteria). RNA libraries were then prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit.

tag: strain

tag: cell type

value: Bacterial cell

tag: genotype

value: C+Y media, 37°C, OD 0.4


title: Replicate 2 Ig control T58A marrow B cells stimulated for 48 hours with IL7

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
Data was aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for CUT&RUN data.
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: Primary marrow B Cells

growth_protocol: Primary B cells were grown in RPMI supplemented with 10% FBS, and either IL7 or LPS, and harvested 48 hours after stimulation.

extract_protocol:
CUT&RUN was performed according to published methods using pA-MNase as secondary reagent. Yeast DNA was spiked into the samples after DNA extraction to normalize signal between samples. Cells were processed on an automated system at the Fred Hutch Cancer Center to carry out MNase cleavage, DNA extraction, and library construction.
Processed on a previously published, automated system at the Fred Hutch Cancer Center that uses KAPA DNA polymerase method for library preparation optimized for recovery of small DNA fragments.

treatment_protocol: Cells were stimulated for 48 hours with IL7 or LPS prior to extraction.

value: Primary marrow B Cells

value: IL7 stimulation, 48 hours


title: Digested control cells, macrophages from CMFBMF, replicate 1

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

institute: University Health Network

description:
CM+FB+MF1_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx

data_processing:
RNA sequencing was executed on a NovaSeq 6000 (Illumina) using a paired-end 2x100bp protocol and multiplexing to obtain a sequencing depth of 30-35 million paired-end reads per sample.
Reads were filtered for quality control and mapped to the human genome (hg19) using STAR aligner (version 2.7.9a).
Count files containing uniquely mapped reads were generated using htseq-count (version 0.11.0), retaining protein-coding genes with non-zero counts. Data were pre-filtered to include only genes expressed by at least one sample.
The DESeq2 package was used in R Studio (R version 4.3.2) to normalize counts and compute differentially expressed genes
Assembly: hg19
Supplementary files format and content: Excel file contains raw counts for each sample
Supplementary files format and content: Excel file contains normalized counts (DESeq2) for each sample

organism: Homo sapiens

source_name: Digested cells

growth_protocol: Biowires were cultured in StemPro-34 SFM (1X) medium (ThermoFisher) containing 2-phospho-L-ascorbic acid (64mg/mL; Sigma), 2% v/v HEPES (1M; ThermoFisher), 1% v/v GlutaMax (100X; ThermoFisher), 1% v/v Penicillin-Streptomycin (10,000U/mL; ThermoFisher), Transferrin (30mg/mL; ROCHE).

extract_protocol:
Biowires were digested in collagenase type I (1370U/mL), hyaluronidase (122U/mL), DNase I (146U/mL), Dispase (1U/mL) , ROCK inhibitor (1uM) and 1uM of Flavopiridol for 40 minutes at 37°C with gentle shaking. After 40 minutes, the digestion mix was pipetted 10 times to physically dissociate cells and was washed in 1mL media. Cells were pelleted (300g for 5 minutes at 4°C) and stained with cell surface antibodies. Cells were stained in FACS buffer (2% heat-inactivated bovine serum in PBS containing 1mM EDTA) with mouse anti-human CD14 (clone M5E2; 1:100) and mouse anti-human CD45 (clone 2D1; 1:100) for 20 minutes at 4°C. Cells were washed once in FACS buffer (2% heat-inactivated bovine serum in PBS containing 1mM EDTA) and spun down 300xg for 5 minutes at 4°C. Finally, cells were resuspended in BD FACS Pre-Sort Buffer with 1:100 DAPI and sorted on Aria Fusion (BD Biosciences) under low pressure (100um nozzle) directly into 350uL of RLT lysis buffer in DNA lobind tubes. Total RNA from sorted hESC-macrophages or hESC-cardiomyocytes was prepared using the Qiagen RNeasy Micro kit with on-column treatment with RNAase-free DNAase.
Sample library preparation using the Takara SMARTer Stranded Total RNA-seq Kit v3

value: Digested cells

tag: cell line

value: hES2 hESC-macrophages

value: hESC-macrophages

value: hES2 (WT)

tag: timepoint


title: Replicate Ig control WT marrow B cells stimulated for 48 hours with IL7

value: WT


title: Biowire, macrophages from MF group, replicate 3

description:
MF3
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx

source_name: Human cardiac microtissues

value: Human cardiac microtissues

value: Day 14


title: D39 CEP:rr10, OD 0.4, Rep2 [RR10-2]


title: D39 CEP:rr10, OD 0.4, Rep1  [RR10-1]


title: Replicate Ig control T58A marrow B cells stimulated for 48 hours with IL7


title: SCMp, EtOH, rep2

description: small RNA analysis

value: EtOH 0.4%


title: RNA pol2 WT marrow B cells stimulated for 48 hours with IL7


title: Digested control cells, macrophages from FBMF, replicate 1

description:
FB+MF1_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx


title: Biowire, macrophages from MF group, replicate 1

description:
MF1
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: Biowire, macrophages from MF group, replicate 2

description:
MF2
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: D39 CEP:rr09, OD 0.4, Rep3 [RR09-3]


title: D39 CEP:rr11, OD 0.4, Rep1  [RR11-1]


title: SCMp, EtOH, rep1

description: small RNA analysis


title: RNA pol2 T58A marrow B cells stimulated for 48 hours with IL7


title: SCMP, IAA, rep3

description: small RNA analysis


title: D39 CEP:rr09, OD 0.4, Rep2 [RR09-2]


title: Biowire, macrophages from FBMF, replicate 3

description:
FB+MF3
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: RNASeq T58A replicate 3 spleen B cells stimulated for 48 hours with LPS pair 3

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
For RNASeq analysis, low quality reads were filtered out prior to alignment to mm10 using TopHat v2.1.0. Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1. Normalization and gene expression results were done using DESeq2, with samples paired by littermate mice.
Assembly: mm10
Supplementary files format and content: For RNA-seq data, DESeq2 count tables with Log2Fold gene expression changes and adjusted p values.

source_name: Primary splenic B Cells

extract_protocol:
Total RNA was extracted using Trizol, and Zymogenetics Direct-Zol Miniprep kit.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 kit.

value: Primary splenic B Cells

value: LPS stimulation, 48 hours


title: Biowire, macrophages from FBMF, replicate 2

description:
FB+MF2
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: SCMp, EtOH, rep3

description: small RNA analysis

value: Seam cells


title: D39 CEP:rr09, OD 0.4, Rep1  [RR09-1]


title: RNASeq T58A replicate 2 spleen B cells stimulated for 48 hours with LPS pair 2


title: Biowire, macrophages from CMFBMF, replicate 3

description:
CM+FB+MF3
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: Biowire, macrophages from FBMF, replicate 1

description:
FB+MF1
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: Elder normal_rep2

type: RNA

city: Guangzhou

first: Jingsong

last: Ou

state: Please Select

address: 58 Zhong Shan Er Road

department: Surgery/Cardiac Surgery

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: miRNA expression of human plasma

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Peripheral Blood

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Plasma was collected from blood anti-coagulated with ethylene diamine tetraaceticacid (EDTA).

value: plasma

tag: gender

value: female

tag: age

tag: individual

value: Elder normal


title: RNASeq T58A replicate 1 spleen B cells stimulated for 48 hours with LPS pair 1


title: Elder normal_rep3

description: miRNA expression of human plasma

value: male


title: D39 CEP:rr08, OD 0.4, Rep3 [RR08-3]

value: Bacterial cell

value: C+Y media, 37°C, OD 0.4


title: Elder normal_rep1

description: miRNA expression of human plasma


title: D39 CEP:rr08, OD 0.4, Rep2 [RR08-2]


title: Biowire, macrophages from CMFBMF, replicate 2

description:
CM+FB+MF2
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: D39 CEP:rr08, OD 0.4, Rep1  [RR08-1]


title: RNASeq WT replicate 3 spleen B cells stimulated for 48 hours with LPS pair 3


title: D39 CEP:rr06, OD 0.4, Rep3 [RR06-3]


title: RNASeq WT replicate 1 spleen B cells stimulated for 48 hours with LPS pair 1


title: RNASeq WT replicate 2 spleen B cells stimulated for 48 hours with LPS pair 2


title: Biowire, macrophages from CMFBMF, replicate 1

description:
CM+FB+MF1
RawCounts_BiowireMF.xlsx
NormalizedCounts_BiowireMF.xlsx


title: D39 CEP:rr06, OD 0.4, Rep2 [RR06-2]


title: RNASeq T58A replicate 3 marrow B cells stimulated for 48 hours with IL7 pair3

value: Primary marrow B Cells

value: IL7 stimulation, 48 hours


title: Young normal _rep2

description: miRNA expression of human plasma

value: Young normal


title: Young normal _rep3

description: miRNA expression of human plasma


title: HC,replicate2,scRNAseq

city: 南京市

first: lijuan

last: chen

state: 江苏省

address: Nanjing City, 建邺区

institute: Nanjing BenQ hospital

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
feature‐barcode matrices were obtained by aligning reads to the human genome (GRCh38 Ensemble: version 100) using CellRanger. Next, downsampling analysis among samples sequenced according to the mapped barcoded reads per cell of each sample was applied, and finally, an aggregated matrix was achieved
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: pharyngopalatine arch mucosa

extract_protocol:
Fresh biopsies of 4 RRPs were collected from the primary papilloma during surgical resection. 3 pharyngopalatine arch mucosa samples were obtained from tonsil hypertrophy as the comparative group.Those Tissues were lysed into single-cell suspensions and subjected to transcriptome profiling using single-cell RNA sequence
Seven samples were loaded onto 10ⅹgenomics chromium single-cell platform, and libraries were sequenced using an illumine platform with 150 bp pair-end sequencing. Sequencing data analysis was performed by Novogene Co., Ltd (Beijing, China). Using the Novogene Cloud Analysis platform(www.magic.novogene.com)

value: pharyngopalatine arch mucosa

tag: age (year)

tag: Sex


title: HC,replicate3,scRNAseq

description: 10x genomics


title: Young normal _rep1

description: miRNA expression of human plasma


title: Elder patient _rep3

description: miRNA expression of human plasma

value: Elder patient


title: HC,replicate1,scRNAseq

description: 10x genomics


title: RNASeq T58A replicate 2 marrow B cells stimulated for 48 hours with IL7 pair 2


title: D39 CEP:rr05, OD 0.4, Rep2 [RR05-2]


title: D39 CEP:rr05, OD 0.4, Rep3 [RR05-3]


title: RNASeq T58A replicate 1 marrow B cells stimulated for 48 hours with IL7 pair 1


title: RNASeq WT replicate 3 marrow B cells stimulated for 48 hours with IL7 pair 3

value: WT


title: RRP,replicate4,scRNAseq

description: 10x genomics

source_name: recurrent respiratory papilloma

value: recurrent respiratory papilloma


title: Elder patient _rep2

description: miRNA expression of human plasma


title: Elder patient _rep1

description: miRNA expression of human plasma


title: Young patient _rep3

description: miRNA expression of human plasma

value: Young patient


title: RRP,replicate3,scRNAseq

description: 10x genomics


title: D39 CEP:rr05, OD 0.4, Rep1  [RR05-1]


title: RNASeq WT replicate 2 marrow B cells stimulated for 48 hours with IL7 pair 2


title: RRP,replicate2,scRNAseq

description: 10x genomics


title: SCNT Obox3 late 2-cell rep2

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

data_processing:
For LET-seq and RNA-seq data, paired-end reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore! with a ‘--clip_R2 3’ option. After the reads were aligned, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts (version 1.6.5) and GENCODE annotation of the mm10 mouse genome (vM25) was used to analyze transcription levels with options ‘-p -O --fraction’. bigWig files were generated by deeptools bamCoverage with options '-bs 25 --normalizeUsing RPKM -ignore chrX chrM chrY --smoothLength 75'. The expression of each annotated gene was quantified by calculating TPM (transcripts per million) using R.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with options  ‘-X 700 --dovetail’ after removing adaptor sequences and low-quality reads by Trim Galore!. bigWig files were generated by bamCoverage from deepTools with parameters ‘-bs 50 --normalizeUsing RPKM --smoothLength 500’. MACS2 was used to call peaks with options ‘-q 0.05 -f BAMPE’.
Assembly: mm10
Supplementary files format and content: bigWig, tab-delimited text files indicating TPM values (for RNA-seq)

growth_protocol: Early embryos were cultured in KSOM. Male mouse embryonic stem cells were cultured with the medium consists of GMEM containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates.

extract_protocol:
For LET-seq and RNA-seq, total RNA from whole-cell lysate was used.  For CUT&RUN, chromatin was digested by protein A- potein G-MNase.
LET-seq protocol was used. For total RNA-seq, SMART-seq stranded kit (TAKARA) was used. For CUT&RUN library preparation, NEBnext Ultra II DNA Library Prep Kit (NEB) was used.

treatment_protocol: For LET-seq with inhibitors, zygotes were cultured in KSOM containing DMSO, 10 μM A-485 or 100 nM TSA from 18 to 24 hphCG, and then cultured in KSOM medium containing the same inhibitor and 1 mM EU from 24 to 27 hphCG. For RNA-seq of mESC samples, plasmids were transfected into mESCs using Lipofectamine 2000.  For RNA-seq of SCNT embryos, MII oocytes were enucleated, and the nuclei of cumulus cells were placed into ooplasm. SCNT embryos were then injected with 10 ng/µl of Obox3 or EGFP mRNA. For CUT&RUN, mESCs were collected at 24 hours after the transfection of pPB-CAG-3xFLAG-Obox3-2A-Puro or pPB-CAG-2A-puro control plasmid.

value: Late 2-cell

value: wild-type


title: D39 CEP:rr04, OD 0.4, Rep3 [RR04-3]


title: RRP,replicate1,scRNAseq

description: 10x genomics


title: SCNT Obox3 late 2-cell rep1


title: RNASeq WT replicate 1 marrow B cells stimulated for 48 hours with IL7 pair 1


title: VSMC, miR-1204, input

data_processing:
Qualities off fastq files were  inspected by fastqc (version 0.20.1).
ChlP-seq reads were timmed from 3' end until the final base had a ouality score > 30. using trim_galore version 0.6.4_dev, discarding reads lelt with < 20 bp.
The sequenced reads (FASTQ format) are mapped using tools such as Bowtie2 (Version 2.5.0). Bowtie2 can consider indels (insertions and deletions) by gapped alignments, which is appropriate for long and/or paired-end reads. After alignment, reads mapped to the same genomic positions are filtered as redundant reads, and the remaining nonredundant reads are used for analysis.
The peak-calling step identifies significantly enriched loci (peaks) in the genome. All peak calling was performed with MACS2 (version 2.1.0) , While is the most commonly used peak-calling tool. Peak-calling results are generally returned in BED format.
Assembly: hg38
Supplementary files format and content: bigwig,narrowpeak

source_name: vascular smooth muscle cell

extract_protocol:
Cells were fixed with 1% fommaldehyde for 10 minutes. After guenching and cell lysis, Chromatin was sonicated using a Focused Ultrasonicator.
ChlP-seg libraries were prepared using the KAPA Hyper Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bio Scientific. 2-5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 18 cycles on the themmocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencout AMPure xP beads from Beckman couter. ibraries were valdalted using the kapa library quantification kit.

value: vascular smooth muscle cell

value: miR-1204 overexpression


title: D39 CEP:rr04, OD 0.4, Rep2 [RR04-2]


title: D39 CEP:rr04, OD 0.4, Rep1  [RR04-1]


title: Cut&Run non-reactive Ig control  WT replicate 2 marrow B cells stimulated for 48 hours with IL7

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
CUT&RUN data was aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for CUT&RUN data.
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed according to published methods using pA-MNase as secondary reagent. Yeast DNA was spiked into the samples after DNA extraction to normalize signal between samples. Cells were processed on an automated system at the Fred Hutch Cancer Center to carry out MNase cleavage, DNA extraction, and library construction.
For CUT&RUN, cells were processed on a previously published, automated system at the Fred Hutch Cancer Center that uses KAPA DNA polymerase method for library preparation optimized for recovery of small DNA fragments.


title: D39 CEP:rr06, OD 0.4, Rep1  [RR06-1]


title: Cut&Run non-reactive Ig control  T58A replicate 2 marrow B cells stimulated for 48 hours with IL7


title: Young patient _rep1

description: miRNA expression of human plasma

value: plasma


title: Young patient _rep2

description: miRNA expression of human plasma

value: female


title: D39 CEP:rr03, OD 0.4, Rep3 [RR03-3]


title: VSMC, miR-1204, ChIP

tag: antibody

value: anti-p53 antibody (Cat.ab1101, Lot.GR3436878-6, UK, Abcam)


title: SCNT EGFP late 2-cell rep1


title: Cut&Run non-reactive Ig control  WT replicate 1 marrow B cells stimulated for 48 hours with IL7


title: D39 CEP:rr03, OD 0.4, Rep2 [RR03-2]

value: Bacterial cell


title: Cut&Run non-reactive Ig control T58A replicate 1 marrow B cells stimulated for 48 hours with IL7


title: ICSI late 2-cell rep2

source_name: BDF1 x BDF1

value: BDF1 x BDF1


title: ICSI late 2-cell rep1


title: Sample20_RF_S100

city: Aviano

first: Federico

last: Pozzo

state: PN

address: via Franco Gallini 2

department: Department of Translational Research

country: Italy

institute: Centro di Riferimento Oncologico (CRO) di Aviano IRCCS

data_processing:
Custom pipeline
Sequence reads were trimmed with fastp using default settings
Trimmed reads were mapped to hg38 using STAR with default parameters and --quant mode for read count.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: Primary CLL

extract_protocol:
RNA was extracted with Rneasy Micro kit (Qiagen). 30-50ng of total RNA were used as input for library preparation
RNA libraries were prepared using the mRNA library Prep Kit (Illumina) According to manufacturer's protocols

value: Primary CLL

value: RF


title: Cut&Run H3K4Me2 WT replicate 2 marrow B cells stimulated for 48 hours with IL7

value: Primary marrow B Cells

value: IL7 stimulation, 48 hours


title: VSMC, miR-ctl, ChIP

value: control


title: D39 CEP:rr01, OD 0.4, Rep3 [RR01-3]

value: C+Y media, 37°C, OD 0.4


title: Cut&Run H3K4Me2 T58A replicate 2 marrow B cells stimulated for 48 hours with IL7


title: SCNT EGFP late 2-cell rep2


title: D39 CEP:rr01, OD 0.4, Rep2 [RR01-2]


title: Sample19_PF_S91

value: PF


title: D39 CEP:rr01, OD 0.4, Rep1  [RR01-1]


title: Late 2-cell siCtrl rep2


title: Sample19_RF_S93


title: Cut&Run H3K4Me2 T58A replicate 1 marrow B cells stimulated for 48 hours with IL7


title: Sample18_RF_S111


title: Cut&Run H3K27Ac WT replicate 2 marrow B cells stimulated for 48 hours with IL7

value: WT


title: VSMC, miR-ctl, input


title: D39 WT, OD 0.4, Rep2 [WT-2]

value: wild type


title: D39 WT, OD 0.4, Rep3 [WT-3]


title: Late 2-cell siCtrl rep1

value: Late 2-cell

value: wild-type


title: Cut&Run H3K27Ac T58A replicate 2 marrow B cells stimulated for 48 hours with IL7


title: D39 CEP:rr03, OD 0.4, Rep1  [RR03-1]


title: D39 WT, OD 0.4, Rep1  [WT-1]


title: Sample18_PF_S102


title: ESC Crxos2 RNA-seq rep1

source_name: hybrid C57BL/6 / 129

value: hybrid C57BL/6 / 129

value: Embryonic stem cell


title: Cut&Run H3K27Ac WT replicate 1 marrow B cells stimulated for 48 hours with IL7


title: ESC Crxos3 RNA-seq rep1


title: ESC Crxos1 RNA-seq rep1


title: Late 2-cell siObox3_2 rep2


title: XR-seq xpc-1 mutant C. elegans mixed stages CPD 1h rep 2

city: College Station

first: Yuchao

last: Jiang

state: TX

address: 3143 TAMU

institute: Texas A&M University

library_source: other

data_processing:
For XR-seq, cutadapt was used to trim reads with adaptor sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG at the 3′-end and to discard untrimmed reads. Bowtie 2 was used for read alignment to the ce11 reference genome, followed by filtering, sorting, deduplication, and indexing. Post-alignment filtering steps were adopted using Rsamtools. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 19-24 bp. For plotting strand-based average repair profiles of the genes, we selected 7061 genes longer than 1 kilobase pair, situated at least 500 base pairs away from neighboring genes. Each gene was evenly divided into 100 bins from the Transcription Start Site (TSS) to the Transcription End Site (TES), and 25 bins (2 kbp) upstream of TSS, 25 bins (2 kbp) downstream of TES. Bed files of the reads were intersected to the 150 bin-divided-gene list by Bedtools intersect with the following commands -d -wa -F 0.5 -S or -s for TS and NTS, respectively22. We present the descriptive properties of our data in Supplementary Table 1. For RNA-seq, reads were aligned using STAR, followed by a filtering step to remove unmapped reads, reads with unmapped mates, reads that do not pass quality controls, reads that are unpaired, and reads that are not properly paired. We only kept the first read from the mate pair to ensure independent measures. Read counts for each gene were obtained using FeatureCounts.
Assembly: ce11
Supplementary files format and content: bed
Library strategy: XR-seq

molecule: other

source_name: Mixed stages

growth_protocol: The C. elegans wild-type (N2 ancestral), csb-1 (RB1801) and xpc-1 (TG2226) strains were obtained from the Caenorhabditis Genetics Center and were cultured under standard conditions at room temperature on nematode growth media (NGM) agar plates with E. coli strain OP50.

extract_protocol:
For XR-seq, supernatants were incubated with 5μL RNase A and then 5μL Proteinase K, purified, and then immunoprecipitated with either anti-CPD antibodies.
For XR-seq, immunoprecipitations were ligated to the adaptors, purified with the antibody used in the first purification, and DNA damage was reversed by CPD photolyase. After PCR amplification, the library was sequenced.

value: Mixed stages

value: UV irradiation induced CPD


title: Sample20_PF_S99


title: Late 2-cell siObox3_2 rep1


title: Cut&Run Myc T58A replicate 1 marrow B cells stimulated for 48 hours with IL7


title: XR-seq xpc-1 mutant C. elegans mixed stages CPD 1h rep 1


title: Sample17_PF_S95


title: Sample17_RF_S97


title: ESC Obox8 RNA-seq rep1


title: ESC Obox7 RNA-seq rep1


title: XR-seq WT no UV C. elegans CPD rep 2

source_name: L1 larvae

value: L1 larvae

value: No UV irradiation


title: Cut&Run H3K4Me2 WT replicate 1 marrow B cells stimulated for 48 hours with IL7


title: Sample16_RF_S78

value: Primary CLL


title: Cut&Run Myc WT replicate 2 narriw B cells stimulated for 48 hours with IL7


title: Cut&Run Myc T58A replicate 2 marrow B cells stimulated for 48 hours with IL7


title: XR-seq WT no UV C. elegans CPD rep 1


title: ESC Obox4ps35 RNA-seq rep1


title: Cut&Run Myc WT replicate 1 marrow B cells stimulated for 48 hours with IL7


title: Cut&Run Myc T58A replicate 1  marrow B cells stimulated for 48 hours with IL7


title: XR-seq WT C. elegans CPD 1h rep 2


title: Sample15_PF_S79


title: ESC Obox4ps27 RNA-seq rep1


title: Sample16_PF_S76


title: ESC Obox2 RNA-seq rep1


title: XR-seq WT C. elegans CPD 1h rep 1


title: Cut&Run non-reactive Ig control  WT replicate 2 spleen B cells stimulated for 48 hours with LPS

value: Primary splenic B Cells

value: LPS stimulation, 48 hours


title: XR- seq csb-1 mutant C. elegans CPD 1h rep 2


title: Cut&Run non-reactive Ig control  T58A replicate 2 spleen B cells stimulated for 48 hours with LPS


title: Sample14_PF_S94


title: XR- seq csb-1 mutant C. elegans CPD 1h rep 1


title: ESC Obox6 RNA-seq rep2


title: Cut&Run non-reactive Ig control  WT replicate 1 spleen B cells stimulated for 48 hours with LPS


title: Mnase_F_fujiB

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
QC, trimming with trimmomatic
mapping with BWA
samtools for creating bam files
R/Rsamtools, GenomicRegions for size selection and coverage calculation
Assembly: Fusarium fujikuroi IMI58289
Supplementary files format and content: trace of nucleosome coverage

organism: Fusarium fujikuroi

growth_protocol: Fungal mycelia were cultivated for three days in liquid ICI (6 mm glutamine) prior crosslinking with 1% formaldehyde.

extract_protocol:
Crosslinked and quick-frozen mycelia (3 days, liquid synthetic ICI, 6 mM glutamine) was treated with MNaseI (60 U/µL, Thermo Fisher Scientific) for 4 minutes. The reaction was stopped by the  addition of 0.5 M EDTA (final conc. 40 mM EDTA). Reverse cross-linking of digested DNA was performed for at least 30 minutes at 65 °C. Subsequently,  samples were diluted and treated with proteinase K (1h and 40°C, Thermo Fisher Scientific) for protein degradation. DNA fragments were extracted  using phenol and separated on an agarose gel to check for successful MNase digestion. Fragmented DNA was cut from the gel at 150 bp and extracted using the  Monarch® DNA Gel Extraction Kit (NEB®).
The quality control, library preparation and sequencing of the samples were performed by the Vienna BioCenter Core Facilities (Vienna, Austria). Library prep and sequencing was performed using poly-A enrichment kit (NEB) and Nextera Library prep kit.

treatment_protocol: no treatment

tag: replicate


title: Cut&Run non-reactive Ig control T58A replicate 1 spleen B cells stimulated for 48 hours with LPS


title: Sample13_PF_S89


title: Mnase_F_fujiA


title: Sample15_RF_S80

value: RF


title: ESC Obox5 RNA-seq rep2


title: Cut&Run H3K4Me2 WT replicate 2 spleen B cells stimulated for 48 hours with LPS


title: ESC Obox5 RNA-seq rep1


title: WT_IC

data_processing:
Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.36
Mapping was performed using BWA on the F. fujikuroi IMI58289 genome assembly.
bw (bigwig) files were prozessed and normalized using samtools, bedtools and wigToBigwig.
Assembly: F. fujikuroi IMI58289
Supplementary files format and content: bigwig

growth_protocol: The F. fujikuroi IMI58289 wild-type strain (FfWT) provided by Commonwealth Mycological Institute, Kew, UK, was used as a parental strain to generate the H2A.Z  knock-down strain (Tetoff::FfH2A.Z), the constitutive H2A.Z overexpression (OE::FfH2A.Z) strain as well as the N- and C-terminal  hemagglutinin (HA)-tagged H2A.Z (HA::FfH2A.Z, FfH2A.Z::HA) strains. Fungal mycelia were cultivated for three days in liquid ICI (6 mm glutamine) prior crosslinking with 1% formaldehyde. For immunoprecipitation, sonicated mycelia were incubated either with an anti-HA (Abcam, 9110),  an anti-H3K27me3- (Active motif, 39155) or an anti-H3K4me3- (CellSignal, 9751)  specific antibody. The assay was performed in biological duplicates,  including input controls for every strain.

extract_protocol:
ChIP standard protocol
Library preparation was don at the Vienna BioCenter Core facilities (Vienna, Austria) using NEB and Nextera Library prep kit.

treatment_protocol: Cultures inoculated with the TetOff::H2A.Z knock down strain were additionally supplemented  with 0-50 µg/mL DOX to facilitate FfH2A.Z gene silencing.

value: input control


title: Tet_off_IC


title: Sample12_PF_S73


title: ESC Obox3 RNA-seq rep2


title: Sample14_RF_S108


title: Cut&Run H3K4Me2 T58A replicate 2 spleen B cells stimulated for 48 hours with LPS


title: ESC Obox1 RNA-seq rep1


title: Cut&Run H3K4Me2 WT replicate 1 spleen B cells stimulated for 48 hours with LPS


title: Sample12_RF_S74


title: ESC Obox3 RNA-seq rep1


title: H2AZ_b

value: HA


title: Cut&Run H3K4Me2 T58A replicate 1 spleen B cells stimulated for 48 hours with LPS


title: H2AZ_a


title: ESC Obox6 RNA-seq rep1


title: ESC Dux RNA-seq rep2


title: Cut&Run H3K27Ac WT replicate 2 spleen B cells stimulated for 48 hours with LPS


title: H3K27_Tet_off_b

value: DOX


title: SK-N-BE2 shMETTL14_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

description:
shMETTL14-2
gene_count_matrix.txt

data_processing:
Raw reads were trimmed using Fastp v0.20.0
Removing low-quality reads and removing reads with size inferior to 50 bp (--length_required 50). Then, the reference genome and gene model annotation files were downloaded from the genome website directly GRCh38(Homo_sapiens.GRCh38.101.gtf).
Clean data were mapped to the reference genome using HISAT2 v 2.1.0. （http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015）Next, the mapped reads of each sample were assembled using StringTie v1.3.6 in a reference-based approach.
All RNAs were quantified as FPKM (Fragments Per Kilobase Million Mapped Reads) by HTSeq(v0.13.5,http://htseq.readthedocs.io/en/release_0.9.1).The formula was defined as FPKM = 106×F/ (NL×10-3), where F is the number of fragments assigned to a certain gene in a certain sample, N is the total number of mapped reads in the certain sample, and L is the length of the certain gene.
Differentially expressed genes were determined by edgeR, and genes withFDR<0.05 and |log2foldchange| >1 were identified as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes readcount values for each Sample.

value: Neuroblastoma cells


title: Sample13_RF_S90


title: Sample11_PF_S98

value: PF


title: ESC Dux RNA-seq rep1


title: Cut&Run H3K27Ac T58A replicate 2 spleen B cells stimulated for 48 hours with LPS


title: SK-N-BE2 shMETTL14_rep1

description:
shMETTL14-1
gene_count_matrix.txt


title: ESC control RNA-seq rep2


title: H3K27_Tet_off_a


title: SK-N-BE2 shNC_rep2

description:
shNC-2
gene_count_matrix.txt

value: shNC


title: Cut&Run H3K27Ac WT replicate 1 spleen B cells stimulated for 48 hours with LPS

value: WT


title: H3K27_WT2


title: Sample11_RF_S109


title: Cut&Run H3K27Ac T58A replicate 1 spleen B cells stimulated for 48 hours with LPS


title: H3K27_WT1


title: SK-N-BE2 shNC_rep1

description:
shNC-1
gene_count_matrix.txt


title: ESC unlabeled RNA rep3

data_processing:
For LET-seq and RNA-seq data, paired-end reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore! with a ‘--clip_R2 3’ option. After the reads were aligned, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts (version 1.6.5) and GENCODE annotation of the mm10 mouse genome (vM25) was used to analyze transcription levels with options ‘-p -O --fraction’. bigWig files were generated by deeptools bamCoverage with options '-bs 25 --normalizeUsing RPKM -ignore chrX chrM chrY --smoothLength 75'. The expression of each annotated gene was quantified by calculating TPM (transcripts per million) using R.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with options  ‘-X 700 --dovetail’ after removing adaptor sequences and low-quality reads by Trim Galore!. bigWig files were generated by bamCoverage from deepTools with parameters ‘-bs 50 --normalizeUsing RPKM --smoothLength 500’. MACS2 was used to call peaks with options ‘-q 0.05 -f BAMPE’.
Assembly: mm10
Supplementary files format and content: bigWig, tab-delimited text files indicating TPM values (for RNA-seq)
Library strategy: LET-seq

value: wild-type


title: Cut&Run Myc WT replicate 2 spleen B cells stimulated for 48 hours with LPS


title: ESC unlabeled RNA rep2

value: Embryonic stem cell


title: H3K4me_Tet_offH2AZ_b


title: H3K4me_Tet_offH2AZ_a


title: iPAX7 in vitro Replicate 1

city: Minneapolis

first: Sarah

last: Crist

state: Minnesota

address: 2231 6th St SE

institute: University of Minnesota

description:
7d_diff_A
7d_diff_A

data_processing:
Reads were trimmed using Trimmomatic (v0.33) and quality control on raw reads was performed with FastQC(v0.11.9) (mean quality score 36) was assessed.
STAR(v2.7.3a) was used to align to human (hg38) and mouse (mm10) reference genomes.
Subtraction of mouse sequences was performed using XenofilteR(v1.6).
Aligned reads were counted for gene associations against the UCSC genes data base with HTSeq(v0.11.0).
Differentially expressed genes were identified using edgeR (v3.42.4, negative binomial)
Assembly: mm10 and hg38
Supplementary files format and content: Comma separated value text files of raw counts for each sample (.CSV) - there is one file for counts mapped to human genome and one file for counts mapped to mouse genome
Supplementary files format and content: Raw sequencing data for each sample (.FASTQ)

source_name: In vitro myotube

extract_protocol:
Total RNA was isolated from iPAX7 in vitro-differentiated myotubes and homogenized tibialis anterior muscles using TRIzol (Invitrogen) and the PureLink RNA mini kit (Invitrogen, #12183025) with on-column DNaseI treatment following the manufacturer’s recommendations.
500 ng of total RNA was used to for generate unique dual-indexed (UDI) TruSeq stranded mRNA libraries.

treatment_protocol: 6–8-week-old male NSG and NSG-mdx4Cv mice were used for these experiments. One day before intramuscular cell transplantation, target muscles (tibialis anterior) were pre-injured with cardiotoxin (15 μl of 10 μM stock).  Myogenic progenitors were injected at 1.65×106 (resuspended in 15 μl of PBS) using a 26 g Hamilton syringe. As control, contralateral legs were injected with the same volume of PBS. Two months after transplantation muscles were collected for RNA isolation.

value: In vitro myotube

value: iPSC-derived myogenic progenitor

value: terminal differentiation


title: Cut&Run Myc T58A replicate 2 spleen B cells stimulated for 48 hours with LPS


title: ESC EU+ RNA rep3


title: Cut&Run Myc T58A replicate 1 spleen B cells stimulated for 48 hours with LPS


title: ESC unlabeled RNA rep1


title: H3K4me_WT2


title: H3K4me_WT1_DOX


title: CARM1-ChIPseq

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed."
The expression peaks were detected by MACS(Model-based Analysis for ChIP-Seq) using the parameter:-f BOWTIE -g hs -n C_Ip -w.
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files were generated using MACS2 and The R programming language-ChIPseeker

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Approximately 5 x 10^7 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibody against CARM1. The DNA was purified with a Qiagen PCR purification kit.
A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation  of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina sequencer following the manufacturer's protocols.

value: untreated

tag: chip antibody

value: CARM1 (Cell Signaling Technology, catlog#:12495S, lot#:2)


title: cKO_input (ChIP-seq)

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

data_processing:
RNA-seq reads were aligned to the GRCm38 genome assembly using g Salmon (v.1.1.0) using default parameters.Expression calculations and differential gene expression analysis were executed by tximport (v1.14.2) and DESeq2 (v1.26.0)  respectively.
DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp. After trimming with trimmomatic (v.0.36), high-quality reads were mapped to mm10 genome with bowtie 2(v2.4.1) using default parameters.Peaks were called with macs2 with default parameters relative to input sample.Manorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data
Genome_build: GRCm38
Supplementary_files_format_and_content: ReadCount.txt, cKO_WT-Diff (RNA-seq samples), bigwig (ChIP-seq samples)

source_name: cerebellum

extract_protocol: Freshly  cerebellar tissues isolated from of WT and EED-/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp.

value: cerebellum

value: post natal day 14

value: EED-/-


title: Input DNA


title: ESC EU+ RNA rep2


title: H3K4me_WT1


title: ESC EU+ RNA rep1


title: OE_H2AZ_T1_2

data_processing:
Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.36
Mapping was performed using BWA
and reverse transcripts were counted using python script HTSeq .
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation .
Assembly: Fusarium fujikuroi IMI58289
Supplementary files format and content: raw counts, RPKM, differential transcription and p-values

growth_protocol: The F. fujikuroi IMI58289 wild-type strain (FfWT) provided by Commonwealth Mycological Institute, Kew, UK, was used as a parental strain to generate the H2A.Z knock-down strain (Tetoff::FfH2A.Z), the constitutive H2A.Z overexpression (OE::FfH2A.Z) strain as well as the N- and C-terminal hemagglutinin (HA)-tagged H2A.Z (HA::FfH2A.Z, FfH2A.Z::HA) strains. Submerged fungal growth was performed in 100 mL Darken pre-culture medium (Darken et al., 1959) on a rotary shaker at 180 rpm, 30°C in constant darkness for 3 days.

extract_protocol:
Isolation of fungal RNA was performed with lyophilized and ground mycelia from cultivation on solid CM or under liquid-standard conditions (ICI supplemented with 6  glutamine) for 3-4 days. Total RNA was extracted from samples, using the RNA reagent TRIzol (Thermo Fisher Scientific) as described in the manufacturer’s manual.
Library preparation and sequencing of the samples was performed by the Vienna BioCenter Core facilities (Vienna, Austria).Library prep and sequencing was performed using poly-A enrichment kit (NEB) and Nextera Library prep kit.

treatment_protocol: Cultures inoculated with the TetOff::H2A.Z knock down strain were additionally supplemented with 0-50 µg/mL DOX to facilitate FfH2A.Z gene silencing. Flasks were incubated on a rotary shaker (180 rpm, 30°C) in the dark. Mycelia were harvested 3-4 days post inoculation (dpi) for RNA isolation.


title: ESC control RNA-seq rep1

value: hybrid C57BL/6 / 129


title: WT_input (ChIP-seq)


title: iPAX7 in vitro Replicate 2

description:
7d_diff_C
7d_diff_C


title: si-OCT4 POVPC treated 3

city: Cleveland

first: Olga

last: Cherepanova

state: Ohio

address: 9620 Carnegie Avenue

department: Cardiovascular and metabolic sciences

institute: Cleveland Clinic Foundation

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 12

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min

scan_protocol: The slides were scanned on an Agilent G2505C microarray scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw intensities were log2 transformed and quantile normalized. After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 12 samples were retained

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48, POVPC 24h, Replicate 3

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

treatment_protocol: Primary mouse aortic smooth muscle cells (MASMC) were isolated and grown as previously described (Cherepanova et al., 2016). For experiments, cells at the 70% confluency were transfected with blocking siOct4 or non-target siRNA (NT siRNA) for 48 hours in serum-free media, followed by the treatment with 10 µg/mL POVPC (Cayman Chem, #10031) or vehicle (DMSO) for 24 hours based on our previous findings (Pidkovka et al., 2007).

value: aortic smooth muscle cells

value: smooth muscle cells


title: OE_H2AZ_T1_1


title: cKO_H3K27ac (ChIP-seq)

value: H3K27ac(ChIP grade,ab4729,abcam)


title: Non-treated ESC non-specific RNA rep2


title: Non-treated ESC non-specific RNA rep1


title: cKO_H3K27me3 (ChIP-seq)

value: H3K27me3（ChIP grade, 07-449, Millipore)


title: Cut&Run Myc WT replicate 1 spleen B cells stimulated for 48 hours with LPS

value: Primary splenic B Cells

value: LPS stimulation, 48 hours


title: si-OCT4 POVPC treated 2

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 11

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48h, POVPC 24h, Replicate 2


title: OE_WT2

value: WT


title: Non-treated ESC unlabeled RNA rep2

value: Embryonic stem cell

value: wild-type


title: si-OCT4 POVPC treated 1

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 10

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48h, POVPC 24h, Replicate 1


title: OE_WT1


title: WT_H3K27ac (ChIP-seq)

extract_protocol:
Freshly  cerebellar tissues isolated from of WT and EED-/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: ESC 3xFLAG-Obox3 CUT&RUN rep2

data_processing:
For LET-seq and RNA-seq data, paired-end reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore! with a ‘--clip_R2 3’ option. After the reads were aligned, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts (version 1.6.5) and GENCODE annotation of the mm10 mouse genome (vM25) was used to analyze transcription levels with options ‘-p -O --fraction’. bigWig files were generated by deeptools bamCoverage with options '-bs 25 --normalizeUsing RPKM -ignore chrX chrM chrY --smoothLength 75'. The expression of each annotated gene was quantified by calculating TPM (transcripts per million) using R.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with options  ‘-X 700 --dovetail’ after removing adaptor sequences and low-quality reads by Trim Galore!. bigWig files were generated by bamCoverage from deepTools with parameters ‘-bs 50 --normalizeUsing RPKM --smoothLength 500’. MACS2 was used to call peaks with options ‘-q 0.05 -f BAMPE’.
Assembly: mm10
Supplementary files format and content: bigWig, tab-delimited text files indicating TPM values (for RNA-seq)
Library strategy: CUT&RUN

value: FLAG (Sigma, M2, F1804)


title: si-OCT4 DMSO treated 3

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 9

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48h, DMSO 24h, Replicate 3


title: cKO3 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff

extract_protocol:
Cerebelum were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.RNA-seq libraries from WT and EED-/-  at 14-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols


title: si-OCT4 DMSO treated 2

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 8

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48h, DMSO 24h, Replicate 2


title: tetoff_H2Az_T2_2

value: DOX


title: Non-treated ESC unlabeled RNA rep1


title: tetoff_H2Az_T2_1


title: ESC 3xFLAG-Obox3 CUT&RUN rep1


title: tetoff_H2Az_T1_2


title: cKO2 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff


title: cKO1 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff


title: ESC negative control CUT&RUN rep1


title: WT_H3K27me3 (ChIP-seq)


title: WT3 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff


title: Parp12KD_rep1

first: Manqi

last: Chen

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
All reads passed filter were trimmed to remove adaptor sequences and low-quality bases using trim_galore(v0.6.4).
Reads were aligned to the mm10 genome reference using STAR(2.7.5b), and the counts were calculated using featureCounts(v2.0.0).
The differentially expressed genes were calculated and normalized using R package DESeq2 (v1.28.1).
Assembly: mm10
Supplementary files format and content: A tab-delimited text file includes raw gene count for all samples.

source_name: Ovary

extract_protocol:
Total RNA was extracted by the RNeasy Micro Kit (Qiagen, Germantown, MD, USA), and then subjected to mRNA isolation using NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA).
Construction of the mRNA library was performed using NEB Next UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual.

value: Ovary

value: Oocyte

value: Parp12 knockdown

value: Direct separation from the ovary


title: si-OCT4 DMSO treated 1

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 7

source_name: Primary mouse aortic smooth muscle cells (MASMC), siOCT4 48h, DMSO 24h, Replicate 1


title: Negative control non-target siRNA POVPC treated 3

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 6

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 3


title: Negative control non-target siRNA POVPC treated 2

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 5

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 2


title: Parp12KD_rep2


title: WT2 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff

value: cerebellum

value: post natal day 14


title: tetoff_H2Az_T1_1


title: WT_DOX1


title: WT_DOX2


title: Negative control non-target siRNA POVPC treated 1

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 4

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 1

value: aortic smooth muscle cells


title: Control_rep2


title: WT1 (RNA-seq)

description: ReadCount.txt, cKO_WT-Diff


title: Control_rep1


title: WT_CDK1as_Halo_CAP-H2_30min_Input(biol rep1)_ChIP-Seq

status: Public on Apr 01 2024

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig

organism: Gallus gallus

source_name: Bursa

growth_protocol: RPMI1640, 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenchng and cell lysis, chromatin was shear using Diagenode Biorupter.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645) AND NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB #E7335). 15ng of template was used for library preparation for input and IP samples and amplified using 11 cycle on the thermocycler. Libraries were size selected at 200bp to 500bp length range using SPRIselect bead from Beckman Coulter. Purified libraries were analysed by Agilent 2100 Bioanalyzer by using Agilent High Sensitivity DNA Kit (#5067-4626).

treatment_protocol: Cells were blocked at G2 with 1NMPP1 (G2). After 1NMPP1 washout, cells were collected at 5 min (early prophase), 7.5 min (late prophase), and 30 min (late prometaphase).

value: Bursa

value: lymphoblast

tag: time

value: 30 min


title: Negative control non-target siRNA DMSO treated 3

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 3

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 3

tag: tissue

value: smooth muscle cells


title: Negative control non-target siRNA DMSO treated 2

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 2

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 2


title: WT_CDK1as_Halo_CAP-H2_30min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_7.5min_Input(biol rep1)_ChIP-Seq

value: 7.5 min


title: WT_CDK1as_Halo_CAP-H2_7.5min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_G2_Input(biol rep2)_ChIP-Seq


title: Negative control non-target siRNA DMSO treated 1

description: Small RNA Array expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 1

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 1


title: WT_CDK1as_Halo_CAP-H2_5min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_7.5min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_G2_Input (biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_30min_Input(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_30min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_30min (biol rep2)_ChIP-Seq

data_processing:
Normalise ChIP/Input with bamCompare -bs 20 --normalizeUsing BPM --exactScaling
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig

value: Halo-Trap Agarose affinity beads (Chromotek #ota)


title: WT_CDK1as_CAP-H-Halo_7.5min_Input(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_5min_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_G2_Input(biol rep2)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_5min_Input(biol rep1)_ChIP-Seq

value: 5 min


title: WT_CDK1as_Halo_CAP-H2_G2(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_7.5min(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_7.5min(biol rep1)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_5min(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_30min(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_5min(biol rep2)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_5min_Input(biol rep1)_ChIP-Seq


title: WT_CDK1as_Halo_CAP-H2_G2(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_30min(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_5min(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_5min(biol rep2)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_G2(biol rep2)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_7.5min(biol rep1)_ChIP-Seq


title: WT_CDK1as_CAP-H-Halo_G2(biol rep1)_ChIP-Seq


title: ppk_delta_t60_riff_rep3

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: rRNA depleted RNA, umi library

data_processing:
Initial read preprocessing, alignment and QC using the IPOD-HR processing pipeline version 2.7.1
overlaps of aligned reads to genes were quantified using the summarizeOverlaps() function of the R package GenomicAlignments (version 1.26.0) running under R 4.0.2, with options  “singleEnd = FALSE, inter.feature = FALSE, ignore.strand = TRUE, mode = "IntersectionStrict",fragments = TRUE”.
ead counts for each feature (gen) were then normalized by the total read count for that sample, and then sequencing depths of genomic features further rescaled by the median abundance of ERCC transcripts in that sample (considering only ERCC transcripts with a relative abundance greater than 5*10-4) in order to provide a relative estimate of per-cell transcript abundance
For each gene, we then fitted an exponential decay equation (y=a*exp(-1*t/b), where y is the normalized transcript abundance, a and b are coefficients to be fitted, and t is the time) to the data for each time course, using the scipy.optimize.curve_fit function from scipy 1.8.0, with default optimization settings, and a and b initialized to 0.001 and 20, respectively; a represents a baseline abundance (at t=0) for each transcript, and b is the exponential decay time constant (in minutes).
Assembly: E coli MG1655 gene product set from regulonDB, plus ERCC spikein mix
Supplementary files format and content: halflives_for_geo.csv – contains the results of the exponential decay fits for each gene/condition combination

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cells

growth_protocol: N-24 WT and Δppk E. coli were supplemented with 150 µg/mL rifampicin (#R3501, Sigma-Aldrich) and incubated at 37°C with 200 rpm shaking.

extract_protocol:
On ice, each sample pellet was resuspended in 90 µl of 1X TE (10 mM Tris pH 7.0, 1 mM EDTA pH 8.0), briefly centrifuged to remove liquid from tube walls and transferred to 1.5 ml tube, and then transferred to 1.5 ml microfuge tubes. Then 1 µl of Ready-Lyse Lysozyme Solution (LGC Biosearch Technologies) was added to each sample and mixed. Samples were incubated at 30°C for 15 min and returned to ice. Then, 10 µl of Proteinase K (Thermo-Fisher) was added to each sample and mixed. Samples were incubated at 23°C for 15 min, with resuspension every two minutes then returned to ice. EERC RNA spike-in control mix (Ambion) was diluted 1:25 in water as one batch (8.6 µl of EERC, 206.4 µl water).Then, 5 µl of the diluted mix was added to each sample, except for Δppk t=60 (no rifampicin) replicate 1, which received 1.6 µl instead of 5 µl. After vortexing the samples, they were clarified by centrifugation (12,000 r.c.f., 30 sec.) and up to 250 µl of clarified lysate was transferred to a new tube. The samples were cleaned using RNA Clean & Concentrator-96 (Zymo Research) per manufacturer's directions for total RNA clean-up, and eluted with 25 µl of water per sample. Each sample was transferred to tubes that contained 60 µl of water, 10 µl of 10X Baseline Zero DNase buffer, 5 µl of Baseline Zero DNase (LGC Biosearch Technologies), and 2 µl of RNase Inhibitor, Murine (recombinant, NEB) in each tube. Samples were incubated at 37°C for 30 min. The samples were re-cleaned using RNA Clean & Concentrator-96 (Zymo Research) per manufacturer's directions for total RNA clean-up, and eluted with 20 µl water per sample. The concentration of RNA was determined using 5 µl samples and Quantifluor RNA system (Promega) per manufacturer's directions for quantitating RNA in multiwell plates.
Appropriate amounts of nuclease-free water were added to 0.1 µg of RNA per sample to achieve 11 µl of starting material for NEBNext rRNA Depletion Kit (Bacterial, NEB). The kit was used per manufacturer's directions to remove rRNA from the samples. Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Samples were prepared per kit directions except that 2.5 µl of diluted (1:100) NEBNext Unique Dual Index UMI Adaptors DNA Set 1 was used instead of the NEBNext Adaptor for Illumina, and that Omega Mag-Bind TotalPure NGS Beads were used instead of NEBNext Sample beads for post second-strand synthesis, post adapter ligation, and post PCR clean-up steps. Pooled libraries were subjected to sequencing on a NextSeq 2000 instrument.

treatment_protocol: Samples were collected before rifampicin addition, or at 10, 30 and 60 min after treatment, and were immediately mixed with RNAProtect® Bacteria Reagent (#1018380, Qiagen); for the post-treatment timepoints, a separate untreated control was collected after the same lag time. Cells were pelleted and stored at -80°C. Each sample was also plated for CFUs at the time of harvest in order to provide a normalization factor (used below). Three biological replicates were performed for each genotype/condition combination.

value: cells

value: delta-ppk with hfq-mcherry

tag: biological replicate

value: biological replicate 3

value: time 60 min

value: rifampicin treated


title: ppk_delta_t30_rep3

description: rRNA depleted RNA, umi library

value: time 30 min

tag: treatment

value: no drug


title: WT_CDK1as_Halo_CAP-H2_30min(biol rep1)_ChIP-Seq


title: ppk_delta_t60_rep3

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_riff_rep3

description: rRNA depleted RNA, umi library

value: time 10 min


title: WT_CDK1as_CAP-H-Halo_G2_Input(biol rep1)_ChIP-Seq


title: ppk_delta_t00_rep3

description: rRNA depleted RNA, umi library

value: time 00 min


title: wt_t30_riff_rep3

description: rRNA depleted RNA, umi library

value: wild-type with hfq-mcherry


title: wt_t10_rep3

description: rRNA depleted RNA, umi library

value: Time 10 min


title: wt_t10_riff_rep3

description: rRNA depleted RNA, umi library


title: wt_t30_rep3

description: rRNA depleted RNA, umi library


title: wt_t60_riff_rep3

description: rRNA depleted RNA, umi library


title: wt_t00_rep3

description: rRNA depleted RNA, umi library

value: Time 0 min


title: ppk_delta_t60_rep2

description: rRNA depleted RNA, umi library

value: biological replicate 2


title: ppk_delta_t30_riff_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t30_rep2

description: rRNA depleted RNA, umi library


title: WT_CDK1as_CAP-H-Halo_7.5min(biol rep2)_ChIP-Seq

value: Bursa

value: lymphoblast


title: ppk_delta_t00_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t60_riff_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_riff_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t30_riff_rep3

description: rRNA depleted RNA, umi library


title: wt_t60_rep2

description: rRNA depleted RNA, umi library


title: wt_t30_rep2

description: rRNA depleted RNA, umi library


title: wt_t10_riff_rep2

description: rRNA depleted RNA, umi library


title: wt_t00_rep2

description: rRNA depleted RNA, umi library


title: wt_t60_riff_rep2

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_rep3

description: rRNA depleted RNA, umi library


title: ppk_delta_t60_riff_rep1

description: rRNA depleted RNA, umi library

value: biological replicate 1


title: wt_t60_rep3

description: rRNA depleted RNA, umi library


title: ppk_delta_t30_riff_rep1

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_rep1

description: rRNA depleted RNA, umi library


title: ppk_delta_t10_riff_rep1

description: rRNA depleted RNA, umi library


title: ppk_delta_t60_rep1

description: rRNA depleted RNA, umi library


title: wt_t60_riff_rep1

description: rRNA depleted RNA, umi library


title: wt_t30_riff_rep1

description: rRNA depleted RNA, umi library


title: wt_t60_rep1

description: rRNA depleted RNA, umi library


title: wt_t30_rep1

description: rRNA depleted RNA, umi library


title: ppk_delta_t00_rep1

description: rRNA depleted RNA, umi library


title: wt_t10_rep1

description: rRNA depleted RNA, umi library


title: wt_t00_rep1

description: rRNA depleted RNA, umi library


title: wt_t10_rep2

description: rRNA depleted RNA, umi library


title: wt_r4_t24_extract

description:
wt_pullVinp_minus_dppk_pullVinp_t24.csv
wt_pulldown_vs_input_t24.csv

data_processing:
Raw RNA-seq reads were preprocessed using the IPOD-HR pipeline version 2.7.1 , acting through the preprocessing and alignment stages
overlaps of aligned reads to genes were quantified using the summarizeOverlaps() function of the R package GenomicAlignments (version 1.26.0) running under R 4.0.2, with options  “singleEnd = FALSE, inter.feature = FALSE, ignore.strand = TRUE, mode = "IntersectionStrict",fragments = TRUE”
Differential expression calling was then performed using DeSeq2 , with a model including terms for the sample genotype, sample type (input or IP), timepoint (0h, 6h, 12h, or 24hr), sequencing preparation batch, and the following interaction terms: genotype:sampletype, timepoint:sampletype genotype:timepoint:sampletype, batch:sampletype.
Multiple hypothesis testing correction was performed using the IHW method .
Assembly: RegulonDB gene set (downloaded March 2023)
Supplementary files format and content: pulldown_t*.csv – shows significance testing for the ppk-independent pulldown strength at a particular timepoint
Supplementary files format and content: wt_pullVinp_minus_dppk_pullVinp_t*.csv – significance testing on the polyP-dependent pulldown effect (that is, log2( [WT IP/WT inp]/[ppk IP/ppk inp]) ) ) at the specified timepoint
Supplementary files format and content: input_abundances_vs_dppk_t*.csv – significance testing for difference in RNAseq (input) levels between WT and ppk cells at the indicated timepoint
Supplementary files format and content: wt_pulldown_vs_input_t*.csv – differential abundance calling for the WT pulldown sample at each timepoint compared with the corresponding input

growth_protocol: WT and ?ppk Hfq-mCherry strains were streaked onto LB agar plates from cryogenic storage and grown at 37°C. Colonies (three biological replicates per strain) were inoculated into N+ Gutnick medium and grown overnight at 37°C with shaking at 200 rpm. The overnight culture was back-diluted to OD600=0.01 in 250 mL N- Gutnick medium.

extract_protocol:
Three biological replicates of samples were extracted in three separate experiments (one per replicate). Each pellet (~ 40 O.D. * mL) was resuspended in 600 µL of lysis buffer (10 mM Tris pH 8.0, 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche, cat. No. 11836170001), 50 mM NaCl, 3 µL of Ready Lyse lysozyme per mL) and incubated for 15 minutes at 30°C. Samples were placed on ice, then sonicated in the ice bath at 25% amplitude for 20 seconds (5 seconds on, 15 seconds off). The samples were clarified by centrifugation (16,000 r.c.f.,10 minutes, 4°C), and the liquid transferred into new microfuge tubes. To each sample, an equal volume of 2x IP buffer (200 mM Tris, pH 8.0, 600 mM NaCl, 4% (v/v) Triton X-100 with 2× protease inhibitors (Roche, cat. No. 11836170001) and 0.2 mg/ml BSA) was added and mixed by inversion. To preclear samples, 100 ?L of pre-washed (add 100ul of beads per sample in microfuge tube, place on magnetic stand, remove storage buffer, add 1 mL 1X IP buffer, mix by inversion, clear using magnetic stand, remove liquid, resuspend in 100 µL of 1x IP buffer per sample) protein G magnetic beads (NEB; lot 101325116) were added to each sample and incubated for 2 hours on a nutating platform at 4°C. Beads were cleared using a magnetic stand, and the liquid was transferred to new 2 mL microfuge tubes. To keep as input material, 100 µL of each sample was transferred to a new tube containing 400 µL of ChIP elution buffer (50 mM Tris, pH 7.0, 10 mM EDTA, 1% (w/v) SDS), mixed, and kept on ice until proteinase K (10 µL per sample; Fermentas, 50 mg/mL) digestion. To each ChIP sample, 8 µL of mCherry Monoclonal Antibody 16D7 (Invitrogen, M11217, lot #XC345714) was added and incubated for 2 hours on a nutating platform at 4°C. To capture the antibodies, 100 ?L of pre-washed (see above) protein G magnetic beads (NEB; lot 101325116) were added to each ChIP sample and incubated 2 hours on a nutating platform. Beads from the ChIP samples were washed, in series, with 1 mL of Buffer A (100 mM Tris pH 8.0, 250mM LiCl, 0.2% (v/v) Triton x-100, 1 mM EDTA), Buffer B (10 mM Tris pH 8.0, 500 mM NaCl, 0.1% (v/v) Triton x-100, 1 mM EDTA, sodium deoxycholate), Buffer C (10 mM Tris pH 8.0, 500 mM NaCl, 0.1% (v/v) Triton x-100, 1 mM EDTA), 1X IP buffer (100 mM Tris pH 8.0, 300 mM NaCl, 2% (v/v) Triton x-100, 1 mM EDTA) and 1X TE (10 mM Tris pH 7.0, 1 mM EDTA). Beads from the ChIP samples were resuspended in 500 ?L ChIP elution buffer. To recover the RNA, for each input and ChIP sample, 10 µL of RNase/DNase free proteinase K was added. After mixing by inversion, all tubes were incubated for 2 hr at 37°C. This was followed by phenol/chloroform extraction clean up (500 ?L of acidic 5:1 phenol/chloroform (VWR, E277) was added, mixed, and allowed to separate into layers at 16,000 r.c.f., 5 minutes, 4°C); the water layer was transferred to a new tube with 500 ?L of 24:1 chloroform/isoamyl alcohol, mixed, allowed to separate as before at 16,000 r.c.f., 5 minutes, 4°C); finally, the water layer was transferred to a new tube). Nucleic acids from the samples were precipitated by the addition of 1/25 volume of 5 M NaCl, 2 ?L of Glycoblue coprecipitant (Invitrogen), 1 volume of 100% (v/v) ethanol and 1 volume of 100% (v/v) isopropanol, mixed, and then incubated for 1 hour at 4°C, then > 2 hr  (up to overnight) at -20°C. Nucleic acids were pelleted via centrifugation (16,000 r.c.f., 15 minutes, 4°C), washed once with ice-cold 95% (v/v) ethanol, and air dried. Pellets were resuspended in 83 ?L of 0.1X TE (1 mM Tris pH 7.0, 0.1 mM EDTA) and stored at -80°C. The DNA was removed from the samples 10 ?L of 10X Baseline-ZERO Buffer plus 5 ?L of Baseline-ZERO DNase (Lucigen) and 2 ?L of murine RNase Inhibitor (NEB), and incubated 37°C for 30 min. The RNA was collected/cleaned using the Zymo RNA Clean and Concentrate Kit-96 per kit directions (Zymo Research) and eluted with either 15 (extracts) or 20 ?L (inputs) of water. The concentration of RNA was determined with 3 ?L of each sample using QuantiFluor RNA System (Promega) and the provided standards.
Input material obtained from Hfq-mCherry RNA ChIP was treated with NEBNext rRNA Depletion Kit (Bacteria) [NEB]. For each input, 11 µL of diluted material (0.15-0.44 µg) was used. Depletion performed per kit directions except that Zymo RNA Clean and Concentrate Kit-96 [Zymo Research, per kit directions (3000 r.c.f., 5 min centrifugation) and eluted with 11 ?L of water] was substituted for the post DNase I digestion bead clean-up in an attempt to preserve small RNAs that may be present. Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and either 5 ?L of rRNA depleted material (inputs) or 5 ?L of RNA (5 - 36 ng) obtained by immunoprecipitation (extracts). Samples were prepared per kit directions except that samples were fragmented for 1 min, the post-second strand synthesis bead clean-up was replaced with an Oligo Clean and Concentrate kit [Zymo Research, per kit directions (3000 r.c.f., 5 min centrifugation) and eluted with 25 ?L of water, and add 25 ?L of water prior to end prep reaction], diluted (1:20)  NEBNext Unique Dual Index UMI Adaptors DNA Set 1 were used instead of the NEBNext Adaptor for Illumina, the post ligation bead binding involved 174 ?L of Axyprep beads (Axygen) and 68 ?L of isopropanol, and the NEBNext Primer Mix was used for the PCR amplification step. Pooled libraries were subjected to Illumina sequencing on a NextSeq platform with 38 x 37 bp paired end reads.

treatment_protocol: After nitrogen starvation for the indicated amount of time, cultures equivalent to 40 mL OD600=1.0 were collected and immediately spun down for 3 min at 13,000×g at 4°C in a fixed-angle rotor. The cell pellets were shock-frozen in a dry ice-ethanol bath, and stored at -80°C.

value: 24 hr

value: nitrogen starvation

tag: sample type

value: mcherry-RIP


title: wt_r4_t06_extract

description:
wt_pullVinp_minus_dppk_pullVinp_t06.csv
wt_pulldown_vs_input_t06.csv

value: cells

value: 06 hr


title: wt_r4_t00_extract

description:
wt_pulldown_vs_input_t0.csv
wt_pullVinp_minus_dppk_pullVinp_t0.csv

value: 00 hr


title: wt_r4_t12_input

value: 12 hr

value: matched input for mcherry RIP


title: 7B 42-2 Liver Met Gstt1 shRNA 2

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description:
CFa13-3
Control_vs_Gstt1_KD_CPM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using application at CLC genomic benchwork v 11.0.1 (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm9 using application at CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed at CLC genomic benchwork
Assembly: mm9

source_name: 42-2 Liver Met

growth_protocol: Lung and Liver metastatic cell lines were derived from spontaneous metastases from the above GEMM models. Cells were maintained in 2D culture conditions (RPMI supplemented with 10% fetal bovine serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cells were infected with lentiviral particles expressing either NT control, Gstt1 shRNA 1 or Gstt1 shRNA 2 using polybrene
n/a

value: 42-2 Liver Met

tag: cell type

value: PDAC Liver Metastatic Tumor Cells

value: Gstt1 shRNA 2 under Puromycin selection

value: cells were infected with lentivirus, selected for 48 hours with puromycin and collected for RNA after one split


title: wt_r4_t12_extract

description:
wt_pullVinp_minus_dppk_pullVinp_t12.csv
wt_pulldown_vs_input_t12.csv

tag: genotype

value: wild-type with hfq-mcherry


title: 4C 6-3 Liver Met Gstt1 shRNA 2

description:
CFa12-2
Control_vs_Gstt1_KD_CPM.txt

source_name: 6-3 Liver Met

tag: cell line

value: 6-3 Liver Met


title: wt_r4_t06_input


title: wt_r4_t00_input


title: wt_t30_riff_rep2

description: rRNA depleted RNA, umi library

value: biological replicate 2

value: time 30 min

value: rifampicin treated


title: ppk_delta_t30_rep1

description: rRNA depleted RNA, umi library

value: delta-ppk with hfq-mcherry

value: biological replicate 1

value: no drug


title: delta_r3_t24_input

value: cells

value: 24 hr

value: nitrogen starvation


title: 5B 13-2 Liver Met Gstt1 shRNA 1

description:
CFa12-3
Control_vs_Gstt1_KD_CPM.txt

source_name: 13-2 Liver Met

value: 13-2 Liver Met

value: Gstt1 shRNA 1 under Puromycin selection


title: wt_t10_riff_rep1

description: rRNA depleted RNA, umi library

value: Time 10 min


title: delta_r3_t12_input

value: 12 hr

value: matched input for mcherry RIP


title: delta_r3_t00_input

value: 00 hr


title: 2C G45-2 Liver Met Gstt1 shRNA 2

description:
CFa11-6
Control_vs_Gstt1_KD_CPM.txt

source_name: G45-2 Liver Met

value: G45-2 Liver Met

value: PDAC Liver Metastatic Tumor Cells

value: Gstt1 shRNA 2 under Puromycin selection

value: cells were infected with lentivirus, selected for 48 hours with puromycin and collected for RNA after one split


title: delta_r3_t06_input

value: 06 hr


title: 2B G45-2 Liver Met Gstt1 shRNA 1

description:
CFa11-5
Control_vs_Gstt1_KD_CPM.txt


title: wt_r3_t12_input

value: wild-type with hfq-mcherry


title: wt_r3_t24_input


title: 3E 42-3 Lung Met Gstt1 shRNA 1

description:
CFa8-9
Control_vs_Gstt1_KD_CPM.txt

source_name: 42-3 Lung Met

value: 42-3 Lung Met

value: PDAC Lung Metastatic Tumor Cells


title: 3G 42-2 Liver Met Gstt1 shRNA 1

description:
CFa8-11
Control_vs_Gstt1_KD_CPM.txt

value: 42-2 Liver Met


title: wt_r3_t06_input

value: cells


title: wt_r4_t24_input

value: 24 hr

value: nitrogen starvation


title: 3B 42-3 Lung Met Gstt1 shRNA 2

description:
CFa11-8
Control_vs_Gstt1_KD_CPM.txt


title: 1F 6-2 Lung Met Gstt1 shRNA 1

description:
CFa8-10
Control_vs_Gstt1_KD_CPM.txt

source_name: 6-2 Lung Met

value: 6-2 Lung Met

value: Gstt1 shRNA 1 under Puromycin selection


title: delta_r2_t24_input

value: delta-ppk with hfq-mcherry


title: 5A 13-2 Liver Met NT Control

description:
CFa11-10
Control_vs_Gstt1_KD_CPM.txt

value: 13-2 Liver Met

value: NT shRNA Control under Puromycin selection


title: 4B 6-3 Liver Met Gstt1 shRNA 1

description:
CFa12-1
Control_vs_Gstt1_KD_CPM.txt

value: 6-3 Liver Met


title: 4A 6-3 Liver Met NT Control

description:
CFa11-9
Control_vs_Gstt1_KD_CPM.txt

value: PDAC Liver Metastatic Tumor Cells


title: delta_r2_t12_input

value: 12 hr

value: matched input for mcherry RIP


title: 2A G45-2 Liver Met NT Control

description:
CFa11-4
Control_vs_Gstt1_KD_CPM.txt

value: G45-2 Liver Met

value: cells were infected with lentivirus, selected for 48 hours with puromycin and collected for RNA after one split


title: delta_r2_t00_input

value: 00 hr


title: 1G 42-2 Liver Met NT Control

description:
CFa8-6
Control_vs_Gstt1_KD_CPM.txt


title: delta_r2_t06_input

value: 06 hr


title: wt_r3_t00_input

value: wild-type with hfq-mcherry


title: 7A 42-2 Liver Met NT Control

description:
CFa13-2
Control_vs_Gstt1_KD_CPM.txt

value: 42-2 Liver Met


title: wt_r2_t24_input

value: cells

value: 24 hr


title: 3F 6-2 Lung Met NT Control

description:
CFa8-5
Control_vs_Gstt1_KD_CPM.txt

value: 6-2 Lung Met

value: PDAC Lung Metastatic Tumor Cells


title: wt_r2_t06_input

value: nitrogen starvation


title: 1E 42-3 Lung Met NT Control

description:
CFa8-4
Control_vs_Gstt1_KD_CPM.txt

value: 42-3 Lung Met


title: DTC3

description:
CFa14-3
mCherry_Populations_DTCs_CPM.txt

source_name: n/a GFP

growth_protocol: GFP and mCherryHigh and mCherryLow sorted cells or GFP positive DTCs from lung tumors of tail vein injected mice

extract_protocol:
RNA was harvested using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher Scientific). A minimum of 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Clontech's SMART-seq v4 Ultra Low Input RNA Kit followed by library preparation using Illumina's Nextera XT kit following manufacturer's protocols.

treatment_protocol:
n/a
n/a

value: n/a GFP

value: PDAC Lung Metastatic Tumor Cells expressing GFP and Gstt1-mCherry

value: 5 days


title: 3A 42-3 Lung Met NT Control

description:
CFa11-7
Control_vs_Gstt1_KD_CPM.txt

value: NT shRNA Control under Puromycin selection


title: delta_r1_t24_input

value: delta-ppk with hfq-mcherry

value: matched input for mcherry RIP


title: wt_r2_t00_input


title: DTC2

description:
CFa14-2
mCherry_Populations_DTCs_CPM.txt


title: DTC1

description:
CFa14-1
mCherry_Populations_DTCs_CPM.txt


title: delta_r1_t12_input

value: 12 hr


title: delta_r1_t06_input


title: 6F_mCherryHigh6

description:
CFa13-1
mCherry_Populations_DTCs_CPM.txt

source_name: n/a GFP/mCherryHigh sorted cells

value: n/a GFP/mCherryHigh sorted cells

value: 6 weeks


title: delta_r1_t00_input

value: 00 hr


title: wt_r1_t24_input

value: wild-type with hfq-mcherry


title: 5F_mCherryLow6

description:
CFa12-6
mCherry_Populations_DTCs_CPM.txt

source_name: n/a GFP/mCherryLow sorted cells

value: n/a GFP/mCherryLow sorted cells


title: 6A_mCherryHigh1

description:
CFa10-8
mCherry_Populations_DTCs_CPM.txt


title: wt_r1_t06_input

value: cells

value: 06 hr


title: 5E_mCherryLow5

description:
CFa12-5
mCherry_Populations_DTCs_CPM.txt


title: 5A_mCherryLow1

description:
CFa10-7
mCherry_Populations_DTCs_CPM.txt


title: wt_r1_t12_input


title: wt_r1_t00_input


title: delta_r3_t24_extract

value: 24 hr

value: mcherry-RIP


title: delta_r3_t12_extract

value: nitrogen starvation


title: 4T4-primary

description:
CFa1-24
CFa1_Bulk_Tissue_CPM.txt

source_name: n/a bulk tissue

growth_protocol: Bulk tumor tissue from orthotopic mouse models

value: n/a bulk tissue

value: BC primary tumor

value: 4T1 derived

value: 28 days


title: delta_r3_t06_extract

value: delta-ppk with hfq-mcherry


title: 4T4-1 lung met

description:
CFa1-23
CFa1_Bulk_Tissue_CPM.txt

value: BC Lung metastatic tumor


title: 4T3-primary

description:
CFa1-22
CFa1_Bulk_Tissue_CPM.txt


title: 4T3-1 lung met

description:
CFa1-21
CFa1_Bulk_Tissue_CPM.txt


title: delta_r3_t00_extract


title: wt_r2_t12_input

value: 12 hr

value: matched input for mcherry RIP


title: 4T2-primary

description:
CFa1-20
CFa1_Bulk_Tissue_CPM.txt


title: wt_r3_t24_extract


title: 4T2-1 lung met

description:
CFa1-19
CFa1_Bulk_Tissue_CPM.txt


title: wt_r3_t12_extract


title: 6E_mCherryHigh5

description:
CFa12-10
mCherry_Populations_DTCs_CPM.txt

value: n/a GFP/mCherryHigh sorted cells

value: PDAC Lung Metastatic Tumor Cells expressing GFP and Gstt1-mCherry

value: 6 weeks


title: wt_r3_t00_extract

value: wild-type with hfq-mcherry

value: 00 hr


title: wt_r3_t06_extract

value: cells

value: 06 hr


title: 4T1-primary

description:
CFa1-18
CFa1_Bulk_Tissue_CPM.txt


title: CF16-2 liver met

description:
CFa1-14
CFa1_Bulk_Tissue_CPM.txt

value: PDAC Liver metastatic tumor

value: 21.14 weeks


title: CF16-3 lung met

description:
CFa1-15
CFa1_Bulk_Tissue_CPM.txt

value: n/a bulk tissue

value: PDAC Lung metastatic tumor


title: delta_r2_t24_extract

value: 24 hr

value: nitrogen starvation

value: mcherry-RIP


title: delta_r2_t06_extract

value: delta-ppk with hfq-mcherry


title: CF15-2 liver met

description:
CFa1-10
CFa1_Bulk_Tissue_CPM.txt

value: 27.71 weeks


title: CF16-primary

description:
CFa1-16
CFa1_Bulk_Tissue_CPM.txt

value: PDAC primary tumor


title: CF15-3 lung met

description:
CFa1-11
CFa1_Bulk_Tissue_CPM.txt


title: delta_r2_t12_extract

value: 12 hr


title: wt_r2_t06_extract


title: delta_r2_t00_extract


title: wt_r2_t12_extract


title: CF13-3 lung met

description:
Cfa1-07
CFa1_Bulk_Tissue_CPM.txt

value: 28 weeks


title: delta_r1_t24_extract


title: CF15-primary

description:
CFa1-12
CFa1_Bulk_Tissue_CPM.txt


title: 4T1-1 lung met

description:
CFa1-17
CFa1_Bulk_Tissue_CPM.txt

value: BC Lung metastatic tumor

value: 4T1 derived

value: 28 days


title: delta_r1_t12_extract

value: cells


title: CF13-primary

description:
CFa1-08
CFa1_Bulk_Tissue_CPM.txt


title: CF6-3 liver met

description:
CFa1-03
CFa1_Bulk_Tissue_CPM.txt

value: 31.29 weeks


title: CF6-2 lung met

description:
CFa1-02
CFa1_Bulk_Tissue_CPM.txt


title: delta_r1_t00_extract

value: 00 hr


title: delta_r1_t06_extract

value: 06 hr


title: PDACLiverMetYFP _5

description:
CFa7-9
CFa7_YFP_GFP_CPM.txt

source_name: n/a YFP sorted cells

growth_protocol: YFP and GFP sorted tumor cells from orthotopic mouse models

value: n/a YFP sorted cells

value: PDAC Liver metastatic tumor cells

value: 28.95 weeks


title: CF6-primary

description:
CFa1-04
CFa1_Bulk_Tissue_CPM.txt

value: n/a bulk tissue


title: wt_r1_t24_extract

value: wild-type with hfq-mcherry

value: 24 hr

value: nitrogen starvation

value: mcherry-RIP


title: PDACLiverMetYFP _1

description:
CFa7-11
CFa7_YFP_GFP_CPM.txt

value: 25.67 weeks


title: wt_r2_t24_extract


title: wt_r1_t12_extract

value: 12 hr


title: wt_r1_t06_extract


title: wt_r1_t00_extract


title: BCLungMetGFP _4

description:
CFa7-3
CFa7_YFP_GFP_CPM.txt

source_name: n/a GFP sorted cells

value: n/a GFP sorted cells

value: BC Lung metastatic tumor cells

value: 4T1-eGFP derived


title: PDACPrimaryYFP _1

description:
CFa7-7
CFa7_YFP_GFP_CPM.txt

value: PDAC primary tumor cells


title: wt_r2_t00_extract

value: cells


title: PDACPrimaryYFP _5

description:
CFa7-8
CFa7_YFP_GFP_CPM.txt


title: A. burtoni, testes, rep3

city: Cambridge

first: Miguel

middle: Vasconcelos

last: Almeida

address: Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

description:
Abu_tes_rep3
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt

data_processing:
Illumina adapters and reads with low-quality calls were filtered out with Trimmomatic v0.39 (Bolger et al., 2014) using options SLIDINGWINDOW:4:28 MINLEN:36.
We mapped trimmed reads to the genome, using STAR v2.5.4b (Dobin et al., 2013) with options --outTmpDir --readFilesCommand zcat ‑‑genomeDir ‑‑readFilesIn {R1} {R2} --outSAMtype BAM SortedByCoordinate ‑‑outFilterType BySJout --outFilterMultimapNmax 150 ‑‑winAnchorMultimapNmax 150 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 ‑‑outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000000 --alignMatesGapMax 100000000 --outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
The resulting BAM files were used as inputs for TEtranscripts v2.2.1 (Jin et al., 2015) with options -t -c --GTF --TE --stranded reverse ‑‑project --SortByPos.
For A. calliptera samples, gene expression (without TEs) was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 ‑2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Acal.txt: Tab-delimited file includes raw counts for genes and TEs in each A. calliptera sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Acal.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. calliptera sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes raw counts for genes and TEs in each Lake Malawi cichlid sample. Output of TEtranscripts, using a curated TE annotation.
Supplementary files format and content: NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: rawCounts_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes raw counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: lengthScaledTPM_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes length scaled TPM counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Abur.txt: Tab-delimited file includes raw counts for genes and TEs in each A. burtoni sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Abur.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. burtoni sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Pnye.txt: Tab-delimited file includes raw counts for genes and TEs in each P. nyererei sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Pnye.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each P. nyererei sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Onil.txt: Tab-delimited file includes raw counts for genes and TEs in each O. niloticus sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Onil.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each O. niloticus sample.

organism: Haplochromis burtoni

source_name: Testes

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Quality control, library preparation (directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene. A. calliptera brain libraries and P.nyererei gonad libraries were prepared differently with the following protocol. We used 50-250 ng of total RNA for library production with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), in conjunction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB #E6440). Samples were then pooled in equimolar amounts and sequenced on a NovaSeq 6000 system (PE150 on one lane of an S1 Flowcell).

value: Testes

value: wild-type


title: A. burtoni, testes, rep4

description:
Abu_tes_rep4
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt


title: BCLungMetGFP _6

description:
CFa7-5
CFa7_YFP_GFP_CPM.txt

value: 28 days


title: BCPrimaryGFP _5

description:
CFa7-2
CFa7_YFP_GFP_CPM.txt

value: BC primary tumor cells


title: A. burtoni, testes, rep1

description:
Abu_tes_rep1
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt


title: KOOTI-WT1  scRNA-seq

city: Yangsan

first: YUNA

last: JO

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

description: 10x chromium Next GEM Single Cell 3’ v3.1 kit

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.1.2 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mouse reference genome (mm10-2020-A)

source_name: tumor

extract_protocol:
To analyze the function of infiltrating cells in the TME, we sorted tumor-infiltrating lymphocytes from tumor-bearing mice.
Use LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) to consult the 10x Genomics Single Cell Protocols Cell Preparation Guide and the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126 respectively) for more information on preparing cells.  Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced using HiSeq platform(Illumina) according to the read length in the user guide.

value: tumor

value: primary cells

value: Tumor-infiltrating lymphocyte


title: A. burtoni, ovary, rep4

description:
Abu_ov_rep4
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt

source_name: Ovary

value: Ovary


title: BCPrimaryGFP _1

description:
CFa7-1
CFa7_YFP_GFP_CPM.txt


title: CF13-2 liver met

description:
CFa1-06
CFa1_Bulk_Tissue_CPM.txt

value: n/a bulk tissue

value: PDAC Liver metastatic tumor

value: 28 weeks


title: OTI-WT2 scRNA-seq


title: A. burtoni, ovary, rep1

description:
Abu_ov_rep1
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt