title: ChIP_SPT5_pSer2_IAA_4h_rep2

city: Daejeon

first: Hae Jin

last: An

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
ChIP_SPT5_pSer2_IAA_4h_r2
ChIP_SPT5-AID_IAA_4h_Ser2p.bw

data_processing:
The raw reads were mapped individually to sacCer3 for experiments and to SpombeASMv2 for spike-in normalization using bowtie2 (version 2.3.4.3).
MACS2 was used to convert the aligned BAM files to bedGraph files with the pileup option.
The bedGraph formats aligned to sacCer3 were normalized with the spike-in mapped reads. BigWig files were generated using bedGraphToBigWig.
For histone ChIP-seq data, the BigWig files were also normalized with H3 values.
Assembly: sacCer3, SpombeASMv2
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in YPD medium and harvested in mid-log phase.

extract_protocol:
ChIP was conducted as reported by Strahl-Bolsinger et al. with several modifications. In brief, 4 OD of S. pombe cells were mixed with 80 OD of S. cerevisiae cells for spike-in normalization. Whole-cell lysates were subjected to 12 cycles of sonication for 20 s using a Branson sonifier SFX550 at 35% amplitude. Adequate time intervals were maintained between each sonication cycle. The immunoprecipitated and input DNA were eluted in elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 1 hour. Subsequently, RNase A (ThermoFisher, EN0531) and proteinase K (Promega, V3021) were added to the eluted DNA for RNA degradation and de-crosslinking. The extracted DNA was purified using a QIAquick PCR purification kit (Qiagen, 28106).
Libraries for RNAPII ChIP-seq were generated using the NEXTflex™ Illumina ChIP-Seq Library Prep kit (BIOO, 5143-02), following the manufacturer’s protocols. For histone ChIP-seq libraries, an NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645) was utilized, as described by the manufacturer.

treatment_protocol: 1mM auxin (3'-IAA) was treated to every AID strain. Final 20uM CMK was treated for inhibiting kinase activity in IS strains.

tag: sample group


title: ChIP_SPT5_pSer2_EtOH_1h_rep2

status: Public on Sep 28 2024

type: SRA

description:
ChIP_SPT5_pSer2_EtOH_1h_r2
ChIP_SPT5-AID_EtOH_1h_Ser2p.bw

library_source: genomic

molecule: genomic DNA

tag: cell line


title: ChIP_SPT5_pSer2_IAA_4h_rep1


title: ChIP_SPT5_pSer2_IAA_1h_rep2

description:
ChIP_SPT5_pSer2_IAA_1h_r2
ChIP_SPT5-AID_IAA_1h_Ser2p.bw


title: Biological replicate 6, pertubation: Influenza

type: RNA

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

country: USA

institute: Duke University

description: Gene expression data from in-vitro perturbed PBMCs

hyb_protocol: 20 ug of antisense cRNA was hybridized for 16+ hr at 45C on GeneChip Human U133A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Midi_euk2v3_450 protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

data_processing: CEL files imported in to R using affy and normalized using the multi-array method for noptical noise and non-specific binding adjustments and quantile normalization implimented in the bioconductor package gcrma

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Perturbed PBMCs

label_protocol: Biotinylated antisense strand cRNA was prepared according to the standard Affymetrix protocol from 2.5 ug total RNA utilizing peptide nucleic acids complimentary to globin mRNA to block amplification of those transcripts(GeneChipÂ® 1 cycle labeling kit with Globin Reduction protocol (Affymetrix) Data was Generated at Expression Analysis, Inc (Durham, NC))

extract_protocol: Total RNA extracted from PaxGene Blood tubes as per the manufacturer's protocol.

tag: biological replicate

tag: perturbation

value: Influenza

tag: perturbation class

value: Viral

tag: cell type

value: Perturbed PBMCs


title: Biological replicate 5, pertubation: Crypt neo

value: Crypt neo

value: Fungal


title: Biological replicate 5, pertubation: Candida

value: Candida


title: ChIP_SPT5_pSer2_IAA_1h_rep1


title: Biological replicate 5, pertubation: St. Pneum

value: St. Pneum

value: Bacterial


title: Biological replicate 5, pertubation: E. coli

value: E. coli


title: ChIP_SPT5_pSer5_IAA_4h_rep2

description:
ChIP_SPT5_pSer5_IAA_4h_r2
ChIP_SPT5-AID_IAA_4h_Ser5p.bw


title: ChIP_SPT5_pSer2_EtOH_1h_rep1


title: ChIP_SPT5_pSer5_IAA_1h_rep2

description:
ChIP_SPT5_pSer5_IAA_1h_r2
ChIP_SPT5-AID_IAA_1h_Ser5p.bw


title: ChIP_SPT5_pSer5_EtOH_1h_rep2

description:
ChIP_SPT5_pSer5_EtOH_1h_r2
ChIP_SPT5-AID_EtOH_1h_Ser5p.bw


title: Biological replicate 5, pertubation: LPS

value: LPS


title: Biological replicate 5, pertubation: Influenza


title: ChIP_SPT5_pSer5_IAA_1h_rep1


title: Biological replicate 6, pertubation: Uninfected

value: Uninfected


title: Biological replicate 4, pertubation: Candida


title: Biological replicate 5, pertubation: Uninfected


title: Biological replicate 4, pertubation: Crypt neo


title: ChIP_SPT5_pSer5_EtOH_1h_rep1


title: Biological replicate 4, pertubation: Crypt gatt

value: Crypt gatt


title: ChIP_SPT5_8WG16_IAA_4h_rep2

description:
ChIP_SPT5_8WG16_IAA_4h_r2
ChIP_SPT5-AID_IAA_4h_8wg16.bw


title: ChIP_SPT5_8WG16_IAA_1h_rep2

description:
ChIP_SPT5_8WG16_IAA_1h_r2
ChIP_SPT5-AID_IAA_1h_8wg16.bw


title: Biological replicate 4, pertubation: E. coli


title: ChIP_SPT5_8WG16_IAA_1h_rep1


title: ChIP_SPT5_8WG16_EtOH_1h_rep1


title: Biological replicate 4, pertubation: St. Pneum


title: ChIP_SPT5_pSer5_IAA_4h_rep1


title: Biological replicate 5, pertubation: Poly I:C

value: Poly I:C


title: ChIP_SPT5_Input_IAA_1h_rep2

description:
ChIP_SPT5_Input_IAA_1h_r2
ChIP_SPT5-AID_IAA_1h_Input.bw


title: Biological replicate 4, pertubation: Poly I:C


title: Biological replicate 4, pertubation: Uninfected


title: Biological replicate 4, pertubation: LPS


title: Biological replicate 4, pertubation: Influenza


title: Biological replicate 3, pertubation: Crypt gatt


title: ChIP_SPT5_Input_IAA_4h_rep2

description:
ChIP_SPT5_Input_IAA_4h_r2
ChIP_SPT5-AID_IAA_4h_Input.bw


title: ChIP_SPT5_Input_EtOH_1h_rep2

description:
ChIP_SPT5_Input_EtOH_1h_r2
ChIP_SPT5-AID_EtOH_1h_Input.bw


title: Biological replicate 3, pertubation: Candida


title: Biological replicate 3, pertubation: Crypt neo


title: ChIP_SPT5_Input_IAA_4h_rep1


title: ChIP_SPT5_8WG16_EtOH_1h_rep2

description:
ChIP_SPT5_8WG16_EtOH_1h_r2
ChIP_SPT5-AID_EtOH_1h_8wg16.bw


title: ChIP_SPT5_Input_IAA_1h_rep1


title: ChIP_SPT5_Input_EtOH_1h_rep1


title: ChIP_SPT5_8WG16_IAA_4h_rep1


title: Biological replicate 3, pertubation: St. Pneum


title: Biological replicate 3, pertubation: Poly I:C


title: ChIP_BUR1_pSer5_CMK_5m_rep2

description:
ChIP_BUR1_pSer5_CMK_5m_r2
ChIP_BUR1-IS_CMK_Ser5p.bw


title: ChIP_BUR1_pSer5_DMSO_5m_rep2

description:
ChIP_BUR1_pSer5_DMSO_5m_r2
ChIP_BUR1-IS_DMSO_Ser5p.bw


title: ChIP_BUR1_pSer5_CMK_5m_rep1


title: Biological replicate 3, pertubation: E. coli


title: Biological replicate 3, pertubation: LPS


title: ChIP_BUR1_pSer5_DMSO_5m_rep1


title: Biological replicate 3, pertubation: Influenza


title: Biological replicate 3, pertubation: Uninfected


title: Biological replicate 2, pertubation: Crypt gatt


title: ChIP_BUR1_8WG16_DMSO_5m_rep2

description:
ChIP_BUR1_8WG16_DMSO_5m_r2
ChIP_BUR1-IS_DMSO_8wg16.bw


title: ChIP_BUR1_8WG16_DMSO_5m_rep1


title: ChIP_BUR1_Input_CMK_5m_rep2

description:
ChIP_BUR1_Input_CMK_5m_r2
ChIP_BUR1-IS_CMK_Input.bw


title: Biological replicate 2, pertubation: E. coli


title: ChIP_BUR1_Input_DMSO_5m_rep2

description:
ChIP_BUR1_Input_DMSO_5m_r2
ChIP_BUR1-IS_DMSO_Input.bw


title: Biological replicate 2, pertubation: Candida


title: ChIP_BUR1_Input_CMK_5m_rep1


title: ChIP_BUR1_Input_DMSO_5m_rep1


title: Biological replicate 2, pertubation: St. Pneum


title: RNA_RRP6_IAA_1h_rep2

description:
mRNA-seq_RRP6-AID_IAA_plus.bw
mRNA-seq_RRP6-AID_IAA_minus.bw

library_source: transcriptomic

data_processing:
The raw reads were mapped to the combined yeast genome (sacCer3 of S. cerevisiae and SpombeASMv2 of S. pombe) using STAR (version 2.7.6a) with clipping of 50 bp from the 3’ end.
The aligned BAM files were sorted and indexed using SAMtools (version 1.14).
BEDTools (version 2.30.0) was used to convert the indexed BAM files to BED formats. The genomecov function of BEDTools was used to generate the coverage of the aligned reads.
The BedGraph files were normalized using the spike-in reads aligned to S. pombe. The normalized BedGraph files were converted to BigWig files using bedGraphToBigWig.
Assembly: sacCer3, SpombeASMv2
Supplementary files format and content: bigwig

molecule: polyA RNA

source_name: Spt5p-FLAG Rrp6p-IAA*-HA

extract_protocol:
Total RNA was extracted from 10 OD cells using a standard hot-phenol RNA extraction method. DNA was eliminated from the total RNA using a TURBO DNA-free kit (Invitrogen, AM1907) at 37°C for 1 h. mRNA was isolated from the total RNA using an NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) following the provided protocol.
Libraries were generated using an NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, E7760).

value: Spt5p-FLAG Rrp6p-IAA*-HA


title: Biological replicate 2, pertubation: LPS


title: Biological replicate 1, pertubation: Crypt gatt


title: Biological replicate 2, pertubation: Crypt neo


title: Biological replicate 2, pertubation: Uninfected


title: RNA_RRP6_EtOH_1h_rep2

description:
mRNA-seq_RRP6-AID_EtOH_plus.bw
mRNA-seq_RRP6-AID_EtOH_minus.bw


title: Biological replicate 1, pertubation: Crypt neo

description: Gene expression data from in-vitro perturbed PBMCs


title: RNA_RRP6_EtOH_1h_rep1


title: RNA_RAT1_IAA_1h_rep2

description:
mRNA-seq_RAT1-AID_IAA_plus.bw
mRNA-seq_RAT1-AID_IAA_minus.bw

source_name: Spt5p-FLAG Rat1p-IAA*-HA

value: Spt5p-FLAG Rat1p-IAA*-HA


title: ChIP_BUR1_8WG16_CMK_5m_rep1


title: RNA_RRP6_IAA_1h_rep1


title: RNA_RAT1_EtOH_1h_rep2

description:
mRNA-seq_RAT1-AID_EtOH_plus.bw
mRNA-seq_RAT1-AID_EtOH_minus.bw


title: RNA_RAT1_IAA_1h_rep1


title: Biological replicate 1, pertubation: Poly I:C


title: RNA_SPT5_IAA_4h_rep2

description:
mRNA-seq_SPT5-AID_IAA_4h_plus.bw
mRNA-seq_SPT5-AID_IAA_4h_minus.bw


title: Biological replicate 1, pertubation: LPS


title: RNA_RAT1_EtOH_1h_rep1


title: Biological replicate 2, pertubation: Poly I:C


title: RNA_SPT5_IAA_1h_rep2

description:
mRNA-seq_SPT5-AID_IAA_1h_plus.bw
mRNA-seq_SPT5-AID_IAA_1h_minus.bw


title: Biological replicate 1, pertubation: Influenza


title: RNA_SPT5_IAA_4h_rep1


title: RNA_SPT5_EtOH_1h_rep2

description:
mRNA-seq_SPT5-AID_EtOH_plus.bw
mRNA-seq_SPT5-AID_EtOH_minus.bw


title: RNA_SPT5_IAA_1h_rep1


title: RNA_SPT4_IAA_4h_rep2

description:
mRNA-seq_SPT4-AID_IAA_4h_plus.bw
mRNA-seq_SPT4-AID_IAA_4h_minus.bw


title: RNA_SPT5_EtOH_1h_rep1


title: Biological replicate 1, pertubation: St. Pneum


title: Biological replicate 2, pertubation: Influenza


title: RNA_SPT4_IAA_1h_rep2

description:
mRNA-seq_SPT4-AID_IAA_1h_plus.bw
mRNA-seq_SPT4-AID_IAA_1h_minus.bw


title: SHR rat strain, male, 12months, standard chow + dexamethasone 3

first: Lukáš

middle: Farhád

last: Mirchi

address: Albertov 4

country: Czech Republic

institute: Charles University PRague

hyb_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC version 4.0.1, Affymetrix, Santa Clara, CA, USA) using GC-MRA as normalization method.

organism: Rattus norvegicus

source_name: liver

label_protocol: biotin

growth_protocol: Only male SHR (n=6) and male PD5 (n=6) were used. Rats were kept under 12h light-dark cycle, fed standard laboratory chow and given access to water ad libitum. After 12 months, half of the SHR rats (n=3) and half of the PD5 rats (n=3) were administered dexamethasone. After that all rats were anesthetized by ether and decapitated. Organs were snap frozen in liquid nitrogen, livers were used for further analysis.

extract_protocol: otal liver RNA was isolated using TRIzol reagent (Invitrogen) and purification was performed using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. UV measurements at 280 and 260 nm and 2100 Bioanalyzer runs using the RNA-6000 Nano-LabChip (Agilent, Böblingen, Germany) were used to ensure the quality and quantity of the extracted RNA Only samples showing RNA integrity numbers (RIN) above 8 were used for furhter analysis.

treatment_protocol: none or dexamethasone (Dexamed, Medochemie) in drinking water (2.6 µg/ml) for 3 days.

tag: tissue

value: liver

tag: Sex

value: male

tag: treatment

value: dexamethasone


title: Biological replicate 1, pertubation: Candida


title: Biological replicate 1, pertubation: Uninfected


title: RNA_SPT4_EtOH_4h_rep1


title: RNA_SPT4_IAA_1h_rep1


title: SHR rat strain, male, 12months, standard chow + dexamethasone 2


title: SHR rat strain, male, 12months, standard chow 2


title: SHR rat strain, male, 12months, standard chow 3


title: PD5 rat strain, male, 12months, standard chow + dexamethasone 3


title: PD5 rat strain, male, 12months, standard chow 3


title: SHR rat strain, male, 12months, standard chow 1


title: PD5 rat strain, male, 12months, standard chow + dexamethasone 2


title: PD5 rat strain, male, 12months, standard chow + dexamethasone 1


title: Biological replicate 1, pertubation: E. coli


title: RNA_SPT4_EtOH_1h_rep1


title: SHR rat strain, male, 12months, standard chow + dexamethasone 1


title: RNA_BUR1_CMK_5m_rep2

description:
mRNA-seq_BUR1-IS_CMK_plus.bw
mRNA-seq_BUR1-IS_CMK_minus.bw


title: ChIP_BUR1_8WG16_CMK_5m_rep2

description:
ChIP_BUR1_8WG16_CMK_5m_r2
ChIP_BUR1-IS_CMK_8wg16.bw


title: PD5 rat strain, male, 12months, standard chow 2


title: RNA_BUR1_DMSO_5m_rep2

description:
mRNA-seq_BUR1-IS_DMSO_plus.bw
mRNA-seq_BUR1-IS_DMSO_minus.bw


title: Small RNA sequencing of Low Worms biological replicate 1

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

description: Low

data_processing:
Adaptor trimming using cutadapt v1.7.1 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -O 6 -m 15
Sequence mapping using bowtie v1.1.1 -a --best --strata -v 0
Assigning reads to genes using featureCounts v1.4.6 -s 2 -t exon -g gene_name -M -O
Counts normalization by total mapped small RNAs using DESeq2 v1.8.1.
Genome_build: C. elegans genome assembly WS235 from WormBase and annotation from Ensembl release 80 with the vector transgene as an additional chromosome
Supplementary_files_format_and_content: Matrix of scaled number of molecules targeting each gene. The individual files representing 22G, 21U, and 26G represent the normalized counts of a specific small RNA class consiting of (22, 21 or 26) nucleotides and starting with the letter (G or U).

organism: Caenorhabditis elegans

source_name: whole multiple worms

growth_protocol: To prepare the ‘High’ and ‘Low’ daf-21p::mCHERRY populations for RNA extraction, P0 worms kept at 16 and 25 ºC were transferred to 20 ºC as L4s (12 worms/plate, 3 replicates per treatment). Four and a half days later, when much of the F1 progeny was gravid, the worms were bleached, washed 3x with M9 and the F2 larvae let to hatch o/n in M9 at 20 ºC. The F2 L1 larvae were washed and plated at a concentration of 1000 worms/plate on standard NGM plates seeded with OP50 bacteria. After 72 hours of growth at 20 ºC, the gravid worms were gently washed of the plates and RNA was extracted.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
1 microgram of total RNA was treated with Antarctic phosphatase (ref. M0289S, NEB) and subsequently with T4 PNK (3' phosphatase minus) (ref. M0236S, NEB) in order to make the 5’ and 3’ ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. Briefly, 3’ adapters and subsequently 5’ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3’ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, libraries were size selected using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 18 to 36 bp were cut from the gel, and DNA was precipitated and eluted in 10 µl EB. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Libraries were pooled and loaded at a concentration of 10 pM onto the flowcell, and were sequenced 1 x 50 on Illumina’s HiSeq 2000.

tag: strain

tag: strain background

tag: developmental stage

value: gravid adult

tag: condition

value: grown at low temperature


title: Small RNA sequencing of Low Worms biological replicate 2

description: Low


title: Small RNA sequencing of High Worms biological replicate 3

description: High

value: grown at high temperature


title: Small RNA sequencing of Low Worms biological replicate 3

description: Low


title: Small RNA sequencing of High Worms biological replicate 2

description: High


title: RNA_BUR1_CMK_5m_rep1


title: PD5 rat strain, male, 12months, standard chow 1


title: RNA_SPT4_EtOH_1h_rep2

description:
mRNA-seq_SPT4-AID_EtOH_plus.bw
mRNA-seq_SPT4-AID_EtOH_minus.bw


title: Small RNA sequencing of High Worms biological replicate 1

description: High


title: CAP_SPT5_IAA_4h_rep2

description:
CAP_SPT5_IAA_4h_r2
PRO-cap_SPT5-AID_IAA_4h_plus.bw
PRO-cap_SPT5-AID_IAA_4h_minus.bw

library_source: other

data_processing:
*library strategy: PRO-seq
BigWig files were generated as previously described (Cheon et al., 2021; Booth et al., 2018) with minor modification to remove PCR duplicates using UMI-tools.
Briefly, 10-bp UMI sequences were removed and kept in the FASTQ name using the function ‘umi_tools extract’ in UMI-tools during adaptor trimming. Duplicates with the same UMI sequences were removed from the BAM files using the ‘umi_tools dedup’ function.
We simply removed UMI sequences of FASTQ and applied spike-in normalization for PRO-cap data processing.
Assembly: sacCer3, SpombeASMv2
Supplementary files format and content: bigwig

molecule: other

extract_protocol:
Nuclear run-on reactions and RNA extractions were performed based on the published protocol (Mahat et al., 2016) and minor conditions are altered as our previous study (Cheon et al., 2021).
Libraries were generated using the published PRO-seq or PRO-cap protocol (Mahat et al., 2016) from RNA fragmentation by base hydrolysis to full-scale PCR amplification. Minor variations in reagents were present, as previously reported (Cheon et al., 2021). To reduce the bias from PCR duplicates, we introduced the 10 nucleotides of UMI (Unique Molecular Identifier) sequences to 3’ adaptor (VRA3-UMI, 5′-/5Phos/NNNNNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/Inverted dT/−3′) of PRO-seq.


title: CAP_SPT5_IAA_1h_rep2

description:
CAP_SPT5_IAA_1h_r2
PRO-cap_SPT5-AID_IAA_1h_plus.bw
PRO-cap_SPT5-AID_IAA_1h_minus.bw


title: CAP_SPT5_EtOH_1h_rep2

description:
CAP_SPT5_EtOH_1h_r2
PRO-cap_SPT5-AID_EtOH_1h_plus.bw
PRO-cap_SPT5-AID_EtOH_1h_minus.bw


title: AR_rhiz1

city: Changchun

first: Tao

last: Zhang

address: Key Laboratory of Chinese Medicine Planting and Development. Changchun University of Chinese Medicin

country: China

institute: Changchun University of Chinese Medicine

description:
AR
AR_rhiz1

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: No reference genome.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Atractylodes lancea

source_name: root

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: root


title: AJ_rhiz3

description:
AJ
AJ_rhiz3


title: AR_rhiz2

description:
AR
AR_rhiz2


title: CAP_SPT5_EtOH_1h_rep1


title: AJ_rhiz1

description:
AJ
AJ_rhiz1


title: AR_rhiz3

description:
AR
AR_rhiz3


title: CAP_SPT5_IAA_4h_rep1


title: PRO_RRP6_IAA_1h_rep2

description:
PRO_RRP6_IAA_1h_r2
PRO-seq_RRP6-AID_IAA_plus.bw
PRO-seq_RRP6-AID_IAA_minus.bw


title: PRO_RRP6_EtOH_1h_rep2

description:
PRO_RRP6_EtOH_1h_r2
PRO-seq_RRP6-AID_EtOH_plus.bw
PRO-seq_RRP6-AID_EtOH_minus.bw


title: AJ_rhiz2

description:
AJ
AJ_rhiz2


title: PRO_RRP6_IAA_1h_rep1


title: PDX_11, R848 treated

city: Boston

first: Christopher

last: Booth

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
STAR was used to align raw reads to hg38 and generate gene counts using --quantMode GeneCounts
Assembly: hg38
Supplementary files format and content: Gene counts for each sample
Supplementary files format and content: Gene TPMs for each sample

source_name: BPDCN PDX

extract_protocol:
Samples from pDCs and BPDCN PDX were collected for total RNA sequencing using the Arcturus PicoPure RNA Isolation Kit (Life Technologies).
Libraries were prepared using the Ovation kit (#0340; Nugen) using 50 ng input total RNA and 20 cycles of amplification.

treatment_protocol: Peripheral blood mononuclear cells were isolated by density gradient centrifugation (Ficoll-Paque PLUS, 17-1440-03; GE Healthcare) from healthy donors. Normal pDCs were enriched using magnetic beads (130-097-415; Miltenyi Biotec) for transcriptomes. CD123+BDCA2+ cells were sorted for normal pDCs, and CD45dimCD123+ cells were sorted for BPDCN PDX tumor cells using a FACSAria (BD Biosciences). For stimulation experiments, pDCs were collected by negative selection using the EasySep Human Plasmacytoid DC Isolation Kit (#17977; StemCell Technologies) to avoid activation by sorting. In all cases, pDCs and BPDCN (from patient and PDX) were >95% pure by flow cytometry. BPDCN tumor cells and normal pDCs were seeded at 1 × 105/mL. Cells were stimulated with 1 μg/mL R848 (tlrl-r848; Invitrogen) for 24 hours.

value: BPDCN PDX

tag: splicing factor_mutation

value: Unknown


title: PDX_10, R848 treated

value: WT


title: PDX_9, Untreated

value: Untreated


title: PDX_9, R848 treated


title: PRO_RAT1_IAA_1h_rep2

description:
PRO_RAT1_IAA_1h_r2
PRO-seq_RAT1-AID_IAA_plus.bw
PRO-seq_RAT1-AID_IAA_minus.bw


title: RNA_BUR1_DMSO_5m_rep1


title: PRO_RRP6_EtOH_1h_rep1


title: PDX_8, Untreated


title: PRO_RAT1_IAA_1h_rep1


title: PDX_8, R848 treated


title: PDX_7, Untreated


title: PRO_RAT1_EtOH_1h_rep1


title: PRO_RAT1_EtOH_1h_rep2

description:
PRO_RAT1_EtOH_1h_r2
PRO-seq_RAT1-AID_EtOH_plus.bw
PRO-seq_RAT1-AID_EtOH_minus.bw


title: PRO_WT_CMK_5m_rep2

description:
PRO_WT_CMK_5m_r2
PRO-seq_WT_CMK_plus.bw
PRO-seq_WT_CMK_minus.bw


title: PRO_WT_DMSO_5m_rep2

description:
PRO_WT_DMSO_5m_r2
PRO-seq_WT_DMSO_plus.bw
PRO-seq_WT_DMSO_minus.bw


title: CAP_SPT5_IAA_1h_rep1


title: PDX_11, Untreated


title: PDX_6, R848 treated


title: PRO_WT_CMK_5m_rep1


title: PDX_5, Untreated


title: PRO_WT_DMSO_5m_rep1


title: PRO_TIR1_IAA_1h_rep2

description:
PRO_TIR1_IAA_1h_r2
PRO-seq_OsTIR1_IAA_plus.bw
PRO-seq_OsTIR1_IAA_minus.bw


title: PDX_10, Untreated


title: PDX_5, R848 treated


title: PDX_6, Untreated


title: ChIP_Histone_SPT5_H4ac_EtOH_1hr_rep2

description:
ChIP_Histone_SPT5_H4ac_EtOH_1hr_r2
ChIP_SPT5-AID_EtOH_H4ac_H3norm.bw


title: ChIP_Histone_SPT5_H4ac_IAA_1hr_rep2

description:
ChIP_Histone_SPT5_H4ac_IAA_1hr_r2
ChIP_SPT5-AID_IAA_H4ac_H3norm.bw


title: PRO_TIR1_EtOH_1h_rep2

description:
PRO_TIR1_EtOH_1h_r2
PRO-seq_OsTIR1_EtOH_plus.bw
PRO-seq_OsTIR1_EtOH_minus.bw


title: PDX_4, Untreated


title: ChIP_Histone_SPT5_H4ac_IAA_1hr_rep1


title: ChIP_Histone_SPT5_H3ac_IAA_1hr_rep2

description:
ChIP_Histone_SPT5_H3ac_IAA_1hr_r2
ChIP_SPT5-AID_IAA_H3ac_H3norm.bw


title: PRO_TIR1_IAA_1h_rep1


title: ChIP_Histone_SPT5_H3ac_EtOH_1hr_rep2

description:
ChIP_Histone_SPT5_H3ac_EtOH_1hr_r2
ChIP_SPT5-AID_EtOH_H3ac_H3norm.bw


title: PDX_4, R848 treated


title: PRO_SPT5_IAA_4h_rep3

description:
PRO_SPT5_IAA_4h_r3
PRO-seq_SPT5-AID_IAA_4h_plus.bw
PRO-seq_SPT5-AID_IAA_4h_minus.bw


title: ChIP_Histone_SPT5_H3ac_IAA_1hr_rep1


title: ChIP_Histone_SPT5_H3K79me3_IAA_1hr_rep2

description:
ChIP_Histone_SPT5_H3K79me3_IAA_1hr_r2
ChIP_SPT5-AID_IAA_H3K79me3_H3norm.bw


title: ChIP_Histone_SPT5_H3ac_EtOH_1hr_rep1


title: PDX_3, R848 treated


title: PDX_7, R848 treated


title: ChIP_Histone_SPT5_H3K79me3_EtOH_1hr_rep2

description:
ChIP_Histone_SPT5_H3K79me3_EtOH_1hr_r2
ChIP_SPT5-AID_EtOH_H3K79me3_H3norm.bw


title: PRO_SPT5_IAA_1h_rep3

description:
PRO_SPT5_IAA_1h_r3
PRO-seq_SPT5-AID_IAA_1h_plus.bw
PRO-seq_SPT5-AID_IAA_1h_minus.bw


title: ChIP_Histone_SPT5_H4ac_EtOH_1hr_rep1


title: PRO_TIR1_EtOH_1h_rep1


title: PDX_2, Untreated


title: ChIP_Histone_SPT5_H3K79me3_IAA_1hr_rep1


title: ChIP_Histone_SPT5_H3K79me3_EtOH_1hr_rep1


title: PRO_SPT5_EtOH_1h_rep3

description:
PRO_SPT5_EtOH_1h_r3
PRO-seq_SPT5-AID_EtOH_plus.bw
PRO-seq_SPT5-AID_EtOH_minus.bw


title: PDX_2, R848 treated


title: PRO_SPT5_IAA_4h_rep2

description:
PRO_SPT5_IAA_4h_r2
PRO-seq_SPT5-AID_IAA_4h_plus.bw
PRO-seq_SPT5-AID_IAA_4h_minus.bw


title: ChIP_Histone_SPT5_H3K36me3_EtOH_1hr_rep2

description:
ChIP_Histone_SPT5_H3K36me3_EtOH_1hr_r2
ChIP_SPT5-AID_EtOH_H3K36me3_H3norm.bw


title: ChIP_Histone_SPT5_H3K36me3_IAA_1hr_rep1


title: PDX_1, Untreated


title: ChIP_Histone_SPT5_H3K36me3_EtOH_1hr_rep1


title: PRO_SPT5_IAA_1h_rep2

description:
PRO_SPT5_IAA_1h_r2
PRO-seq_SPT5-AID_IAA_1h_plus.bw
PRO-seq_SPT5-AID_IAA_1h_minus.bw


title: ChIP_Histone_SPT5_H3K36me3_IAA_1hr_rep2

description:
ChIP_Histone_SPT5_H3K36me3_IAA_1hr_r2
ChIP_SPT5-AID_IAA_H3K36me3_H3norm.bw


title: PDX_1, R848 treated


title: ChIP_Histone_SPT5_Input_IAA_1hr_rep2

description:
ChIP_Histone_SPT5_Input_IAA_1hr_r2
ChIP_SPT5-AID_IAA_Histone_Input.bw


title: PRO_SPT5_EtOH_1h_rep2

description:
PRO_SPT5_EtOH_1h_r2
PRO-seq_SPT5-AID_EtOH_plus.bw
PRO-seq_SPT5-AID_EtOH_minus.bw


title: ChIP_Histone_SPT5_Input_EtOH_1hr_rep2

description:
ChIP_Histone_SPT5_Input_EtOH_1hr_r2
ChIP_SPT5-AID_EtOH_Histone_Input.bw


title: pDC_3, Untreated

source_name: Normal pDC

value: Normal pDC


title: ChIP_Histone_SPT5_Input_IAA_1hr_rep1


title: PRO_SPT5_IAA_1h_rep1


title: SW48 Cas9, Unsorted, biol rep 2

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

country: Canada

data_processing:
*library strategy: amplicon-seq
Raw read files (FASTQ) were aligned to the referene tiling library and normalized using an in-house software package written in R/C++
Read count matrix was generated for guide-by-sample analysis using an in-house software package written in R/C++
Assembly: ZNRF3 tiling library (sgRNA_library.csv)
Supplementary files format and content: CSV containing read count matrix (guidelevel.counts.csv)
Supplementary files format and content: CSV containing statistical outputs for guide-by-sample analysis (guidelevel.statistics.csv)

growth_protocol: SW49 Cas9 cells were maintained in RPMI 1640 at 37˚C. Growth media was supplemented with 10% fetal bovine serum (FBS; Sigma, F4135), 2 mM L-Glutamine and 100 U/ml Penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
Genomic DNA was isolated with the Gentra Puregene Cell Kit (158788, Qiagen)
guide RNAs were PCR amplified from genomic DNA and a library was constructed using xGen (IDT) NGS adapters and indices for Illumina sequencing

treatment_protocol: Cells were seeded in triplicates and treated with 1 µM DCP or DMSO for 1 h.

value: epithelial

tag: genotype

value: DCP


title: ChIP_Histone_SPT5_Input_EtOH_1hr_rep1


title: pDC_3, R848 treated


title: ChIP_Histone_BUR1_H4ac_CMK_20m_rep2

description:
ChIP_Histone_BUR1_H4ac_CMK_20m_r2
ChIP_BUR1-IS_CMK_H4ac_H3norm.bw


title: PDX_3, Untreated


title: SW48 Cas9, Unsorted, biol rep 3


title: PRO_SPT5_IAA_4h_rep1


title: pDC_2, Untreated


title: SW48 Cas9, Unsorted, biol rep 1


title: pDC_2, R848 treated


title: ChIP_Histone_BUR1_H4ac_DMSO_20m_rep2

description:
ChIP_Histone_BUR1_H4ac_DMSO_20m_r2
ChIP_BUR1-IS_DMSO_H4ac_H3norm.bw


title: PRO_SPT5_EtOH_1h_rep1


title: ChIP_Histone_BUR1_H4ac_CMK_20m_rep1


title: pDC_1, Untreated


title: SW48 Cas9, DCP, Top10% ZNRF3, biol rep 2


title: pDC_1, R848 treated


title: ChIP_Histone_BUR1_H4ac_DMSO_20m_rep1


title: PRO_SPT4_EtOH_1h_rep2

description:
PRO_SPT4_EtOH_1h_r2
PRO-seq_SPT4-AID_EtOH_plus.bw
PRO-seq_SPT4-AID_EtOH_minus.bw


title: scOVCA5_CD45

city: Kyoto

first: Shuh

last: Narumiya

state: Kyoto

address: Yoshidahonmachi

department: Department of Drug Discovery Medicine

country: Japan

institute: Kyoto University

description:
Chromium 10x Single Cells 3' v3.1
Metadata.csv

library_source: transcriptomic single cell

data_processing:
fastq files were aligned to GRCh38-2020-A_build reference genome from 10x Genomics using Cell Ranger
Assembly: GRCh38-2020-A_build (10x Genomics)
Supplementary files format and content: tar archive of CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell type annotation file: Metadata.csv

source_name: ovarian cancer

extract_protocol:
Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform
scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000

value: ovarian cancer

value: primary cell


title: SW48 Cas9, DMSO, Top10% ZNRF3, biol rep 3

value: DMSO


title: PRO_SPT4_IAA_4h_rep1


title: ChIP_Histone_BUR1_H3ac_DMSO_20m_rep2

description:
ChIP_Histone_BUR1_H3ac_DMSO_20m_r2
ChIP_BUR1-IS_DMSO_H3ac_H3norm.bw


title: scOVCA4_CD45


title: SW48 Cas9, DCP, Top10% ZNRF3, biol rep 3


title: SW48 Cas9, DMSO, Top10% ZNRF3, biol rep 2


title: PRO_SPT4_IAA_1h_rep1


title: SW48 Cas9, DMSO, Top10% ZNRF3, biol rep 1


title: scOVCA3_CD45


title: PRO_SPT4_EtOH_1h_rep1


title: scOVCA2_CD45


title: ChIP_Histone_BUR1_H3ac_CMK_20m_rep1


title: PRO_Bur1-IS_CMK_20min_rep2

description:
PRO_BUR1-IS_CMK_20min_rep2
PRO-seq_BUR1-IS_CMK_20m_plus.bw
PRO-seq_BUR1-IS_CMK_20m_minus.bw


title: ChIP_Histone_BUR1_H3ac_DMSO_20m_rep1


title: PRO_SPT4_IAA_4h_rep2

description:
PRO_SPT4_IAA_4h_r2
PRO-seq_SPT4-AID_IAA_4h_plus.bw
PRO-seq_SPT4-AID_IAA_4h_minus.bw


title: PRO_SPT4_IAA_1h_rep2

description:
PRO_SPT4_IAA_1h_r2
PRO-seq_SPT4-AID_IAA_1h_plus.bw
PRO-seq_SPT4-AID_IAA_1h_minus.bw


title: scOVCA1_CD45


title: ChIP_Histone_BUR1_H3K79me3_DMSO_20m_rep2

description:
ChIP_Histone_BUR1_H3K79me3_DMSO_20m_r2
ChIP_BUR1-IS_DMSO_H3K79me3_H3norm.bw


title: SW48 Cas9, DCP, Top10% ZNRF3, biol rep 1


title: ChIP_Histone_BUR1_H3ac_CMK_20m_rep2

description:
ChIP_Histone_BUR1_H3ac_CMK_20m_r2
ChIP_BUR1-IS_CMK_H3ac_H3norm.bw


title: scCRC5_CD45

source_name: colorectal cancer

value: colorectal cancer


title: PRO_Bur1-IS_CMK_10min_rep2

description:
PRO_BUR1-IS_CMK_10min_rep2
PRO-seq_BUR1-IS_CMK_10m_plus.bw
PRO-seq_BUR1-IS_CMK_10m_minus.bw


title: RR-3

city: shanghai

first: Jia-Cheng

last: Jin

address: 600 Yishan Rd

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Assembly: mm10 for rnaseq
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)

organism: Mus musculus

source_name: bone marrow

extract_protocol:
we conducted a comparative RNA sequencing (RNA-seq) analysis on primary murine hematopoietic cells transduced with either empty vector or RUNX1-RARA.
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. (m6A-seq)
Libraries were generated using the NR605-02 V8 RNA-seq Library Prep Kit for Illumina and sequenced with Illumina NovaSeq6000.(RNA-seq)

value: bone marrow

value: primary murine hematopoietic cells

value: RUNX1-RARA overexpression


title: RR-1


title: RR-2


title: ChIP_Histone_BUR1_H3K79me3_CMK_20m_rep1


title: scCRC4_CD45


title: PRO_Bur1-IS_CMK_5min_rep2

description:
PRO_BUR1-IS_CMK_5min_rep2
PRO-seq_BUR1-IS_CMK_5m_plus.bw
PRO-seq_BUR1-IS_CMK_5m_minus.bw


title: ChIP_Histone_BUR1_H3K79me3_DMSO_20m_rep1


title: PRO_Bur1-IS_CMK_1min_rep2

description:
PRO_BUR1-IS_CMK_1min_rep2
PRO-seq_BUR1-IS_CMK_1m_plus.bw
PRO-seq_BUR1-IS_CMK_1m_minus.bw


title: ChIP_Histone_BUR1_H3K36me3_CMK_20m_rep2

description:
ChIP_Histone_BUR1_H3K36me3_CMK_20m_r2
ChIP_BUR1-IS_CMK_H3K36me3_H3norm.bw


title: WT-1

value: empty-vector


title: scCRC1_CD45


title: PRO_BUR1-IS_ctrl_rep2

description:
PRO_BUR1-IS_ctrl_rep2
PRO-seq_BUR1-IS_DMSO_plus.bw
PRO-seq_BUR1-IS_DMSO_minus.bw


title: scCRC2_CD45


title: WT-2


title: scBRCA6_CD45

source_name: breast cancer

value: breast cancer


title: PRO_Bur1-IS_CMK_20min_rep1


title: ChIP_Histone_BUR1_H3K79me3_CMK_20m_rep2

description:
ChIP_Histone_BUR1_H3K79me3_CMK_20m_r2
ChIP_BUR1-IS_CMK_H3K79me3_H3norm.bw


title: PRO_Bur1-IS_CMK_15min_rep2

description:
PRO_BUR1-IS_CMK_15min_rep2
PRO-seq_BUR1-IS_CMK_15m_plus.bw
PRO-seq_BUR1-IS_CMK_15m_minus.bw


title: PRO_Bur1-IS_CMK_15min_rep1


title: Ko-2

city: Xuzhou

first: Nianli

last: Liu

address: West Huaihai Road

institute: Xuzhou Medical University

data_processing:
A 2 × 150 bp paired-end (PE) configuration was used for sequencing, and HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) was used for image processing and base calling.
Assembly: Homo_sapiens.GRCh37.91
Supplementary files format and content: excel files include FPKM values for each sample

source_name: cell culture

growth_protocol: Huh7 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% streptomycin/penicillin.

extract_protocol:
RNA was extracted using TRIZOL reagent.
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.

treatment_protocol: None.

value: cell culture

value: cancer cell

value: RABIF KO


title: Ko-3


title: ChIP_Histone_BUR1_H3K36me3_DMSO_20m_rep2

description:
ChIP_Histone_BUR1_H3K36me3_DMSO_20m_r2
ChIP_BUR1-IS_DMSO_H3K36me3_H3norm.bw


title: ChIP_Histone_BUR1_Input_CMK_20m_rep2

description:
ChIP_Histone_BUR1_Input_CMK_20m_r2
ChIP_BUR1-IS_CMK_Histone_Input.bw


title: ChIP_Histone_BUR1_H3K36me3_DMSO_20m_rep1


title: WT-3


title: scBRCA5_CD45


title: Ko-1


title: PRO_Bur1-IS_CMK_5min_rep1


title: ChIP_Histone_BUR1_H3K36me3_CMK_20m_rep1


title: scBRCA4_CD45


title: PRO_Bur1-IS_CMK_10min_rep1


title: C3

value: wide type


title: scCRC3_CD45


title: ChIP_Histone_BUR1_Input_DMSO_20m_rep2

description:
ChIP_Histone_BUR1_Input_DMSO_20m_r2
ChIP_BUR1-IS_DMSO_Histone_Input.bw


title: scBRCA3_CD45

description:
Chromium 10x Single Cells 3' v3.1
Metadata.csv


title: ChIP_Histone_BUR1_Input_CMK_20m_rep1


title: scBRCA1_CD45


title: C1


title: ChIP_Histone_BUR1_Input_DMSO_20m_rep1


title: PRO_BUR1-IS_ctrl_rep1


title: iNeuron Day 26 Rep 4

status: Public on Sep 27 2024

city: Adelaide

first: Alison

last: Gardner

state: SA

address: AHMS, Uni of Adelaide, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

data_processing:
FASTQ files were aligned and mapped to the Human genome assembly GRCh38/hg38 with HISAT2, StringTie and Ballgown (Kim, D., et al (2019). Nat Biotechnol 37, 907-915).
Salmon was used to generate read counts (Patro, R., et al. (2017) Nat Methods 14, 417-419).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed files of .TXT type, are of tab-delimited format, and have readcount content for each sample.

source_name: skin

growth_protocol: Transdifferentiation of hunam dermal fibroblasts as described in Zhou-Yang, L., et al (2021) Methods Mol Biol 2352, 73-96.

extract_protocol:
RNA extraction from iNeurons was performed using TRIzol (Thermo Fisher Scientific) as per manufactures protocol, with further processing using the RNeasy Plus Mini Kit and RNase-free DNase Set. RNA concentrations were determined using  Qubit RNA BR
The quality of RNA was first assessed based on the RNA Integrity Number (RIN) evaluated using the 2100 Bioanalyzer system (Agilent, Santa Clara, USA) as per the manufacturer’s instructions. Libraries were generated using the Universal Plus RNA-Seq Library Kit (Tecan, Mannedorf, Switzerland) using rRNA depletion as per manufactures instructions. Conversion to MGI library was performed using the MGIEasy Universal Library Conversion Kit (MGI, Shenzhen, China). The MGI-compatible libraries were pooled in equimolar concentration and sequenced on the DNBSEQ-G400 Flow Cell Large (MGI, Shenzhen, China) to a minimum of 8 × 107 paired-end 150bp reads

value: skin

value: Dermal Fibroblast

value: Wildtype

value: day 26


title: iNeuron Day 26 Rep 2


title: iNeuron Day 26 Rep 3


title: iNeuron Day 26 Rep 1


title: iNeuron Day 20 Rep 2

value: day 20


title: iNeuron Day 20 Rep 4


title: iNeuron Day 20 Rep 3


title: iNeuron Day 20 Rep 1


title: iNeuron Day 10 Rep 2

value: day 10


title: iNeuron Day 0 Rep 3

value: day 0


title: iNeuron Day 0 Rep 2


title: iNeuron Day 10 Rep 3


title: C2


title: iNeuron Day 0 Rep 4


title: iNeuron Day 0 Rep 1


title: PRO_Bur1-IS_CMK_1min_rep1


title: 72h induced 3

city: Research Unit for Molecular Medicine (MMF)

first: Peter

last: Bross

state: Region Midt

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University and Aarhus University Hospital

data_processing:
Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC (Babraham Bioinformatics). Adaptor removal and trimming of low-quality ends were performed using Trim Galore with default settings (Babraham Bioinformatics). Gene expression was quantified using Salmon against decoy-aware reference transcriptomes (GRCh38). Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 , applying a false discovery rate (FDR) threshold of less than 0.05.
Assembly: GRCh38
Supplementary files format and content: Comma-delimited files contain raw data for each sample

growth_protocol: HEK293 cells with tetracycline-inducible dominant-negative ATPase-deficient mutant (HSP60-D423A) previously established using the Flp-In T-REx system (Invitrogen). HSP60-WT and HSP60-D423A cells were sub-cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) supplemented with 10% fetal bovine serum, 0.29 mg/mL glutamine, 0.1 streptomycin mg/mL, 100 units penicillin/mL, 15 µg/mL blasticidin (Invitrogen) and 100 µg/ml hygromycin B (Invitrogen). Cells were cultured at 37°C, 85% humidity, and 5% CO2.

extract_protocol:
On the day of the collection, cells were washed with warm PBS once, 3 mL ice-cold PBS was added to the flasks, and cells were detached with a cell scraper (VWR, #734-2602) and collected into a pre-chilled falcon tube in 3 repeated steps. Samples were centrifuged at 400 g for 3 minutes at 4°C. After the last centrifugation step, PBS was removed, 250 µL of TRIzol (Invitrogen, #15596-018) was added, and the sample snap-frozen on dry ice, and stored at -80°C for later use for RNA sequencing. RNA isolation was performed using TRIzol, including DNase treatment with DNA-free Kit (Ambion, AM1906) according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate (BioTek, Agilent). Quality control analysis was performed with an automated 4200 TapeStation System (Agilent, G2991AA), and RNA integrity number (RIN) values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 9.3 and 8.3 for all samples of the cell and zebrafish models, respectively.
Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non-stranded and polyA-selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.

treatment_protocol: Expression of the HSP60-D423A transgene was induced with 50 ng/mL tetracycline in culture media for 48h or 72h, respectively. The medium was changed every other day and the day before measurements to maintain the tetracycline concentration constant in the culture medium.

value: Flp-In T-REx

value: Human embryonic kidney

value: tetracycline 72h


title: 72h induced 2


title: 48h induced 2

value: tetracycline 48h


title: uninduced-3

value: untreated


title: uninduced-2


title: 72h induced 1


title: 48h induced 3


title: 48h induced 1


title: D880CD8beads110post30TRAC

city: Munich

first: Laurenz

middle: Thomas

last: Ursch

address: Trogerstraße 30

country: Germany

institute: TUM

data_processing:
Screening for deletion using CRISPResso2 (V2.2.7)
Reads for each deletion were normalised and displayed in a cumulative way
Assembly: hg38
Supplementary files format and content: .txt file with the range of deletions

source_name: PBMCs

growth_protocol: PBMCs were enriched for CD4 or CD8 T cells usingMojoSortHuman CD4 T Cell Isolation Kit (Biolegend) or MojoSort™ Human CD8 T Cell Isolation Kit (Biolegend), respectively. The freshly obtained T cells were cultured in complete Roswell Park Memorial Institute (cRPMI) medium, consisting of RPMI 1640 (ThermoFisher) supplemented with 5 mmol/l HEPES (ThermoFisher), 2 mmol/l glutamine (ThermoFisher), 50 µg/ml penicillin/streptomycin (ThermoFisher), 5 mmol/l nonessential amino acids (ThermoFisher), 5 mmol/l sodium pyruvate (ThermoFisher) and 10% FBS (Sigma-Aldrich) at a concentration of 1x106cells/ml for 24 - 48 hrs at 37°C before Cas9 RNP nucleofection.

extract_protocol:
cells were resuspended in DNA Quick Extraction solution (Lucigen) to lyse the cells and extract genomic DNA. The cell lysate was incubated at 65 °C for 5 min, then 95 °C for 5 min, and stored at −20 °C.
A 25 µl PCR-reaction contained 10 µl of genomic DNA, 0.5 µl 10 µM primer forward, 0.5 µl 10 µM primer reverse,  12.5 µl 2x GoTaq Long PCR Master Mix (Promega) and 1.5 µl H2O. The thermocycler setting consisted of one step at 95 °C for 1 min; followed by 18 cycles at 98°C for  10 s, 65°C for 15 s and 72°C for 15 s (wherein the annealing temperature was decreased by 0.5 °C per cycle); followed by 15 cycles at 98°C for 10 s, 58°C for 15 s and 72°C for 15 s; with one final step at 72°C for 5 min. The PCR products were cleaned up using AMPure beads according to the manufacturer's recommendations (Beckmann Coulter) and eluted in 50 µl 10 mM Tris. For barcoding, 2 µl of the purified DNA were added to 10 µl of 2x GoTaq Long PCR Master Mix, 2 µl of Nextera XT index 1 (i7) primer, 2 µl of Nextera XT index 2 (i5) primer (Illumina) and 4 µl of H2O. The PCR reactions were heated up to 95 °C for 3 min, followed by 8 cycles of 95°C for  30 s, 55°C for 30 s and 72°C for 30 s and a further elongation step for 5 min at 72°C. The second PCR products were again purified with AMPure beads and eluted in  27.5 µl 10 mM Tris. Cleaned-up PCR products were quantified using the SpectraMax Quant AccuBlue HighRange dsDNA Kit (Molecular Devices) on the SpectraMax 3x instrument (Molecular Devices). Equal amounts of DNA/sample were pooled and sequenced on an Illumina MiSeq instrument (Illumina) with a MiSeq Reagent Nano Kit v2 (500-cycles) (Illumina) according to the manufacturer’s recommendations.
Amplicon-Sequencing

treatment_protocol: 80 µM crRNA (IDT) and 80µMtracrRNA(IDT) were mixed in a 1:1 ratio and incubated for 5 min at 96°C to generate 40 µMcrRNA:tracRNA duplexes (gRNA sequences: Suppl. Table 1). An equal volume of 40 µM Streptococcus pyrogenes Cas9-NLS (made in-house;59; Cas9 expression plasmid pMJ915 (Addgene)) was carefully added to the crRNA-tracrRNAduplex and incubated for 20 min at room temperature (RT) to generate 20 µM Cas9 RNPs. 1x106cells were resuspended in 20 µl P3 buffer with Supplement 1 (LONZA) and 4 µl 20 µM Cas9 RNP and 1 µl of100 µM electroporation enhancer (Sigma-Aldrich) were added. T cells were nucleofected in 96 well reaction cuvettes (LONZA) using program EH-115 on theLonza 4D-Nucleofector (LONZA). Directly after nucleofection, 80 µlcRPMIwere added to the reaction cuvette. After resting for 30 min at 37°C the cells were transferred to a 96 well-plate and either activated withDynabead Human T-Activator CD3/CD28 (ThermoFisher) in a cell: bead ratio of 10:1 and cultured with 100 U/ml IL-2 (Peprotech) or cultured with 0.5 ng/ml IL-7 (Peprotech) and 0.5 ng/ml IL-15 (Peprotech) (“non-activated” T cells). IL-2 was replenished on day 6 of culture. 0.5 µM PFT-µ (Sigma) or 30 µM cyclic PFT-α (Hölzel Diagnostika) were added directly after nucleofection in the resting medium, as well as in the cultivation medium.

value: PBMCs

value: TRAC-KO

value: 30mol/l  Pifithrin-alpha


title: uninduced-1


title: D880CD815ICpre30TRAC


title: D880CD8beads11Cytopre30TRAC


title: iNeuron Day 10 Rep 4


title: iNeuron Day 10 Rep 1


title: D880CD8beads11pre0TRAC


title: D875CD8beads110post0TRAC


title: D880CD8beads11Cytopre0TRAC


title: D880CD8beads11pre30TRAC


title: D875CD8beads110post30TRAC


title: D871CD8beads110post0TRAC


title: D871CD8beads110post30TRAC


title: D875CD815ICpre30TRAC


title: D875CD815ICpre0TRAC


title: D871CD8beads11Cytopre30TRAC


title: D875CD8beads11Cytopre30TRAC


title: D871CD815ICpre30TRAC


title: D871CD8beads11Cytopre0TRAC


title: D875CD8beads11pre0TRAC


title: D875CD8beads11pre30TRAC


title: D871CD815ICpre0TRAC


title: D829CD4DMSOTRAC


title: D875CD8beads11Cytopre0TRAC


title: D829CD430aTRAC


title: D871CD8beads11pre0TRAC


title: D871CD8beads11pre30TRAC


title: D880CD815ICpre0TRAC


title: D829CD830aTRAC


title: D880CD8beads110post0TRAC


title: D829CD8DMSOTRAC


title: D827CD430aTRAC


title: D827CD830aTRAC


title: D827CD8DMSOTRAC


title: S37

data_processing:
Screening for deletion using CRISPResso2 (V2.2.7)
Reads for each deletion were normalised and displayed in a cumulative way
Assembly: hg38
Supplementary files format and content: .txt file with the range of deletions
Library strategy: Amplicon-Sequencing

extract_protocol:
cells were resuspended in DNA Quick Extraction solution (Lucigen) to lyse the cells and extract genomic DNA. The cell lysate was incubated at 65 °C for 5 min, then 95 °C for 5 min, and stored at −20 °C.
A 25 µl PCR-reaction contained 10 µl of genomic DNA, 0.5 µl 10 µM primer forward, 0.5 µl 10 µM primer reverse,  12.5 µl 2x GoTaq Long PCR Master Mix (Promega) and 1.5 µl H2O. The thermocycler setting consisted of one step at 95 °C for 1 min; followed by 18 cycles at 98°C for  10 s, 65°C for 15 s and 72°C for 15 s (wherein the annealing temperature was decreased by 0.5 °C per cycle); followed by 15 cycles at 98°C for 10 s, 58°C for 15 s and 72°C for 15 s; with one final step at 72°C for 5 min. The PCR products were cleaned up using AMPure beads according to the manufacturer's recommendations (Beckmann Coulter) and eluted in 50 µl 10 mM Tris. For barcoding, 2 µl of the purified DNA were added to 10 µl of 2x GoTaq Long PCR Master Mix, 2 µl of Nextera XT index 1 (i7) primer, 2 µl of Nextera XT index 2 (i5) primer (Illumina) and 4 µl of H2O. The PCR reactions were heated up to 95 °C for 3 min, followed by 8 cycles of 95°C for  30 s, 55°C for 30 s and 72°C for 30 s and a further elongation step for 5 min at 72°C. The second PCR products were again purified with AMPure beads and eluted in  27.5 µl 10 mM Tris. Cleaned-up PCR products were quantified using the SpectraMax Quant AccuBlue HighRange dsDNA Kit (Molecular Devices) on the SpectraMax 3x instrument (Molecular Devices). Equal amounts of DNA/sample were pooled and sequenced on an Illumina MiSeq instrument (Illumina) with a MiSeq Reagent Nano Kit v2 (500-cycles) (Illumina) according to the manufacturer’s recommendations.

tag: concentration

value: PFTa


title: S9


title: S5


title: S34


title: S38


title: S33


title: S31


title: S32


title: S3


title: S28


title: S20


title: S27


title: S19


title: S15


title: S11


title: S14


title: LM90


title: S16


title: S12


title: D827CD4DMSOTRAC


title: LM859


title: LM862


title: LM860


title: LM87


title: LM861


title: LM857


title: LM856


title: LM855

value: PFTu


title: LM854


title: LM850


title: LM851


title: LM849


title: LM848


title: LM85


title: LM844


title: LM88


title: LM84


title: LM797


title: LM787


title: LM792


title: LM795


title: LM784


title: LM783


title: LM785


title: LM858


title: LM863


title: LM778


title: LM782


title: LM800


title: LM82


title: LM845


title: LM775


title: LM777


title: LM786


title: LM774


title: CFII-150'

city: Hannover

first: Claudio

last: Rodriguez Gonzalez

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

data_processing:
The processing of the raw sequencing data was performed using nfcore/rnaseq and Nextflow bioinformatics tools.
Data normalization and differential gene expression was analyzed with the bioinformatics tool Galaxy (version 20.05, RCU Genomics, Hannover Medical School, Germany) using default settings.
Assembly: The reference genome used to annotate the data was taken from GENCODE.org (Homo sapiens: GRCh38.p13; release 34).
Supplementary files format and content: tab-delimited text file includes raw counts of each sample

source_name: iPSC derived macrophage

extract_protocol:
RNA was isolated using a RNeasy Micro Kit (Qiagen) following manufacturer’s instructions and subsequently preserved at -80°C
220ng of total RNA per sample underwent a process of mRNA enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Afterwards, stranded cDNA libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Procedures were done downscaling 2/3 the initial volumes described in the user manual and one extra purification step was performed at the end of the protocol using Agencourt AMPure XP Beads (Beckman Coulter).

value: iPSC derived macrophage

value: CF

value: P.aeruginosa 150'


title: CFII-60'

value: P.aeruginosa 60'


title: CFII-NoInf

value: No infected


title: CFII-450'

value: P.aeruginosa 450'


title: LM742


title: CFI-150'


title: LM773


title: LM740


title: CFI-NoInf


title: CFI-60'


title: LM739


title: WTII-450'

value: WT


title: LM736


title: WTII-60'


title: LM737


title: WTII-NoInf


title: WTI-450'


title: LM734


title: CFI-450'


title: LM733


title: LM730


title: LM728


title: LM731


title: WTI-60'


title: WTI-NoInf


title: LM727


title: LM725


title: LM63


title: LM63c


title: x03Mlg_TGFB_Mir9LOF_H3K4me3_ChIP

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

country: France

institute: CNRS Director of Research

data_processing:
The raw reads' visualization was trimmed using Trimmomatic (Bolger et al. 2014), min a length of 15 bp and Quality score of a minimum of 15.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings.
PCR duplicated were removed using MarkDuplicates.jar from Picard-tools (v.1.119)
Mitochondrial Chr was removed from bam mapped files using (awk '{if($3 != "chrM" && $3 != "chrUn"){print $0}}')
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Peaks calling for H3k4me3 marker MACS3 callpeak, with settings ( --broad -g mmu -q 0.001 --keep-dup 1 --fix-bimodal --nomodel --extsize 1000).
After call peaks, high signal areas from the mm10 blacklist were removed using bedtools intersept (v2.30.0), settings (-wa -v). Where -a is the peak file ad -b is the edited blacklist from mm10 genome from (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz).
Peaks were annotated with annotatePeaks.pl from homer to the mm10 reference (default settings)
Assembly: mm10 from UCSC
Supplementary files format and content: BigWig files and Annotated peak files

source_name: MLg (ATCC CCL-206)

growth_protocol: MLg (mouse fibroblast cell) were grown according to manufacture's recommendation

extract_protocol:
Cells were transfected with antagomiR probes (Ambion) using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions, and harvested 24 h later for further analysis. Anti-hsa-miR-Mir9-5p (Ambion, #17000), and Anti-miR negative control (Ambion, #17010) were transfected at 60 nM final concentrations. Following 20 h after transfection, TGFB1 signaling was induced with 5 ng/ml final concentration of human recombinant TGFB1 (Sigma-Aldrich) for 4 h.
TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications. Instead of gel-based size selection before the final PCR step, libraries were size selected by SPRI-bead-based approach after the final PCR with 18 cycles. In detail, samples were 1stcleaned up by 1x bead: DNA ratio to eliminate residuals from PCR reaction, followed by a 2-sided-bead cleanup step with an initial 0.6x bead:DNA ratio to exclude larger fragments. The supernatant was transferred to a new tube and incubated with additional beads in 0.2x bead:DNA ratio to eliminate smaller fragments, like adapter and primer dimers. Bound DNA samples were washed with 80% ethanol, dried, and resuspended in TE buffer. Library integrity was verified with LabChip Gx Touch (Perkin Elmer).

treatment_protocol: ChIP-seq was performed as described previously [https://doi.org/10.1038/s41588-018-0139-3]

value: MLg (ATCC CCL-206)

value: lung fibroblast

value: Tgfb treatment and Anti-hsa-miR-Mir9-5p (Ambion, #17000)

tag: antibody


title: x01Mlg_Ctr_H3K4me3_ChIP


title: LM62c


title: WTII-150'


title: MLE-12_Mir9LOF_G4_CaT

data_processing:
The raw reads' visualization was trimmed using Trimmomatic (Bolger et al. 2014), min a length of 15 bp and Quality score of a minimum of 15.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 settings (--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700)
PCR duplicated were removed using MarkDuplicates.jar from Picard-tools (v.1.119)
Mitochondrial Chr was removed from bam mapped files using (awk '{if($3 != "chrM" && $3 != "chrUn"){print $0}}')
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Peaks calling for H3k4me3 marker MACS3 callpeak, with settings ( --broad -g mmu -q 0.001 --keep-dup 1 --fix-bimodal --nomodel --extsize 1000). Peaks for H3k27ac were called with MACS3 callpeak, settings ( --broad -g mmu -q 0.001 --keep-dup 1 --fix-bimodal --nomodel --extsize 200) and G4 was called with MCAS14 setting ( p1e3 for the p-value).
After call peaks, high signal areas from the mm10 blacklist were removed using bedtools intersept (v2.30.0), settings (-wa -v). Where -a is the peak file ad -b is the edited blacklist from mm10 genome from (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz).
Peaks were annotated with annotatePeaks.pl from homer to the mm10 reference (default settings)
Assembly: mm10 from UCSC
Supplementary files format and content: BigWig files and Annotated peak files
Library strategy: Cut&Tag

growth_protocol: MLg (mouse fibroblast cell) and MLE-12 (mouse epithelial cells) were grown according to manufacture's recommendation

extract_protocol:
Cells were transfected with Anti-hsa-miR-Mir9-5p (Ambion, #17000 were transfected at 60 nM final concentrations using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions and harvested 48 h later for further analysis.
TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications. Instead of gel-based size selection before the final PCR step, libraries were size selected by SPRI-bead-based approach after the final PCR with 18 cycles. In detail, samples were 1stcleaned up by 1x bead: DNA ratio to eliminate residuals from PCR reaction, followed by a 2-sided-bead cleanup step with an initial 0.6x bead:DNA ratio to exclude larger fragments. The supernatant was transferred to a new tube and incubated with additional beads in 0.2x bead:DNA ratio to eliminate smaller fragments, like adapter and primer dimers. Bound DNA samples were washed with 80% ethanol, dried, and resuspended in TE buffer. Library integrity was verified with LabChip Gx Touch (Perkin Elmer).

treatment_protocol: CUT&Tag experiments were performed as described previously [PMID: 31036827, PMID: 34792172]

value: Anti-hsa-miR-Mir9-5p (Ambion, #17000)

value: BG4 (Millipore, # MABE917)


title: LM62

value: PBMCs


title: LM61c


title: MLg_Ctr_G4_CaT_r1

value: Anti-miR Inhibitor Negative Ctr #1 (Ambion AM17010)


title: MLg_Mir9LOF_G4_CaT_r1


title: LM610


title: MLE-12_Ctr_G4_CaT_r1


title: WTI-150'


title: MLE-12_H3K4me3_CaT_Ctr


title: LM60c


title: LM609

value: TRAC-KO


title: MLE-12_H3K27ac_CaT_Ctr


title: MLE-12_H3K27ac_CaT_Mir9-LOF


title: MLE-12_H3K4me3_CaT_Mir9-LOF


title: LM607

value: PFTa


title: MLg_H3K27ac_CaT_Ctr


title: MLg_H3K27ac_CaT_Mir9-LOF


title: LM608


title: MLg_H3K4me3_CaT_Mir9-LOF


title: LM61


title: x02Mlg_TGFB_H3K4me3_ChIP

value: Tgfb treatment


title: LM605


title: LM606


title: LM604


title: MLg_H3K4me3_CaT_Ctr


title: LM603


title: DFX_3uM

first: Nathan

middle: Elias

last: Jeffries

address: 185 Cambridge St MCPZN 4400

department: CRM

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
CellRanger (v7.1.0) was used for sequences alignment and generate read counts per gene in each cell.
Downstream analysis was performed using the Seurat 3.2.3 package (Butler et al, 2018)
Exclude cells with <200 expressed genes, genes expressed in <3 cells and cells with mitochondrial transcripts > 20%
Assembly: GRCh38
Supplementary files format and content: Cellranger output files -Tab separated values files and Matrix files

source_name: in vitro adult BM

growth_protocol: A mixture of bone marrow (BM) aspirate and peripheral blood (PB) collected from a healthy donor was lineage-depleted using a Miltenyi kit (130-092-211; columns 130042401) and cultured in aMEM (Gibco 12571-063) with recombinant human SCF (50 ng/mL) and GCSF (10 ng/mL) for 5 days

extract_protocol: none provided

treatment_protocol: Cells were treated with either 1.5 uM DFX, 3 uM DFX, or an equal volume DMSO for the duration of culture

value: in vitro adult BM

value: Hematopoietic

value: 3 uM DFX


title: DMSO_2

description: 10x Genomics

value: DMSO


title: LM59c


title: LM59


title: LM60

value: PFTu


title: DMSO_1

description: 10x Genomics


title: LM58c


title: LM58


title: LM57pd


title: LM56


title: LM55pd


title: LM55


title: LM56pd


title: LM54


title: LM53pd


title: LM52pd


title: LM53


title: LM510


title: LM51


title: LM509


title: LM508


title: LM52


title: DFX_1_5uM

description: 10x Genomics

value: 1.5 uM DFX


title: LM506


title: LM505


title: LM504


title: LM503


title: LM502


title: LM501


title: LM500


title: LM50


title: LM498


title: LM499


title: LM497


title: LM57


title: LM496


title: LM54pd


title: LM494


title: LM491


title: LM493


title: LM490


title: LM492


title: LM46


title: LM483


title: LM49


title: LM45


title: LM45c


title: LM481


title: LM507


title: LM47


title: LM48


title: LM43c


title: LM44c


title: LM435


title: LM44


title: LM433


title: LM434


title: LM432


title: LM431


title: LM430


title: LM43


title: LM429


title: LM495


title: LM42c


title: LM428


title: LM426


title: LM427


title: LM420


title: LM422


title: LM42


title: LM417


title: LM416


title: LM423


title: LM412


title: LM41


title: LM410


title: LM415


title: LM40c


title: LM413


title: LM41c


title: LM40


title: LM39pd


title: LM38


title: LM38pd


title: LM37pd


title: LM376


title: LM36pd


title: LM37


title: LM39


title: LM367


title: LM421


title: LM364


title: LM363


title: LM361


title: LM362


title: LM360


title: LM36


title: LM35pd


title: LM34pd


title: LM35


title: LM359


title: LM382


title: LM332


title: LM331


title: LM379


title: LM330


title: LM373


title: LM339


title: LM34


title: LM33


title: LM370


title: LM327


title: LM325


title: LM324


title: LM329


title: LM314


title: LM32


title: LM313


title: LM312


title: LM310


title: LM304


title: LM311


title: LM302


title: LM303


title: LM30


title: LM308


title: LM301


title: LM298


title: LM31


title: LM323


title: LM29


title: LM291


title: LM300


title: LM285


title: LM296


title: LM297


title: LM299


title: LM284


title: LM293


title: LM288


title: LM321


title: LM281


title: LM28


title: LM290


title: LM292


title: LM279


title: LM278


title: LM309


title: LM276


title: LM275


title: LM273


title: LM269


title: LM287


title: LM264


title: LM266


title: LM257


title: LM267


title: LM256


title: LM254


title: LM247


title: LM251


title: LM245


title: LM253


title: LM250


title: LM252


title: LM249


title: LM243


title: LM242


title: Tepotinib-treated, ROI 077

type: protein

city: Darmstadt

first: Manon

middle: A

last: Simard

address: Frankfurterstraße 250

department: Research Unit Oncology

institute: Merck Healthcare KGaA

description:
20231006_P1001660003346A_P1001660003346A_08.RCC
DNA barcode cleaved from RNA probe

scan_protocol: Scanned using the GeoMx DSP (NanoString Technologies)

data_processing: For an nCounter readout, the collected samples were first hybridized overnight to the GeoMx Hyb Code master mixes, consisting of probes U and R in hybridization buffer, as outlined in the GeoMx nCounter protein readout user guide. Hybridization products were then pooled for readout on the MAX/FLEX nCounter system. RCC files were loaded back onto the GeoMx instrument for downstream analysis in the GeoMx Analysis Suite.

molecule: protein

source_name: METex14 NSCLC

label_protocol: Following BOND Rx protocol, slides were incubated overnight at 37 ˚C with the selected protein panels: Immune Cell Profiling, Immune Cell Typing, Immune Activation Status, IO Drug Targets, PI3K/AKT Signaling; as well as the morphology markers: TTF1, CD3 and CD33. The following day, post-fixation of section was performed, after washing the slides 3 times in TBS-T for 10 minutes, using 4% paraformaldehyde in a humidity chamber for 30 minutes. Slides were then washed twice for 2 minutes in TBS-T. Nuclear staining was then performed in a humidity chamber using SYTO13 DNA stain for 15 minutes. Slides were finally washed twice in TBS-T before being loaded into the GeoMx DSP instrument.

growth_protocol: FFPE blocks, tepotinib-treated surgical resection was obtained following 42 days of tepotinib treatment

treatment_protocol: The slide preparation was performed as per GeoMx DSP Slide Preparation Protocol using the Semi-Automated BOND Rx protocol. In brief, 5 µm tissue sections were positioned in the GeoMx imaging area on a SuperFrost Plus slide. Sections were incubated at 60 ˚C for over 30 minutes prior to BOND Rx protocol. BOND Rx protocol consisted of Bake & Dewax, HIER for 20 minutes with ER1.

value: female

tag: tumor type

value: NSCLC

tag: mutation

tag: tnm

tag: ttf1 staining

value: negative

value: Periphery


title: Tepotinib-treated, ROI 076

description:
20231006_P1001660003346A_P1001660003346A_07.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 078

description:
20231006_P1001660003346A_P1001660003346A_09.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 075

description:
20231006_P1001660003346A_P1001660003346A_06.RCC
DNA barcode cleaved from RNA probe

value: positive

value: Tumor


title: LM241

value: PBMCs


title: Tepotinib-treated, ROI 073

description:
20231006_P1001660003346A_P1001660003346A_04.RCC
DNA barcode cleaved from RNA probe


title: LM272


title: W3: Rong Chang pig, 730 days

city: Chengdu

first: Hongling

address: Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
The raw data was filtered using Trimmomatic-0.36 (parameters: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLUMINACLIP:adapter.fa:2:30:7)
Bismark (0.16.3) was used to compare methylation data (parameters: --score_min L, 0, -0.2, -X 700 --dovetail)
Assembly: Sscrofa11.1
Supplementary files format and content: *.mC_level_Identification_stat.txt.gz: the mC identification results for each sample
(1) Chromosome: chromosome ID
(2) Position: cytosine coordinate at genome
(3) Strand: strand information of the cytosine
(4) mC count: the number of methylated cytosines
(5) umC count: the number of unmethylated cytosines
(6) Methylation level: ML=mC/(mC+umC)
(7) Context: contexts in which the cytosine is located
(8) Pvalue: p value of binomial distribution test
(9) Corrected pvalue: adjusted p value

organism: Sus scrofa

source_name: Liver

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013
DNA methylation-sensitive extraction, bisulfite treatment, DNA fragmentation, library construction, PCR amplification and high-throughput sequencing

value: Liver

tag: age

value: 730 days


title: W1: Rong Chang pig, 730 days


title: LM240

tag: cell type


title: B3: Rong Chang pig, 21 days

tag: tissue

value: 21 days


title: LM244

value: PFTa


title: B1: Rong Chang pig, 21 days


title: LM24


title: Tepotinib-treated, ROI 079

description:
20231006_P1001660003346A_P1001660003346A_10.RCC
DNA barcode cleaved from RNA probe

tag: Sex


title: Tepotinib-treated, ROI 071

description:
20231006_P1001660003346A_P1001660003346A_02.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 070

description:
20231006_P1001660003346A_P1001660003346A_01.RCC
DNA barcode cleaved from RNA probe


title: A3: Rong Chang pig, 0 days

value: 0 days


title: LM238


title: S-41037-VIP

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-delimited files contain raw counts for each sample

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Nr. 74034)
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.

tag: cell line

tag: sorted cell_type

value: murine intestinal organoid line

value: sorted Lgr5-EGFP+ cells

tag: bio rep

tag: treatment

value: vip

tag: irradiation

value: control


title: A2: Rong Chang pig, 0 days


title: S-41037-VIP-IR

value: irradiated


title: LM239


title: LM236


title: S-41037-Control


title: S-41036-VIP


title: Tepotinib-treated, ROI 069

description:
20231006_P1001660003346A_P1001660003346A_12.RCC
DNA barcode cleaved from RNA probe

value: female


title: Tepotinib-treated, ROI 074

description:
20231006_P1001660003346A_P1001660003346A_05.RCC
DNA barcode cleaved from RNA probe

value: NSCLC


title: S-41036-VIP-IR


title: LM235


title: S-41036-Control


title: Tepotinib-treated, ROI 068

description:
20231006_P1001660003346A_P1001660003346A_11.RCC
DNA barcode cleaved from RNA probe

value: negative


title: S-41036-Control-IR


title: Tepotinib-treated, ROI 067

value: Periphery


title: Tepotinib-treated, ROI 072

description:
20231006_P1001660003346A_P1001660003346A_03.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 066


title: S-41032-VIP


title: S-41032-VIP-IR


title: LM233


title: S-41037-Control-IR


title: S-41032-Control-IR


title: Tepotinib-treated, ROI 065

value: positive


title: S-41002-VIP


title: Tepotinib-treated, ROI 064

value: Tumor


title: S-41002-Control


title: S-41002-Control-IR


title: S-41002-VIP-IR


title: Tepotinib-treated, ROI 063


title: LM231

value: PBMCs


title: m40696-VIP-BR4


title: LM232


title: Tepotinib-treated, ROI 061


title: m40669-Ctrl-BR3


title: m40669-VIP-BR3


title: LM229


title: LM23


title: m40562-Ctrl-BR2


title: Tepotinib-treated, ROI 062


title: m40562-VIP-BR2


title: m40696-Ctrl-BR4


title: Tepotinib-treated, ROI 059


title: LM227


title: S-41032-Control


title: LM230


title: m40465-VIP-BR1


title: Tepotinib-treated, ROI 060


title: m40465-Ctrl-BR1


title: LM226


title: Tepotinib-treated, ROI 058


title: m40066-vip-BR4-TR2

value: whole organoid

tag: technical rep


title: m40066-vip-BR4-TR1


title: LM225

tag: genotype


title: m40065-vip-BR3-TR1


title: m40065-vip-BR3-TR2


title: m40065-control-BR3-TR1


title: LM234


title: LM22


title: LM224


title: Tepotinib-treated, ROI 055


title: m40062-control-BR2-TR2


title: Tepotinib-treated, ROI 056


title: m40062-control-BR2-TR1


title: LM21pd

tag: concentration

value: PFTu


title: m40061-vip-BR1-TR2


title: m40062-vip-BR2-TR1


title: m40061-vip-BR1-TR1


title: m40061-control-BR1-TR1


title: LM20pd


title: Tepotinib-treated, ROI 053


title: m40061-control-BR1-TR2


title: Tepotinib-treated, ROI 052


title: Tepotinib-treated, ROI 051


title: 04MLg_RNAs_riZero_Tgfb_Mir9_LOF

data_processing:
trimmomatic version 36.0 was used to trim raw files as followed (java -jar trimmomatic-0.36.jar SE -threads 8 -phred33 sample.fastq .trim.fq ILLUMINACLIP:${TRUE_SEQ_ADAP}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15 CROP:60 HEADCROP:15)
RNA-Seq reads were mapped to the mm10 reference genome using bowtie2 -D 15 -R 3 -N 0 -L 20 -i S,1,0.56 -k 1 -p8
amples were quantified using analyzeRepeats.pl (mm10 –count exons –strand both –noadj).
Differential expression was quantified and normalized using  Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR.
log2fc was the log2(norm_RPKM_from_Mir9_LOF/norm_RPKM_from_CTR)
Assembly: mm10
Supplementary files format and content: Excel differential expression data

growth_protocol: Mlg cells were grown accoring to manufacture recommendation

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
True-seq

treatment_protocol: Cells were transfected with antagomiR probes (Ambion) using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions, and harvested 24 h later for further analysis. Anti-hsa-miR-Mir9-5p (Ambion, #17000), and Anti-miR negative control (Ambion, #17010) were transfected at 60 nM final concentrations. Following 20 h after transfection, TGFB1 signaling was induced with 5 ng/ml final concentration of human recombinant TGFB1 (Sigma-Aldrich) for 4 h.

value: MLg (ATCC CCL-206)

value: WT


title: LM20

value: PFTa


title: Tepotinib-treated, ROI 057


title: 03MLg_RNAs_riZero_Tgfb

source_name: Tgfb


title: 02MLg_RNAs_riZero_Mir9_LOF


title: LM19pd


title: m40062-vip-BR2-TR2

value: murine intestinal organoid line


title: Tepotinib-treated, ROI 050


title: Tepotinib-treated, ROI 054


title: LM21


title: 03MLg_K4m3_HICHIP_Tgfb_antiMir9

data_processing:
HiCHIP-seq paired-end reads were aligned to the mm10 genome, duplicate reads were removed, reads were assigned to MboI restriction fragments, filtered into valid interactions, and the interaction matrices were generated using the HiC-Pro pipeline default settings (Servant et al., 2015). The contig file of the HiC-pro was set to allow validPairs at any distance from each other.
HiC-Pro valid interaction reads were then used to detect significant interaction were obtained using
first: Maketaglibraries were made as followed (makeTagDirectory output_PCA_ucsc smaple_R1_mm10.bwt2merged.bam,sample_R2_mm10.bwt2merged.bam -tbp 1 -genome mm10 -checkGC -restrictionSite GATC.
Second: we used (runHiCpca.pl sample_mer25_50 sample_PCA_ucsc -res 25000 -superRes 50000 -genome mm10 -cpu 16)
Next. We used analyzeHiC as followed (analyzeHiC sample_PCA_ucsc -res 1000000 -interactions sample_significantInteractions.txt -nomatrix )
Only Interaction looping between the H3K4me3 peaks and the TSS (+/-2kb) fromMir9 candidate genes were considered. The seetings were (annotateInteractions.pl Sample_significan mm10 Sample_output_filterk4m9 -filter H4k4me3_HICHIP-seq_peaks -filter2 TSS2kb_fMir9_genes -cpu 16 -washu -pvalue 0.01
Further the mapped merge bam files ouput from HiC-pro was processed as ChiP-seq to perform Peak calling, using (peak_call -i $R1 -o ${yolo1}-peak -r $RE -f 0.01 -a $chr -w 8 . Taken from https://github.com/ChenfuShi/HiChIP_peaks
To calculate the breadth of H3K4me3 peaks, we first performed summary statistics of the peak size from the merged peak list. If the size of a peak was equal to or higher than the top 75 % of peaks quantile 3(Q3) was consider wide (>=2.7kb). If the peak was between Q3 and Q2 was consider medium size peak (<2.7kb and >2kb). The narrow Hek4me3 paks were in the bottom 25% peaks, Q1 or less (< 2kb)
Assembly: mm10
Supplementary files format and content: validPairs
Library strategy: HICHIP-seq

source_name: MLg

extract_protocol: Nextera DNA library preparation kit

tag: transfection

value: Tgfb treatment and Anti-hsa-miR-Mir9-5p (Ambion, #17000)

tag: antibody


title: 01MLg_K4m3_HICHIP_Ctr


title: 02MLg_K4m3_HICHIP_Tgfb

value: Tgfb treatment


title: Tepotinib-treated, ROI 048

tag: tumor type

tag: mutation


title: LM18pd


title: Tepotinib-treated, ROI 049

tag: tnm

tag: ttf1 staining


title: LM18

tag: cell type


title: 01MLg_Mir9_ChIRP

data_processing:
Raw reads were trimmed with Trimmomatic-0.36 with the parameters (ILLUMINACLIP:${ADAPTERS}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 CROP:70 HEADCROP:10.
The trimmed reads were mapping using Bowtie2 (default settings) to the zebrafish genome from ucsc versionmm10 from ucsc.
Mapped reads were converted to from sam to bam by the help of samtools.
PCR duplicates were removed from the bam files with the help of MarkDuplicates.jar from Picard1.119.
Bam files were merged by the help of bamtools merge and from the merged files the bigwig files were created. We used bamCoverage from deptools (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
for Peak calling, MCAS14 was used with a (macs14 -t ChIRP -c Inp -f BAM -p 1e-3 -g 1.87e9 --nomodel --shiftsize 30 -n) and  -p 1e-3 -g 1.87e9 --nomodel --shiftsize 100. With the aim to capture Mir9 different DNA enriched areas. Both peaks results were merged with bedtools merge (bedtools merge -d 100 -i cat_PEAKS_s_2.bed) with differen Annotation with annotatePeaks.pl from homer.
Assembly: mm10
Supplementary files format and content: BigWig files
Library strategy: ChIRP-seq

source_name: Mlg

growth_protocol: MLg (ATCC CCL-206) were grown at 37°c according to the manufacturer recommendation

extract_protocol:
Chromatin was diluted in two times volume of hybridization buffer (750mM NaCl, 1% SDS, 50mM Tris 7.0, 1mM EDTA, 15% formamide, add 1% of DTT, PMSF, PI, and 0.1% of RNase inhibitor (Promega). 150pmol of probes (Biotinylated tilling oligo of mature Mir9 or Mirctrl) added to ml of diluted chromatin, which was mixed by end-to-end rotation at 37°C for 4h. Streptavidin-magnetic C1 beads (Invitrogen) were washed three times in nuclear lysis buffer, blocked with 500ng/μl yeast total RNA, and 1mg/ml BSA for 1h at room temperature, and washed three times again in nuclear lysis buffer before resuspended in its original volume. 100µl of washed/blocked C1 beads were added per 100pmol of probes, and the whole reaction was mixed for another 30min at 37°C. beads:biotin-probes:RNA:chromatin adducts were captured by magnets (Invitrogen) and washed five times with40× beads volume of wash buffer (2× SSC, 0.5% SDS, add 1% DTT, PMSF and PI). After last wash buffer was removed carefully with P-10 pipette so that no trace volume was left behind. Beads are now poised for different elution protocols depending on downstream assays. Beads were resuspended in 3× original volume DNA elution buffer (50mM NaHCO3, 1% SDS, 200mM NaCl), and DNA was eluted with a cocktail of 100μg/ml RNase-A (Sigma-Aldrich). Chromatin was reverse crosslinked at 65°C overnight. DNA was then extracted purify the DNA with qiaquick columns according to manufacturer’s instructions
NEXseq

treatment_protocol: Endogenous Mir9-ChIRP was performed as described in PMID: 21963238[78] with slight modifications. MLE-12 and MLg cells were crosslinked, 1% formaldehyde in PBS for 10min at room temperature. Crosslinking was then quenched with 0.125M glycine for 5min. Cells were rinsed again with PBS, scraped into falcon tubes, and pelleted at 800x g for formaldehyde crosslinking and cell pellets were then snap frozen in liquid nitrogen and can be stored in -80°C indefinitely.


title: Tepotinib-treated, ROI 047

tag: tissue


title: LM17pd


title: NSC34_siQk3

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

institute: Niigata University

data_processing:
alignment with OLego
to have BAM and Bed file
transcript level and alternative splicing events with Quantas
Assembly: mm10
Supplementary files format and content: .txt gene_id gene_symbol, Tag_Number, RPKM, start and end position, strand and isoform tag_number

growth_protocol: NSC34 cells were cultured in 10% FCS DMEM medium

extract_protocol:
Total RNA was obtained from each three biological replicates of NSC34 cells reatment with control siRNA and three different siRNA for Qk gene. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using Illumina TruSeq protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions.
TruSeq RNA Sample Prep Kit v2

value: siRNA for Qk gene


title: 02MLg_Inp_ChIRP


title: NSC34_siQk2


title: Tepotinib-treated, ROI 046

tag: Sex


title: LM17


title: Tepotinib-treated, ROI 045


title: NSC34_NC3

value: control siRNA


title: NSC34_NC2


title: LM16pd


title: 01MLg_RNAs_riZero_Ctr

source_name: Ctr

tag: cell line


title: LM19


title: LM16


title: NSC34_siQk1


title: OPC_siQk_3

source_name: mouse primary OPC

growth_protocol: Mouse primary cultured oligodendrocyte precurssor cells were obtained form (PMID:24003195)

extract_protocol:
Total RNA was obtained from each three biological replicates of mouse primary OPC treatment with control siRNA and three different siRNA for Qk gene. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using Illumina TruSeq protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions.
TruSeq RNA Sample Prep Kit v2

tag: sirna


title: Tepotinib-treated, ROI 044

value: female


title: 04MLg_K4m3_HICHIP_Mir9_LOF

value: Anti-hsa-miR-Mir9-5p (Ambion, #17000)


title: OPC_siQk_2


title: LM15


title: OPC_siQk_1


title: LM140


title: OPC_NC_3


title: OPC_NC_2


title: Tepotinib-treated, ROI 042

value: NSCLC


title: Tepotinib-treated, ROI 041

value: negative

value: Periphery


title: OPC_NC_1


title: AC16 cells, AGO2-KO, 3

city: Wuhan

first: zhan

last: jiabing

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: ribosome footprints

data_processing:
library strategy: Ribo-seq
Low quality reads were filtered by fastp. Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 20-40bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed.
Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2-pass setting enabled. The reads mapped to classical noncoding RNAs (including long noncoding RNAs, microRNA precursors) were abandoned. Then remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment.
Three-nucleotide periodicity was plotted using the riboWaltz R package[6] as described. For RFs with specific length (e.g. RFs with length of 30nt), reads were assigned to frame 1,2,or 3 according to their position of 5’end in transcripts of protein coding gene, then proportion of total RFs in fame 1, 2 and 3 were calculated among all protein coding genes. Because the translocation of ribosomes occurs along the mRNA one codon at a time, the potential of single-codon resolution pauses were investigated. Using PausePred（https://pausepred.ucc.ie/）, which infers the locations of ribosome pauses, global single codon pauses were analyzed.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. Reads counts in the open reading frame of coding genes was calculated by software RSEM,and the gene expression level was normalized by using FPKM (fragment per kilobase of transcript per million mapped reads) method
Assembly: Homo sapiens (Ensembl_release109)

extract_protocol:
Cells pellet were immediately frozen in liquid nitrogen and ground to power in liquid nitrogen with a mortar and pestle, then dissolved in 400μL of lysis buffer. The resuspended extracts in lysis buffer were transferred to new microtubes, pipetted several times and incubated on ice for 10 min. Then cells were triturated ten times through a 26-G needle. The lysate was centrifuged at 20000g for 10min at 4℃, and the supernatant was collected. To prepare RFs , 10μL of RNase I (NEB, Ipswich, MA, USA) and 6μL of DNase I (NEB, Ipswich, MA, USA) were added to 400μL of lysate，which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10μL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next, 10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017). short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China).
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM X10 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: AGO2 knock out


title: AC16 cells, AGO2-KO, 2

description: ribosome footprints


title: Tepotinib-treated, ROI 040

value: positive

value: Tumor


title: LM14

value: PBMCs


title: AC16 cells, AGO2-KO, 1

description: ribosome footprints


title: LM138


title: AC16 cells, WT, 3

description: ribosome footprints

value: wild type


title: NSC34_NC1


title: Tepotinib-treated, ROI 039


title: Tepotinib-treated, ROI 038


title: AC16 cells, WT, 2

description: ribosome footprints


title: LM13


title: Tepotinib-treated, ROI 043


title: AC16 cells, WT, 1

description: ribosome footprints


title: Tepotinib-treated, ROI 037


title: Neutrophils, WT, infected-2

city: Auckland

first: Chris

last: Hall

address: 85 Park Road, Grafton

country: New Zealand

institute: The University of Auckland

description:
WTInfected_2
WTinfected_vs_Per2infected_geneDEsign_results.csv

data_processing:
The filtered clean reads were mapped to the Danio rerio reference genome (GRCz10) by HISAT2.
Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software.
DESeq was used to analyze the DEGs between sets of two groups as a control-treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05.
Assembly: GRCz10
Supplementary files format and content: Comma-separated values file show FPKM, Log2FC, and adj P value of DEGs comparing Per2Infected and WTInfected samples.

organism: Danio rerio

source_name: Neutrophil

growth_protocol: Tg(lyz:DsRED2) zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions

extract_protocol:
Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS-isolation of 1,000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART-Seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio)
Libraries were made using the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: At 52 hours post fertilization (4 hours after lights on), Tg(lyz:DsRED2)/WT and Tg(lyz:DsRED2);per2-/- zebrafish larvae we infected with 1,000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.

tag: developmental stage

value: larvae

value: Neutrophil

tag: infection

value: Salmonella typhimurium


title: Neutrophils, WT, infected-3

description:
WTInfected_3
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: Neutrophils, WT, infected-4

description:
WTInfected_4
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: LM12

tag: treatment

value: PFTu


title: LM116

value: TRAC-KO

value: PFTa


title: Tepotinib-treated, ROI 036


title: Neutrophils, WT, infected-1

description:
WTInfected_1
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: LM115


title: Neutrophils, per2, infected-3

description:
per2Infected_3
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: Neutrophils, per2, infected-2

description:
per2Infected_2
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: Neutrophils, per2, infected-4

description:
per2Infected_4
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: LM114


title: Neutrophils, per2, infected-1

description:
per2Infected_1
WTinfected_vs_Per2infected_geneDEsign_results.csv


title: Tepotinib-treated, ROI 034


title: LM112


title: Tepotinib-treated, ROI 033


title: LM113


title: 4098

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline,  which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file includes information about differential methylated positions with q-values less than 0.01 and methylation  differences greater than the absolute value of 25 and their annotations.
Supplementary files format and content: A tab-delimited text file includes information about differential methylated regionss with q-values less than 0.01 and methylation  differences greater than the absolute value of 25 and their annotations. The regional analysis used a 500-bp sliding window with a 250-bp overlap and a minimum of five CpG per regions
Library strategy: Enzymatic methyl-seq (EM-seq)

organism: Bos taurus

source_name: Blood

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

value: Blood

value: MRG


title: Tepotinib-treated, ROI 031

value: female


title: 3067


title: LM110


title: 5034

value: MSG


title: LM11


title: 8002


title: 5055


title: 7059


title: Tepotinib-treated, ROI 030

description:
20231006_P1001660003346A_P1001660003346A_09.RCC
DNA barcode cleaved from RNA probe

value: NSCLC

value: negative


title: 3020


title: LM109


title: Tepotinib-treated, ROI 029

description:
20231006_P1001660003346A_P1001660003346A_08.RCC
DNA barcode cleaved from RNA probe


title: LM111


title: Tepotinib-treated, ROI 028

description:
20231006_P1001660003346A_P1001660003346A_07.RCC
DNA barcode cleaved from RNA probe


title: 8010


title: Tepotinib-treated, ROI 035

description:
20231006_P1001660003346A_P1001660003346A_02.RCC
DNA barcode cleaved from RNA probe

value: Periphery


title: shRNA SCN5A 6

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

description:
RNA-sequencing data of breast cancer cell-line xenograph in mouse
human xenograft in mouse

data_processing:
Samples split with BBSplit from BBMap 39.0 against mm10 and hg38
hg38 reads aligned with Rsubread
Count matrix created with Rsubread
Differential Expression Calculated with DeSeq2
Assembly: hg38
Supplementary files format and content: csv text file of the Count matrix created with Rsubread
Supplementary files format and content: csv text file of the  output from DeSeq2

source_name: breast

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's protocols.

value: breast

tag: cage

value: shRNA SCN5A


title: shRNA SCN5A 4

tag: genotype


title: shRNA SCN5A 5


title: L892

value: PBMCs

tag: concentration


title: 5067


title: Tepotinib-treated, ROI 027

description:
20231006_P1001660003346A_P1001660003346A_06.RCC
DNA barcode cleaved from RNA probe

value: positive

value: Tumor


title: shRNA SCN5A 3


title: Tepotinib-treated, ROI 026

description:
20231006_P1001660003346A_P1001660003346A_05.RCC
DNA barcode cleaved from RNA probe


title: shRNA SCN5A 2


title: Tepotinib-treated, ROI 032

description:
20231006_P1001660003346A_P1001660003346A_11.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 025

description:
20231006_P1001660003346A_P1001660003346A_04.RCC
DNA barcode cleaved from RNA probe


title: L891


title: Tepotinib-treated, ROI 024

description:
20231006_P1001660003346A_P1001660003346A_03.RCC
DNA barcode cleaved from RNA probe


title: Control 6

value: control


title: L890


title: Control 5


title: Control 3


title: Control 4


title: L889


title: Control 1


title: L888


title: Tepotinib-treated, ROI 023


title: Control 2


title: L887


title: L886


title: LM10


title: Tepotinib-treated, ROI 022

description:
20231006_P1001660003346A_P1001660003346A_01.RCC
DNA barcode cleaved from RNA probe


title: L855


title: L885


title: Tepotinib-treated, ROI 021

description:
20231006_P1001660003346A_P1001660003346A_12.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 019

description:
20231006_P1001660003346A_P1001660003346A_10.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 017


title: L853


title: L854


title: Tepotinib-treated, ROI 018


title: Tepotinib-treated, ROI 020


title: L852


title: shRNA SCN5A 1


title: Tepotinib-treated, ROI 015


title: Tepotinib-treated, ROI 016


title: Tepotinib-treated, ROI 014


title: L850


title: L848


title: L847


title: L851


title: L846


title: Tepotinib-treated, ROI 013


title: Tepotinib-treated, ROI 012


title: Tepotinib-treated, ROI 011


title: L845


title: L844


title: L843


title: L842


title: Tepotinib-treated, ROI 008


title: L841