title: rnaseq_dtag_dtag3

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen).
RNA sequencing libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq 6000 with paired-end 150bp reads

treatment_protocol: For differentiation, high-density cultures (~80% confluency) were switched to differentiation media (DMEM, 2% horse serum (HS, Gibco®16050–122), penicillin 100 U/ml, and streptomycin 100μg/ml) to induce myotube formation. Myotubes at indicated days post differentiation were used for further analysis.


title: rnaseq_dtag_dtag2

status: Public on Feb 02 2024

type: SRA

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

country: USA

institute: Boston Childrens Hospital

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: C2C12 cells were grown following the standard protocol (Doynova et al., 2017). C2C12 myoblasts were propagated at 37°C, 5% CO2 in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Omega Scientific) and antibiotics (penicillin 100 U/ml, streptomycin 100μg/ml, Thermo Fisher Scientific).

tag: cell line

tag: cell type

value: myoblast

tag: genotype

value: dTag-Matr3 depleted

tag: treatment

tag: time

tag: replicate

tag: antibody


title: rnaseq_dtag_dtag1


title: rnaseq_dtag_dmso3

value: DMSO


title: rnaseq_dtag_dmso2


title: rnaseq_wt_42

value: myotube

value: wildtype

value: growth


title: rnaseq_wt_41


title: rnaseq_dtag_dmso1


title: rnaseq_wt_02


title: slamseq_washout_dmso2

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)
Library strategy: SLAM-seq

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep (Zymo Research) according to the manufacturer’s instructions except including 0.1 mM DTT to all buffers. Thiol modification was performed by 10 mM iodoacetamide treatment followed by quenching with 20 mM DTT. RNA was purified by ethanol precipitation
RNA-seq libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq 6000 with paired-end 150bp reads

treatment_protocol: C2C12 cells were seeded the day before the labeling experiment that allows exponential growth (50%-80% confluency for experiment). 0.5 × 106 C2C12 cells per replicate was incubated with 500 nM dTAG47/DMSO for 4h. (For washout experiments, after 4hrs. treatment with dTAG/DMSO, cells were washed twice with 1X PBS and grown for 5 days before S4U labeling). S4U labeling was performed by adding S4U to a final concentration of 100μM for an additional hour.

value: DMSOwashout + S4U labling


title: rnaseq_wt_03


title: rnaseq_matr3_ko_41


title: rnaseq_matr3_ko_43


title: rnaseq_matr3_ko_02


title: rnaseq_matr3_ko_01


title: WT-2, scRNA-seq

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

library_source: transcriptomic single cell

data_processing:
Cellranger Arc 2.0.0
Signac 1.5.0 Processing
MACS2 peak calling
Harmony correction of PCA and LSI
Label transfer from reference dataset
Slingshot 2.8.0 pseudotime
Assembly: mm10
Supplementary files format and content: final.arid1a.msobj.pseudotime.rds (Signac object), corresponds to both the scRNA and scATAC
Supplementary files format and content: Signac fragment files
Supplementary files format and content: arid1a.csm.broad.hrna.sl.rds (a slingshot pseudotime analysis object)

source_name: Spleen

extract_protocol:
GC cells from splenocytes of Arid1a WT/WT, cKO/WT and cKO/cKO were sorted by flow cytometry
Cells underwent nuclei preparation procedure according to the 10x protocol. Then, about 20,000 nuclei were placed into a 10x Chromium X instrument. The remainder of the library preparation steps were conducted in accordance with the manufacturer's protocol
Single Cell Multiome

tag: tissue

value: Spleen

value: GCB

value: Arid1a WT/WT

value: SRBC Immunization


title: WT-3, scRNA-seq


title: WT-1, scRNA-seq


title: Arid1aHet-2, scRNA-seq

value: Arid1a cKO/WT


title: Arid1aHom-1, scRNA-seq

value: Arid1a cKO/cKO


title: Arid1aHet-1, scRNA-seq


title: Arid1aHom-2, scATAC-seq

library_source: genomic single cell

molecule: genomic DNA


title: WT-3, scATAC-seq


title: WT-2, scATAC-seq


title: Arid1aHet-2, scATAC-seq


title: WT-1, scATAC-seq


title: Arid1aHom-1, scATAC-seq


title: Treg, VAT_TCR

city: New York

first: Nicholas

last: Arpaia

address: 701 West 168th Street

department: Microbiology & Immunology

institute: Columbia University

description:
Hashtag 1-3 are normal diet and Hashtag 4-7 are NASH.
NT018

data_processing:
Libraries were then sequenced on an Illumina NovaSeq 6000
CellRanger 6.1.2 was used to process the sequencing data
Analysis was subsequently performed using Seurat 4.2.0
Supplementary files format and content: tar file containing processed CellRanger output for barcodes, features, matrix

source_name: VAT

extract_protocol:
Viable CD4+GFP+ cells were sorted using a FACS Aria cell sorter
10x Genomics Single Cell 5’ workflow for gene expression, cell hashing, and full-length V(D)J T cell receptor sequencing

treatment_protocol: Single cell RNA-seq (cell hashing and TCRseq) of Treg cells enriched via FACS from the liver, spleen and visceral adipose tissue from Foxp3GFP mice fed normal chow or a NASH diet.

value: VAT

value: Treg cells

tag: strain

tag: Sex

value: male

value: multiplexed sample:control and NASH


title: Treg, VAT_HTO


title: rnaseq_matr3_ko_42


title: Arid1aHet-1, scATAC-seq


title: rnaseq_wt_01

value: myoblast


title: Arid1aHom-2, scRNA-seq


title: Treg, VAT_GEX


title: Treg, spleen_TCR

description:
Hashtag 1-3 are normal diet and Hashtag 4-7 are NASH.
NT016

source_name: spleen

value: spleen


title: Treg, liver_TCR

description:
Hashtag 1-3 are normal diet and Hashtag 4-7 are NASH.
NT017

source_name: liver

value: liver


title: mouse MLL-AF9+ Pik3cg-knockout L-GMPs, biol rep 3

first: Jean

last: Zhao

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
GuHao_12
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx

data_processing:
Data processing was used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform with default settings for all steps.
Assembly: Mouse: AmpliSeq_Mouse_Transcriptome_v1 (AmpliSeq_Mouse_Transcriptome_V1_Designed.bed);Human  hg19_AmpliSeq_Transcriptome_v1.1 (hg19_AmpliSeq_Transcriptome_21K_v1.bed)
Supplementary files format and content: xlsx: Tab-separated values and matrix file

source_name: bone marrow

extract_protocol:
Mouse MLL-AF9+ L-GMPs were sorted from primary transplantation recipients. Lin-CD34+CD38- PDX cells were sorted from PDX mouse models upon vehilce or IPI-549 treatment in vivo. Sorted L-GMP cells or  Lin-CD34+CD38- PDX cells were homogenized in 1 mL of TRIZOL reagent and 0.2 mL of chloroform was added to the samples. Samples were vortexed vigorously for 15 seconds and then incubated at 4℃ for 10 minutes. After centrifugation at 12, 000 g for 15 minutes at 4℃, upper aqueous phase of the samples was carefully removed to a new tube and the total RNA was purified by RNAeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction.
RNA libraries were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification.
Ion AmpliSeq Transcriptome Mouse Gene Expression Manual Chef-S5; Ion AmpliSeq Transcriptome Human Gene Expression Panel

treatment_protocol: NSG/NSG-SGM3 mice injected with PDX cells were treated once daily by oral gavage with vehicle (5% NMP and 95% PEG 400) and 15 mg/kg of IPI-549 24 hours post transplantation.

value: bone marrow

value: MLL-AF9+ AML cells

value: L-GMPs


title: Treg, liver_GEX


title: Treg, liver_HTO


title: mouse MLL-AF9+ Pik3cg-knockout L-GMPs, biol rep 2

description:
GuHao_11
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx


title: H3K9me3_IRD3_REIID

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: ChIP was performed using anti-H3K9me3 antibody (ab8898) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to grow cultures at 32˚C, described in detail in methods

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with H3K9me3 antibody (Abcam, ab8898). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at room temperature.

value: H3K9me3 immunoprecipitated DNA

tag: reference

value: Whole-cell extract DNA


title: mouse MLL-AF9+ wild-type L-GMPs, biol rep 3

description:
GuHao_09
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx

value: Wild-type


title: mouse MLL-AF9+ Pik3cg-knockout L-GMPs, biol rep 1

description:
GuHao_10
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx


title: Treg, spleen_GEX


title: Treg, spleen_HTO


title: HSC in NASH, AregFl/Fl Foxp3YFP-cre, cKO

data_processing:
Libraries were then sequenced on an Illumina NovaSeq 6000
CellRanger 6.1.2 was used to process the sequencing data
Analysis was subsequently performed using Seurat 4.2.0
Supplementary files format and content: .tar, tar archive containing the main outputs from a cellranger count analysis

extract_protocol:
Viable nucleated cells were sorted using a FACS Aria cell sorter
10x Genomics Single Cell Gene Expression 3’ workflow

treatment_protocol: Single cell RNA-seq of hepatic stellate cells enriched via FACS from the liver of AregFl/Fl (control) or AregFl/Fl Foxp3YFP-cre (conditional knockout) mice fed a NASH diet.

value: Hepatic stellate cells

value: AregFl/Fl Foxp3YFP-cre

tag: background strain

tag: disease state

value: NASH


title: HSC in NASH, AregFl/Fl control

value: AregFl/Fl


title: mouse MLL-AF9+ wild-type L-GMPs, biol rep 1

description:
GuHao_07
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx


title: RNA-Seq of lung, adult female mouse, E3

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

country: China

institute: Children’s Hospital Zhejiang University School of Medicine

data_processing:
bcl2fastq softwae was used to filter the raw data and then FastQC software got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Assembly: GRCm38
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: lung

extract_protocol:
The totla RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols
poly A enriched RNASeq

value: lung

value: female

value: LPS+PD

value: 12 weeks old


title: Spyo67

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Edge-Pro for alignment to Spyo09 genome as reference and quantification
DESeq2 for differential gene expression
Assembly: Spyo09 genome CP136951 and CP136852
Supplementary files format and content: A csv file including counts of each gene for all 12 isolates

organism: Streptococcus pyogenes

source_name: throat

growth_protocol: cultured in LIM broth

extract_protocol:
Total RNA were extracted using Trizol (Invitrogen) and DirectZol (Zymo Research) .
TruSeq Stranded mRNA kit with RiboZero bacterial rRNA depletion

value: Non-invasive ST28/EMM-1


title: Spyo65


title: RNA-Seq of lung, adult female mouse, E2


title: RNA-Seq of lung, adult female mouse, Model3

value: LPS


title: RNA-Seq of lung, adult female mouse, Model2


title: Spyo43

source_name: wound

value: invasive ST28/EMM-1


title: H3K9me3_IRD1_REIID


title: RNA-Seq of lung, adult female mouse, Con3

value: normal


title: mouse MLL-AF9+ wild-type L-GMPs, biol rep 2

description:
GuHao_08
Column names: Genes, GuHao_07, GuHao_08, GuHao_09, GuHao_10, GuHao_11, GuHao_12
HG_PIK3CG_mouse_transcriptome.xlsx

value: bone marrow

value: MLL-AF9+ AML cells


title: RNA-Seq of lung, adult female mouse, Model1


title: Spyo35

source_name: blood


title: H3K9me3_WT_REIID

value: WT

value: H3K9me3 immunoprecipitated DNA

tag: fraction


title: RNA-Seq of lung, adult female mouse, Con2


title: Spyo10

source_name: urine


title: RNA-Seq of lung, adult female mouse, Con1


title: Spyo70

source_name: skin


title: Spyo16


title: BMP7-2

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

data_processing:
Raw reads in fastq format were aligned to mouse genome mm10 using subjunc function in subread package (Version 2.0.3). Mapped reads for each sample were counted for each gene in annotation files in GTF format (genecode.vM30.annotation.gtf),using the FeatureCounts function in subread package.
Assembly: mm39
Supplementary files format and content: Gene expression profile in txt format

source_name: Mammary gland

extract_protocol: 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Mammary gland

value: medium with BMP7


title: Spyo37


title: Spyo61


title: Spyo01


title: BMP7-1


title: RNA-Seq of lung, adult female mouse, E1


title: BMP7-3


title: Ctrl-3

value: medium without BMP7


title: Ctrl-2


title: Hepatic stellate cells, Areg, sample 5

data_processing:
Libraries were then sequenced using Illumina NovaSeq 6000, with multiplexed samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0).
Differentially expressed genes were assessed through DESeq2
Assembly: Ensembl v96, Mouse:GRCm38.p6
Supplementary files format and content: .tsv, abundance output from Kallisto that includes estimated counts, TPM, effective length for each transcript.

extract_protocol:
Cells were lysed with Trizol Reagent, and RNA was extracted using a Qiagen kit
Poly-A pull-down to enrich mRNAs from total RNA, then library construction using Illumina TruSeq chemistry

treatment_protocol: Quiescent hepatic stellate cells were isolated and cultured for 5 hours, then stimulated with recombinant mouse Areg (500 ng/mL) or control for 4 hours in starving media.

value: liver

value: Hepatic Stellate Cells

value: C57BL/6 male

value: Areg (500 ng/mL)


title: H3K9me3_IRD2_REIID

value: Whole-cell extract DNA


title: Spyo06


title: Orc1_G1_input

library_source: genomic

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the Star aligner (Dobin et al. 2013) and RPM normalized bedgraphs were generated using the Star –outWigNorm option. RPM normalized bedgraphs for IPs were converted to wigs, normalized to DNA input by subtraction saved in bedgraph format using Deeptools (Ramirez et al. 2016). Values that were negative after input subtraction were set to zero in the final bedgraph.

growth_protocol: Growth in EMM and YEA, 26°C and 36°C, 30°C

extract_protocol:
Cells were crosslinked using 3% PFA at room temperature for 30 min. Cells were spun at 2,000g for 10 min and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1M-smt0 ade6-M210 his2 orp1::5xFLAG-orp1 cdc10-v50

tag: chip antibody

value: ANTI-FLAG M2 affinity gel

tag: growth

value: Growth in YEA 36degreeC

tag: fixation

value: 3percent PFA


title: BrdU_210527_WT_S4

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT cdc25-22

value: anti-BrdU IgG1 (Becton Dickinson-cloneB44)

value: Growth in EMM 36degreeC and 26degreeC

value: 0,1percent NaN3


title: Hepatic stellate cells, Areg, sample 4


title: Orc1_G1


title: Spyo09

source_name: synovial Fluid


title: Low CH4, La+, Bioreactor, biological replicate 2

city: «Sirius» Federal Territory

first: Semyon

last: Kolmykov

state: Krasnodar region

address: Olympic Ave., 1

country: Russia

institute: Sirius University of Science and Technology

data_processing:
The reads were mapped to the Methylotuvimicrobium alcaliphilum 20ZR (ASM96853v1) reference genome using the Bowtie2 algorithm v2.5.1. Illumina standard adapters were removed using Trim Galore software before mapping when it’s necessary. The mapped reads were quantified with featureCounts using gene features from the RefSeq annotations (GCF_000968535.2). Reads that aligned to ribosomal genes were filtered out.
Assembly: ASM96853v1
Supplementary files format and content: Tab-delimeted text file includes raw counts for each sample

organism: Methylotuvimicrobium alcaliphilum 20Z

growth_protocol: A DASbox mini bioreactor (0.5 L working volume; 250 ml culture) with two individual bioreactor units was used for bioreactor cultures.

extract_protocol:
Cells were pelleted by centrifugation at 4700 rpm for 15 min, and RNA was extracted using a RNeasy kit and treated with PureLink DNaseI (ThermoFisher Scientific) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions. Samples were sequenced on an Illumina HiSeq2500 with ∼50 million/sample SR50 reads by IGM Genomics Center, University of California, San Diego

treatment_protocol: Samples (45 ml) of bioreactor cultures (two biological replicates per tested growth condition: La-optimum and Ca-optimum) were collected  and immediately transferred into tubes containing 5 ml of the stop solution (5% water-equilibrated phenol in ethanol).

tag: culture type

value: Bioreactor DASbox/continuous

value: Growth medium:P(La)3% low CH4 (methane limitation) PH:8.7-9 N:NO3 S:SO4 C:CH4 Metals:+La +W +Cu


title: Mcm2_210412_G2

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan  cdc25-22  otr1R(Sph1)::ura4+

value: Abcam anti-GFP 290

value: Growth in YEA 36degreeC and 26degreeC


title: Low CH4, La+, Bioreactor, biological replicate 1


title: CH4, La+, Bioreactor,  biological replicate 2

value: Growth medium:P(La)3% CH4 PH:8.7-9 N:NO3 S:SO4 C:CH4 Metals:+La +W +Cu


title: BrdU_210729_Swi6Δ_S2

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT swi6::natN2 cdc25-22


title: CH4, La+, Bioreactor,  biological replicate 1


title: Hepatic stellate cells, Areg, sample 3

value: liver

tag: cell type

value: Hepatic Stellate Cells

value: C57BL/6 male

value: Areg (500 ng/mL)


title: Input_210412

tag: genotype


title: BrdU_210729_Swi6Δ_S3


title: Ctrl-1

value: Mammary gland

tag: cell line

tag: treatment

value: medium without BMP7


title: Low CH4, Ca+, Bioreactor, biological replicate 1

value: Growth medium:P3% low CH4 (methane limitation) PH:8.7-9 N:NO3 S:SO4 C:CH4 Metals:+Ca +W +Cu


title: Hepatic stellate cells, Areg, sample 1


title: CH4, Ca+, Bioreactor,  biological replicate 1

value: Growth medium:P3% CH4 PH:8.7-9 N:NO3 S:SO4 C:CH4 Metals:+Ca +W +Cu


title: Mcm2_220818_IRΔ2_S

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4/ura4-D18/-DS/E mcm2-GFP:kanMx, IR-delta2, cdc25-22

value: 3percent PFA


title: CH4, Ca+, Bioreactor,  biological replicate 2

value: Bioreactor DASbox/continuous


title: Hepatic stellate cells, control, sample 5

value: control


title: Low CH4, Ca+, Bioreactor, biological replicate 2


title: Hepatic stellate cells, Areg, sample 2


title: Input_220818_IRΔ2


title: BrdU_210527_ WT_S3

description: BrdU_210527_ WT_S3

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT cdc25-22

value: anti-BrdU IgG1 (Becton Dickinson-cloneB44)

value: Growth in EMM 36degreeC and 26degreeC

value: 0,1percent NaN3


title: Hepatic stellate cells, control, sample 4


title: Hepatic stellate cells, control, sample 3


title: Scramble control RNA-seq rep2

city: Guangzhou

first: Peng

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with ENCODE RNA-seq pipeline.
Assembly: hg38
Supplementary files format and content: tsv files with FPKM and TPM values for each gene

organism: Homo sapiens

source_name: Human erythroblasts

growth_protocol: Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.

extract_protocol:
Cells were homogenized using TRIzol (Life Technologies). RNA was extracted using RNeasy Mini Kit (Qiagen).
Sequencing libraries were constructed from 500 ng of DNase-treated, total RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB cat# 6310) for rRNA depletion, followed by the TruSeq Stranded Total kit (Illumina cat# 20020598) for cDNA synthesis and library preparation according to manufacturer’s specifications.

value: Adult peripheral blood

value: CD34+ derived erythroblasts

tag: differentiation

value: Day 13

value: Scramble control


title: Mcm2_220818_WT_S

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan  cdc25-22  otr1R(Sph1)::ura4+

value: Abcam anti-GFP 290

value: Growth in YEA 36degreeC and 26degreeC


title: Let-7 KD HIC2 ChIP-seq rep2

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800.
Assembly: hg38
Supplementary files format and content: bigWig files with read coverage

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Samples were processed for library construction for Illumina sequencing using NEBNext UltraII for DNA Library Prep Kit (NEB cat# E7645S) according to NEB's instructions.

value: Day 11

value: Let-7 KD

value: HIC2 (Proteintech, 22788-1-AP)


title: Input_220818_WT

value: 3percent PFA


title: Mcm2_210412_S


title: Hepatic stellate cells, control, sample 1

value: liver

value: Hepatic Stellate Cells

value: C57BL/6 male


title: Let-7 KD RNA-seq rep1


title: Hepatic stellate cells, control, sample 2

value: control


title: Mcm2_220520_Swi6Δ_S

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan swi6::natN2 cdc25-22


title: Scramble control HIC2 ChIP-seq rep2


title: Scramble control HIC2 ChIP-seq rep1


title: Let-7 KD HIC2 ChIP-seq rep1


title: Let-7 KD RNA-seq rep2


title: Spleen Tconv cells, CCl4, sample 5

extract_protocol:
Cells were FACS-sorted into Trizol Reagent, and RNA was extracted using a Qiagen kit
Clontech Ultra Low v4 kit for cDNA synthesis followed by NexteraXT

treatment_protocol: CD4+ Treg and Tconv cells were FACS purified from livers and spleens of male Foxp3GFP mice, either control, CCl4 treated, or fed the CDAA-HFD diet.

value: spleen

value: Spleen Tconv cells

value: male


title: Input let-7 KD

value: Adult peripheral blood

value: CD34+ derived erythroblasts


title: Let-7 KD GATA1 ChIP-seq rep1


title: Input_220520_Swi6Δ


title: Let-7 KD GATA1 ChIP-seq rep2


title: Scramble control GATA1 ChIP-seq rep2

value: Scramble control


title: Spleen Tconv cells, CCl4, sample 3


title: Spleen Tconv cells, CCl4, sample 4


title: Scramble control GATA1 ChIP-seq rep1


title: Let-7 KD rep4 [Capture-C]

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Assembly: hg38
Supplementary files format and content: bigwig files with the normalized Capture-C interaction signals
Library strategy: Capture-C

extract_protocol:
Cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal).
Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).


title: Mcm2_220520_WT_S

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan  cdc25-22  otr1R(Sph1)::ura4+

value: Abcam anti-GFP 290


title: Spleen Tconv cells, CCl4, sample 2


title: Let-7 KD rep3 [Capture-C]

value: Day 11


title: BrdU_210527_IRΔ2_S

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT IR-delta2 cdc25-23

value: anti-BrdU IgG1 (Becton Dickinson-cloneB44)

value: Growth in EMM 36degreeC and 26degreeC

value: 0.1percent NaN3


title: Scramble control rep4 [Capture-C]


title: Spleen Tconv cells, CCl4, sample 1


title: Spleen Tconv cells, control, sample 3


title: Let-7 KD rep1 [Capture-C]

value: Let-7 KD


title: Let-7 KD rep2 [Capture-C]


title: Input_210527_IRΔ2

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT IR-delta2 cdc25-22


title: Spleen Tconv cells, control, sample 2

value: control


title: BrdU_210927_Swi6Δ_S

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT swi6::natN2 cdc25-22


title: Scramble control rep3 [Capture-C]


title: Input_210927_Swi6Δ


title: Scramble control RNA-seq rep1

value: Day 13


title: Scramble control rep1 [Capture-C]


title: Input_220520_WT

value: Growth in YEA 36degreeC and 26degreeC

value: 3percent PFA


title: Input scramble control

value: Adult peripheral blood


title: Let-7 KD ATAC-seq rep2

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800
Assembly: hg38
Supplementary files format and content: bigWig files with read coverage

extract_protocol:
50-100k cells were lysised with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin, then incubated with Tagment DNA Enzyme (Illumina) for 30 minutes at 37C. DNA was purified with Qiagen MinElute Reaction Cleanup Kit.
Library fragments were amplified using Phusion High-Fidelity PCR Master Mix with HF Buffer (ThermoFisher cat#F531S) and custom v2_Ad1 and v2_Ad2 unique dual indexes (Mezger, et al., 2018, Nat Commun).

value: CD34+ derived erythroblasts


title: Spleen Tconv cells, control, sample 1

value: spleen

value: Spleen Tconv cells

value: male


title: Spleen Treg cells, CCl4, sample 5

value: Spleen Treg cells


title: Scramble control ATAC-seq rep2

value: Day 11

value: Scramble control


title: Let-7 KD ATAC-seq rep1


title: Spleen Treg cells, CCl4, sample 4


title: Input_210527_WT

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT cdc25-22

value: anti-BrdU IgG1 (Becton Dickinson-cloneB44)

value: Growth in EMM 36degreeC and 26degreeC


title: Scramble control ATAC-seq rep1


title: BrdU_210527_ WT_S1

description: BrdU_210527_ WT_S1

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT cdc25-23

value: 0.1percent NaN3


title: Scramble control rep2 [Capture-C]


title: Spleen Treg cells, CCl4, sample 3


title: Input_220501_G2

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan  cdc25-22  otr1R(Sph1)::ura4+

value: Abcam anti-GFP 290


title: Input_220501_S

value: Growth in YEA 36degreeC and 26degreeC


title: Spleen Treg cells, control, sample 3

value: control


title: Mcl1_S_210914

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcl1-GFP:kanMx  cdc25-24

value: 3percent PFA


title: Spleen Treg cells, control, sample 1

value: spleen


title: Mcl1_G2_210914

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcl1-GFP:kanMx  cdc25-23


title: Liver Tconv cells, CCl4, sample 5

value: liver

value: Liver Tconv cells

value: male


title: Liver Tconv cells, CCl4, sample 3


title: Liver Tconv cells, CCl4, sample 4


title: U-2932 - TAK981 - 8 hr - replicate 2 - ATACseq

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 E duarte rd

institute: City of Hope

data_processing:
RNA seq: Trimmomatic trimming of fastq files and star mapping to GRCH38, DESeq2 DGE
ATAC seq: Trimmomatic trimming of fastq files and Bowtie2 mapping to hg19, MACS2 peak calling, bedtools, DESeq2 differential peak calling, HOMER motif analysis
Assembly: RNA seq: GRCH38 ATAC seq: hg19

extract_protocol:
Total RNA/DNA was isolated using the E.Z.N.A. HP Total RNA/DNA Isolation Kit (Omega Bio-tek).
performed via novogene, polyA enrichment and PCR duplciation removal, cDNA reverse transcription

value: B cell - DLBCL

value: WT


title: Spleen Treg cells, CCl4, sample 1

value: Spleen Treg cells


title: Mcm2_220501_S


title: Spleen Treg cells, CCl4, sample 2


title: Spleen Treg cells, control, sample 2


title: Liver Tconv cells, CCl4, sample 2


title: U-2932 - TAK981 - 8 hr - replicate 1 - ATACseq


title: BrdU_210527_WT_S2

value: mat1M-smt0 leu1-32 his2 ura4::ura4+-Pnmt1-TK ade6::ade6+-Padh1-hENT cdc25-24

value: anti-BrdU IgG1 (Becton Dickinson-cloneB44)

value: Growth in EMM 36degreeC and 26degreeC


title: Mcm2 _220501_G2

description: Mcm2 _220501_G2

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcm2-GFP:kan  cdc25-22  otr1R(Sph1)::ura4+


title: Liver Tconv cells, CCl4, sample 1


title: Input_210914

value: mat1M-smt0 leu1-32 ade6-M216 his2 ura4-DS/E mcl1-GFP:kanMx  cdc25-22

value: Abcam anti-GFP 290


title: U-2932 - TAK981 - 0 hr - replicate 1 - ATACseq


title: OCI-LY3 - TAK981 - 8 hr - replicate 2 - ATACseq


title: Liver Tconv cells, control, sample 2

value: control


title: Liver Tconv cells, control, sample 3


title: OCI-LY3 - TAK981 - 8 hr - replicate 1 - ATACseq


title: Liver Tconv cells, control, sample 1


title: OCI-LY3 - TAK981 - 0 hr - replicate 2 - ATACseq


title: OCI-LY3 - TAK981 - 0 hr - replicate 1 - ATACseq


title: Liver Treg cells, CCl4, sample 5

value: Liver Treg cells


title: U-2932 - TAK981 - 0 hr - replicate 2 - ATACseq


title: Liver Treg cells, CCl4, sample 4


title: Liver Treg cells, CCl4, sample 3


title: U-2932 - TAK981 - 0 hr - replicate 2 - RNAseq


title: U-2932 - TAK981 - 8 hr - replicate 2 - RNAseq


title: U-2932 - TAK981 - 0 hr - replicate 1 - RNAseq


title: Liver Treg cells, control, sample 3


title: Liver Treg cells, CCl4, sample 2


title: Liver Treg cells, CCl4, sample 1


title: OCI-LY19 - TAK981 - 8 hr - replicate 2 - RNAseq


title: Liver Treg cells, control, sample 2


title: OCI-LY19 - TAK981 - 8 hr - replicate 1 - RNAseq


title: Liver Treg cells, control, sample 1


title: sertoli cells, SE,  2

city: 呼和浩特市

first: 代玲

last: 宋

state: 内蒙古自治区

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区

institute: lnner Mongolia Key Laboratory of Equine Science Research and Technology Innovation

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: ftp://ftp.ensembl.org/pub/release-107/fasta/equus_caballus/dna/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Equus caballus

source_name: testis

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: testis

value: sertoli cells

value: SE event occurred in MEI1 gene


title: sertoli cells, MXE,  3

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区

value: MXE event occurred in MEI1 gene


title: sertoli cells, SE,  1

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区


title: sertoli cells, MXE,  2

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区


title: OCI-LY19 - TAK981 - 0 hr - replicate 2 - RNAseq


title: sertoli cells, SE,  3

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区


title: Fgfr2 KO,scRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gene expression profile in txt format

extract_protocol: none provided

value: Mammary gland

value: Epithelial cells

value: Fgfr2 KO


title: OCI-LY3 - TAK981 - 8 hr - replicate 2 - RNAseq

value: B cell - DLBCL

value: WT


title: Ctrl,scRNA-seq

description: 10x Genomics


title: OCI-LY3 - TAK981 - 8 hr - replicate 1 - RNAseq


title: U-2932 - TAK981 - 8 hr - replicate 1 - RNAseq


title: OCI-LY3 - TAK981 - 0 hr - replicate 2 - RNAseq


title: Rarres1-KO 18-month male (normal) 5 [T18_KO7N]

city: Goyang-si

first: Kyungtae

last: Kim

state: Gyeonggi-do

address: 323 Ilsan-ro

country: South Korea

institute: National Cancer Center

data_processing:
RNA-seq reads were trimmed using Trimmomatic version 0.36.
RNA-seq reads were aligned to the mm10 genome assembly using STAR version 2.5.2b.
Counts of reads and FPKM (Fragments Per Kilobase of transcript per million mapped reads) were calculated using RSEM version 1.3.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including a matrix of read counts and FPKM, respectively

source_name: Rarres1-KO 18-month male (normal)_lung

growth_protocol: All mice were housed in a pathogen-free barrier environment.

extract_protocol: Total RNA and genomic DNA were extracted from lung.

treatment_protocol: No treatment

tag: strain background

tag: gentotype/variation

tag: age

value: 18 months after birth

value: male

value: lung

tag: pathology

value: Non-tumor


title: Rarres1-KO 18-month male (normal) 4 [T18_KO6N]

tag: Sex

tag: tissue


title: Rarres1-KO 18-month male (normal) 2 [T18_KO2N]


title: OCI-LY3 - TAK981 - 0 hr - replicate 1 - RNAseq


title: Rarres1-KO 18-month male (normal) 1 [T18_KO1N]


title: HL10 - TAK981 - 8 hr - replicate 1 - RNAseq


title: Rarres1-KO 18-month male (tumor) 6 [T18_KO6T]

source_name: Rarres1-KO 18-month male (tumor)_lung

value: Tumor


title: HL10 - TAK981 - 8 hr - replicate 2 - RNAseq


title: H3-FLAG ChIP in IRD2 clr3D cells

description: ChIP was performed using anti-FLAG M2 afffinity gel (Sigma-Aldrich A2220) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol. Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner. Scanned on an Agilent G2505B scanner.

data_processing:
Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.
Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

source_name: early log. growing cells

label_protocol:
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol:
Cells carrying pINV1-H3.2-FLAG plasmid grown in EMM-Leu + 8% glucose media to OD 0.1- 0.15 were synchronized by adding 15 mM HU for 4 h before shifting the cells to EMM-Leu-glucose + 4% sucrose media containing 15mM HU for 2 h to induce the expression of H3-FLAG.
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) . Cultures were grown at 30˚C.

extract_protocol:
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with anti-FLAG M2 afffinity gel (Sigma-Aldrich A2220). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam, ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 20 min.
Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. DMA was also added to the fixation of cells to be used in Pds5 ChIPs. Prior fixation cells were incubated at 18˚C for 2h (Pds5 ChIPs).

value: IR-D2 clr3D cells

tag: antibody

value: Whole-cell extract DNA


title: Rarres1-KO 18-month male (tumor) 3 [T18_KO3T]


title: sertoli cells, MXE,  1

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区


title: HL10 - TAK981 - 0 hr - replicate 2 - RNAseq


title: OCI-LY19 - TAK981 - 0 hr - replicate 1 - RNAseq


title: H3-FLAG ChIP in IRD2 cells

value: IR-D2 cells

tag: fraction


title: HL10 - TAK981 - 0 hr - replicate 1 - RNAseq


title: H3-FLAG ChIP in clr3D cells

value: clr3D cells


title: Rarres1-KO 18-month male (tumor) 1 [T18_KO1T]


title: Wild-type 18-month male 3 [T18_WT3]

source_name: Wild-type 18-month male_lung

value: Wild-type


title: Wild-type 18-month male 2 [T18_WT2]


title: H3-FLAG ChIP in WT cells

value: Wild type cells


title: Tcell_3

city: Shinjuku-ku

first: Mitsuru

last: Ishikawa

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
RNA-seq libraries were sequenced using paired-end reads (50 nt for read1 and 25 nt for read2) using an Illumina NextSeq 500 instrument.
The reads obtained were  counted using featureCounts.
Fragments per kilo base of transcripts per million mapped fragments (FPKM) values were calculated from the mapped reads by normalization to the total counts and transcripts.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Raw data were preprocessed and normalized using the limma package in R. All further calculations were performed on log2 transformed data.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM value for each sample.

source_name: T cells

growth_protocol: T cell expansion from human PBMCs in vitro.

extract_protocol:
Total RNA were extracted by using QIAGEN miRNeasy Kit.
Total RNA quality was assessed using a bioanalyzer to ensure that the RNA integrity number (RIN) was > 7.0.  After poly (A) + RNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module, double-stranded cDNA libraries (RNA-seq libraries) were prepared using the SMARTer Stranded RNA-Seq Kit v2, according to the manufacturer's instructions.

treatment_protocol: NeuroD1, BAZ or OSKM genes were overexpressed by infecting Sendai virus.

value: T cells

value: 0+0 factors


title: Wild-type 18-month male 1 [T18_WT1]


title: HeLa 4sU labelled chromatin-associated RNA

city: Philadelphia

first: Allison

last: Cote

state: PA

address: 415 Curie Blvd

institute: University of Pennsylvania

data_processing:
Paired-end reads were aligned to the ENSEMBLE GRCh38 (release-86) reference genome using STAR (v2.5.1a) with default parameters (except for readFilesCommand=cat, limitIObufferSize=200000000, limitBAMsortRAM=64000000000, outReadsUnmapped=Fastx, outSAMtype=BAM SortedByCoordinate, outSAMattributes=All, outFilterMultimapNmax=101, outSJfilterOverhangMin=3 1 1 1, outSJfilterDistToOtherSJmin=0 0 0 0, alignIntronMin=11, alignEndsType=EndToEnd).
Splicing index calculations were determined by summing the number of spliced and unspliced read pairs that span exon junctions by at least 3 nucleotides and calculating the total spliced read pairs divided by the total unspliced read pairs for each gene; splicing index = 2 × spliced read pairs / (5’SS unspliced + 3’SS unspliced read pairs).
Assembly: ENSEMBLE GRCh38
Supplementary files format and content: mapped counts, and text files of calculated splicing indices

source_name: HeLa S3

growth_protocol: HeLa S3 cells (ATCC, CCL-2.2) were maintained in DMEM media containing 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin to 75% confluency.

extract_protocol:
Plates were washed twice with 1X PBS and cells were lifted by scraping. Labeled cells were collected by centrifugation at 500 g for 2 minutes. Nuclei were collected by lysing samples of 10M cells in 200 μl cytoplasmic lysis buffer (0.15% (vol/vol) NP-40 (Thermo Fisher Scientific, 28324), 10 mM Tris-HCl (pH 7.0), and 150 mM NaCl) for 2 min, layering over a 500 μl sucrose cushion (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (wt/vol) sucrose), and centrifuging at 16,000 g for 10 minutes. The nuclei pellet was washed in 800 μl wash buffer (0.1% (vol/vol) Triton X-100, 1 mM EDTA, in 1X PBS) and collected by centrifuging at 1,150 g for 1 minute. Nuclei were resuspended in 200 μl glycerol buffer (20 mM Tris-HCl (pH 8.0), 75 mM NaCl, 0.5 mM EDTA, 50% (vol/vol) glycerol, 0.85 mM DTT), and mixed with 200 μl nuclei lysis buffer (1% (vol/vol) NP-40, 20 mM HEPES (pH 7.5), 300 mM NaCl, 1 M urea, 0.2 mM EDTA, 1 mM DTT) by pulse vortex and incubated on ice for 2 minutes. The chromatin pellet was collected by centrifugation at 18,500 g for 2 minutes and resuspended in 1X PBS. All steps were performed at 4°C and buffers were prepared with 25 μM α-amanitin (Sigma, A2263), 0.05U/μl SUPERase.In (ThermoFisher Scientific, AM2694), and protease inhibitor mix (Roche, 11873580001). Chromatin-associated RNA was extracted using Qiazol lysis reagent (Qiagen, 79306) following the manufacturer’s instructions. For more details about cell harvest, please see (Smith et al 1998).  50ug RNA were subjected to 4sU purification. In brief, labeled RNA (1 μg / 10 μl) was incubated with 10% biotinylation buffer (100mM Tris pH 7.5, 10mM EDTA) and 20% EZ-Link Biotin-HPDP (1 mg/mL resuspended in DMF, Thermo Fisher Scientific, 21341) for 1.5 hours 24°C in the dark and 800 rpm to mix. RNA was purified by shaking the sample with a 1:1 volume of chloroform/isoamylacohol (24:1), separating using a phase-lock tube at 16,000 g for 5 min, and performing isopropanol precipitation. For more detials, please see (Girard et al 2011) and (Wang et al 1990).
Biotinylated RNA was separated using the μMACS streptavidin kit (Miltenyi Biotec, 130-074-101) by mixing with μMACS streptavidin beads at a 2:1 ratio by volume at 800 rpm and 24°C for 15 min. RNA-streptavidin beads mix was transferred to the μMACS column and washed with wash buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween 20) at 65°C and room temperature 3 times each. Selected RNA was eluted off the magnet using the reducing agent, DTT (0.1M), and purified using the miRNeasy micro kit (Qiagen, 217084) with on-column DNase I treatment (Qiagen, 79254). For the poly(A) depleted sample, the RNA was first concentrated using the RNA Clean and Concentrator kit (ZymoResearch, R1015). 10 μL Oligo(dT) Dynabeads (ThermoFisher, 61002) were washed in 10 μL Binding Buffer (20mM Tris.HCl pH 7.5, 1M LiCl, and 2mM EDTA). The sample was mixed with 10 μl binding buffer, heated to 65°C for 2 min, moved to ice, and mixed with 1 μl SUPERase.In (ThermoFisher Scientific, AM2694). The sample and beads were mixed thoroughly and annealed by rotating continuously on a mixer for 5 minutes at room temperature. Poly(A) RNAs were collected on a magnet while depleted supernatant was removed and purified using the RNA Clean and Concentrator kit (ZymoResearch, R1015). Illumina sequencing libraries were prepared using the Ovation Universal RNA-seq System (NUGEN, 0343-32) with Universal Human rRNA strand selection reagent (NUGEN, S01859) following the manufacturer’s instructions.

treatment_protocol: Cells were labeled in media containing 500 μM 4-thiouridine (4sU, Sigma, T4509) for 7.5 minutes to label nascent RNA.

value: HeLa S3


title: Rarres1-KO 10-month male 3 [T10_KO3]

source_name: Rarres1-KO 10-month male_lung

value: 10 months after birth


title: Tcell_2


title: Rarres1-KO 10-month male 2 [T10_KO2]


title: Rarres1-KO 10-month male 1 [T10_KO1]


title: Rarres1-KO 18-month male (normal) 3 [T18_KO3N]


title: Tcell_1


title: Wild-type 10-month male 3 [T10_WT3]

source_name: Wild-type 10-month male_lung


title: iPiN-4F_3

source_name: iPS cells

value: iPS cells

value: iPSC-derived iN

value: 0+4 factors


title: iPiN-4F_2


title: iPiN-4F_1


title: Wild-type 10-month male 1 [T10_WT1]

value: male


title: Wild-type 10-month male 2 [T10_WT2]

value: lung


title: Rarres1-KO embryo 3 [T00_KO3]

source_name: Rarres1-KO embryo_lung

value: embryonic day 19.5

value: Non-tumor


title: iPiN-1F_2

value: 0+1 factors


title: iPS_3

value: 4+0 factors


title: Rarres1-KO embryo 1 [T00_KO1]


title: iPiN-1F_3


title: Wild-type embryo 3 [T00_WT3]

source_name: Wild-type embryo_lung


title: Wild-type embryo 2 [T00_WT2]


title: HeLa 4sU labelled chromatin-associated RNA - minA


title: iPiN-1F_1


title: Wild-type embryo 1 [T00_WT1]


title: Rarres1-KO embryo 2 [T00_KO2]


title: iPS_1


title: TiN-8F_3

source_name: Peripheral blood cells

value: Peripheral blood cells

value: T cell-derived iN

value: 4+4 factors


title: TiN-8F_2


title: A549, siCSTF2&T, Nuc, biol rep 3

city: Daejeon

first: Yoosik

state: Daejeon

address: Daejeon

institute: KAIST

data_processing:
Raw paired-end RNA sequencing reads produced in this paper were mapped to the reference human genome (build hg38) with HISAT2 v.2.1.0 using default parameters except with the option “--rna-strandness RF”. The raw RNA sequencing reads from the other studies were mapped using default parameters. Only uniquely and concordantly mapped reads were selected using samtools and then used for further analyses.
To assign and summarize genomic features, the featureCounts function of the Rsubread v2.8.2 R package was used with transcriptome information from the GENCODE v27 or RepeatMasker pre-masked for hg38. For the GENCODE, only protein-coding transcripts that have a transcript_support_level of 1 or 2 were used.
For the Nuc/Cyt ratio, Translational efficiency, and J2 enrichment calculation, raw read counts were normalized into Reads per Million (RPM) and used.
DESeq2 v1.34.0 R package analyzed the differentially expressed genes (DEGs) with the summarized raw read counts for each gene. For the gene set enrichment analysis (GSEA) and over-representation analysis, clusterProfiler v4.2.2 R package and DOSE v.3.20.1 R package were used. Hallmark gene sets were obtained from the Molecular Signatures Database (MSigDB) v7.4. For the secondary structure prediction of RNAs, RNAfold web server33 was used.
Assembly: hg38
Supplementary files format and content: A csv file for normalized counts

extract_protocol:
For mRNA-seq following subcellular fractionation, RNAs were obtained using Trizol and Trizol LS. Purified RNAs was digested with DNase I.  For J2 fCLIP-seq, RNAs purified using acid phenol:chloroform extraction and DNA contaminant were digested using DNase I.
For mRNA-seq following subcellular fractionation, TruSeq Stranded mRNA Sample Prep Kit (Illumina) was used.  For J2 fCLIP-seq, TruSeq Stranded Total RNA with Ribo-zero H/M/R Gold kit (Illumina) was used.
For mRNA-seq following subcellular fractionation, RNA-Seq.  For J2 fCLIP-seq, RIP-Seq.

treatment_protocol: For mRNA-seq following subcellular fractionation, cells were fractionated into the cytosol and the nuclear fractions using NE-PER Nuclear and Cytoplasmic Extract Reagent kit (Thermo Scientific) following the manufacturer's protocol.  For J2 fCLIP-seq, cells were fixed with 0.1% formaldehyde at room temperature (RT) for 10 min. Immediately, cells were quenched by adding glycine and incubated at RT for additional 10 min. Crosslinked cells were lysed in the fCLIP lysis buffer (20 mM Tris-HCl pH 7.5, 15 mM NaCl, 10 mM EDTA, 0.5% NP-40, 0.1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) and sonicated 2 times, 15 min each for complete lysis. The lysate was then immunoprecipitated using J2 antibody for 3 h in the fCLIP lysis buffer supplemented with 50 U/ml of RNase T1. Urea elution buffer (200 mM Tris-HCl pH 7.5, 100 mM NaCl, 20 mM EDTA, 2% SDS, and 7 M Urea) was used to elute J2 interactome from the resin. RNA was then decrosslinked and separated from J2 by incubating 65℃ for at least 12 h with 2 mg/ml Proteinase K.

value: Human lung carcinoma

value: a mixture of siCSTF2 and siCSTF2T

tag: sample type

value: Nuclear polyA RNA


title: TiN-8F_1


title: A549, siCSTF2&T, Cyt, biol rep 3

value: cytoplasmic polyA RNA


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-1, Dcp2 depletion

city: Berkeley

first: Joseph

middle: Heimlich

last: Lobel

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: UC berkeley

data_processing:
Adaptors were trimmed with Cutadapt (Martin 2011) and aligned to peptide library with bowtie2 (Langmead 2012).
Each amplicon count corresponding to a peptide was counted with SamTools (Li, 2009)
Assembly: Custom list of DNA sequences encoding 50 amino acid peptides
Supplementary files format and content: text file containing read counts for each peptide for each sample
Library strategy: Amplicon sequencing

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast were grown in synthetic media minus uracil for 16 hour in a custom turbidostat before being flow sorted (McGeachy 2019)

extract_protocol:
After flow sorting, RNA was extract by phenol/choloroform followed by ethanol precipitation
Libraries were prepared by constructing cDNA from total cellular mRNA using dT priming. Peptide constucts were amplifeid from cDNA with oJL090 and oJL109, followed by 2nd step amplification with indexing primers for illumina sequencing

treatment_protocol: For yeast expressing degron tagged nucleases, cells were grown in synthetic media minus uracil + 0.5 mM indole-3-acetic acid (Sigma I3750)

tag: strain

value: yeast

value: citirine-boxB, mScarlet-pp7, Dcp2::Dcp2-V5-mAID, OsTir1

value: 0.5 mM indole-3-acetic acid


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Dcp2 depletion


title: A549, siCSTF2&T, Nuc, biol rep 2


title: TiN-5F_3

value: 4+1 factors


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Dcp2 depletion


title: A549, siCSTF2&T, Cyt, biol rep 2


title: TiN-5F_2


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Dcp2 depletion


title: A549, siCSTF2&T, Nuc, biol rep 1


title: TiN-5F_1


title: iPS_2

value: iPS cells


title: A549, siCSTF2&T, Cyt, biol rep 1


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Dcp2 depletion


title: DSP.1001660005046.D.E12

city: Los Angeles

first: Jina

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

data_processing:
We used GeoMxWorkflow to preprocess the data using NanoStringNCTools and GeomxTools R packages. We ran running the ROI segmentation and probe quality control process, the genes with a minimum LOQ of 1 and fewer than 5% of segments were removed.
The expression values of these genes were normalized using upper quartile normalization method, and slide batch effects among the ROIs were corrected using the ComBat-seq R package.
For further removal of outlier, we performed t-distributed stochastic neighbor embedding (t-SNE) plot analysis and excluded the outlier ROI (DSP.1001660005046.D.C06) from the analysis
Assembly: GeoMx Human Whole Transcriptome Atlas
Supplementary files format and content: GeoMx processed expression data,csv format

source_name: Placental Tissue -Accreta invasion

extract_protocol:
Control, PAS-invasion, or PAS-opposite were mounted on the same slide (3 matched pairs on 3 slides) before hybridization with the Cancer Transcriptome Atlas (CTA) panel of probes corresponding to 1,825 genes (NanoString).  Following hybridization, the slides were scanned on the GeoMx instrument with the workspace used to select regions of interest (ROI)
The NanoString GeoMx Digital Spatial Profiler(DSP) protocol
Spatial transcriptomics

value: Placental Tissue -Accreta invasion


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-2 , Dcp2 depletion


title: A549, siLuc, Nuc, biol rep 3

value: siLuc


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-2 , Dcp2 depletion


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Dcp2 depletion


title: DSP.1001660005046.D.E11

description: NanoString GeoMx Digital Spatial Profiler(DSP)


title: A549, siLuc, Cyt, biol rep 3


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Dcp2 depletion


title: A549, siLuc, Nuc, biol rep 2


title: A549, siLuc, Cyt, biol rep 2


title: DSP.1001660005046.D.E09


title: A549, siLuc, Nuc, biol rep 1


title: DSP.1001660005046.D.E08


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Dcp2 depletion


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Dcp2 depletion


title: DSP.1001660005046.D.E07


title: DSP.1001660005046.D.E06


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-1, Pop2 depletion

value: citirine-boxB, mScarlet-pp7, Pop2::Pop2-V5-mAID, OsTir1


title: A549, siCSTF2&T, J2

value: total RNA


title: DSP.1001660005046.D.F01


title: SC31_PDX_E2

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using SpaceRanger's default settings
Gene expression level of Refseq coding genes were quantified using SpaceRanger's default settings
Assembly: mm10
Supplementary files format and content: text files containing the raw gene expression count
Library strategy: Spatial Transcriptomics

source_name: SC31 breast cancer PDX

growth_protocol: GS3 and SC31 tumor pieces were implanted into the 4th mammary fat pads of 9-11-week-old NOD-SCID/IL2Rγ−/− mice.

extract_protocol:
Fresh frozen tissue were OCT embeded, and 10µm frozen sections were cut with cryostat
Spatail transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufactrue's construction

treatment_protocol: Once the implanted tumors were established, placebo or E2 (1 mg) pellet were implanted subcutaneously. To ensure that there was enough tumor mass remaining for the analysis, GS3 tumors were implanted in intact mice and treated with E2 only for 1 week, or with placebo for 2 weeks, while SC31 tumors were implanted in ovariectomized mice and were treated for 6 weeks. After the treatment periods, tumor samples were collected, and spatial transcriptomics was performed.

value: SC31 breast cancer PDX


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Pop2 depletion


title: DSP.1001660005046.D.E05


title: A549, siCSTF2&T, Input


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Pop2 depletion


title: SC31_PDX_Placebo

value: Placebo


title: A549, siLuc, Cyt, biol rep 1


title: DSP.1001660005046.D.E04


title: A549, siLuc, J2


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-1, Dcp2 depletion


title: GS3_PDX_E2

source_name: GS3 breast cancer PDX

value: GS3 breast cancer PDX


title: DSP.1001660005046.D.E10


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Pop2 depletion


title: GS3_PDX_Placebo


title: DSP.1001660005046.D.E03


title: A549, siLuc, Input


title: MD6_RNA_3

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

data_processing:
Quality of the reads was checked using FastQC and trimmed using Trimmomatic v0.39
Reads were aligned to the human genome hg19 using Tophat2
Further analysis was performed using HOMER. Tag Directories were created for each of the three replicates per cell type and genes were annotated using analyzeRepeats.pl rna hg19 –rpkm
For differential expression analysis, analyzeRepeats.pl rna hg19 –raw was run to get the raw counts needed as an input for edgeR. Differential expression analyses were undertaken using the edgeR v3.20.9 and limma v3.34.9 software packages
Lowly expressed genes were filtered with the filterByExpr function from edgeR. Compositional differences between libraries were normalized using the trimmed mean of log expression ratios method (TMM), counts were transformed to log2-CPM and differential expression was assessed
Assembly: hg19
Supplementary files format and content: table containing normalized gene expression values for differential analysis
Supplementary files format and content: table containing rpkm-normalized gene expression values used as input for IMAGE

growth_protocol: Cells were seeded at maintenance density four days before collection. Three biological replicates per condition were collected.

extract_protocol:
Cells were directly lysed on plates, and tissue collected from primary lung tumours (PT) was lysed with TRIzol (Thermo Fisher cat. #15596026), and total RNAs were extracted according to the manufacturer’s instructions. ontaminating genomic DNA was removed by DNase (Qiagen cat. #79254) digestion. RNA quality and concentration were assessed using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226), respectively.
RNA-seq libraries were prepared by using the TruSeq® Stranded Total RNA (Illumina #20020596) supplemented with Illumina Ribo-Zero plus rRNA Depletion Kit (Illumina #20037135) starting from 500 ng of total RNA.Libraries were sequenced on an Illumina HiSeq 2500 with SE 50 bp.

value: metastasis-derived cell line

value: WT


title: MD6_RNA_2


title: DSP.1001660005046.D.E01

source_name: Placental Tissue -Accreta opposite

value: Placental Tissue -Accreta opposite


title: DSP.1001660005046.D.E02


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-2 , Pop2 depletion


title: NPCs, J2 fCLIP

source_name: Neural progenitor Cells (NPC)

value: Neural progenitor Cells (NPC)


title: NPCs, Input


title: MD6_RNA_1


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-1, Pop2 depletion


title: HeLa, Nuc, biol rep 2

source_name: HeLa

value: HeLa

value: Human cervical carcinoma

value: Nuclear polyA RNA


title: XD6_RNA_3

source_name: XD

value: XD

value: primary tumor-derived cell line


title: DSP.1001660005046.D.D12


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Pop2 depletion

value: yeast

value: 0.5 mM indole-3-acetic acid


title: DSP.1001660005046.D.D11


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Pop2 depletion


title: DSP.1001660005046.D.D10


title: HeLa, Cyt, biol rep 2

value: cytoplasmic polyA RNA


title: HeLa, Nuc, biol rep 1


title: XD2_RNA_1


title: DSP.1001660005046.D.D09


title: HeLa, Cyt, biol rep 1


title: tIMEC_RNA_3

source_name: tIMEC

value: tIMEC

value: mammary epthelial cell-derived cell line


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Pop2 depletion

value: citirine-boxB, mScarlet-pp7, Pop2::Pop2-V5-mAID, OsTir1


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Pop2 depletion


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Pop2 depletion


title: DSP.1001660005046.D.D08


title: DSP.1001660005046.D.D07


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-2 , Ccr4 depletion

value: citirine-boxB, mScarlet-pp7, Ccr4::Ccr4-V5-mAID, OsTir1


title: tIMEC_RNA_2


title: tIMEC_RNA_1


title: RNA-Seq of THP-1 cell, LPS+PD, 7

data_processing:
bcl2fastq softwae was used to filter the raw data and then FastQC software got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Assembly: GRCh38
Supplementary files format and content: Excel file includes FPKM values for each Sample

extract_protocol:
The total RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols
poly A enriched RNASeq

value: human monocytic leukemia cell

value: wildtype

value: LPS+PD


title: RNA-Seq of THP-1 cell, LPS+PD, 8


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-1, Ccr4 depletion


title: PT_ATAC_7

data_processing:
Quality of the reads was checked using FastQC and trimmed using Trimmomatic v0.39
Reads were aligned to the human genome hg19 using BowTie2
SAM files were processed using samtools v1.10
Tag directories for the merged files were created and peaks were called with callPeaks hg19 –peak size 500 –distance 1000 –L 0 –C 3 using HOMER
Differential accessibility analysis was undertaken using the edgeR v3.20.9 and limma v3.34.9 software packages (McCarthy et al., 2012; Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, 2015). Normalization factors were calculated with calcNormFactors using the TMM. Differential accessibility between all cell types was assessed using the quasi-likelihood (QL) framework of the edgeR package. P-values were adjusted for multiple testing using the Benjamini-Hochberg method. Peaks with a FDR below 0.1% and absolute fold change > 0.5 were defined as differentially accessible regions. Peaks were annotated using the assignChromosomeRegion function in the ChiPpeakAnno (Zhu et al., 2010) (v 3.18.2') package in R.
Assembly: hg19
Supplementary files format and content: bigwig files of replicates
Supplementary files format and content: peak list with cpm-normalized counts and differential accessibiity analysis

source_name: PT

growth_protocol: Four biological replicates for each cell population were considered. 50000 cells for each replicate were harvested and washed once with PBS; nuclei were isolated together with homogenized tissues collected from primary lung tumours (PT) (Poli et al., 2018).

extract_protocol:
Samples were resuspended in 50uL Tn5 transposase mixture: 1x Tagment DNA Buffer, 0.5uL Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, Illumina). Transposition reaction was incubated at 37°C for 45 minutes, followed by DNA isolation using a Qiagen MinElute PCR purification kit (QIAGEN, Hilden, Germany).
Libraries were amplified for 5 cycles using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with primers (0.5uM each) from (Buenrostro et al., 2015) and the following the following cycling program: 5 minutes at 72°C, 30 s at 98°C, followed by 5 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. To avoid overamplification of libraries, 2uL of the eluted DNA were subjected to a side-qPCR for defining the optimal number of PCR cycles for each sample.The remaining libraries were subjected to a second round of PCR in a volume of 50uL with NEBNext High-fidelity 2x PCR master mix, respective primers (1.25uM each) and the following thermal cycles: 30 s hot-start at 98°C, followed by 7-13 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. The final libraries were purified using Agencourt AMPure XP beads, eluted in 30uL Tris HCl 10mM pH 8 and quantified using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226)

value: PT

value: primary tumor-derived sample


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Ccr4 depletion


title: XD4_RNA_2

value: WT


title: DSP.1001660005046.D.D05

value: Placental Tissue -Accreta opposite


title: RNA-Seq of THP-1 cell, LPS, 6

value: LPS


title: PT_ATAC_6


title: RNA-Seq of THP-1 cell, LPS, 5


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Ccr4 depletion


title: DSP.1001660005046.D.D04


title: PT_ATAC_4


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Ccr4 depletion


title: RNA-Seq of THP-1 cell, LPS, 4


title: PT_ATAC_2


title: RNA-Seq of THP-1 cell, LPS+PD, 9


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Ccr4 depletion


title: DSP.1001660005046.D.D02


title: RNA-Seq of THP-1 cell, control, 3

value: control


title: MD6_ATAC_3

value: metastasis-derived cell line


title: DSP.1001660005046.D.C12

source_name: Placental Tissue -Control

value: Placental Tissue -Control


title: RNA-Seq of THP-1 cell, control, 2


title: DSP.1001660005046.D.D06


title: DSP.1001660005046.D.D01


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-2 , Ccr4 depletion

value: yeast

value: 0.5 mM indole-3-acetic acid


title: MD6_ATAC_4


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Ccr4 depletion


title: DSP.1001660005046.D.C11


title: MD6_ATAC_2


title: MD6_ATAC_1


title: 6h-EV

city: Seongnam

first: Seung Woo

last: Choi

state: Gyeonggi

address: 82, Gumi-ro 173beon-gil, Bundang-gu

institute: Seoul National University Bundang Hospital

data_processing:
Paired-ended transcriptome reads were mapped to the human reference genome GRCh38 using the HISAT2 software (version 2.1.0) to generate aligned reads.
Transcript assembly was performed using StringTie software (version 2.1.3b).
After assembly, the abundance of the transcript was estimated using read count and normalized values of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: GRCh38
Supplementary files format and content: The Excel file for the expression profile of known genes included count, FPKM and TPM values for each sample.

growth_protocol: Human immortalized RPEs (RPE-1s, CRL-4000™) were purchased from ATCC and cultured in DMEM/F-12 supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using TRIzol™ reagent(Invitrogen, 15596026) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols (Library Protocol TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E).

treatment_protocol: Extracellular vesicles (2 × 10^9 particles/ml) and/or all-trans-retinal (25 μM, Sigma-Aldrich) were treated to the RPE-1s (2.5 × 10^6 cells) for 1 or 6 hours of cultivation according to the condition of each group.

value: epithelial cell

value: hTERT-immortalized cell

value: extracellular vesicles only

tag: time

value: 6 hours


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Ccr4 depletion

value: citirine-boxB, mScarlet-pp7, Ccr4::Ccr4-V5-mAID, OsTir1


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-1, Ccr4 depletion


title: DSP.1001660005046.D.D03


title: DSP.1001660005046.D.C10


title: 6h-CTL


title: DSP.1001660005046.D.C09


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Ccr4 depletion


title: XD_ATAC_6

value: XD

value: primary tumor-derived cell line


title: DSP.1001660005046.D.C08


title: 6h-atRAL

value: all-trans-retinal only


title: XD_ATAC_4


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2

value: citirine-boxB, mScarlet-pp7


title: DSP.1001660005046.D.C07


title: RNA-Seq of THP-1 cell, control, 1

value: human monocytic leukemia cell

value: wildtype


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2


title: XD_ATAC_1


title: DSP.1001660005046.D.C06


title: 1h-CTL

value: 1 hour


title: DSP.1001660005046.D.C05


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2


title: 1h-atRAL_EV

value: all-trans-retinal & extracellular vesicles


title: tIMEC_ATAC_3

value: tIMEC

value: mammary epthelial cell-derived cell line


title: XD_ATAC_7


title: tIMEC_ATAC_4


title: 1h-atRAL


title: DSP.1001660005046.D.C03

value: Placental Tissue -Control


title: Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1

value: yeast


title: tIMEC_ATAC_2


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1, Ccr4 depletion

value: 0.5 mM indole-3-acetic acid


title: tIMEC_ATAC_1


title: GS1_PDX_Control

description: 37894_GS1-ovariectomy-plus-without-E2-pellet

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger's default settings
Assembly: mm10
Supplementary files format and content: text files containing the raw gene expression count

source_name: GS1 breast cancer PDX

growth_protocol: GS1 tumor pieces were implanted into the 4th mammary fat pads of 11-13-week-old ovariectomized NOD-SCID/IL2Rγ−/− mice.

extract_protocol:
single cell suspension were prepare from GS1 breast cancer PDX, and the single cell emulsion were generated on 10xGenomics Chromium with 3' Solution V3.1 kit
single cell sequencing libraries were prepared with Chromium Next GEM Single Cell 3' v3.1 kit

treatment_protocol: For E2 and E2 + ICI groups, E2 pellets (1 mg) were inserted subcutaneously at the time of tumor implantation. Once the tumor mass was established (10 weeks after the tumor implantation), ICI (5 mg) was administered once weekly via subcutaneous injection for 4 weeks in E2 + ICI group. Sterile saline was administered as vehicle in control and E2 groups. 16 weeks after the tumor implantation, the tumor tissues were collected and were processed for single-cell preparation. Single-cell samples from two biological replicates were combined, and scRNA-seq was performed.

value: GS1 breast cancer PDX

value: Control


title: 1h-EV

value: epithelial cell

value: hTERT-immortalized cell

value: extracellular vesicles only


title: 48_S48

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

data_processing:
Transcript reads were aligned and quantified relative to the “Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI using Salmon v1.9.0. Quality control of the alignment was performed via MultiQC v1.1345. Finally, counts were filtered and normalized (cpm + 0,0001) using EdgeR v3.38 R package. Low expressed genes were excluded using filterByExpr function with default parameters. The conserved counts were normalized as counts per million, plus 0.0001 to avoid null values, then log2 transformed.
Differential gene expression analysis was performed with the dearseq v.1.8.4 package using a mixed model with variance component test to calculate the adjusted p values and with limma v3. package to obtain the fold-change in expression.
Assembly: Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI
Supplementary files format and content: normalized as counts per million (log2)

organism: Chlorocebus sabaeus

source_name: Blood

extract_protocol:
Whole blood was sampled in tempus buffer (ThermoFisher Scientific). Total RNA was purified from whole blood using the Tempus Spin RNA Isolation Kit (ThermoFisher Scientific). RNA samples were depleted of globin mRNA using the Globinclear Kit (Invitrogen)
mRNA library preparation using the NEB Kit (NEBNext Biolab). Libraries were sequenced on an Illumina HiSeq 2500 V4 system.

treatment_protocol: 9 African green monkeys (AGM) were vaccinated with CD40.NiV+Poly-ICLC  at D0 and D21

tag: subject

tag: timepoint

value: F

value: Blood

value: Vaccin


title: Far Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1

tag: cell type

tag: genotype

value: citirine-boxB, mScarlet-pp7


title: DSP.1001660005046.D.C01

source_name: No Template Control

value: No Template Control


title: GS1_PDX_E2+ICI

description: 37893_GS1-ovariectomy-plus-with-E2-pellet-plus-ICI-treatment

tag: treatment


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1


title: 47_S47


title: cr_yy1_dtag43

city: Boston

first: Stuart

last: Orkin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN experiments were carried out as described (Janssens et al., 2019, Meers et al, 2019) with modifications. Briefly, ~0.5x106 cells were collected and incubated with primary antibody on a nutator at 4°C overnight. After washing away unbound antibody, protein A-MNase was added at 700ng/ml and incubated for 1h at 4°C. Samples were washed again and placed in a 0°C metal block. To activate protein A-MNase, CaCl2 was added to a final concentration of 2mM. The reaction was incubated at 0°C for and stopped by chelating Ca2+. The CUT&RUN fragments were released from the insoluble nuclear chromatin at 37°C for 30min. Digested chromatin in the supernatant were collected and then digested by proteinase K at 50°C for 1h. DNA was extracted by phenol chloroform extraction, ethanol precipitation. The antibodies used were: Matr3, Proteintech, 12202-2-AP; CTCF, Abcam, ab70303; Rad21, Abcam, ab992; YY1, santa cruz, sc-7341X; MyoD, Santa cruz, sc-32758 X; H3K27Ac, millipore, MABE647; H3K4me3, active motif, 39159; Rabbit Anti-Mouse IgG H&L, abcam, ab46540.
For transcription factors (TF), libraries were constructed using the library preparation manual of “NEBNext® Ultra™ II DNA Library Prep Kit for Illumina”, NEB E7645, with modification (Liu et al., 2018). Briefly, dA-tailing temperature was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. After adaptor ligation, 1.87x volume of AMPure XP beads was added to the reaction to ensure high recovery efficiency of short fragments. After 12 cycles of PCR amplification, the reaction was cleaned up with 1.2x volume of AMPure XP beads. For histone markers, libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina”, NEB E7645, per manufacturer’s instruction with modification. Briefly, after end repair and adapter ligation, 1.1x volume of AMPure XP beads was added to the reaction for DNA cleanup. After 12 cycles of PCR amplification, the reaction was cleaned up with 1.1x volume of AMPure XP beads. 16-24 barcoded libraries were quantified and mixed at equal molar ratio. Library was loaded to a NextSeq 500/550 High Output Kit v2 (75 cycles), and sequenced in the NextSeq 500 platform. To enable determination of fragment length, paired-end sequencing was performed (2x42 bp, 6 bp index)

treatment_protocol: As for acute depletion, dTag-Matr3 cells were treated with DMSO/dTAG47 (500nM) for indicated hours. As for steady state, Matr3KO cells and wildtype cells were used.

tag: cell line

value: myoblast

value: dTag-Matr3 depleted

tag: replicate


title: r2-MD6-noEU

data_processing:
.Raw reads were quality controlled using FastQC and trimmed using Trimmomatic v0.31
Reads were aligned to the human genome hg19 using BowTie2.
SAM files were further processed and duplicates were removed using samtools v1.10
‘MultiBamSummary’ of Deeptools v3.1.2 was used to retrieve the counts per sample over the RefSeq-transcript model in bed format.
Counts transformed to FPKM values and spike-in normalized as described in Palozola et al., 2021)
Assembly: hg19
Supplementary files format and content: count table of spike-in normalized expression values [fpkm]
Supplementary files format and content: bigwig files of merged replicates per treatment

extract_protocol:
For the analysis of nascent RNA expression, cells were treated with RA as described above and pulse-labeled with 0.5 mM 5-ethynyluridine for 30 min at 37°C and 5% CO2. After pulse-labeling, total RNA was isolated using TRIzol and purified RNA was further processed using the Click-iTTM Nascent RNA Capture Kit (Invitrogen, C10365)
In brief, 5-EU incorporated RNA was biotinylated, purified and pulled down using Dynabeads™ MyOne™ Streptavidin T1 beads. Before the pulldown, biotinylated custom-made spike-in RNAs #1 (2.5e-5 ug) and #2 (2.5-e-4 ug) (expression vectors kindly provided by Kenneth Zaret, University of Pennsylvania) were added to 1 ug of biotinylated RNA. After washing the beads, cDNA was directly generated off the beads using the Universal Plus Total RNA-Seq with NuQuant kit (Tecan) as described by the manufacturer with the following modifications: fragmentation time was increased to 10 min and after second strand synthesis, beads were collected on a magnet and supernatant was transferred to a new tube for subsequent steps. Quality of the libraries was assessed using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226), pooled and sequenced on an Illumina NovaSeq6000 with 150 bp PE.

treatment_protocol: Cells were treated with  1µM atRA treatment (30min for the pulse samples), for 2h with 1µM atRA for the primed samples and for 2h with 1µM atRA (primed), followed by a short atRA treatment for 30min 36 hours after the priming to obtain the primed + pulse samples.

value: unlabeled control


title: DSP.1001660005046.D.C04


title: Far Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-2


title: cr_yy1_dtag42


title: r1-MD6-noEU


title: 45_S45

value: M


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-2, sequencing-1


title: cr_yy1_dtag41


title: GS1_PDX_E2

description: 37895_GS1-ovariectomy--plus-with-E2-pellet


title: 6h-atRAL_EV

value: all-trans-retinal & extracellular vesicles

value: 6 hours


title: DSP.1001660005046.D.C02

value: Placental Tissue -Control


title: Right bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-2

value: yeast


title: r4-MD6-2h-30min

value: 2h priming + 30min retinoic acid pulse


title: cr_yy1_dmso43

value: DMSO


title: r3-MD6-2h-30min


title: 43_S43


title: Left bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-1


title: Left bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-2


title: r2-MD6-2h-30min


title: cr_yy1_dmso42


title: Far Right bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-2


title: cr_yy1_dmso41


title: 41_S41


title: Far Left bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-2


title: cr_rad21_dtag43


title: r4-MD6-2h

value: 2h retinoic acid priming


title: r1-MD6-2h-30min

value: 2h primimg + 30min retinoic acid pulse


title: 40_S40

value: F


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-2


title: cr_rad21_dtag42


title: 44_S44

value: Blood


title: Unsorted reporter yeast expressing wildtype idr  librry, replicate-1, sequencing-1


title: 38_S38

value: Vaccin


title: Right bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-1

value: citirine-boxB, mScarlet-pp7


title: r1-MD6-2h


title: cr_rad21_dmso43


title: r3-MD6-2h


title: Left bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-1


title: 37_S37


title: cr_rad21_dmso42


title: 42_S42


title: r4-MD6-30min

value: 30 min retinoic acid pulse


title: 36_S36


title: 46_S46


title: r2-MD6-2h


title: Far Right bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-1


title: 35_S35


title: r3-MD6-30min


title: 34_S34


title: r2-MD6-30min


title: Far Left bin of Sort-seq on iRFP/RFP ratio with wildtype idr library, replicate-1


title: cr_rad21_dmso41

value: myoblast


title: cr_myod_wt01

value: wildtype

value: growth

value: MyoD


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-2, sequencing-1, from yfp


title: cr_myod_wt02


title: cr_rad21_dtag41

value: dTag-Matr3 depleted


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-1, sequencing-2, from yfp


title: r1-MD6-30min


title: 39_S39

value: M


title: 33_S33


title: cr_myod_ko02


title: r3-MD6-contr

value: control


title: 31_S31


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-1, sequencing-1, from yfp

value: yeast


title: cr_myod_dtag43 (matr3.ko and yy1.ko) (for double ko comparison)

value: dTag-Matr3 depleted, YY1ko


title: cr_myod_ko01


title: 32_S32


title: r1-MD6-contr


title: 29_S29

description: No

value: No


title: cr_myod_dtag42 (matr3.ko and yy1.ko) (for double ko comparison)


title: Left bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-2


title: 30_S30

description: No


title: r2-MD6-contr


title: cr_myod_dtag41 (matr3.ko and yy1.ko) (for double ko comparison)


title: 28_S28

description: No